ENTRY       gmx00910                    Pathway
NAME        Nitrogen metabolism - Glycine max (soybean)
DESCRIPTION The biological process of the nitrogen cycle is a complex interplay among many microorganisms catalyzing different reactions, where nitrogen is found in various oxidation states ranging from +5 in nitrate to -3 in ammonia. The core nitrogen cycle involves four reduction pathways and two oxidation pathways. Nitrogen fixation [MD:M00175] is the process of reducing atmospheric molecular nitrogen to ammonia, a biologically useful reduced form incorporated into amino acids and other vital compounds. The ability of fixing atmospheric nitrogen by the nitrogenase enzyme complex is present in restricted prokaryotes (diazotrophs). The other reduction pathways are assimilatory nitrate reduction [MD:M00531] and dissimilatory nitrate reduction [MD:M00530] both for conversion to ammonia, and denitrification [MD:M00529]. Denitrification is a respiration in which nitrate or nitrite is reduced as a terminal electron acceptor under low oxygen or anoxic conditions, producing gaseous nitrogen compounds (N2, NO and N2O) to the atmosphere. The two oxidation pathways are nitrification [MD:M00528] and anaerobic ammonium oxidation (anammox). Nitrification is the oxidation of ammonia (NH3) with oxygen into nitrite followed by the oxidation of nitrite into nitrate. The first step is performed by ammonia-oxidizing microorganisms (e.g., Nitrosomonas and Nitrosococcus) and the second step by nitrite-oxidizing microorganisms (e.g., Nitrobacter). Anammox is a biochemical process of oxidizing ammonium (NH4+) into dinitrogen gas (N2) using nitrite as an electron acceptor. It occurs in the anammoxosome, a membrane bound compartment inside the cytoplasm, of anammox bacteria (e.g., Planctomycetes).
CLASS       Metabolism; Energy metabolism
PATHWAY_MAP gmx00910  Nitrogen metabolism
MODULE      gmx_M00531  Assimilatory nitrate reduction, nitrate => ammonia [PATH:gmx00910]
DBLINKS     GO: 0006807
ORGANISM    Glycine max (soybean) [GN:gmx]
GENE        100527923  acetamidase/formamidase family protein [KO:K01455] [EC:3.5.1.49]
            547946  NRT2; NRT2 protein [KO:K02575]
            100807710  high affinity nitrate transporter 2.4 [KO:K02575]
            100803196  high affinity nitrate transporter 2.5 [KO:K02575]
            100787888  high affinity nitrate transporter 2.5 [KO:K02575]
            100782969  high affinity nitrate transporter 2.4 [KO:K02575]
            100813471  putative nitrate reductase 1 [KO:K10534] [EC:1.7.1.1 1.7.1.2 1.7.1.3]
            100818642  nitrate reductase [NADH] 2 [KO:K10534] [EC:1.7.1.1 1.7.1.2 1.7.1.3]
            100818103  nitrate reductase [NADH] 2 [KO:K10534] [EC:1.7.1.1 1.7.1.2 1.7.1.3]
            732634  INR2; inducible nitrate reductase [NADH] 2 [KO:K10534] [EC:1.7.1.1 1.7.1.2 1.7.1.3]
            100775519  ferredoxin--nitrite reductase, chloroplastic isoform X2 [KO:K00366] [EC:1.7.7.1]
            732631  NIR; nitrate reductase precursor [KO:K00366] [EC:1.7.7.1]
            547687  GDH1; glutamate dehydrogenase 1 [KO:K00261] [EC:1.4.1.3]
            547688  GDH2; glutamate dehydrogenase 2 [KO:K00261] [EC:1.4.1.3]
            100801250  glutamate dehydrogenase 2 [KO:K00261] [EC:1.4.1.3]
            100801991  glutamate dehydrogenase 1 [KO:K00261] [EC:1.4.1.3]
            100789509  uncharacterized protein LOC100789509 [KO:K00261] [EC:1.4.1.3]
            100793231  glutamate dehydrogenase 2 [KO:K00261] [EC:1.4.1.3]
            100777869  glutamate dehydrogenase 1 isoform X1 [KO:K00261] [EC:1.4.1.3]
            100809032  NADP-specific glutamate dehydrogenase isoform X1 [KO:K00262] [EC:1.4.1.4]
            100788009  NADP-specific glutamate dehydrogenase isoform X1 [KO:K00262] [EC:1.4.1.4]
            548036  GS-2; glutamine synthetase precursor [KO:K01915] [EC:6.3.1.2]
