# List of top-scoring protein chains for t2k-100-30-str2 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 1pq1A 196 4.37e-02 f.1.4.1 -12055 1q4mA 221 1.50e-01 unknown_sccs -1910 1jcrA 377 2.07e-01 a.118.6.1 66506 1bxlA 181 2.24e-01 1maz f.1.4.1 43396 1kn1A 160 3.29e-01 a.1.1.3 77455 1jcqA 382 3.77e-01 a.118.6.1 66504 1ld8A 382 3.79e-01 a.118.6.1 73838 1af3 196 4.10e-01 1maz f.1.4.1 43397 1d8dA 377 4.14e-01 1ft1A a.118.6.1 19185 1mgn 154 4.82e-01 1a6m a.1.1.2 15097 2spo 154 5.31e-01 1a6m a.1.1.2 15053 1maz 221 5.38e-01 1maz f.1.4.1 43393 1bzpA 153 5.42e-01 1a6m a.1.1.2 15020 1tbmA 326 6.22e-01 1t7pA 698 6.29e-01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1qbqA 333 8.17e-01 1ft1A a.118.6.1 19187 1hg2A 289 8.90e-01 1hg5A unknown_sccs -401 unknown_sccs -1630 2bidA 197 9.80e-01 2bidA f.1.4.1 43398 1ft1A 377 9.91e-01 1ft1A a.118.6.1 19186 1h5uA 842 1.01e+00 1a8i c.87.1.4 60655 1htjF 210 1.14e+00 1htjF a.91.1.1 61254 1nrfA 262 1.15e+00 e.3.1.1 -11780 1n97A 389 1.26e+00 a.104.1.1 80335 1ks8A 433 1.29e+00 a.102.1.2 77519 1hf8A 289 1.29e+00 1hg5A unknown_sccs -399 unknown_sccs -1628 1gdj 153 1.32e+00 2gdm a.1.1.2 15213 1lh1 153 1.49e+00 2gdm a.1.1.2 15222 2lh2 153 1.49e+00 2gdm a.1.1.2 15220 1flcB 175 1.54e+00 1flcB h.3.1.1 45716 2gdm 153 1.58e+00 2gdm a.1.1.2 15212 1allA 160 1.67e+00 1qgwC a.1.1.3 15647 1foeA 377 1.68e+00 1foeA a.87.1.1 18517 b.55.1.1 26969 1jf0A 195 1.71e+00 1ej3A a.39.1.5 62926 1l2iA 261 1.76e+00 a.123.1.1 73503 1rqjA 299 1.93e+00 a.128.1.1 -1774 1mbd 153 2.01e+00 1a6m a.1.1.2 15033 1a6m 151 2.01e+00 1a6m a.1.1.2 15018 1iwgA 1053 2.21e+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 1c8kA 842 2.44e+00 1a8i c.87.1.4 35491 1e6qM 501 2.47e+00 1e70M c.1.8.4 28920 1e4mM 501 2.54e+00 1e70M c.1.8.4 59226 1e70M 501 2.54e+00 1e70M c.1.8.4 28926 1miwA 404 2.66e+00 a.173.1.1 79162 d.218.1.4 79163 1l7vA 326 2.73e+00 f.22.1.1 73672 1be3C 379 2.92e+00 1be3C f.32.1.1 75805 f.21.1.2 75806 1hg5A 289 3.05e+00 1hg5A unknown_sccs -400 unknown_sccs -1629 1qv1A 195 3.27e+00 a.39.1.5 -830 1l6nA 289 3.43e+00 a.61.1.1 73624 a.73.1.1 73625 1cnt3 187 3.44e+00 1cnt3 1yveJ 524 3.54e+00 1qmgA a.100.1.2 18790 c.2.1.6 30187 1qmgA 524 3.62e+00 1qmgA a.100.1.2 18785 c.2.1.6 30182 1el4A 195 3.78e+00 1ej3A a.39.1.5 59453 1rfmA 344 3.82e+00 c.122.1.1 -8032 1dbhA 354 3.99e+00 1awe a.87.1.1 18514 b.55.1.1 26967 1amz 435 4.16e+00 1csh a.103.1.1 18884 1a8i 842 4.29e+00 1a8i c.87.1.4 35490 1fnnA 389 4.34e+00 1fnnA a.4.5.11 16129 c.37.1.20 32426 1csc 433 4.35e+00 1csh a.103.1.1 18886 1odoA 408 4.47e+00 a.104.1.1 -1463 1cg5A 141 4.49e+00 1abwA a.1.1.2 15406 1cnt1 187 4.49e+00 1cnt3 1csh 435 4.64e+00 1csh a.103.1.1 18880 1gpb 842 4.71e+00 1a8i c.87.1.4 35478 1hiwA 133 4.78e+00 1hiwA a.61.1.1 18122 3ertA 261 4.86e+00 3erdA a.123.1.1 19292 1kx9A 112 5.26e+00 unknown_sccs 