# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-scores 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 1wolA 122 1.22e-18 1ufbA 127 1.55e-14 a.24.16.3 99331 1o3uA 135 1.41e-12 a.24.16.3 86615 1wwpA 119 5.48e-01 1h1wA 289 8.87e-01 d.144.1.7 83460 1eg7A 557 9.07e-01 1eg7A c.37.1.10 32241 1uu3A 310 1.13e+00 d.144.1.7 99999 2g0qA 173 2.75e+00 3grx 82 3.06e+00 1aba c.47.1.1 32769 1a17 166 3.15e+00 1a17 a.118.8.1 19206 1e2aA 105 3.45e+00 1e2aA a.7.2.1 16322 1knzA 164 3.83e+00 e.34.1.1 68709 1wkbA 810 3.85e+00 1khoA 370 3.98e+00 a.124.1.1,b.12.1.3 72489,72490 1qcrF 103 4.44e+00 1be3F f.27.1.1 43676 2e2aA 105 4.61e+00 a.7.2.1 88499 1hu4A 288 4.91e+00 1hu4A 1n5dA 288 4.91e+00 c.2.1.2 80030 2anxA 146 5.27e+00 16vpA 366 5.55e+00 16vpA d.180.1.1 42601 1lqaA 346 5.63e+00 c.1.7.1 84674 2frvB 536 5.80e+00 1h2rL e.18.1.1 43291 1kamA 194 5.88e+00 c.26.1.3 72254 1gtxA 472 6.30e+00 1gtxA 1pmzA 86 6.49e+00 a.39.1.10 104195 1v3wA 173 6.50e+00 b.81.1.5 100291 1ouvA 273 6.55e+00 a.118.18.1 93570 1wtyA 119 6.82e+00 2ag5A 246 7.29e+00 1ppjF 110 7.41e+00 f.27.1.1 104262 1ohvA 472 7.90e+00 c.67.1.4 93031 1k47A 337 8.10e+00 d.14.1.5,d.58.26.4 72040,72041 1adt 356 8.12e+00 1anv a.54.1.1,g.51.1.1,g.51.1.1 17887,45362,45368 1t46A 313 8.69e+00 d.144.1.7 106397 1qhdA 398 8.91e+00 1qhdA a.115.1.2,b.19.1.1 63324,63325 1na3A 91 8.95e+00 k.38.1.1 85481 1zq4A 693 9.21e+00 1j30A 144 9.50e+00 a.25.1.1 90806 1q0sA 259 9.55e+00 c.66.1.28 95509 1x6vA 630 1.02e+01 1yf3A 259 1.02e+01 1izmA 184 1.12e+01 a.199.1.1 90725 1gs5A 258 1.12e+01 c.73.1.2 70395 1mo0A 275 1.14e+01 c.1.1.1 79329 1usyA 275 1.15e+01 1uarA 285 1.18e+01 c.46.1.2,c.46.1.2 107762,107763 1w3iA 293 1.26e+01 c.1.10.1 109152 2cfuA 658 1.29e+01 2ftzA 284 1.30e+01 1frvB 536 1.33e+01 1h2rL e.18.1.1 43296 1swxA 209 1.41e+01 a.224.1.1 106075 1tph1 247 1.44e+01 1amk 1kiyA 374 1.46e+01 a.128.1.5 72555 1r2rA 248 1.49e+01 c.1.1.1 96875 2crbA 97 1.53e+01 1yyqA 374 1.58e+01 1e7uA 961 1.58e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 2avpA 70 1.68e+01 1lox 662 1.71e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1mldA 314 1.73e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 2pgd 482 1.85e+01 2pgd a.100.1.1,c.2.1.6 18778,30190 2fkzA 155 1.87e+01 1va4A 279 1.90e+01 c.69.1.12 108458 1tfjA 219 1.97e+01 1bccF 109 1.98e+01 1be3F f.27.1.1 43700 1v7nV 163 1.98e+01 a.26.1.2 100476 1wbeA 209 1.99e+01 1cjcA 460 2.02e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1sfjA 