# List of top-scoring protein chains for t2k-100-30-bys 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 1ks8A 433 3.35e-02 a.102.1.2 77519 1vk3A 615 1.61e-01 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1pq1A 196 2.04e-01 f.1.4.1 -12055 1foeA 377 2.45e-01 1foeA a.87.1.1 18517 b.55.1.1 26969 1af3 196 4.14e-01 1maz f.1.4.1 43397 1kgnA 329 5.74e-01 a.25.1.2 68584 1b3uA 588 7.31e-01 1b3uA a.118.1.2 19135 1jcrA 377 8.71e-01 a.118.6.1 66506 1qbqA 333 1.27e+00 1ft1A a.118.6.1 19187 1cnt2 187 1.38e+00 1cnt3 1vsgA 364 1.41e+00 1vsgA h.4.1.1 45782 1d8dA 377 1.55e+00 1ft1A a.118.6.1 19185 1rh5A 436 1.70e+00 unknown_sccs -12298 1maz 221 1.72e+00 1maz f.1.4.1 43393 1l2iA 261 1.72e+00 a.123.1.1 73503 1dn1B 267 1.78e+00 1dn1B a.47.2.1 17771 1ld8A 382 1.79e+00 a.118.6.1 73838 1bp7A 152 1.89e+00 1bp7A d.95.2.1 40568 1n00A 321 1.94e+00 a.65.1.1 85241 1qs1A 462 1.97e+00 1qs1A d.166.1.1 42260 d.166.1.1 42261 1a8i 842 1.99e+00 1a8i c.87.1.4 35490 1ojhA 65 2.07e+00 1gpb 842 2.11e+00 1a8i c.87.1.4 35478 1n97A 389 2.23e+00 a.104.1.1 80335 1tbmA 326 2.33e+00 1hiwA 133 2.40e+00 1hiwA a.61.1.1 18122 3ertA 261 2.40e+00 3erdA a.123.1.1 19292 1jcqA 382 2.41e+00 a.118.6.1 66504 1cii 602 2.69e+00 1cii f.1.1.1 43381 h.4.3.1 45787 1flcB 175 2.79e+00 1flcB h.3.1.1 45716 1fjgM 126 2.82e+00 1fjfM a.156.1.1 16293 1dvpA 220 2.86e+00 1dvpA a.118.9.2 19216 g.50.1.1 45358 1c8kA 842 2.91e+00 1a8i c.87.1.4 35491 3erdA 261 3.09e+00 3erdA a.123.1.1 19293 1g9zA 152 3.18e+00 1bp7A d.95.2.1 60408 1bxlA 181 3.18e+00 1maz f.1.4.1 43396 1odoA 408 3.35e+00 a.104.1.1 -1463 1t7pA 698 3.43e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1kx9A 112 3.51e+00 unknown_sccs 77602 1ft1A 377 3.74e+00 1ft1A a.118.6.1 19186 1a32 88 3.91e+00 1a32 a.16.1.2 16384 1aisA 182 4.04e+00 1ytbA d.129.1.1 41288 d.129.1.1 41289 1ng6A 148 4.10e+00 a.182.1.1 85670 1evsA 187 4.21e+00 1evsA a.26.1.1 16845 1aj3 110 4.25e+00 1cunA a.7.1.1 16319 1cnt3 187 4.28e+00 1cnt3 1dbhA 354 4.56e+00 1awe a.87.1.1 18514 b.55.1.1 26967 1ow4A 129 4.59e+00 a.39.2.1 -876 1cnt1 187 4.70e+00 1cnt3 1htjF 210 4.80e+00 1htjF a.91.1.1 61254 1jytA 163 4.89e+00 b.94.1.1 67489 1h5uA 842 4.91e+00 1a8i c.87.1.4 60655 