77602 3erdA 261 5.42e+00 3erdA a.123.1.1 19293 1aj8A 371 5.48e+00 1aj8A a.103.1.1 18900 1aj3 110 5.72e+00 1cunA a.7.1.1 16319 1jf2A 195 6.02e+00 1ej3A a.39.1.5 62930 1li5A 461 6.07e+00 a.27.1.1 73912 c.26.1.1 73913 1evsA 187 6.11e+00 1evsA a.26.1.1 16845 1ez3A 127 6.15e+00 1dn1B a.47.2.1 17768 1ssqA 267 6.19e+00 1cnt2 187 6.22e+00 1cnt3 1j7yB 146 6.29e+00 a.1.1.2 66427 1yveI 524 6.31e+00 1qmgA a.100.1.2 18789 c.2.1.6 30186 1lrzA 426 6.39e+00 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1phb 414 6.52e+00 1phd a.104.1.1 18906 1kgnA 329 6.71e+00 a.25.1.2 68584 1mldA 314 6.92e+00 2cmd c.2.1.5 30122 d.162.1.1 42089 1po5A 476 7.04e+00 a.104.1.1 -1467 1n46A 258 7.13e+00 a.123.1.1 85315 1phg 414 7.16e+00 1phd a.104.1.1 18910 1ezwA 349 7.24e+00 1ezwA c.1.16.3 29558 5cpp 414 7.55e+00 1phd a.104.1.1 18935 6cts 433 8.15e+00 1csh a.103.1.1 18891 1qcrC 378 8.17e+00 1be3C f.32.1.1 75931 f.21.1.2 75932 1bouA 139 8.17e+00 1bouA a.88.1.1 18521 1qmqA 414 8.22e+00 1phd a.104.1.1 18907 1iwhB 146 8.28e+00 a.1.1.2 76883 1mhyB 395 8.31e+00 1mtyB a.25.1.2 16781 1vom 762 8.40e+00 1lvk b.34.3.1 24577 c.37.1.9 32174 1huw 166 8.62e+00 1huw a.26.1.1 16831 1oyeA 1049 8.95e+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 1f3aA 222 9.10e+00 1pgtA a.45.1.1 17701 c.47.1.5 32995 1is2A 661 9.11e+00 a.29.3.2 71382 a.29.3.2 71383 e.6.1.2 71384 3nodB 423 9.12e+00 1nseA d.174.1.1 42513 1h5zA 455 9.27e+00 a.104.1.1 -1456 1oc2A 348 9.31e+00 c.2.1.2 -5753 1ash 150 9.38e+00 1ash a.1.1.2 15622 1v92A 46 9.89e+00 a.5.2.3 -357 1lvk 762 1.01e+01 1lvk b.34.3.1 24576 c.37.1.9 32173 1phd 414 1.03e+01 1phd a.104.1.1 18913 1ihgA 370 1.03e+01 2cpl a.118.8.1 62380 b.62.1.1 62381 1hg4A 279 1.05e+01 1lbd a.123.1.1 19333 2bgu 351 1.07e+01 1c3jA c.87.1.1 35460 1c3jA 351 1.07e+01 1c3jA c.87.1.1 35459 1jg7A 351 1.07e+01 1c3jA c.87.1.1 62945 1jixA 351 1.10e+01 1c3jA c.87.1.1 63081 1b4uA 139 1.10e+01 1bouA a.88.1.1 18523 7aatA 401 1.10e+01 1ajsA c.67.1.1 34250 1hkcA 917 1.11e+01 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1dz4A 414 1.12e+01 1phd a.104.1.1 18903 1bmfA 510 1.12e+01 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1e1dA 553 1.12e+01 1e1dA e.26.1.1 43363 1qs1A 462 1.14e+01 1qs1A d.166.1.1 42260 d.166.1.1 42261 1fd9A 213 1.16e+01 1fd9A d.26.1.1 59771 1gntA 553 1.19e+01 e.26.1.1 70290 1e2uA 553 1.20e+01 1e1dA e.26.1.1 43362 1n00A 321 1.21e+01 a.65.1.1 85241 1s9pA 227 1.25e+01 1dxtB 147 1.26e+01 1abwA a.1.1.2 15450 1babB 146 1.27e+01 1abwA a.1.1.2 15414 1bu7A 455 1.28e+01 1bu7A a.104.1.1 18937 1ih7A 903 1.30e+01 1clqA c.55.3.5 62375 e.8.1.1 62376 1d0yA 761 1.31e+01 1lvk b.34.3.1 24581 c.37.1.9 32178 1klo 162 1.32e+01 1klo g.3.11.2 44326 g.3.11.2 44327 g.3.11.2 44328 1ua4A 455 1.39e+01 c.72.1.3 -8416 1clqA 903 1.39e+01 1clqA c.55.3.5 33717 e.8.1.1 43006 1gnlA 544 1.39e+01 