# List of top-scoring protein chains for t2k-100-30-alpha hidden Markov model. # HMM and HMM E-value scores computed by SAM (c) 1992-2001 Regents of the University of California, Santa Cruz # Sequence Alignment and Modeling Software System # http://www.cse.ucsc.edu/research/compbio/sam.html # ----------------- Citations (SAM, SAM-T99, HMMs) -------------------- # R. Hughey, A. Krogh, Hidden Markov models for sequence analysis: # Extension and analysis of the basic method, CABIOS 12:95-107, 1996. # K. Karplus, C. Barrett, R. Hughey, Hidden Markov models for detecting # remote protein homologies, Bioinformatics 14(10):846-856, 1998. # A. Krogh et al., Hidden Markov models in computational biology: # Applications to protein modeling, JMB 235:1501-1531, Feb 1994. # # FSSP representative for each protein chain taken from FSSP: # ------------------Citations (FSSP) ----------------------------------- # L. Holm and C. Sander (1996) Mapping the protein universe. Science 273:595-602. # #SCOP domains found in each protein chain taken from SCOP: # ------------------Citations (SCOP) ----------------------------------- #Murzin A. G., Brenner S. E., Hubbard T., Chothia C. (1995). #SCOP: a structural classification of proteins database for the investigation of sequences and structures. #J. Mol. Biol. 247, 536-540. Sequence_ID Length Target_Evalue FSSP-rep SCOP_domain SCOP_suid 5S 5N 12S 6S 12S 10N 1bvqA 141 6.51e-07 1bvqA d.38.1.1 38542 1lo7A 141 1.19e-06 1c8uA 285 1.52e-04 1c8uA d.38.1.3 38547 d.38.1.3 38548 1koqA 253 1.58e-01 2cba b.74.1.1 27964 1iq0A 592 2.05e-01 a.27.1.1 66257 c.26.1.1 66258 d.67.2.1 66259 2bpa1 426 2.10e-01 2bpa1 1dqeA 137 3.42e-01 1dqeA a.39.2.1 17388 1al0F 426 3.85e-01 2bpa1 b.10.1.1 23274 1kopA 223 4.05e-01 2cba b.74.1.1 27966 1b65A 375 4.10e-01 1b65A d.154.1.1 42020 3pcgM 238 4.11e-01 3pchM b.3.6.1 22742 3pchM 238 4.44e-01 3pchM b.3.6.1 22748 1tf4A 605 6.27e-01 1tf4A a.102.1.2 18827 b.2.2.2 22393 1ihkA 174 8.34e-01 1bfg b.42.1.1 62384 1dabA 539 8.67e-01 1dabA b.80.1.7 28049 2pcdM 238 9.28e-01 3pchM b.3.6.1 22760 1whi 122 9.60e-01 1whi b.39.1.1 24810 1eo9B 241 1.03e+00 3pchM b.3.6.1 22826 1vcaA 202 1.07e+00 1vcaA b.1.1.3 21649 b.1.1.4 21685 1nfiA 301 1.07e+00 1a3qA b.1.1.5 21942 b.2.5.1 22455 1bzyA 217 1.19e+00 1qk3A c.61.1.1 34071 1hf2A 210 1.22e+00 1hf2A b.80.3.1 60992 c.102.1.1 60993 1pcfA 66 1.31e+00 1pcfA d.18.1.1 38142 2pia 321 1.31e+00 