238 2.05e+01 2c31A 568 2.10e+01 113l 164 2.16e+01 1l92 d.2.1.3 36678 2btzA 394 2.19e+01 2chgA 226 2.27e+01 1b8dA 164 2.28e+01 1cpcA a.1.1.3 15665 1np8A 159 2.31e+01 a.39.1.8 92022 1wmaA 276 2.35e+01 1b4cA 92 2.37e+01 1b4cA a.39.1.2 17169 1iujA 106 2.40e+01 d.58.4.5 90701 1on0A 158 2.42e+01 d.108.1.1 87095 1uwkA 557 2.43e+01 e.51.1.1 108065 1jfaA 374 2.46e+01 a.128.1.5 66622 1e8xA 961 2.47e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1wcrA 103 2.50e+01 1elwA 118 2.51e+01 1a17 a.118.8.1 19207 1spvA 184 2.54e+01 c.50.1.2 98957 1p2xA 159 2.56e+01 a.40.1.1 104062 1b8oA 284 2.56e+01 1b8oA c.56.2.1 33762 1pprM 312 2.60e+01 1pprM a.131.1.1,a.131.1.1 19502,19503 1e8yA 966 2.62e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 103l 167 2.62e+01 1l92 d.2.1.3 36870 1jagA 241 2.64e+01 c.37.1.1 66463 163l 164 2.64e+01 1l92 d.2.1.3 36658 1t9kA 347 2.67e+01 c.124.1.5 106721 1hi0P 664 2.67e+01 1hi0P e.8.1.6 61051 1hhsA 664 2.68e+01 1hi0P e.8.1.6 61045 1uvjA 664 2.68e+01 e.8.1.6 100045 1b8aA 438 2.70e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1itkA 731 2.73e+01 a.93.1.3,a.93.1.3 71417,71418 1v37A 177 2.77e+01 1liaA 164 2.87e+01 1cpcA a.1.1.3 15661 1mmoD 512 2.95e+01 1mhyD a.25.1.2 16770 1ptmA 329 2.99e+01 c.77.1.3 95104 1ji6A 589 3.00e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1ca1 370 3.00e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1sflA 238 3.06e+01 1dd5A 185 3.10e+01 1dd5A d.67.3.1 39564 2evrA 246 3.10e+01 1xrhA 351 3.11e+01 1tzvA 142 3.14e+01 a.79.1.1 107526 1d7mA 101 3.14e+01 1d7mA h.1.10.1 45628 2fq4A 192 3.17e+01 2fymA 431 3.19e+01 2eshA 118 3.21e+01 1jfgA 374 3.23e+01 a.128.1.5 66636 1is1A 185 3.26e+01 d.67.3.1 83704 1mho 88 3.26e+01 1b4cA a.39.1.2 17171 1hfeS 123 3.33e+01 1hfeS a.137.4.1 19640 1qwiA 143 3.37e+01 d.227.1.1 96474 1f1eA 154 3.38e+01 a.22.1.2 64927 1p5sA 203 3.45e+01 a.40.1.1 94147 2b2hA 399 3.51e+01 1p5zB 263 3.53e+01 c.37.1.1 87815 1qhfA 240 3.55e+01 1qhfA c.60.1.1 33960 1t98A 287 3.60e+01 1be3F 110 3.65e+01 1be3F f.27.1.1 43668 1w9yA 319 3.66e+01 1a8h 500 3.73e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1siqA 392 3.75e+01 a.29.3.1,e.6.1.1 105585,105586 3gcb 470 3.76e+01 3gcb d.3.1.1 37032 1a6r 471 3.77e+01 3gcb d.3.1.1 37033 1rxwA 336 3.78e+01 a.60.7.1,c.120.1.2 98059,98060 1ti6A 875 3.86e+01 b.52.2.2,c.81.1.1 106974,106975 1sceA 112 3.89e+01 1puc d.97.1.1 40676 4pfk 319 3.92e+01 3pfk c.89.1.1 