# List of top-scoring protein chains for t04-100-30-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 1ihp 438 5.95e-02 1ihp c.60.1.2 33993 1sz2A 332 1.60e-01 1q18A 332 2.08e-01 c.55.1.7,c.55.1.7 104470,104471 1tbmA 326 2.65e-01 a.211.1.2 106744 6gsvA 217 3.06e-01 1b8xA a.45.1.1,c.47.1.5 17633,32925 2c4jA 218 4.41e-01 1xw5A 217 5.45e-01 1b4pA 217 8.26e-01 a.45.1.1,c.47.1.5 83158,83159 1qwoA 442 8.51e-01 c.60.1.2 104620 1zejA 293 1.07e+00 1eemA 241 1.40e+00 1eemA a.45.1.1,c.47.1.5 17717,33011 1mzbA 136 1.74e+00 a.4.5.42 91497 2fiyA 309 1.90e+00 1jhgA 101 2.02e+00 1jhgA a.4.12.1 19009 2fu4A 83 2.08e+00 2iu5A 195 2.39e+00 1bd8 156 2.40e+00 1bd8 d.211.1.1 19157 1qfxA 460 2.57e+00 1qfxA c.60.1.2 33994 1jpaA 312 2.71e+00 d.144.1.7 67011 1hp5A 512 2.99e+00 1hp4A c.1.8.6,d.92.2.1 61113,61114 1zd3A 555 3.11e+00 1zv1A 65 3.23e+00 1vj5A 555 3.30e+00 c.108.1.2,c.69.1.11 100799,100800 1jakA 512 3.62e+00 c.1.8.6,d.92.2.1 66472,66473 1y3nA 490 5.88e+00 1x1fA 149 6.26e+00 2gsvA 80 6.87e+00 1zboA 210 7.20e+00 1es5A 262 7.68e+00 1skf e.3.1.1 42679 1esiA 262 7.71e+00 1skf e.3.1.1 42682 1kpsB 171 8.87e+00 a.118.12.1 68787 2aheA 267 9.65e+00 1w1oA 534 1.10e+01 d.58.32.4,d.145.1.1 109071,109072 1jk8B 190 1.19e+01 1iakB b.1.1.2,d.19.1.1 63147,63148 2esnA 310 1.31e+01 1ohfA 644 1.37e+01 b.121.4.8 93014 1kblA 873 1.48e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1h6zA 913 1.58e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1tzvA 142 1.58e+01 a.79.1.1 107526 1xgkA 352 1.61e+01 1okcA 297 1.70e+01 f.42.1.1 93248 1o5hA 214 1.73e+01 a.191.1.1 92497 1jb0I 38 1.74e+01 1jb0I f.23.17.1 62826 1sszA 34 1.76e+01 j.35.1.1 105999 1gewA 356 1.78e+01 1gewA c.67.1.1 60470 1im5A 180 1.79e+01 c.33.1.3 66211 1n1jA 93 1.87e+01 a.22.1.3 79813 1nd7A 374 1.93e+01 d.148.1.1 91817 1g7oA 215 1.93e+01 1g7oA a.45.1.1,c.47.1.5 60332,60333 1sqgA 429 2.05e+01 a.79.1.3,c.66.1.38 105912,105913 1zq9A 285 2.08e+01 1fg7A 356 2.10e+01 1gewA c.67.1.1 59819 2furA 209 2.17e+01 1ufaA 520 2.17e+01 a.8.3.3,c.6.2.4 99329,99330 1fhuA 320 2.20e+01 1fhuA c.1.11.2,d.54.1.1 29234,38878 7atjA 308 2.23e+01 1bgp a.93.1.1 18673 1x6vA 630 2.24e+01 1v4aA 440 2.26e+01 a.24.16.4,d.218.1.9 108350,108351 1t92A 116 2.27e+01 1rh9A 373 2.31e+01 1uk5A 111 2.31e+01 a.7.7.1 99487 1no1A 126 2.37e+01 a.179.1.1 85913 1vls 146 2.42e+01 1vls a.24.2.1 16532 1z98A 281 2.49e+01 1t1uA 639 2.49e+01 4crxA 322 2.50e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1z2uA 150 2.54e+01 1hs6A 611 2.57e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1or7A 194 2.59e+01 a.4.13.2,a.177.1.1 87332,87333 2b7aA 293 2.60e+01 1ewfA 456 2.64e+01 1bp1 d.83.1.1,d.83.1.1 40024,40025 1ad3A 452 2.64e+01 1ad3A c.82.1.1 35335 1yozA 116 2.70e+01 1z2nX 324 2.71e+01 1br1B 150 2.75e+01 1wdcC a.39.1.5 17309 1p4cA 380 2.90e+01 c.1.4.1 94100 1ycsB 239 2.93e+01 1ycsB d.211.1.1,b.34.2.1 