# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1tljA 213 8.90e-30 1hv8A 367 4.95e-01 1hv8A c.37.1.19 32405 c.37.1.19 32406 1rkqA 282 5.38e-01 c.108.1.10 -6847 1kwkA 645 8.81e-01 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1kwgA 645 1.15e+00 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 2ctc 307 1.42e+00 1aye c.56.5.1 33802 1f0xA 571 1.64e+00 1f0xA d.58.32.2 39483 d.145.1.1 41746 1p5dX 463 1.66e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1w1kA 560 2.07e+00 1t7pA 698 2.23e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 2ctb 307 2.33e+00 1aye c.56.5.1 33803 1e8gA 560 2.37e+00 1qltA d.58.32.1 39455 d.145.1.1 41718 1k2yX 463 2.53e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1yme 309 2.86e+00 1aye c.56.5.1 33804 1vaoA 560 3.39e+00 1qltA d.58.32.1 39461 d.145.1.1 41724 6cpa 307 3.45e+00 1aye c.56.5.1 33816 1s98A 107 3.46e+00 1gpjA 404 3.48e+00 a.151.1.1 65451 c.2.1.7 65452 d.58.39.1 65453 1a3gA 308 3.67e+00 1daaA e.17.1.1 43286 1gz0A 253 3.72e+00 c.116.1.1 76391 d.79.3.3 76392 1qltA 560 4.03e+00 1qltA d.58.32.1 39457 d.145.1.1 41720 1m4lA 307 4.73e+00 c.56.5.1 78604 1m2oA 768 4.82e+00 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 1ofuX 119 4.96e+00 c.37.1.22 86976 1r94A 118 5.17e+00 b.124.1.1 -4402 1eps 427 5.86e+00 1eps d.68.2.2 39586 1bd3A 243 5.92e+00 1bd3A c.61.1.1 34098 1rpjA 288 6.55e+00 2dri c.93.1.1 35656 1ayyA 151 6.68e+00 1apyA d.153.1.5 42016 1gio 125 6.81e+00 7rsa d.5.1.1 37304 1f7uA 607 6.84e+00 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1hl6A 165 6.97e+00 d.58.7.1 83609 1gw5S 142 7.71e+00 d.110.4.2 70633 1eqfA 280 7.97e+00 1eqfA a.29.2.1 16972 a.29.2.1 16973 1mu5A 471 8.04e+00 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1agi 125 8.89e+00 7rsa d.5.1.1 37303 1bpr 191 9.13e+00 1dkzA unknown_sccs 43319 1a8q 274 9.74e+00 1brt c.69.1.12 34702 2irfG 113 1.04e+01 2irfG a.4.5.23 16185 1gudA 288 1.08e+01 c.93.1.1 83326 1j5yA 187 1.09e+01 a.4.5.1 71592 d.94.2.1 71593 1ftrA 296 1.10e+01 1ftrA d.58.33.1 39485 d.58.33.1 39486 1ufkA 254 1.16e+01 unknown_sccs -8103 1dkxA 219 1.17e+01 1dkzA unknown_sccs -446 unknown_sccs -3061 1p4kA 295 1.17e+01 d.153.1.5 87772 1dkzA 219 1.18e+01 1dkzA unknown_sccs -445 unknown_sccs -3060 1j3mA 129 1.20e+01 1oo0B 110 1.26e+01 d.58.7.1 87183 1aw7A 194 1.27e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 1np3A 338 1.28e+01 a.100.1.2 85946 c.2.1.6 85947 1b65A 375 1.33e+01 1b65A d.154.1.1 42020 1rk8A 165 1.36e+01 d.58.7.1 -10018 1i1kA 309 1.55e+01 1daaA e.17.1.1 61533 3tss 194 1.56e+01 1aw7A b.40.2.2 25160 d.15.6.1 37749 1kczA 413 1.57e+01 c.1.11.2 68451 d.54.1.1 68452 1p9rA 418 1.60e+01 c.37.1.11 -7142 1b8oA 284 1.70e+01 1b8oA c.56.2.1 33762 1o0xA 262 1.73e+01 d.127.1.1 80755 1l5jA 865 1.78e+01 a.118.15.1 73592 c.8.2.1 73593 c.83.1.1 73594 1b7fA 168 1.79e+01 1b7fA d.58.7.1 39169 d.58.7.1 39170 1qo7A 394 1.80e+01 1qo7A c.69.1.11 34697 1dp4A 435 1.81e+01 1dp4A c.93.1.1 35710 1iyeA 309 2.00e+01 e.17.1.1 83786 1p2fA 220 2.01e+01 a.4.6.1 87720 c.23.1.1 87721 1ln1A 214 2.07e+01 d.129.3.2 74038 1g6sA 427 2.11e+01 1eps d.68.2.2 39584 1f1oA 431 2.21e+01 1f1oA a.127.1.1 19433 9gafA 295 2.24e+01 1apyA d.153.1.5 42008 1clqA 903 2.25e+01 1clqA c.55.3.5 33717 e.8.1.1 43006 1bs2A 607 2.29e+01 1bs2A a.27.1.1 16930 c.26.1.1 31597 d.67.2.1 39563 1brwA 433 2.37e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1jeyB 565 2.39e+01 1jeqB unknown_sccs -4431 unknown_sccs -7995 1b3nA 412 2.43e+01 1dd8A c.95.1.1 35966 c.95.1.1 35967 1kas 412 2.43e+01 1dd8A c.95.1.1 35964 c.95.1.1 35965 1jeqB 565 2.54e+01 1jeqB unknown_sccs -4432 unknown_sccs -7996 1ohvA 472 2.54e+01 c.67.1.4 -8181 1ykfA 352 2.61e+01 1pedA b.35.1.2 24757 c.2.1.1 29773 1daaA 282 2.63e+01 1daaA e.17.1.1 43270 1qwiA 143 2.84e+01 d.227.1.1 -11183 1p27B 106 2.91e+01 d.58.7.1 -10020 1ts3A 194 2.98e+01 1aw7A b.40.2.2 25168 d.15.6.1 37757 1g99A 408 2.99e+01 1g99A c.55.1.2 33457 c.55.1.2 33458 1dtdA 303 3.06e+01 1aye c.56.5.1 33823 1k47A 337 3.10e+01 d.14.1.5 72040 d.58.26.4 72041 1qupA 222 3.12e+01 1qupA b.1.8.1 22301 d.58.17.1 39352 1pkn 530 3.20e+01 1a49A b.58.1.1 27042 c.1.12.1 29271 c.49.1.1 33125 1aye 401 3.41e+01 1aye c.56.5.1 33824 d.58.3.1 39065 1lyvA 306 3.41e+01 c.45.1.2 74348 1mml 265 3.51e+01 1mml e.8.1.2 43015 1dkgD 383 3.52e+01 1ba1 c.55.1.1 33427 c.55.1.1 33428 1khxA 227 3.59e+01 b.26.1.1 68631 1bs0A 384 3.91e+01 1bs0A c.67.1.4 34490 1hgeA 328 3.96e+01 1hgeA b.19.1.2 23816 1ytn 306 3.99e+01 1ytw c.45.1.2 32688