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1pne 140 1.63e+00 1pne d.110.1.1 40866 1lylA 504 1.73e+00 1lylA b.40.4.1 25261 d.104.1.1 40717 2pcdA 200 1.74e+00 3pchA b.3.6.1 22665 3pcnA 200 1.87e+00 3pchA b.3.6.1 22725 1fmaD 81 1.91e+00 1fmaD d.15.3.1 37643 1fm0D 81 1.94e+00 1fmaD d.15.3.1 37642 3pcgA 200 1.97e+00 3pchA b.3.6.1 22647 1fil 139 2.00e+00 1pne d.110.1.1 40869 1dboA 506 2.30e+00 1dbgA b.80.1.4 28034 3pchA 200 2.39e+00 3pchA b.3.6.1 22653 1erxA 184 2.40e+00 1np1A b.60.1.1 27164 1e1oA 504 2.53e+00 1lylA b.40.4.1 25258 d.104.1.1 40714 2ae2A 260 2.53e+00 1bdb c.2.1.2 29945 1jjyA 636 2.60e+00 1jjyA e.26.1.2 63141 1cvsC 225 2.64e+00 1cvsC b.1.1.4 21726 b.1.1.4 21727 1qqtA 551 2.68e+00 1qqtA a.27.1.1 16923 c.26.1.1 31590 g.41.1.1 45175 1np4A 184 2.73e+00 1np1A b.60.1.1 27166 2bb8 71 2.75e+00 2bb8 d.10.1.1 37480 1cskA 71 2.82e+00 1ckaA b.34.2.1 24513 1p32A 209 3.11e+00 1p32A d.25.1.1 38379 1bb8 71 3.18e+00 2bb8 d.10.1.1 37478 1g7tA 594 3.44e+00 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1krs 120 3.53e+00 1krs b.40.4.1 25256 1ffyA 917 3.54e+00 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 3.54e+00 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1qg3A 195 3.55e+00 1qg3A b.1.2.1 21993 b.1.2.1 21994 1xgsA 295 3.65e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1g7sA 594 3.75e+00 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1f4lA 551 4.11e+00 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1dbgA 506 4.13e+00 1dbgA b.80.1.4 28033 1np1A 184 4.38e+00 1np1A b.60.1.1 27155 1koiA 184 4.42e+00 b.60.1.1 68725 1h5uA 842 4.82e+00 1a8i c.87.1.4 60655 1ca1 370 4.93e+00 1ca1 a.124.1.1 19340 b.12.1.3 23648 1qhvA 195 5.01e+00 1qhvA b.21.1.1 23842 1cor 82 5.28e+00 451c a.3.1.1 15903 1hnoA 280 5.37e+00 1hnoA c.14.1.3 61095 1ospH 218 5.39e+00 1igtB b.1.1.1 20117 b.1.1.2 21147 1p32C 209 5.41e+00 1p32A d.25.1.1 38381 1i31A 314 5.62e+00 1bw8A b.2.7.1 22481 1ca4A 168 5.65e+00 1d0aB b.8.1.1 23238 h.1.2.1 45445 1aw8E 91 5.67e+00 1aw8B 1az9 457 5.85e+00 1az9 c.55.2.1 33547 d.127.1.1 41164 1czyC 168 5.88e+00 1d0aB b.8.1.1 23222 h.1.2.1 45429 1xypA 190 5.89e+00 1axkA b.29.1.11 24327 1l0wA 580 6.01e+00 1eo1A 124 6.11e+00 1eo1A c.55.5.1 33739 1ca9A 192 6.12e+00 1d0aB b.8.1.1 23244 h.1.2.1 45451 1ibcB 88 6.17e+00 1pauB 1bmqB 88 6.20e+00 1pauB 1cwvA 492 6.39e+00 1cwvA b.1.14.1 22373 b.1.14.1 22374 b.1.14.1 22375 b.1.14.1 22376 d.169.1.3 42442 1lcl 142 6.52e+00 1lcl b.29.1.3 