# List of top-scoring protein chains for t2k-100-30-str2-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 1.16e-18 1ufbA 127 1.57e-14 a.24.16.3 99331 1o3uA 135 2.35e-12 a.24.16.3 86615 1h1wA 289 3.49e-01 d.144.1.7 83460 1uu3A 310 3.74e-01 d.144.1.7 99999 1wwpA 119 4.49e-01 16vpA 366 2.09e+00 16vpA d.180.1.1 42601 1wkbA 810 3.09e+00 3grx 82 3.11e+00 1aba c.47.1.1 32769 1khoA 370 3.34e+00 a.124.1.1,b.12.1.3 72489,72490 1knzA 164 3.47e+00 e.34.1.1 68709 1eg7A 557 3.78e+00 1eg7A c.37.1.10 32241 2g0qA 173 4.27e+00 1e2aA 105 4.53e+00 1e2aA a.7.2.1 16322 1qbgA 272 4.64e+00 1d4aA c.23.5.3 31227 1a17 166 4.80e+00 1a17 a.118.8.1 19206 1kbqA 273 5.03e+00 c.23.5.3 68391 1d4aA 273 5.03e+00 1d4aA c.23.5.3 31219 2pgd 482 5.13e+00 2pgd a.100.1.1,c.2.1.6 18778,30190 1gs5A 258 5.72e+00 c.73.1.2 70395 2e2aA 105 5.74e+00 a.7.2.1 88499 2frvB 536 6.18e+00 1h2rL e.18.1.1 43291 1v3wA 173 6.28e+00 b.81.1.5 100291 1pmzA 86 6.68e+00 a.39.1.10 104195 1ouvA 273 6.69e+00 a.118.18.1 93570 2anxA 146 7.05e+00 1on0A 158 7.12e+00 d.108.1.1 87095 1ppjF 110 7.51e+00 f.27.1.1 104262 1t46A 313 7.74e+00 d.144.1.7 106397 2ag5A 246 8.50e+00 1qcrF 103 8.51e+00 1be3F f.27.1.1 43676 1e7uA 961 8.57e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1wtyA 119 8.76e+00 1ufhA 180 9.85e+00 d.108.1.1 88485 1na3A 91 9.89e+00 k.38.1.1 85481 1mldA 314 1.07e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1frvB 536 1.13e+01 1h2rL e.18.1.1 43296 1np8A 159 1.14e+01 a.39.1.8 92022 1gtxA 472 1.20e+01 1gtxA 1t8qA 336 1.21e+01 c.1.18.3 106669 1mtyB 384 1.25e+01 1mtyB a.25.1.2 16740 1adt 356 1.26e+01 1anv a.54.1.1,g.51.1.1,g.51.1.1 17887,45362,45368 1ydyA 356 1.30e+01 2cfuA 658 1.30e+01 1ohvA 472 1.31e+01 c.67.1.4 93031 1f1eA 154 1.33e+01 a.22.1.2 64927 1mmoB 384 1.35e+01 1mtyB a.25.1.2 16768 1bccF 109 1.41e+01 1be3F f.27.1.1 43700 1tfjA 219 1.43e+01 1izmA 184 1.46e+01 a.199.1.1 90725 1usyA 275 1.50e+01 1w3iA 293 1.51e+01 c.1.10.1 109152 1e8yA 966 1.51e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1ti6A 875 1.52e+01 b.52.2.2,c.81.1.1 106974,106975 1swxA 209 1.53e+01 a.224.1.1 106075 1wbeA 209 1.57e+01 1hu4A 288 1.60e+01 1hu4A 1n5dA 288 1.60e+01 c.2.1.2 80030 2evrA 246 1.65e+01 1e8xA 961 1.66e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1k47A 337 1.66e+01 d.14.1.5,d.58.26.4 72040,72041 1itkA 731 1.79e+01 