e.26.1.1 70287 1hkbA 917 1.40e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1d9cA 121 1.42e+01 1d9cA a.26.1.3 16901 1bgeB 175 1.43e+01 1bgc a.26.1.1 16824 1gm7A 209 1.44e+01 d.153.1.2 65302 1czaN 917 1.45e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1aijL 281 1.47e+01 6prcL f.26.1.1 43461 1iygA 133 1.48e+01 a.118.8.1 76947 1n8vA 112 1.48e+01 unknown_sccs 85457 1ng6A 148 1.50e+01 a.182.1.1 85670 1taq 832 1.58e+01 1taq a.60.7.1 18082 c.120.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1vsgA 364 1.60e+01 1vsgA h.4.1.1 45782 1irdB 146 1.61e+01 a.1.1.2 66287 1j9aA 184 1.62e+01 c.55.3.5 84135 1a99A 344 1.66e+01 1pot c.94.1.1 35812 1h8eA 510 1.69e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1hq3B 126 1.70e+01 1aoiD a.22.1.1 16444 1fobA 334 1.71e+01 c.1.8.3 83255 1fjgM 126 1.74e+01 1fjfM a.156.1.1 16293 1qsdA 106 1.74e+01 1qsdA a.7.5.1 16335 1i3dA 146 1.75e+01 a.1.1.2 61587 1ldjA 760 1.82e+01 a.4.5.34 73847 a.118.17.1 73848 e.40.1.1 73849 1ecxA 384 1.87e+01 1ecxA c.67.1.3 34431 1e79A 510 1.87e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1uaaA 673 1.92e+01 1pjr c.37.1.19 32401 c.37.1.19 32402 1mplA 349 1.94e+01 e.3.1.1 79387 1pieA 419 1.97e+01 d.14.1.5 -9075 unknown_sccs -10120 1or0A 160 2.00e+01 d.153.1.2 -11415 1tys 265 2.00e+01 1bkpA d.117.1.1 40937 1ow4A 129 2.04e+01 a.39.2.1 -876 3pte 349 2.08e+01 3pte e.3.1.1 42687 1h97A 147 2.08e+01 1h97A a.1.1.2 60812 1ji8A 111 2.09e+01 d.203.1.1 66733 1ka3A 90 2.10e+01 a.150.1.1 72239 1iv8A 720 2.12e+01 b.71.1.1 76842 c.1.8.1 76843 1o7xD 377 2.12e+01 a.103.1.1 81174 1q59A 172 2.13e+01 f.1.4.1 -12062 1io7A 368 2.17e+01 1f4tA a.104.1.1 18971 1on2A 142 2.19e+01 a.4.5.24 87103 a.76.1.1 87104 1rzhL 281 2.23e+01 f.26.1.1 -12215 1eca 136 2.26e+01 1flp a.1.1.2 15209 1ecd 136 2.26e+01 1flp a.1.1.2 15211 1dgkN 917 2.28e+01 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1iqpA 327 2.29e+01 a.80.1.1 62649 c.37.1.20 62650 1kmiZ 214 2.31e+01 h.4.11.1 72752 1ci9A 392 2.34e+01 e.3.1.1 64767 1p9sA 300 2.35e+01 b.47.1.4 87999 1r9lA 309 2.36e+01 c.94.1.1 -8700 1ddbA 195 2.36e+01 1ddbA f.1.4.1 43399 1kyhA 276 2.37e+01 c.72.1.4 73222 1hvbA 349 2.38e+01 3pte e.3.1.1 42686 1nm8A 616 2.39e+01 c.43.1.3 85872 c.43.1.3 85873 1eco 136 2.40e+01 1flp a.1.1.2 15208 1ge9A 184 2.41e+01 1dd5A d.67.3.1 60463 1mh3A 421 2.45e+01 a.4.1.1 79112 c.94.1.1 79113 1rp4A 389 2.45e+01 1umvX 122 2.46e+01 a.133.1.2 -1994 1eg5A 384 2.49e+01 1ecxA c.67.1.3 34429 1ht9A 76 2.49e+01 4icb a.39.1.1 61252 1hwxA 501 2.58e+01 1hwyA c.2.1.7 30250 c.58.1.1 33898 1q8iA 783 2.61e+01 c.55.3.5 -7635 e.8.1.1 -11885 1e3aA 260 2.64e+01 1ajqA d.153.1.2 41838 1cqxA 403 2.64e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1i7gA 287 2.69e+01 a.123.1.1 71121 1mumA 295 2.70e+01 c.1.12.7 85108 1ux5A 411 2.74e+01 unknown_sccs -1768 1evfA 264 