24216 1hnuA 280 6.55e+00 1hnoA c.14.1.3 61096 2scuB 388 6.56e+00 2scuB c.23.4.1 31141 d.142.1.4 41562 1kxgA 152 6.72e+00 1ecfA 504 6.92e+00 1ecfB c.61.1.1 34053 d.153.1.1 41820 1dmzA 158 7.16e+00 1qu5A b.26.1.2 23921 1ckaA 57 7.77e+00 1ckaA b.34.2.1 24459 1hdkA 141 7.90e+00 b.29.1.3 65807 1a28A 256 8.22e+00 1a28A a.123.1.1 19290 1ex2A 189 8.22e+00 1ex2A c.51.4.2 33225 1aw8B 91 8.46e+00 1aw8B 1hmpA 217 8.49e+00 1qk3A c.61.1.1 34075 1mdc 133 8.58e+00 1hmt b.60.1.2 27198 1hmt 132 8.81e+00 1hmt b.60.1.2 27169 1d0aB 168 8.82e+00 1d0aB b.8.1.1 23224 h.1.2.1 45431 1dceA 567 9.26e+00 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 1svb 395 9.29e+00 1svb b.1.1.5 21814 f.10.1.1 43827 1fts 295 9.30e+00 1ng1 a.24.13.1 16968 c.37.1.10 32279 1g7rA 594 9.60e+00 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1ez1A 392 9.71e+00 1ez1A b.84.2.1 28248 c.30.1.1 31655 d.142.1.2 41500 1lox 662 9.90e+00 1lox a.119.1.2 19238 b.12.1.1 23638 2reb 352 9.93e+00 2reb c.37.1.11 32282 d.48.1.1 38767 2ms2A 129 9.93e+00 1msc d.85.1.1 40049 1cne 270 1.01e+01 1ndh b.43.4.2 25661 c.25.1.1 31551 2gwxA 267 1.01e+01 2prgA a.123.1.1 19323 1aipE 405 1.01e+01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1je5A 206 1.02e+01 1je5A b.40.4.7 62909 1eyzA 392 1.06e+01 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1ha3A 405 1.12e+01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1pvc2 271 1.13e+01 1aym2 1gtrA 553 1.14e+01 1gtrA b.53.1.2 26939 c.26.1.1 31578 1czyA 168 1.15e+01 1d0aB b.8.1.1 23220 h.1.2.1 45427 1msc 129 1.16e+01 1msc d.85.1.1 40039 1lm8V 160 1.18e+01 1ecfB 504 1.21e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 1gefA 123 1.26e+01 1gefA c.52.1.18 60465 1qq8A 214 1.26e+01 1qq8A a.132.1.1 19508 1cd8 114 1.28e+01 1cd8 b.1.1.1 19714 1vpc 45 1.28e+01 1vpc j.11.1.1 46138 1pls 113 1.29e+01 1pls b.55.1.1 26965 1ijtA 128 1.31e+01 1bfg b.42.1.1 62510 1rrpB 134 1.32e+01 1rrpB b.55.1.3 26995 2hvm 273 1.35e+01 1cnv c.1.8.5 28985 1qlyA 58 1.35e+01 1bbzA b.34.2.1 24530 3ullA 132 1.38e+01 3ullA b.40.4.3 25282 1fwyA 331 1.41e+01 1fwyA b.81.1.4 28064 c.68.1.5 34522 1gm6A 175 1.42e+01 1i07A 60 1.42e+01 1aojA b.34.2.1 61477 1icjA 168 1.43e+01 1bs4A d.167.1.1 42284 1mkaA 171 1.47e+01 1mkaA d.38.1.2 38543 1fx3A 169 1.48e+01 1fx3B d.33.1.1 38524 1f2tB 148 1.49e+01 1f2tB 1hv9A 456 1.49e+01 1fwyA b.81.1.4 28060 c.68.1.5 34518 1aj6 219 1.49e+01 1aj6 d.122.1.2 41106 1quqA 129 1.50e+01 1quqA b.40.4.3 