1f3aA 222 4.94e+00 1pgtA a.45.1.1 17701 c.47.1.5 32995 1nm8A 616 5.19e+00 c.43.1.3 85872 c.43.1.3 85873 1s9pA 227 5.35e+00 1bf5A 545 5.62e+00 1bg1A a.47.1.1 17766 b.2.5.5 22460 d.93.1.1 40526 1gaxA 862 5.78e+00 1gaxA a.2.7.3 75842 a.27.1.1 75843 b.51.1.1 26893 c.26.1.1 31595 1qkmA 255 5.81e+00 3erdA a.123.1.1 19309 1vd5A 377 5.82e+00 1k3yA 221 5.87e+00 a.45.1.1 77245 c.47.1.5 77246 1el4A 195 6.08e+00 1ej3A a.39.1.5 59453 1ej3A 191 6.17e+00 1ej3A a.39.1.5 17259 1mijA 152 6.51e+00 a.4.1.1 79150 1n8vA 112 6.63e+00 unknown_sccs 85457 1k3lA 221 6.63e+00 a.45.1.1 77229 c.47.1.5 77230 1oyeA 1049 6.85e+00 d.58.44.1 87587 d.58.44.1 87588 d.58.44.1 87589 d.58.44.1 87590 d.225.1.1 87591 d.225.1.1 87592 f.35.1.1 87593 f.35.1.1 87594 1jixA 351 6.87e+00 1c3jA c.87.1.1 63081 1jg7A 351 6.94e+00 1c3jA c.87.1.1 62945 1ai7A 209 7.04e+00 1ajqA d.153.1.2 41845 1c3jA 351 7.05e+00 1c3jA c.87.1.1 35459 1rp4A 389 7.06e+00 1iwgA 1053 7.24e+00 d.58.44.1 76874 d.58.44.1 76875 d.58.44.1 76876 d.58.44.1 76877 d.225.1.1 76878 d.225.1.1 76879 f.35.1.1 76880 f.35.1.1 76881 2bgu 351 7.31e+00 1c3jA c.87.1.1 35460 1upkA 341 7.34e+00 unknown_sccs -1565 1li5A 461 7.51e+00 a.27.1.1 73912 c.26.1.1 73913 1dk5A 322 7.51e+00 1dk5A a.65.1.1 18192 1qv1A 195 7.63e+00 a.39.1.5 -830 1on2A 142 7.89e+00 a.4.5.24 87103 a.76.1.1 87104 1vjs 483 7.97e+00 1bli b.71.1.1 27714 c.1.8.1 28701 1avqA 228 8.04e+00 1avqA c.52.1.13 33326 1aua 296 8.21e+00 1aua a.5.3.1 16290 c.13.1.1 30882 1rqjA 299 8.29e+00 a.128.1.1 -1774 1gk9A 260 8.30e+00 d.153.1.2 65246 1b5l 172 8.30e+00 1b5l a.26.1.3 16900 1jobA 162 8.51e+00 1f35A b.94.1.1 63207 1jqnA 883 8.59e+00 c.1.12.3 77159 1ua4A 455 8.62e+00 c.72.1.3 -8416 1ajqA 209 8.68e+00 1ajqA d.153.1.2 41840 1e3aA 260 8.76e+00 1ajqA d.153.1.2 41838 1jf0A 195 8.84e+00 1ej3A a.39.1.5 62926 1ji8A 111 9.09e+00 d.203.1.1 66733 1bs4A 168 9.30e+00 1bs4A d.167.1.1 42287 1f35A 162 9.33e+00 1f35A b.94.1.1 59628 1kn1A 160 9.58e+00 a.1.1.3 77455 1ge9A 184 9.63e+00 1dd5A d.67.3.1 60463 1pieA 419 9.93e+00 d.14.1.5 -9075 unknown_sccs -10120 1ez3A 127 1.01e+01 1dn1B a.47.2.1 17768 1jf2A 195 1.03e+01 1ej3A a.39.1.5 62930 1gseA 221 1.03e+01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1nrfA 