a.93.1.3,a.93.1.3 71417,71418 1uwkA 557 1.79e+01 e.51.1.1 108065 1v7nV 163 1.79e+01 a.26.1.2 100476 1zq4A 693 1.81e+01 1qhdA 398 1.87e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 1b8aA 438 1.88e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1ca1 370 2.02e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1j30A 144 2.10e+01 a.25.1.1 90806 1a8h 500 2.11e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1x6vA 630 2.13e+01 1mp8A 281 2.14e+01 d.144.1.7 91384 1ii6A 368 2.22e+01 1bg2 c.37.1.9 62413 1ireB 228 2.31e+01 b.34.4.4 76770 1ugpB 226 2.33e+01 b.34.4.4 107832 113l 164 2.38e+01 1l92 d.2.1.3 36678 1qwiA 143 2.38e+01 d.227.1.1 96474 1is1A 185 2.38e+01 d.67.3.1 83704 2avpA 70 2.39e+01 1qxoA 388 2.44e+01 d.258.1.1 96539 2crbA 97 2.45e+01 1lox 662 2.53e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1ry6A 360 2.55e+01 c.37.1.9 98090 1va4A 279 2.55e+01 c.69.1.12 108458 1b4cA 92 2.57e+01 1b4cA a.39.1.2 17169 1zrzA 364 2.58e+01 1hhsA 664 2.66e+01 1hi0P e.8.1.6 61045 1uvjA 664 2.66e+01 e.8.1.6 100045 1fz1C 389 2.67e+01 1mtyB a.25.1.2 16746 1rxwA 336 2.67e+01 a.60.7.1,c.120.1.2 98059,98060 1hi0P 664 2.68e+01 1hi0P e.8.1.6 61051 1alvA 173 2.70e+01 1alvA a.39.1.8 17370 2fkzA 155 2.71e+01 1u6mA 199 2.76e+01 1b8dA 164 2.79e+01 1cpcA a.1.1.3 15665 1p5sA 203 2.85e+01 a.40.1.1 94147 2chgA 226 2.85e+01 1d7mA 101 2.87e+01 1d7mA h.1.10.1 45628 1kiyA 374 2.90e+01 a.128.1.5 72555 1cjcA 460 2.92e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1wcrA 103 3.02e+01 1yyqA 374 3.03e+01 1liaA 164 3.03e+01 1cpcA a.1.1.3 15661 1myt 146 3.06e+01 1a6m a.1.1.2 15207 1etxA 98 3.13e+01 1fipA a.4.1.12 18978 1siqA 392 3.19e+01 a.29.3.1,e.6.1.1 105585,105586 1cnpA 90 3.19e+01 4icb a.39.1.2 17161 103l 167 3.24e+01 1l92 d.2.1.3 36870 1wp1A 474 3.27e+01 1f9aA 168 3.31e+01 1f9aA c.26.1.3 31602 1io7A 368 3.36e+01 1f4tA a.104.1.1 18971 1onxA 390 3.42e+01 b.92.1.7,c.1.9.13 87176,87177 1f89A 291 3.42e+01 d.160.1.1 64988 1uarA 285 3.43e+01 c.46.1.2,c.46.1.2 107762,107763 2ftzA 284 3.45e+01 1rztA 331 3.45e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1tph1 247 3.47e+01 1amk 1w7jA 795 3.57e+01 1l7bA 92 3.58e+01 c.15.1.2 91053 1t98A 287 3.63e+01 3gcb 470 3.65e+01 3gcb d.3.1.1 37032 1dd5A 185 3.68e+01 1dd5A d.67.3.1 39564 1a6r 471 3.70e+01 3gcb d.3.1.1 37033 1elwA 118 3.72e+01 1a17 a.118.8.1 