# HOMEP data set - homologous pairs of membrane protein structures
# (Supplementary) Table 3 - definition of transmembrane domains in each of the structures
# from Forrest et al, Membrane protein homology modeling, Biophys J 2006
#
# Note that the original file contains incorrect entries for cytochrome c oxidase
# That mistake is corrected here 06.10.2019 by LRF
# thanks to Sjors van Heuveln, Bioinformatics Master Student @ VU Amsterdam
# for noticing the mistake!
#
# Opsins
# TM,,1m0l-s,1m0l-e,,1h68-s,1h68-e,,1e12-s,1e12-e,,1u19-s,1u19-e,,,,,,
1,A,9,31,A,4,26,A,29,51,A,37,59,,,,,,
2,A,39,62,A,33,56,A,59,82,A,72,96,,,,,,
3,A,80,101,A,70,91,A,106,127,A,111,135,,,,,,
4,A,105,124,A,95,114,A,131,150,A,154,173,,,,,,
5,A,133,155,A,122,144,A,160,182,A,199,222,,,,,,
6,A,167,192,A,156,181,A,192,217,A,250,275,,,,,,
7,A,204,226,A,193,215,A,230,252,A,288,309,,,,,,
# 
#Cytochrome c oxidase
#TM,,1v54-s,1v54-e,,1m56-s,1m56-e,,1ar1-s,1ar1-e
1,A,12,42,A,26,56,A,28,58
2,A,51,87,A,92,128,A,84,120
3,A,95,117,A,136,158,A,128,150
4,A,142,171,A,186,215,A,178,207
5,A,183,214,A,227,258,A,219,250
6,A,228,262,A,272,306,A,264,298
7,A,270,291,A,313,334,A,305,326
8,A,299,328,A,342,371,A,334,363
9,A,336,359,A,379,402,A,371,394
10,A,371,401,A,414,444,A,406,436
11,A,407,434,A,450,477,A,442,469
12,A,445,478,A,488,521,A,480,513
13,B,15,47,B,49,81,B,26,58
14,B,60,87,B,99,126,B,76,103
# 
# Cytochrome bc1
# TM,,1bcc-s,1bcc-e,,1ntm-s,1ntm-e,,1kb9-s,1kb9-e,,,,,,,,,
1,C,30,54,C,29,53,C,28,52,,,,,,,,,
2,C,77,104,C,76,103,C,75,102,,,,,,,,,
3,C,111,131,C,110,130,C,111,131,,,,,,,,,
4,C,173,204,C,172,203,C,173,204,,,,,,,,,
5,C,224,246,C,223,245,C,224,246,,,,,,,,,
6,C,273,308,C,272,307,C,273,308,,,,,,,,,
7,C,320,341,C,319,340,C,320,341,,,,,,,,,
8,C,346,378,C,345,377,C,346,378,,,,,,,,,
9,D,198,232,D,198,232,D,263,297,,,,,,,,,
10,E,30,61,E,30,61,E,50,81,,,,,,,,,
11,G,34,69,G,34,69,H,45,80,,,,,,,,,
12,J,20,46,J,20,46,I,17,43,,,,,,,,,
# 
# Aquaporins
# TM,,1j4n-s,1j4n-e,,1rc2-s,1rc2-e,,1fx8-s,1fx8-e,,,,,,,,,
1,A,12,33,B,3,24,A,9,30,,,,,,,,,
2,A,51,88,B,36,73,A,41,78,,,,,,,,,
3,A,95,119,B,80,104,A,85,109,,,,,,,,,
4,A,140,160,B,134,154,A,148,168,,,,,,,,,
5,A,170,205,B,162,196,A,179,214,,,,,,,,,
6,A,211,230,B,205,224,A,233,252,,,,,,,,,
#
# PRC
# TM,,1prc-s,1prc-e,,1eys-s,1eys-e,,1ogv-s,1ogv-e,,,,,,,,,
1,L,33,55,L,33,55,L,33,55,,,,,,,,,
2,L,83,111,L,91,119,L,83,111,,,,,,,,,
3,L,116,139,L,124,147,L,116,139,,,,,,,,,