2.75e+01 1bkpA d.117.1.1 40932 1di1A 300 2.76e+01 1di1A a.128.1.4 19446 1r88A 280 2.80e+01 c.69.1.3 -8298 1qqqA 264 2.80e+01 1bkpA d.117.1.1 40931 1n0uA 842 2.83e+01 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1yfm 488 2.84e+01 1furA a.127.1.1 19413 1bf5A 545 2.85e+01 1bg1A a.47.1.1 17766 b.2.5.5 22460 d.93.1.1 40526 1kn1B 161 2.86e+01 a.1.1.3 77456 1iqvA 218 2.87e+01 1rss a.75.1.1 62661 1gnc 178 2.92e+01 1bgc a.26.1.1 16821 1ca1 370 2.99e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1ai7A 209 3.03e+01 1ajqA d.153.1.2 41845 1s5lB 510 3.04e+01 1upkA 341 3.05e+01 unknown_sccs -1565 1dn1B 267 3.07e+01 1dn1B a.47.2.1 17771 1blu 82 3.08e+01 2fdn d.58.1.1 38948 1gmjA 84 3.09e+01 h.4.8.1 65310 1fjgT 106 3.18e+01 1fjfT a.7.6.1 16338 1vk3A 615 3.21e+01 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 2abk 211 3.23e+01 2abk a.96.1.1 18743 1fm2A 169 3.27e+01 1fm2A d.153.1.2 59877 1ajqA 209 3.27e+01 1ajqA d.153.1.2 41840 1qhaA 917 3.27e+01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1hwyA 501 3.32e+01 1hwyA c.2.1.7 30262 c.58.1.1 33910 1i1rB 181 3.32e+01 1i1rB a.26.1.1 61548 1ea1A 455 3.34e+01 1ea1A a.104.1.1 18970 1o7xB 377 3.36e+01 a.103.1.1 81172 1dguA 183 3.36e+01 1dguA a.39.1.5 17333 1f45B 197 3.38e+01 1f45B a.26.1.1 59642 1ni3A 392 3.39e+01 c.37.1.8 80531 d.15.10.2 80532 1pnkA 209 3.40e+01 1ajqA d.153.1.2 41839 1jnrA 643 3.40e+01 a.7.3.1 66966 c.3.1.4 66967 d.168.1.1 66968 2tscA 264 3.44e+01 1bkpA d.117.1.1 40952 1fcbA 511 3.44e+01 1gox c.1.4.1 28620 d.120.1.1 41087 1hjp 203 3.45e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1otvA 259 3.47e+01 unknown_sccs -1915 1vj7A 393 3.49e+01 unknown_sccs -1265 unknown_sccs -9814 1n9bA 265 3.55e+01 e.3.1.1 85463 1nznA 126 3.56e+01 a.118.8.1 -1616 1oxjA 173 3.57e+01 a.60.1.2 87517 a.118.1.13 87518 1dvpA 220 3.59e+01 1dvpA a.118.9.2 19216 g.50.1.1 45358 1k8kG 151 3.61e+01 a.118.13.1 68313 1ik9A 213 3.62e+01 b.59.1.1 66176 h.1.11.1 66177 1dvkA 173 3.66e+01 1dvkA a.72.1.1 18319 1l8nA 679 3.67e+01 c.1.8.10 84564 d.92.2.2 84565 1n4kA 381 3.69e+01 unknown_sccs 79992 b.42.6.1 79993 1mlwA 301 3.70e+01 d.178.1.1 79289 1bsjA 168 3.70e+01 1bs4A d.167.1.1 42302 1lngA 87 3.71e+01 d.201.1.1 74045 1ivg 388 3.74e+01 2qwc b.68.1.1 27578 1clc 639 3.75e+01 1clc a.102.1.2 18835 b.1.18.2 21872 1aua 296 3.77e+01 1aua a.5.3.1 16290 c.13.1.1 30882 1ci8A 392 3.79e+01 e.3.1.1 64765 1jdc 429 3.81e+01 1jdc b.71.1.1 27789 c.1.8.1 28776 1ej3A 191 3.84e+01 1ej3A a.39.1.5 17259 2gwxA 267 3.85e+01 2prgA a.123.1.1 19323 1bs4A 168 3.86e+01 1bs4A d.167.1.1 42287 1id3B 102 3.90e+01 a.22.1.1 66113 7catA 506 3.91e+01 1cf9A e.5.1.1 42781 1m2oA 768 3.93e+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 1k9dA 679 3.94e+01 c.1.8.10 77292 d.92.2.2 77293 1kbjA 412 3.96e+01 c.1.4.1 72280 1t3uA 104 3.99e+01 unknown_sccs -9325