19207 2fq4A 192 3.72e+01 1tzvA 142 3.74e+01 a.79.1.1 107526 1gcb 454 3.75e+01 3gcb d.3.1.1 37034 1pprM 312 3.77e+01 1pprM a.131.1.1,a.131.1.1 19502,19503 1xq8A 140 3.85e+01 1xrhA 351 3.86e+01 1i5pA 633 3.88e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1o5hA 214 3.88e+01 a.191.1.1 92497 1fipA 98 4.10e+01 1fipA a.4.1.12 18980 1nlnA 204 4.13e+01 d.3.1.7 91962 1p2xA 159 4.14e+01 a.40.1.1 104062 1idrA 136 4.15e+01 1dlyA a.1.1.1 62301 2genA 197 4.28e+01 1tueB 218 4.30e+01 b.91.1.1 107324 2ex3B 264 4.33e+01 1adeA 431 4.34e+01 1adeA c.37.1.10 32213 1pn0A 665 4.34e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 2bcqA 335 4.37e+01 1kr7A 110 4.38e+01 a.1.1.4 72890 2bf9A 36 4.41e+01 1x92A 199 4.43e+01 1kfuS 184 4.54e+01 a.39.1.8 68574 1t9kA 347 4.55e+01 c.124.1.5 106721 2coiA 386 4.56e+01 1lylA 504 4.56e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 109l 164 4.58e+01 1l92 d.2.1.3 36781 103m 154 4.65e+01 1a6m a.1.1.2 15124 1mtyD 512 4.67e+01 1mhyD a.25.1.2 16742 1p5zB 263 4.69e+01 c.37.1.1 87815 1jcdA 52 4.72e+01 h.1.16.1 84157 163l 164 4.74e+01 1l92 d.2.1.3 36658 1ag8A 499 4.77e+01 1bpwA c.82.1.1 35341 3fisA 98 4.86e+01 1fipA a.4.1.12 18994 1xjdA 345 4.90e+01 1hfeS 123 4.93e+01 1hfeS a.137.4.1 19640 2eshA 118 4.96e+01 1puc 105 5.02e+01 1puc d.97.1.1 40675 1b8oA 284 5.05e+01 1b8oA c.56.2.1 33762 1jchA 551 5.12e+01 b.101.1.1,b.110.1.1,h.4.9.1 66491,66492,66493 1jchC 551 5.12e+01 b.101.1.1,b.110.1.1,h.4.9.1 66495,66496,66497 1r2rA 248 5.15e+01 c.1.1.1 96875 1xg2B 153 5.16e+01 1ppt 36 5.30e+01 1ppt j.6.1.1 46089 1ydwA 362 5.31e+01 1e1oA 504 5.34e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 2a61A 145 5.36e+01 1t3tA 1303 5.39e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1kamA 194 5.42e+01 c.26.1.3 72254 1yn9A 169 5.45e+01 155l 164 5.46e+01 1l92 d.2.1.3 36762 1mmoD 512 5.47e+01 1mhyD a.25.1.2 16770 1om2A 95 5.49e+01 1om2A a.23.4.1 16520 1mo0A 275 5.52e+01 c.1.1.1 79329 1cwwA 102 5.54e+01 1cy5A a.77.1.3 18434 1vjpA 394 5.56e+01 c.2.1.3,d.81.1.3 100828,100829 1pvvA 315 5.71e+01 c.78.1.1,c.78.1.1 95190,95191 1eysL 280 5.73e+01 6prcL f.26.1.1 43515 1ynmA 247 5.77e+01 165l 164 5.77e+01 1l92 d.2.1.3 36680 120l 164 5.78e+01 1l92 d.2.1.3 36720 111l 164 5.84e+01 1l92 d.2.1.3 36661 152l 164 5.88e+01 1l92 d.2.1.3 36904 159l 164 5.91e+01 1l92 d.2.1.3 36682 