19155,24553 1gwuA 309 3.00e+01 a.93.1.1 83351 1y5iC 225 3.02e+01 1w07A 659 3.03e+01 1m6kA 251 3.12e+01 e.3.1.1 78695 2afdA 88 3.13e+01 1xo0A 324 3.14e+01 1mun 225 3.14e+01 1mun a.96.1.2 18744 1yy7A 213 3.22e+01 1whrA 124 3.25e+01 2afaA 425 3.29e+01 1x91A 153 3.32e+01 1tueA 212 3.33e+01 c.37.1.20 107323 2fkzA 155 3.34e+01 1n3gA 113 3.35e+01 d.204.1.1 79962 1gcqC 70 3.36e+01 1gcpA b.34.2.1 60436 2g62A 325 3.36e+01 2fqmA 75 3.40e+01 1r4wA 226 3.40e+01 c.47.1.13 97050 2afwA 329 3.40e+01 1repC 251 3.51e+01 1repC a.4.5.10,a.4.5.10 16125,16126 1im8A 244 3.56e+01 c.66.1.14 66212 1ytaA 180 3.56e+01 1k6xA 352 3.57e+01 c.2.1.2 68238 1xrsA 516 3.65e+01 1d6gA 47 3.65e+01 1d6gA g.33.1.1 44976 1dbwA 126 3.66e+01 1dbwA c.23.1.1 31095 1n8vA 112 3.70e+01 a.118.21.1 85457 1fsu 492 3.77e+01 1auk c.76.1.2 35032 2gw6A 123 3.85e+01 2occH 85 3.94e+01 2occH a.51.1.1 17796 1hdiA 413 3.95e+01 16pk c.86.1.1 60964 1rzhL 281 4.01e+01 f.26.1.1 98164 2a9iA 113 4.04e+01 2gdjA 264 4.15e+01 1hbzA 498 4.15e+01 1cf9A e.5.1.1 60937 1x23A 155 4.26e+01 1xl7A 612 4.30e+01 1gjwA 637 4.33e+01 b.71.1.1,c.1.8.1 60582,60583 2occC 261 4.36e+01 1ocrC f.25.1.1 43520 2bbrA 195 4.36e+01 1nw3A 416 4.45e+01 c.66.1.31 86288 2c78A 405 4.47e+01 1h2sA 225 4.48e+01 f.13.1.1 76578 1ha3A 405 4.50e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1zkeA 83 4.52e+01 1mp8A 281 4.52e+01 d.144.1.7 91384 1exmA 405 4.53e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1tkeA 224 4.54e+01 1gweA 503 4.56e+01 e.5.1.1 70667 1qo7A 394 4.57e+01 1qo7A c.69.1.11 34697 2aawA 222 4.76e+01 1qd9A 124 4.85e+01 1qu9A d.79.1.1 39758 1m98A 317 4.92e+01 a.175.1.1,d.17.4.6 78866,78867 1jhdA 396 4.93e+01 b.122.1.3,c.26.1.5 66712,66713 1b74A 254 5.01e+01 1b74A c.78.2.1,c.78.2.1 35264,35265 1jmtB 28 5.01e+01 2f1sA 186 5.01e+01 2csgA 424 5.04e+01 1hlrA 907 5.06e+01 1vlbA 907 5.08e+01 a.56.1.1,d.15.4.2,d.41.1.1,d.133.1.1 108739,108740,108741,108742 1n1fA 159 5.10e+01 a.26.1.3 79803 1nu7D 282 5.21e+01 a.8.6.1,a.8.6.1 92191,92192 1t7rA 269 5.21e+01 a.123.1.1 106635 1tu7A 208 5.26e+01 1xioA 261 5.28e+01 1n2fA 142 5.35e+01 d.227.1.1 79853 1pn0A 665 5.40e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1ds1A 324 5.48e+01 1drtA b.82.2.2 28127 2g6tA 306 5.56e+01 1pw4A 451 5.62e+01 f.38.1.1 95198 1r5zA 323 5.65e+01 f.40.1.1 97135 1pgjA 478 5.77e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 1dik 874 5.83e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1jgjA 217 5.84e+01 1c3wA f.13.1.1 62952 1k2xA 177 5.86e+01 d.153.1.5 90929 1v9mA 323 5.87e+01 f.40.1.1 100543 2ccmA 191 5.88e+01 1dugA 234 5.89e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 1thg 544 5.92e+01 1thg c.69.1.17 34763 1h2vC 771 5.92e+01 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1lghA 56 5.93e+01 1lghA f.3.1.1 43733 1z6gA 218 5.97e+01 1jvr 137 5.99e+01 1jvr a.61.1.2 18132 1ewqA 765 