25303 1j9qA 341 1.53e+01 1nif b.6.1.3 62765 b.6.1.3 62766 1c3mA 147 1.53e+01 1jotA b.77.3.1 27983 1vkxA 273 1.54e+01 1a3qA b.1.1.5 21941 b.2.5.1 22454 2gdm 153 1.57e+01 2gdm a.1.1.2 15212 1euoA 180 1.57e+01 1np1A b.60.1.1 27163 1qtqA 553 1.64e+01 1gtrA b.53.1.2 26940 c.26.1.1 31579 1chmA 401 1.66e+01 1chmA c.55.2.1 33545 d.127.1.1 41142 1ris 101 1.71e+01 1ris d.58.14.1 39314 1qfhA 212 1.72e+01 1qfhA b.1.1.5 21893 b.1.1.5 21894 1fxjA 331 1.73e+01 1fwyA b.81.1.4 28062 c.68.1.5 34520 1hms 132 1.74e+01 1hmt b.60.1.2 27168 1php 394 1.76e+01 16pk c.86.1.1 35452 1cr1A 296 1.77e+01 1cr1A c.37.1.11 32286 1ee2A 373 1.79e+01 2ohxA b.35.1.2 24663 c.2.1.1 29679 1k9vF 201 1.82e+01 c.23.16.1 68365 1b64 91 1.82e+01 1b64 d.58.12.1 39306 1smlA 269 1.82e+01 1smlA d.157.1.1 42053 1as8A 343 1.84e+01 1nif b.6.1.3 23074 b.6.1.3 23075 1louA 101 1.84e+01 1ris d.58.14.1 39323 1g2aA 168 1.92e+01 d.167.1.1 65109 1i1jA 108 1.96e+01 1i1jA b.34.2.1 61531 1ihoA 283 1.98e+01 1ihoA c.26.1.4 62390 1vcc 77 2.01e+01 1vcc d.121.1.1 41092 1tsm 316 2.02e+01 1bkpA d.117.1.1 41024 1dgrW 93 2.03e+01 1caxB 1bsjA 168 2.07e+01 1bs4A d.167.1.1 42302 1e3mA 800 2.17e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1cqmA 101 2.17e+01 1ris d.58.14.1 39321 1bxxA 285 2.18e+01 1bw8A b.2.7.1 22483 1bs4A 168 2.20e+01 1bs4A d.167.1.1 42287 1stfI 98 2.20e+01 1stfI d.17.1.2 38006 1enfA 212 2.21e+01 3seb b.40.2.2 25198 d.15.6.1 37787 1avwB 171 2.23e+01 1wba b.42.4.1 25599 1xat 212 2.25e+01 2xat b.81.1.3 28059 1dgwY 93 2.26e+01 1caxB 1c1lA 136 2.28e+01 1c1lA b.29.1.3 24219 1iazA 179 2.28e+01 1iazA b.97.1.1 62131 2ohxA 374 2.30e+01 2ohxA b.35.1.2 24669 c.2.1.1 29685 1lh1 153 2.31e+01 2gdm a.1.1.2 15222 1bdo 80 2.32e+01 1bdo b.84.1.1 28214 1c8kA 842 2.34e+01 1a8i c.87.1.4 35491 1gaxA 862 2.37e+01 1gaxA a.27.1.1 16928 b.51.1.1 26893 c.26.1.1 31595 1et7A 341 2.39e+01 1nif b.6.1.3 23070 b.6.1.3 23071 1fx3B 169 2.43e+01 1fx3B d.33.1.1 38525 1g2oA 268 2.44e+01 1b8oA c.56.2.1 60228 1bw8A 321 2.48e+01 1bw8A b.2.7.1 22482 1ao0A 459 2.55e+01 1ecfB c.61.1.1 34049 d.153.1.1 41816 1lx7A 253 2.59e+01 2hfh 109 2.60e+01 2hfh a.4.5.14 16145 1bwwA 109 2.62e+01 8fabA b.1.1.1 20518 1ezvI 55 2.62e+01 1be3J f.2.1.8 59553 1f2dA 341 2.66e+01 1f2dA c.79.1.1 35298 1aojA 60 2.67e+01 1aojA b.34.2.1 24555 1gcvA 140 2.69e+01 1cg5B a.1.1.2 15410 1vcbC 160 2.70e+01 1vcbC b.3.3.1 22535 1umuA 116 2.70e+01 1umuA b.87.1.1 28382 1f0xA 571 2.73e+01 1f0xA d.58.32.2 