1r2zA 274 5.92e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1a1s 314 5.92e+01 1othA c.78.1.1,c.78.1.1 35258,35259 167lA 164 5.95e+01 1l92 d.2.1.3 36937 1i8oA 114 5.95e+01 1ycc a.3.1.1 61979 1vybA 238 5.96e+01 d.151.1.1 108897 1in4A 334 6.01e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1jfaA 374 6.02e+01 a.128.1.5 66622 1hh7A 114 6.03e+01 1ycc a.3.1.1 15896 122l 164 6.12e+01 1l92 d.2.1.3 36667 1qf5A 431 6.13e+01 1adeA c.37.1.10 32212 138l 164 6.22e+01 1l92 d.2.1.3 36679 114l 164 6.23e+01 1l92 d.2.1.3 36663 1ag9A 175 6.28e+01 1rcf c.23.5.1 31178 1llmC 88 6.29e+01 g.37.1.1,g.37.1.1 91059,91060 1rt8A 513 6.33e+01 a.40.1.1 105095 130l 164 6.34e+01 1l92 d.2.1.3 36638 129l 164 6.38e+01 1l92 d.2.1.3 36660 1in6A 334 6.39e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 166l 164 6.39e+01 1l92 d.2.1.3 36681 1x9zA 188 6.39e+01 1kfnA 56 6.39e+01 h.1.16.1 72422 1ji6A 589 6.41e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1o04A 500 6.45e+01 c.82.1.1 86508 125l 164 6.45e+01 1l92 d.2.1.3 36672 118l 164 6.46e+01 1l92 d.2.1.3 36642 161l 164 6.48e+01 1l92 d.2.1.3 36636 119l 164 6.50e+01 1l92 d.2.1.3 36622 1osa 148 6.51e+01 1cll a.39.1.5 17300 142l 164 6.53e+01 1l92 d.2.1.3 36874 1c3cA 429 6.54e+01 1c3cA a.127.1.1 19425 131l 164 6.56e+01 1l92 d.2.1.3 36685 156l 164 6.62e+01 1l92 d.2.1.3 36709 1ii2A 524 6.64e+01 c.91.1.1,c.109.1.1 66146,66147 2thiA 379 6.65e+01 2thiA c.94.1.1 35794 1pme 380 6.67e+01 1hcl d.144.1.7 41653 2fsrA 195 6.72e+01 160l 164 6.72e+01 1l92 d.2.1.3 36748 1u00A 227 6.73e+01 1q0sA 259 6.75e+01 c.66.1.28 95509 112l 164 6.75e+01 1l92 d.2.1.3 36677 5croA 66 6.84e+01 1orc a.35.1.2 17044 139l 164 6.84e+01 1l92 d.2.1.3 36643 1rlhA 173 6.92e+01 d.256.1.1 97646 1tazA 365 6.95e+01 a.211.1.2 106734 1jfgA 374 6.97e+01 a.128.1.5 66636 145l 164 6.99e+01 1l92 d.2.1.3 36860 158l 164 6.99e+01 1l92 d.2.1.3 36747 1fohA 664 7.04e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1ah7 245 7.06e+01 1ah7 a.124.1.1 19339 1lw9A 164 7.07e+01 d.2.1.3 84727 1jagA 241 7.09e+01 c.37.1.1 66463 170l 164 7.10e+01 1l92 d.2.1.3 36968 1f60A 458 7.14e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1pzxA 289 7.15e+01 c.119.1.1 95484 2f1kA 279 7.16e+01 1rkbA 173 7.17e+01 1y21A 282 7.18e+01 126l 164 7.26e+01 1l92 d.2.1.3 36699 1tvoA 368 7.30e+01 1oshA 232 7.31e+01 a.123.1.1 93496 