262 1.04e+01 e.3.1.1 -11780 1nznA 126 1.05e+01 a.118.8.1 -1616 1aj8A 371 1.06e+01 1aj8A a.103.1.1 18900 1ka3A 90 1.06e+01 a.150.1.1 72239 1gm7A 209 1.08e+01 d.153.1.2 65302 1ffkT 154 1.08e+01 1ffkT d.59.1.1 39527 1e8aA 91 1.10e+01 1b4cA a.39.1.2 17188 1miwA 404 1.10e+01 a.173.1.1 79162 d.218.1.4 79163 1d9cA 121 1.12e+01 1d9cA a.26.1.3 16901 1top 162 1.14e+01 1ncx a.39.1.5 17223 1pnkA 209 1.16e+01 1ajqA d.153.1.2 41839 1ncx 162 1.16e+01 1ncx a.39.1.5 17222 1mlwA 301 1.18e+01 d.178.1.1 79289 1fx8A 281 1.19e+01 f.19.1.1 43651 1id3B 102 1.19e+01 a.22.1.1 66113 1auwA 468 1.21e+01 1auwA a.127.1.1 19416 1qmqA 414 1.21e+01 1phd a.104.1.1 18907 1ezwA 349 1.22e+01 1ezwA c.1.16.3 29558 1mr3F 181 1.23e+01 c.37.1.8 79422 1l6nA 289 1.23e+01 a.61.1.1 73624 a.73.1.1 73625 1f5xA 208 1.25e+01 1f5xA a.87.1.1 18516 1lnwA 147 1.27e+01 a.4.5.28 78104 1h97A 147 1.27e+01 1h97A a.1.1.2 60812 1dguA 183 1.28e+01 1dguA a.39.1.5 17333 2bidA 197 1.28e+01 2bidA f.1.4.1 43398 1cr6B 554 1.29e+01 1cr6B c.108.1.2 43338 c.69.1.11 34688 1ndbA 596 1.31e+01 c.43.1.3 80411 c.43.1.3 80412 1kiyA 374 1.31e+01 a.128.1.5 72555 1jr5A 90 1.34e+01 a.150.1.1 67113 1mldA 314 1.34e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1icjA 168 1.35e+01 1bs4A d.167.1.1 42284 1hg4A 279 1.36e+01 1lbd a.123.1.1 19333 1qsdA 106 1.36e+01 1qsdA a.7.5.1 16335 1s5lA 344 1.41e+01 1uzbA 516 1.44e+01 c.82.1.1 -8552 1dz4A 414 1.46e+01 1phd a.104.1.1 18903 1k3kA 158 1.49e+01 f.1.4.1 72017 1fca 55 1.51e+01 2fdn d.58.1.1 38945 1hf8A 289 1.52e+01 1hg5A unknown_sccs -399 unknown_sccs -1628 1hg2A 289 1.53e+01 1hg5A unknown_sccs -401 unknown_sccs -1630 1octC 156 1.54e+01 1au7A a.4.1.1 15991 a.35.1.1 17017 1oxjA 173 1.56e+01 a.60.1.2 87517 a.118.1.13 87518 7aatA 401 1.57e+01 1ajsA c.67.1.1 34250 1l0oC 243 1.62e+01 a.4.13.2 73405 1af5 126 1.63e+01 1bp7A d.95.2.1 40572 1dgfA 497 1.69e+01 1cf9A e.5.1.1 42782 1hg5A 289 1.69e+01 1hg5A unknown_sccs -400 unknown_sccs -1629 1p9bA 442 1.72e+01 c.37.1.10 -7115 1ik9A 213 1.78e+01 b.59.1.1 66176 h.1.11.1 66177 1ssqA 267 1.78e+01 1gw5A 621 1.85e+01 a.118.1.10 70629 1rfmA 344 1.88e+01 c.122.1.1 -8032 1k7wA 468 1.90e+01 a.127.1.1 72130 1nd7A 