35582 1o5hA 214 3.99e+01 a.191.1.1 92497 1e1oA 504 4.03e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 3pfk 319 4.03e+01 3pfk c.89.1.1 35581 159l 164 4.04e+01 1l92 d.2.1.3 36682 1ufhA 180 4.06e+01 d.108.1.1 88485 1u5dA 108 4.09e+01 1mtyD 512 4.10e+01 1mhyD a.25.1.2 16742 1myt 146 4.11e+01 1a6m a.1.1.2 15207 2gmyA 153 4.21e+01 1t0qA 498 4.21e+01 a.25.1.2 106220 1gcb 454 4.21e+01 3gcb d.3.1.1 37034 1bq3B 246 4.27e+01 1qhfA c.60.1.1 33979 2a61A 145 4.28e+01 1etxA 98 4.41e+01 1fipA a.4.1.12 18978 1f60A 458 4.41e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1ireB 228 4.43e+01 b.34.4.4 76770 1ugpB 226 4.46e+01 b.34.4.4 107832 1r2zA 274 4.47e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1ii2A 524 4.52e+01 c.91.1.1,c.109.1.1 66146,66147 1e9iA 431 4.56e+01 c.1.11.1,d.54.1.1 64818,64819 2aelA 374 4.62e+01 1hzdA 272 4.64e+01 c.14.1.3 65969 2genA 197 4.67e+01 109l 164 4.86e+01 1l92 d.2.1.3 36781 1d4aA 273 4.88e+01 1d4aA c.23.5.3 31219 1uocA 289 4.88e+01 c.55.3.9 99686 155l 164 4.89e+01 1l92 d.2.1.3 36762 2b0jA 358 4.94e+01 2bf9A 36 4.95e+01 1qo7A 394 4.96e+01 1qo7A c.69.1.11 34697 1kbqA 273 4.98e+01 c.23.5.3 68391 1qbgA 272 5.11e+01 1d4aA c.23.5.3 31227 1cz1A 394 5.13e+01 1cz1A c.1.8.3 28839 1ur4A 399 5.14e+01 1mp8A 281 5.14e+01 d.144.1.7 91384 152l 164 5.16e+01 1l92 d.2.1.3 36904 1fipA 98 5.19e+01 1fipA a.4.1.12 18980 2fiqA 420 5.21e+01 1ah7 245 5.21e+01 1ah7 a.124.1.1 19339 1w79A 489 5.26e+01 1xg2B 153 5.26e+01 1bif 469 5.28e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1jcdA 52 5.28e+01 h.1.16.1 84157 120l 164 5.36e+01 1l92 d.2.1.3 36720 165l 164 5.37e+01 1l92 d.2.1.3 36680 1o5iA 249 5.45e+01 c.2.1.2 92499 1zdrA 164 5.57e+01 167lA 164 5.61e+01 1l92 d.2.1.3 36937 1zcdA 388 5.61e+01 1dw9A 156 5.62e+01 1dw9A a.35.1.4,d.72.1.1 17065,39596 114l 164 5.63e+01 1l92 d.2.1.3 36663 1ctn 540 5.64e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1o7fA 469 5.66e+01 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 2f1kA 279 5.69e+01 138l 164 5.69e+01 1l92 d.2.1.3 36679 1tueB 218 5.70e+01 b.91.1.1 107324 111l 164 5.71e+01 1l92 d.2.1.3 36661 1ynmA 247 5.72e+01 122l 164 5.76e+01 1l92 d.2.1.3 36667 125l 164 5.78e+01 1l92 d.2.1.3 36672 2c4wA 176 5.79e+01 130l 164 5.86e+01 1l92 d.2.1.3 36638 1h97A 147 5.88e+01 1h97A a.1.1.2 60812 2bcgG 453 5.88e+01 166l 164 5.88e+01 1l92 d.2.1.3 36681 1mek 120 5.91e+01 1erv c.47.1.2 32775 129l 164 5.91e+01 1l92 d.2.1.3 36660 161l 164 