5.99e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1vpqA 273 6.02e+01 1hf8A 289 6.05e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1vi0A 206 6.06e+01 a.4.1.9,a.121.1.1 100720,100721 1f7uA 607 6.07e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1s6lA 212 6.13e+01 1aj8A 371 6.24e+01 1aj8A a.103.1.1 18900 1li5B 461 6.30e+01 a.27.1.1,c.26.1.1 73914,73915 1ogsA 497 6.34e+01 b.71.1.2,c.1.8.3 86997,86998 1j8mF 297 6.37e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 2b3oA 532 6.39e+01 1j8yF 297 6.39e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1sheA 103 6.40e+01 d.274.1.1 105551 1jae 471 6.42e+01 1smd b.71.1.1,c.1.8.1 27773,28760 2cchB 260 6.49e+01 1v9jA 113 6.55e+01 d.52.6.1 100542 1rxqA 178 6.58e+01 a.213.1.1 105118 1ssqA 267 6.60e+01 b.81.1.6 105993 1qwyA 291 6.62e+01 b.84.3.2 96509 1px5A 349 6.65e+01 a.160.1.2,d.218.1.6 95277,95278 1f44A 324 6.73e+01 a.60.9.1,d.163.1.1 64982,64983 1y82A 157 6.77e+01 1paqA 189 6.83e+01 a.118.1.14 94413 1sq5A 308 6.84e+01 c.37.1.6 105882 1axdA 209 6.85e+01 1gnwA a.45.1.1,c.47.1.5 17730,33024 1gdeA 389 6.98e+01 c.67.1.1 60456 1e8yA 966 7.00e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1rypH 205 7.07e+01 d.153.1.4 41876 1yfsA 465 7.08e+01 1e7uA 961 7.08e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1zrzA 364 7.16e+01 1fzqA 181 7.22e+01 1hurA c.37.1.8 32060 1q3eA 207 7.23e+01 b.82.3.2 95669 1b06A 210 7.23e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1mw5A 187 7.24e+01 d.259.1.1 91477 2a2rA 210 7.28e+01 1zvzA 279 7.29e+01 1fpoA 171 7.29e+01 1fpoA a.2.3.1,a.23.1.1 15693,16487 1ni3A 392 7.34e+01 c.37.1.8,d.15.10.2 80531,80532 1oktA 211 7.35e+01 a.45.1.1,c.47.1.5 93272,93273 1x8vA 455 7.36e+01 1xp3A 307 7.38e+01 1iqrA 420 7.41e+01 a.99.1.1,c.28.1.1 66275,66276 1b8aA 438 7.42e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1pd21 199 7.52e+01 1pd21 1i9gA 280 7.58e+01 c.66.1.13 62090 1x74A 360 7.61e+01 2gwdA 449 7.68e+01 2bnfB 241 7.74e+01 2fpmA 322 7.76e+01 1o17A 345 7.76e+01 a.46.2.1,c.27.1.1 80765,80766 2fikA 287 7.78e+01 2dbnA 461 7.80e+01 2c2nA 339 7.84e+01 1i7dA 659 7.88e+01 1d6mA e.10.1.1 61886 2cygA 312 8.03e+01 1ux5A 411 8.04e+01 a.207.1.1 100144 2ctoA 93 8.06e+01 2cqsA 842 8.22e+01 1lvaA 258 8.23e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 2a2fX 325 8.25e+01 1h3nA 878 8.33e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1au1A 166 8.38e+01 1ifa a.26.1.3 16889 1pgtA 210 8.39e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 1ji7A 89 8.39e+01 a.60.1.1 71682 1dp4A 435 8.51e+01 1dp4A c.93.1.1 35710 1yarA 233 8.59e+01 1ykhA 108 8.60e+01 1iqcA 308 8.62e+01 a.3.1.5,a.3.1.5 66266,66267 1ufzA 83 8.65e+01 a.5.9.1 107821 1tqyB 415 8.82e+01 c.95.1.1,c.95.1.1 107247,107248 1v54H 85 8.83e+01 a.51.1.1 100329 1li5A 461 8.84e+01 a.27.1.1,c.26.1.1 73912,73913 1tml 286 8.94e+01 1tml c.6.1.1 30656