39483 d.145.1.1 41746 1jmcA 246 2.76e+01 1jmcA b.40.4.3 25300 b.40.4.3 25301 1f5mB 180 2.78e+01 1f5mB d.110.2.1 40896 1jzgA 128 2.80e+01 b.6.1.1 67855 1c0aA 585 2.83e+01 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1cr0A 296 2.89e+01 1cr1A c.37.1.11 32287 1cb0A 283 2.94e+01 1cb0A c.56.2.1 33790 1dgrM 93 2.95e+01 1caxB b.82.1.2 28101 1fs0E 138 2.95e+01 1aqt a.2.10.1 59997 b.93.1.1 59998 1f28A 297 2.95e+01 1bkpA d.117.1.1 59608 1lid 131 2.99e+01 1hmt b.60.1.2 27184 1azu 128 2.99e+01 1nwpA b.6.1.1 23007 1ktpB 172 3.02e+01 830cA 168 3.03e+01 1ck7A d.92.1.11 40400 1gpwB 201 3.04e+01 c.23.16.1 65461 1bwzA 274 3.11e+01 1bwzA d.21.1.1 38337 d.21.1.1 38338 1jkeA 145 3.21e+01 c.110.1.1 66791 1jr7A 311 3.24e+01 b.82.2.3 63255 1dj7B 75 3.27e+01 1dj7B b.34.4.3 24598 1kl9A 182 3.27e+01 1ayyA 151 3.28e+01 1apyA d.153.1.5 42016 2afgA 140 3.28e+01 1bfg b.42.1.1 25514 1pvxA 194 3.29e+01 1axkA b.29.1.11 24341 1g2bA 62 3.30e+01 1tud b.34.2.1 24488 1quqB 121 3.30e+01 1quqB b.40.4.3 25305 2xat 212 3.38e+01 2xat b.81.1.3 28058 1umuB 116 3.39e+01 1umuA b.87.1.1 28383 1mn1 357 3.41e+01 1arv a.93.1.1 18667 1prgA 270 3.46e+01 2prgA a.123.1.1 19314 1cpcL 172 3.51e+01 1qgwC a.1.1.3 15646 1cqyA 99 3.51e+01 1b9zA b.3.1.1 22527 1qu5A 182 3.51e+01 1qu5A b.26.1.2 23922 1hkbA 917 3.53e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1ab8A 220 3.57e+01 1azsA d.58.29.1 39414 1f5mA 180 3.59e+01 1f5mB d.110.2.1 40895 1cpcB 172 3.61e+01 1qgwC a.1.1.3 15644 1gpb 842 3.61e+01 1a8i c.87.1.4 35478 1i78A 297 3.66e+01 f.4.4.1 66046 2mjpA 193 3.71e+01 1b78A c.51.4.1 33223 1eulA 994 3.72e+01 1eulA f.2.1.10 43726 1eikA 77 3.73e+01 1eikA d.78.1.1 39751 1qhaA 917 3.74e+01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1fyhA 258 3.74e+01 1d9cA a.26.1.3 16907 a.26.1.3 16908 1ayl 541 3.77e+01 1ayl c.91.1.1 64718 c.109.1.1 64719 1ema 236 3.77e+01 1ema d.22.1.1 38339 1f20A 435 3.81e+01 b.43.4.1 64932 c.25.1.4 64933 1qupA 222 3.86e+01 1qupA b.1.8.1 22301 d.58.17.1 39352 1f02T 66 3.87e+01 1f02T j.67.1.1 46360 2lh2 153 3.87e+01 2gdm a.1.1.2 15220 1i7gA 287 3.88e+01 1je0A 236 3.90e+01 c.56.2.1 66581 1tif 78 3.90e+01 1tif d.15.8.1 37836 1hkcA 917 3.90e+01 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1gs5A 258 3.91e+01 1cauA 181 3.93e+01 1dgwA b.82.1.2 28102 1hlrA 907 3.94e+01 a.56.1.1 65850 d.15.4.2 65851 d.41.1.1 65852 d.133.1.1 65853 1h6rA 236 3.95e+01 d.22.1.1 65683 1vapA 123 3.98e+01 1poa a.133.1.2 19548