5.91e+01 1l92 d.2.1.3 36636 142l 164 5.93e+01 1l92 d.2.1.3 36874 131l 164 5.95e+01 1l92 d.2.1.3 36685 119l 164 6.01e+01 1l92 d.2.1.3 36622 118l 164 6.05e+01 1l92 d.2.1.3 36642 6acn 754 6.07e+01 1amj c.8.2.1,c.83.1.1 30721,35397 1cnpA 90 6.07e+01 4icb a.39.1.2 17161 6pfkA 319 6.08e+01 3pfk c.89.1.1 35583 1aazA 87 6.09e+01 1aba c.47.1.1 32761 1edqA 540 6.10e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1dwkA 156 6.11e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 3fisA 98 6.12e+01 1fipA a.4.1.12 18994 1uuqA 440 6.16e+01 c.1.8.3 100015 1k9tA 540 6.22e+01 b.1.18.2,c.1.8.5,d.26.3.1 77298,77299,77300 1ii6A 368 6.24e+01 1bg2 c.37.1.9 62413 156l 164 6.27e+01 1l92 d.2.1.3 36709 145l 164 6.27e+01 1l92 d.2.1.3 36860 1iioA 84 6.29e+01 a.39.4.1 66150 1ry6A 360 6.31e+01 c.37.1.9 98090 1yoyA 175 6.34e+01 139l 164 6.35e+01 1l92 d.2.1.3 36643 1wp1A 474 6.37e+01 112l 164 6.38e+01 1l92 d.2.1.3 36677 1i8oA 114 6.39e+01 1ycc a.3.1.1 61979 1xq8A 140 6.40e+01 1r6rA 100 6.47e+01 a.190.1.1 97158 160l 164 6.48e+01 1l92 d.2.1.3 36748 1alvA 173 6.53e+01 1alvA a.39.1.8 17370 1qazA 351 6.54e+01 1qazA a.102.3.1 18848 1cw0A 155 6.55e+01 1vsrA c.52.1.15 33333 158l 164 6.56e+01 1l92 d.2.1.3 36747 170l 164 6.58e+01 1l92 d.2.1.3 36968 1om2A 95 6.64e+01 1om2A a.23.4.1 16520 1lylA 504 6.66e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1mioB 458 6.67e+01 1qguB c.92.2.3 35602 1evsA 187 6.70e+01 1evsA a.26.1.1 16845 1io7A 368 6.70e+01 1f4tA a.104.1.1 18971 2ae5B 528 6.71e+01 1rkbA 173 6.72e+01 1hh7A 114 6.72e+01 1ycc a.3.1.1 15896 1ppt 36 6.73e+01 1ppt j.6.1.1 46089 2thiA 379 6.74e+01 2thiA c.94.1.1 35794 1lw9A 164 6.81e+01 d.2.1.3 84727 1u6mA 199 6.81e+01 1g01A 364 6.82e+01 7a3hA c.1.8.3 60161 1tcvA 287 6.83e+01 1ann 318 6.88e+01 1avc a.65.1.1 18151 126l 164 6.92e+01 1l92 d.2.1.3 36699 2f2bA 246 6.92e+01 1g0cA 364 6.95e+01 7a3hA c.1.8.3 60165 1ykhA 108 7.01e+01 1gk1B 522 7.02e+01 196l 164 7.04e+01 1l92 d.2.1.3 36927 1jchA 551 7.09e+01 b.101.1.1,b.110.1.1,h.4.9.1 66491,66492,66493 1jchC 551 7.09e+01 b.101.1.1,b.110.1.1,h.4.9.1 66495,66496,66497 1o6lA 337 7.13e+01 d.144.1.7 81092 1xjdA 345 7.16e+01 1apxA 249 7.16e+01 1ryc a.93.1.1 18669 1or0B 528 7.18e+01 1puc 105 7.19e+01 1puc d.97.1.1 40675 1l92 164 7.26e+01 1l92 d.2.1.3 36629 195l 164 7.30e+01 1l92 d.2.1.3 36841 1nlnA 204 7.33e+01 d.3.1.7 91962 1ahr 146 7.34e+01 1cll a.39.1.5 17287 144l 164 7.34e+01 1l92 d.2.1.3 36893 2arsA 262 7.37e+01 1d3yA 301 