374 1.91e+01 d.148.1.1 -11394 1gtxA 472 1.96e+01 1gtxA 1bk5A 422 1.98e+01 1bk5A a.118.1.1 19130 1m48A 133 1.98e+01 a.26.1.2 74443 1rj1A 151 1.99e+01 unknown_sccs -753 7catA 506 2.00e+01 1cf9A e.5.1.1 42781 1v92A 46 2.00e+01 a.5.2.3 -357 1j9aA 184 2.01e+01 c.55.3.5 84135 1kl9A 182 2.02e+01 b.40.4.5 72681 1h6kA 757 2.02e+01 unknown_sccs 60675 unknown_sccs 60676 unknown_sccs 60677 1ldfA 281 2.03e+01 f.19.1.1 73845 2bce 581 2.05e+01 2bce c.69.1.1 34625 1ohvA 472 2.07e+01 c.67.1.4 -8181 1bli 483 2.07e+01 1bli b.71.1.1 27715 c.1.8.1 28702 1q4mA 221 2.08e+01 unknown_sccs -1910 1r88A 280 2.12e+01 c.69.1.3 -8298 1i7wA 538 2.16e+01 3bct a.118.1.1 61909 1euvA 221 2.17e+01 1euvA d.3.1.7 37133 1allA 160 2.23e+01 1qgwC a.1.1.3 15647 1hx1B 114 2.23e+01 1hx1B a.7.7.1 61350 1deeG 54 2.24e+01 1fc2C a.8.1.1 16343 1orsC 132 2.28e+01 f.14.1.1 87353 1ef8A 261 2.29e+01 1ef8A c.14.1.3 30921 1jplA 171 2.29e+01 a.118.9.2 67027 1ezfA 340 2.32e+01 1ezfA a.128.1.2 19440 1us0A 316 2.36e+01 c.1.7.1 -5233 1vj7A 393 2.37e+01 unknown_sccs -1265 unknown_sccs -9814 1qs2A 401 2.38e+01 1qs1A d.166.1.1 42268 d.166.1.1 42269 1gnc 178 2.39e+01 1bgc a.26.1.1 16821 1d3yA 301 2.40e+01 1d3yA e.12.1.1 43252 1g2aA 168 2.41e+01 d.167.1.1 65109 1cqxA 403 2.49e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1ht9A 76 2.49e+01 4icb a.39.1.1 61252 1bsjA 168 2.51e+01 1bs4A d.167.1.1 42302 1eblB 317 2.57e+01 1hn9A c.95.1.1 35975 c.95.1.1 35976 1lfkA 398 2.58e+01 a.104.1.1 77926 1m2oA 768 2.59e+01 a.71.2.1 78480 b.2.8.1 78481 c.62.1.2 78482 d.109.2.1 78483 g.41.10.1 78484 1ecxA 384 2.59e+01 1ecxA c.67.1.3 34431 1ihgA 370 2.59e+01 2cpl a.118.8.1 62380 b.62.1.1 62381 1qqeA 292 2.64e+01 1qqeA a.118.8.1 19210 2acr 315 2.70e+01 1frb c.1.7.1 28674 1iqpA 327 2.71e+01 a.80.1.1 62649 c.37.1.20 62650 1mv8A 436 2.75e+01 a.100.1.4 85128 c.2.1.6 85129 c.26.3.1 85130 1l8wA 348 2.77e+01 a.154.1.1 73704 1bzpA 153 2.77e+01 1a6m a.1.1.2 15020 1l1jA 239 2.78e+01 b.47.1.1 84516 2fdn 55 2.78e+01 2fdn d.58.1.1 38944 1r7jA 95 2.79e+01 1jyoE 105 2.80e+01 d.184.1.2 67487 1cqzA 554 2.82e+01 1cr6B c.108.1.2 43339 c.69.1.11 34689 2tmkA 216 2.82e+01 3tmkA c.37.1.1 31928 4ts1A 319 2.83e+01 2ts1 c.26.1.1 31565 