4,L,171,198,L,179,206,L,171,198,,,,,,,,,
5,L,226,249,L,234,257,L,226,249,,,,,,,,,
6,M,53,77,M,54,78,M,54,78,,,,,,,,,
7,M,110,138,M,111,139,M,112,140,,,,,,,,,
8,M,143,166,M,144,167,M,145,168,,,,,,,,,
9,M,198,224,M,199,225,M,200,226,,,,,,,,,
10,M,260,283,M,261,284,M,262,285,,,,,,,,,
#
# ClC
# TM,,1kpl-s,1kpl-e,,1ots-s,1ots-e,,,,,,,,,,,,
1,A,33,68,A,33,68,,,,,,,,,,,,
2,A,78,117,A,78,117,,,,,,,,,,,,
3,A,124,166,A,124,166,,,,,,,,,,,,
4,A,171,201,A,171,201,,,,,,,,,,,,
5,A,215,232,A,215,232,,,,,,,,,,,,
6,A,251,283,A,251,283,,,,,,,,,,,,
7,A,288,306,A,288,306,,,,,,,,,,,,
8,A,311,325,A,311,324,,,,,,,,,,,,
9,A,330,378,A,330,378,,,,,,,,,,,,
10,A,386,416,A,386,416,,,,,,,,,,,,
11,A,422,458,A,422,458,,,,,,,,,,,,
12,B,33,68,B,33,68,,,,,,,,,,,,
13,B,78,117,B,78,117,,,,,,,,,,,,
14,B,124,166,B,124,166,,,,,,,,,,,,
15,B,171,201,B,171,201,,,,,,,,,,,,
16,B,215,232,B,215,232,,,,,,,,,,,,
17,B,251,283,B,251,283,,,,,,,,,,,,
18,B,288,306,B,288,306,,,,,,,,,,,,
19,B,311,325,B,311,324,,,,,,,,,,,,
20,B,330,378,B,330,378,,,,,,,,,,,,
21,B,386,416,B,386,416,,,,,,,,,,,,
22,B,422,458,B,422,458,,,,,,,,,,,,
# 
# Reductases
# TM,,1l0v-s,1l0v-e,,1kqf-s,1kqf-e,,1qla-s,1qla-e,,,,,,,,,
1,C,23,46,C,12,36,C,25,49,,,,,,,,,
2,C,66,90,C,52,76,C,78,101,,,,,,,,,
3,D,10,35,C,110,134,C,122,147,,,,,,,,,
4,D,62,85,C,152,174,C,169,192,,,,,,,,,
#
# MFST
# TM,,1pw4-s,1pw4-e,,1pv6-s,1pv6-e,,,,,,,,,,,,
1,A,29,54,A,10,36,,,,,,,,,,,,
2,A,63,88,A,42,68,,,,,,,,,,,,
3,A,93,113,A,74,93,,,,,,,,,,,,
4,A,120,148,A,104,134,,,,,,,,,,,,
5,A,156,180,A,140,163,,,,,,,,,,,,
6,A,190,207,A,169,185,,,,,,,,,,,,
7,A,252,277,A,219,244,,,,,,,,,,,,
8,A,288,314,A,258,284,,,,,,,,,,,,
9,A,320,338,A,287,305,,,,,,,,,,,,
10,A,349,373,A,314,338,,,,,,,,,,,,
11,A,382,411,A,347,375,,,,,,,,,,,,
12,A,413,434,A,378,400,,,,,,,,,,,,
#
# Porins
# TM,,1osm-s,1osm-e,,2omf-s,2omf-e,,1e54-s,1e54-e,,1pho-s,1pho-e,,1prn-s,1prn-e,,2por-s,2por-e
1,A,10,23,_,10,23,A,3,16,_,10,23,_,1,14,_,1,14
2,A,31,44,_,36,49,A,28,45,_,31,44,_,26,39,_,20,33
3,A,51,58,_,56,63,A,52,59,_,51,58,_,46,53,_,40,47
4,A,78,82,_,85,89,A,78,82,_,78,82,_,70,74,_,60,64
5,A,87,92,_,94,99,A,86,91,_,87,92,_,78,83,_,68,73
6,A,129,134,_,136,141,A,137,142,_,130,135,_,132,137,_,118,123
7,A,145,151,_,152,158,A,149,155,_,146,152,_,143,149,_,129,135
8,A,176,184,_,173,181,A,171,179,_,167,175,_,163,171,_,149,157
9,A,189,197,_,185,193,A,183,191,_,181,189,_,175,183,_,161,169