7.37e+01 1d3yA e.12.1.1 43252 1d7kA 421 7.38e+01 7odcA b.49.2.3,c.1.6.1 26486,28648 1n3lA 372 7.41e+01 c.26.1.1 79966 1pn0A 665 7.42e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 140l 164 7.46e+01 1l92 d.2.1.3 36891 164l 164 7.54e+01 1l92 d.2.1.3 36714 1xhlA 297 7.58e+01 c.2.1.2 109591 198l 164 7.61e+01 1l92 d.2.1.3 36785 1r1dA 247 7.61e+01 c.69.1.29 96813 1wt4A 73 7.63e+01 197l 164 7.63e+01 1l92 d.2.1.3 36911 199l 164 7.65e+01 1l92 d.2.1.3 36855 1adeA 431 7.68e+01 1adeA c.37.1.10 32213 143l 164 7.68e+01 1l92 d.2.1.3 36857 1kfnA 56 7.68e+01 h.1.16.1 72422 1wn0A 145 7.77e+01 1idrA 136 7.79e+01 1dlyA a.1.1.1 62301 1cpcA 162 7.79e+01 1cpcA a.1.1.3 15643 3bifA 468 7.80e+01 1bif c.37.1.7,c.60.1.4 31962,34008 1s6cA 183 7.80e+01 a.39.1.5 98594 2c1vA 338 7.80e+01 1ui0A 205 7.85e+01 c.18.1.2 99411 1h1nA 305 7.89e+01 c.1.8.3 70855 1ykuA 136 7.94e+01 1kmiZ 214 7.95e+01 h.4.11.1 72752 1xkqA 280 7.97e+01 180lA 164 7.97e+01 1l92 d.2.1.3 36867 1uwoA 92 7.98e+01 4icb a.39.1.2 17174 1irl 133 7.98e+01 3inkC a.26.1.2 16883 1x92A 199 7.99e+01 123l 164 8.00e+01 1l92 d.2.1.3 36697 1b7bA 310 8.02e+01 1b7bA c.73.1.1 34963 1cwwA 102 8.03e+01 1cy5A a.77.1.3 18434 1zrzA 364 8.04e+01 1fm2B 520 8.05e+01 1fm2B 1iqcA 308 8.06e+01 a.3.1.5,a.3.1.5 66266,66267 1fztA 211 8.07e+01 1qhfA c.60.1.1 60158 157l 164 8.08e+01 1l92 d.2.1.3 36717 1sjiA 350 8.08e+01 2bifA 469 8.12e+01 1bif c.37.1.7,c.60.1.4 31963,34009 103m 154 8.12e+01 1a6m a.1.1.2 15124 1brwA 433 8.17e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1z2iA 358 8.18e+01 1v93A 296 8.18e+01 c.1.23.1 100532 1i60A 278 8.19e+01 c.1.15.4 71118 1onxA 390 8.25e+01 b.92.1.7,c.1.9.13 87176,87177 1neyA 247 8.29e+01 c.1.1.1 80449 1u00A 227 8.31e+01 1y0kA 209 8.32e+01 1ah4 315 8.41e+01 1frb c.1.7.1 28684 1l1zA 274 8.43e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 2fcwA 109 8.44e+01 1vlgA 176 8.45e+01 a.25.1.1 108816 1gzsB 165 8.46e+01 a.168.1.1 76425 1o82A 70 8.58e+01 a.64.2.1 92630 2c8mA 262 8.61e+01 146l 164 8.68e+01 1l92 d.2.1.3 36763 1h6pA 203 8.75e+01 a.146.1.1 60690 2f60K 64 8.76e+01 1c1gD 284 8.77e+01 1c1gA h.1.5.1 45576 1cfpA 92 8.77e+01 1b4cA a.39.1.2 17172 1xo5A 183 8.78e+01 1ivhA 394 8.78e+01 3mdeA a.29.3.1,e.6.1.1 16608,42869 128l 164 8.81e+01 1l92 d.2.1.3 36634 1gw5S 142 8.88e+01 d.110.4.2 70633 1hvyA 288 8.90e+01 1bkpA d.117.1.1 41049 1mwwA 128 8.96e+01 d.80.1.4 91483 1anv 356 8.97e+01 1anv a.54.1.1,g.51.1.1,g.51.1.1 17890,45365,45371