1qazA 351 2.85e+01 1qazA a.102.3.1 18848 1nh1A 330 2.86e+01 unknown_sccs -11798 1gcvA 140 2.88e+01 1cg5B a.1.1.2 15410 3tmkA 216 2.91e+01 3tmkA c.37.1.1 31920 1pwmA 316 2.95e+01 c.1.7.1 -5232 1el3A 316 3.00e+01 1frb c.1.7.1 28672 1ek1A 554 3.05e+01 1cr6B c.108.1.2 43335 c.69.1.11 34685 1omrA 201 3.09e+01 a.39.1.5 -854 1kqfB 294 3.10e+01 d.58.1.5 75900 f.23.22.1 75901 1dghB 498 3.12e+01 1cf9A e.5.1.1 42791 1jfaA 374 3.17e+01 a.128.1.5 66622 1g7dA 106 3.17e+01 1g7dA a.71.1.1 18318 1eg5A 384 3.18e+01 1ecxA c.67.1.3 34429 1hzpA 335 3.19e+01 1hn9A c.95.1.1 61455 c.95.1.1 61456 1sqsA 242 3.19e+01 unknown_sccs -6433 1eblA 317 3.22e+01 1hn9A c.95.1.1 35973 c.95.1.1 35974 1v64A 108 3.23e+01 1khvA 516 3.29e+01 e.8.1.4 68627 1fntc 245 3.30e+01 1a99A 344 3.32e+01 1pot c.94.1.1 35812 1bdc 60 3.40e+01 1fc2C a.8.1.1 16350 1iygA 133 3.42e+01 a.118.8.1 76947 1qdbA 473 3.43e+01 1qdbA a.138.1.3 19688 1e3oC 160 3.45e+01 1au7A a.4.1.1 59197 a.35.1.1 59198 1mumA 295 3.45e+01 c.1.12.7 85108 1ih7A 903 3.46e+01 1clqA c.55.3.5 62375 e.8.1.1 62376 1p0iA 529 3.48e+01 c.69.1.1 -8291 1fu1B 203 3.49e+01 1fu1B b.59.1.1 27077 h.1.11.1 45631 1tf4A 605 3.50e+01 1tf4A a.102.1.2 18827 b.2.2.2 22393 1oc2A 348 3.50e+01 c.2.1.2 -5753 1no5A 114 3.51e+01 unknown_sccs -9785 1c1kA 217 3.52e+01 1c1kA a.120.1.1 19239 1bjz 207 3.53e+01 2tct a.4.1.9 16065 a.121.1.1 19242 1jeqA 609 3.55e+01 1jeqA a.140.2.1 64748 unknown_sccs -4427 unknown_sccs -7991 1dofA 403 3.55e+01 1c3cA a.127.1.1 19429 1fxxA 482 3.62e+01 1fxxA c.55.3.5 33726 1mmoG 162 3.65e+01 1mtyG a.23.3.1 16512 1qb4A 883 3.66e+01 c.1.12.3 74640 1qcwA 410 3.68e+01 1gox c.1.4.1 28622 1fd9A 213 3.73e+01 1fd9A d.26.1.1 59771 1jihA 531 3.78e+01 unknown_sccs -10212 unknown_sccs -11922 1bmfA 510 3.78e+01 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1od2A 805 3.85e+01 c.14.1.4 86821 c.14.1.4 86822 1eq1A 166 3.88e+01 a.63.1.1 64910 1hn9A 317 3.93e+01 1hn9A c.95.1.1 35977 c.95.1.1 35978 1q8iA 783 3.94e+01 c.55.3.5 -7635 e.8.1.1 -11885 1phb 414 3.95e+01 1phd a.104.1.1 18906 1qkrA 188 3.96e+01 1qkrA a.24.9.1 16628 1a79A 171 3.99e+01 1a79A c.52.2.1 33340 d.75.1.1 39739 1fcbA 511 4.00e+01 1gox c.1.4.1 28620 d.120.1.1 41087