10,A,216,224,_,212,220,A,204,212,_,208,216,_,192,200,_,182,190
11,A,229,237,_,225,233,A,217,225,_,221,229,_,206,214,_,195,203
12,A,254,262,_,255,263,A,239,247,_,245,253,_,222,230,_,230,238
13,A,269,278,_,270,279,A,254,263,_,260,269,_,236,244,_,244,253
14,A,293,300,_,294,301,A,273,280,_,284,291,_,252,259,_,262,269
15,A,306,314,_,307,315,A,285,293,_,297,305,_,265,273,_,275,283
16,A,333,341,_,331,339,A,323,331,_,321,329,_,280,288,_,292,300
# 
# Sugar Porins
# TM,,1af6-s,1af6-e,,2mpr-s,2mpr-e,,1oh2-s,1oh2-e,,,,,,,,,
1,A,2,13,A,2,13,R,74,85,,,,,,,,,
2,A,39,48,A,39,48,R,116,125,,,,,,,,,
3,A,58,68,A,58,68,R,135,145,,,,,,,,,
4,A,80,89,A,80,89,R,159,168,,,,,,,,,
5,A,98,103,A,98,103,R,180,185,,,,,,,,,
6,A,126,131,A,126,131,R,209,214,,,,,,,,,
7,A,138,148,A,138,148,R,222,232,,,,,,,,,
8,A,169,177,A,169,177,R,244,252,,,,,,,,,
9,A,187,195,A,187,195,R,256,264,,,,,,,,,
10,A,212,221,A,212,221,R,287,296,,,,,,,,,
11,A,227,236,A,227,236,R,306,315,,,,,,,,,
12,A,267,279,A,277,289,R,334,346,,,,,,,,,
13,A,284,296,A,294,306,R,351,363,,,,,,,,,
14,A,303,314,A,313,324,R,372,383,,,,,,,,,
15,A,320,333,A,330,343,R,389,402,,,,,,,,,
16,A,338,352,A,348,362,R,413,427,,,,,,,,,
17,A,362,373,A,372,383,R,439,450,,,,,,,,,
18,A,410,419,A,416,425,R,472,481,,,,,,,,,
# 
# TonB CR
# TM,,1fep-s,1fep-e,,1nqe-s,1nqe-e,,1kmo-s,1kmo-e,,1qfg-s,1qfg-e,,,,,,
1,A,154,162,A,137,145,A,224,232,A,161,169,,,,,,
2,A,172,181,A,149,158,A,243,252,A,173,182,,,,,,
3,A,186,198,A,163,175,A,257,269,A,189,201,,,,,,
4,A,228,239,A,197,208,A,278,289,A,210,221,,,,,,
5,A,244,256,A,213,225,A,294,306,A,226,238,,,,,,
6,A,282,296,A,243,257,A,333,347,A,275,289,,,,,,
7,A,301,316,A,261,276,A,352,367,A,294,309,,,,,,
8,A,338,353,A,289,304,A,378,393,A,348,363,,,,,,
9,A,362,375,A,310,323,A,403,416,A,373,386,,,,,,
10,A,405,419,A,333,347,A,442,456,A,438,452,,,,,,
11,A,424,436,A,351,363,A,460,472,A,456,468,,,,,,
12,A,439,450,A,366,377,A,488,499,A,484,495,,,,,,
13,A,456,467,A,383,394,A,505,516,A,501,512,,,,,,
14,A,505,516,A,413,424,A,535,546,A,527,538,,,,,,
15,A,521,533,A,429,441,A,551,563,A,545,557,,,,,,
16,A,561,572,A,459,470,A,581,592,A,576,587,,,,,,
17,A,578,587,A,475,484,A,604,613,A,593,602,,,,,,
18,A,605,614,A,501,510,A,634,643,A,623,632,,,,,,
19,A,619,631,A,514,526,A,647,659,A,641,653,,,,,,
20,A,654,663,A,544,553,A,681,690,A,666,675,,,,,,
21,A,669,677,A,559,567,A,699,707,A,685,693,,,,,,
22,A,715,724,A,585,594,A,732,741,A,716,725,,,,,,