            547621  GS1GAMMA2; glutamine synthetase cytosolic isozyme 2 [KO:K01915] [EC:6.3.1.2]
            547798  GS1-GAMMA; glutamine synthetase cytosolic isozyme 2 [KO:K01915] [EC:6.3.1.2]
            100817922  glutamine synthetase PR-2 [KO:K01915] [EC:6.3.1.2]
            547953  GS; glutamine synthetase nodule isozyme [KO:K01915] [EC:6.3.1.2]
            548082  GS; glutamine synthetase cytosolic isozyme 1 [KO:K01915] [EC:6.3.1.2]
            547620  GS1alpha; cytosolic glutamine synthetase alpha [KO:K01915] [EC:6.3.1.2]
            100780873  glutamine synthetase leaf isozyme, chloroplastic isoform X1 [KO:K01915] [EC:6.3.1.2]
            100794457  glutamine synthetase leaf isozyme, chloroplastic [KO:K01915] [EC:6.3.1.2]
            100815931  glutamate synthase [NADH], amyloplastic isoform X1 [KO:K00264] [EC:1.4.1.14]
            548016  ferredoxin-dependent glutamate synthase, chloroplastic [KO:K00284] [EC:1.4.7.1]
            100809299  ferredoxin-dependent glutamate synthase, chloroplastic-like isoform X1 [KO:K00284] [EC:1.4.7.1]
            100305967  CYN; cyanate hydratase [KO:K01725] [EC:4.2.1.104]
            547671  CA1; carbonic anhydrase [KO:K01673] [EC:4.2.1.1]
            100781868  carbonic anhydrase, chloroplastic isoform 1 [KO:K01673] [EC:4.2.1.1]
            100803945  carbonic anhydrase 2 isoform X1 [KO:K01673] [EC:4.2.1.1]
            100812124  uncharacterized protein LOC100812124 [KO:K01673] [EC:4.2.1.1]
            100500448  carbonic anhydrase, chloroplastic isoform 1 [KO:K01673] [EC:4.2.1.1]
            100810496  carbonic anhydrase isoform 1 [KO:K01673] [EC:4.2.1.1]
            100811331  beta carbonic anhydrase 5, chloroplastic [KO:K01673] [EC:4.2.1.1]
            100782859  beta carbonic anhydrase 5, chloroplastic isoform X2 [KO:K01673] [EC:4.2.1.1]
            100807954  beta carbonic anhydrase 5, chloroplastic isoform X1 [KO:K01673] [EC:4.2.1.1]
            100808326  carbonic anhydrase 2 [KO:K01673] [EC:4.2.1.1]
            100306209  alpha carbonic anhydrase 4 [KO:K01674] [EC:4.2.1.1]
            100784540  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            100797935  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            100777574  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            100811978  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            100797401  alpha carbonic anhydrase 1-like precursor [KO:K01674] [EC:4.2.1.1]
            100799362  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            100781864  alpha carbonic anhydrase 4 [KO:K01674] [EC:4.2.1.1]
            100776677  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            106797392  alpha carbonic anhydrase 4 [KO:K01674] [EC:4.2.1.1]
            100810249  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            100776144  alpha carbonic anhydrase 7 isoform X1 [KO:K01674] [EC:4.2.1.1]
            106796394  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            100819340  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
            102660002  alpha carbonic anhydrase 7 [KO:K01674] [EC:4.2.1.1]
COMPOUND    C00011  CO2
            C00014  Ammonia
            C00025  L-Glutamate
            C00058  Formate
            C00064  L-Glutamine
            C00088  Nitrite
            C00169  Carbamoyl phosphate
            C00192  Hydroxylamine
            C00244  Nitrate
            C00288  HCO3-
            C00488  Formamide
            C00533  Nitric oxide
            C00697  Nitrogen
            C00726  Nitrile
            C00887  Nitrous oxide
            C01417  Cyanate
            C01563  Carbamate
            C05361  Hydrazine
            C06058  Nitroalkane
REFERENCE   PMID:14702404
  AUTHORS   Scott JD, Ludwig RA
  TITLE     Azorhizobium caulinodans electron-transferring flavoprotein N electrochemically couples pyruvate dehydrogenase complex activity to N2 fixation.