1dj8A 89 7.38e+01 1bg8A a.57.1.1 17919 1be3F 110 7.39e+01 1be3F f.27.1.1 43668 1y0kA 209 7.39e+01 1r6rA 100 7.49e+01 a.190.1.1 97158 1yoyA 175 7.49e+01 2f2bA 246 7.50e+01 157l 164 7.52e+01 1l92 d.2.1.3 36717 2b2hA 399 7.58e+01 196l 164 7.58e+01 1l92 d.2.1.3 36927 1si6X 282 7.58e+01 1brwA 433 7.64e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1sjiA 350 7.66e+01 1irl 133 7.66e+01 3inkC a.26.1.2 16883 1ysc 421 7.67e+01 1ivyA c.69.1.5 34652 1l92 164 7.72e+01 1l92 d.2.1.3 36629 2gtrA 261 7.72e+01 195l 164 7.74e+01 1l92 d.2.1.3 36841 1o6lA 337 7.74e+01 d.144.1.7 81092 144l 164 7.77e+01 1l92 d.2.1.3 36893 164l 164 7.79e+01 1l92 d.2.1.3 36714 1v37A 177 7.79e+01 1xtcA 194 7.83e+01 1lt3A d.166.1.1 42259 140l 164 7.85e+01 1l92 d.2.1.3 36891 197l 164 7.93e+01 1l92 d.2.1.3 36911 1ahr 146 7.93e+01 1cll a.39.1.5 17287 1vydA 116 7.95e+01 a.3.1.1 108900 198l 164 7.97e+01 1l92 d.2.1.3 36785 1q52A 314 8.00e+01 c.14.1.3 95846 1wt4A 73 8.00e+01 1mho 88 8.05e+01 1b4cA a.39.1.2 17171 180lA 164 8.05e+01 1l92 d.2.1.3 36867 1ryp2 233 8.06e+01 1ryp2 1fjgB 256 8.06e+01 1fjfB c.23.15.1 31400 143l 164 8.07e+01 1l92 d.2.1.3 36857 1c1gD 284 8.07e+01 1c1gA h.1.5.1 45576 1oe9A 795 8.08e+01 b.34.3.1,c.37.1.9 92792,92793 1ykhA 108 8.13e+01 2aelA 374 8.14e+01 199l 164 8.16e+01 1l92 d.2.1.3 36855 1c1gB 284 8.18e+01 1c1gB h.1.5.1 45574 1p36A 164 8.19e+01 d.2.1.3 93978 1o1xA 155 8.19e+01 c.121.1.1 86553 2b5gA 171 8.27e+01 1uwoA 92 8.29e+01 4icb a.39.1.2 17174 2fmlA 273 8.29e+01 1v1rA 400 8.30e+01 c.36.1.11 108272 1nkpB 83 8.30e+01 a.38.1.1 80574 128l 164 8.31e+01 1l92 d.2.1.3 36634 2arsA 262 8.35e+01 1d3yA 301 8.36e+01 1d3yA e.12.1.1 43252 1u5dA 108 8.38e+01 1kmiZ 214 8.39e+01 h.4.11.1 72752 1wzdA 215 8.40e+01 2f60K 64 8.40e+01 1fm2B 520 8.42e+01 1fm2B 1cpcA 162 8.45e+01 1cpcA a.1.1.3 15643 1nhyA 219 8.47e+01 a.45.1.1,c.47.1.5 80520,80521 1wmaA 276 8.54e+01 1f16A 192 8.57e+01 1f16A f.1.4.1 43400 1zesA 125 8.57e+01 1evsA 187 8.62e+01 1evsA a.26.1.1 16845 123l 164 8.68e+01 1l92 d.2.1.3 36697 1g0u1 266 8.68e+01 1cw0A 155 8.71e+01 1vsrA c.52.1.15 33333 1c2rA 116 8.73e+01 1ycc a.3.1.1 15887 1wn0A 145 8.78e+01 1ifm 46 8.84e+01 1ql1A h.1.4.1 45557 1iioA 84 8.89e+01 a.39.4.1 66150 146l 164 8.90e+01 1l92 d.2.1.3 36763 2arkA 188 8.91e+01 1cv8 174 8.97e+01 1cv8 d.3.1.1 37089 1npsA 88 8.97e+01 1prs b.11.1.1 23622