  JOURNAL   Microbiology 150:117-26 (2004)
            DOI:10.1099/mic.0.26603-0
REFERENCE   PMID:17408485
  AUTHORS   Kneip C, Lockhart P, Voss C, Maier UG
  TITLE     Nitrogen fixation in eukaryotes--new models for symbiosis.
  JOURNAL   BMC Evol Biol 7:55 (2007)
            DOI:10.1186/1471-2148-7-55
REFERENCE   PMID:11004450
  AUTHORS   Whittaker M, Bergmann D, Arciero D, Hooper AB
  TITLE     Electron transfer during the oxidation of ammonia by the chemolithotrophic bacterium Nitrosomonas europaea.
  JOURNAL   Biochim Biophys Acta 1459:346-55 (2000)
            DOI:10.1016/S0005-2728(00)00171-7
REFERENCE   PMID:15528644
  AUTHORS   Cabello P, Roldan MD, Moreno-Vivian C
  TITLE     Nitrate reduction and the nitrogen cycle in archaea.
  JOURNAL   Microbiology 150:3527-46 (2004)
            DOI:10.1099/mic.0.27303-0
REFERENCE   PMID:11921398
  AUTHORS   Stolz JF, Basu P
  TITLE     Evolution of nitrate reductase: molecular and structural variations on a common function.
  JOURNAL   Chembiochem 3:198-206 (2002)
            DOI:10.1002/1439-7633(20020301)3:2/3<198::AID-CBIC198>3.0.CO;2-C
REFERENCE   PMID:18021072
  AUTHORS   Morozkina EV, Zvyagilskaya RA
  TITLE     Nitrate reductases: structure, functions, and effect of stress factors.
  JOURNAL   Biochemistry (Mosc) 72:1151-60 (2007)
            DOI:10.1134/S0006297907100124
REFERENCE   PMID:19247843
  AUTHORS   Jetten MS, Niftrik L, Strous M, Kartal B, Keltjens JT, Op den Camp HJ
  TITLE     Biochemistry and molecular biology of anammox bacteria.
  JOURNAL   Crit Rev Biochem Mol Biol 44:65-84 (2009)
            DOI:10.1080/10409230902722783
REFERENCE   PMID:22221911
  AUTHORS   Luesken FA, Wu ML, Op den Camp HJ, Keltjens JT, Stunnenberg H, Francoijs KJ, Strous M, Jetten MS
  TITLE     Effect of oxygen on the anaerobic methanotroph 'Candidatus Methylomirabilis oxyfera': kinetic and transcriptional analysis.
  JOURNAL   Environ Microbiol 14:1024-34 (2012)
            DOI:10.1111/j.1462-2920.2011.02682.x
REFERENCE   PMID:26610024
  AUTHORS   Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M
  TITLE     Complete nitrification by Nitrospira bacteria.
  JOURNAL   Nature 528:504-9 (2015)
            DOI:10.1038/nature16461
REFERENCE   PMID:26610025
  AUTHORS   van Kessel MA, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJ, Kartal B, Jetten MS, Lucker S
  TITLE     Complete nitrification by a single microorganism.
  JOURNAL   Nature 528:555-9 (2015)
            DOI:10.1038/nature16459
REL_PATHWAY gmx00220  Arginine biosynthesis
            gmx00250  Alanine, aspartate and glutamate metabolism
            gmx00460  Cyanoamino acid metabolism
            gmx00630  Glyoxylate and dicarboxylate metabolism
KO_PATHWAY  ko00910
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