# List of top-scoring protein chains for t2k-100-30-bys-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.soe.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 3h3mA 126 4.56e-12 2jg0A 535 6.21e-02 a.102.1.9 148034 2cy8A 453 3.80e-01 2jx0A 135 4.59e-01 2crbA 97 8.28e-01 a.7.16.1 130737 3eb2A 300 1.43e+00 3bc1B 59 2.36e+00 3bomA 142 2.36e+00 2rd3A 223 2.54e+00 2qk2A 242 3.17e+00 3dghA 483 3.40e+00 1epwA 1290 3.76e+00 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 2fztA 79 3.79e+00 a.46.3.1 134476 2ccyA 128 4.12e+00 2ccyA a.24.3.2 16544 1eyhA 144 4.14e+00 1eduA a.118.9.1 19214 2of3A 266 4.29e+00 1eduA 149 4.54e+00 1eduA a.118.9.1 19215 1n8vA 112 4.70e+00 a.118.21.1 85457 1h0aA 158 4.81e+00 a.118.9.1 76434 2a1dD 329 5.36e+00 1gc5A 467 5.46e+00 1gc5A c.72.1.3 60429 1nu7D 282 5.70e+00 a.8.6.1,a.8.6.1 92191,92192 2avkA 136 5.79e+00 1o9iA 266 5.80e+00 a.25.1.3 92671 1jkvA 266 5.85e+00 a.25.1.3 71719 1xkyA 301 6.96e+00 c.1.10.1 122094 3ibxA 221 7.21e+00 1jr3A 373 7.64e+00 a.80.1.1,c.37.1.20 63245,63246 2ux0A 143 7.75e+00 d.17.4.7 152231 2qcxA 263 7.84e+00 2pqxA 245 8.04e+00 1jocA 125 8.61e+00 g.50.1.1,h.1.21.1 66990,66991 1woyA 500 8.79e+00 a.27.1.1,c.26.1.1 121130,121131 1pd3A 58 9.36e+00 a.30.3.1 94512 1a8h 500 9.49e+00 1a8h 3hjeA 704 9.52e+00 3lkeA 263 1.01e+01 2i76A 276 1.01e+01 a.100.1.10,c.2.1.6 147535,147536 1mx0A 472 1.09e+01 a.156.1.3,d.14.1.3,d.122.1.2 79618,79619,79620 1ufaA 520 1.11e+01 a.8.3.3,c.6.2.4 99329,99330 2hs5A 239 1.12e+01 a.4.5.6,a.78.1.1 147379,147380 1ihgA 370 1.13e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 2vj4A 294 1.19e+01 3lbxB 185 1.21e+01 1ek9A 428 1.30e+01 1ek9A f.5.1.1 43809 2gkpA 167 1.30e+01 d.351.1.1 147129 2qqyA 149 1.33e+01 2v6xA 85 1.37e+01 1b3uA 588 1.38e+01 1b3uA a.118.1.2 19135 1kfrA 147 1.43e+01 a.1.1.2 72424 1idpA 172 1.43e+01 d.17.4.1 83685 3stdA 165 1.43e+01 3stdA d.17.4.1 38073 1hkxA 147 1.49e+01 d.17.4.7 83567 1b9xC 246 1.49e+01 1b9yC c.47.1.6 33053 2dobA 83 1.50e+01 2uubT 106 1.51e+01 a.7.6.1 139951 3cp5A 124 1.55e+01 3kj0A 158 1.57e+01 3cqxC 88 1.64e+01 3cjhB 64 1.67e+01 3dplC 382 1.70e+01 1sqsA 242 1.70e+01 c.23.5.5 98968 1h97A 147 1.70e+01 1h97A a.1.1.2 60812 1fcyA 236 1.71e+01 2lbd a.123.1.1 19282 1dhpA 292 1.71e+01 1dhpA c.1.10.1 29097 1ykhB 132 1.73e+01 a.252.1.1 123519 1l2iA 261 1.75e+01 a.123.1.1 73503 1or3A 165 1.75e+01 1nfn a.24.1.1 16522 2d5bA 500 1.75e+01 a.27.1.1,c.26.1.1 131268,131269 3kezA 461 1.80e+01 2gscA 128 1.80e+01 a.29.16.1 147169 1nfn 191 1.82e+01 1nfn 1gs9A 165 1.89e+01 a.24.1.1 83313 1aoa 275 1.89e+01 1aoa 1pbe 394 1.93e+01 1pbe 1pbeA 394 1.93e+01 c.3.1.2,d.16.1.2 30338,37869 1woqA 267 1.93e+01 c.55.1.10,c.55.1.10 109462,109463 3hr0A 263 1.98e+01 2vqeT 106 2.07e+01 a.7.6.1 153444 2lbd 267 2.07e+01 2lbd 2oxoA 103 2.08e+01 2z5kA 890 2.08e+01 2d7dB 40 2.09e+01 2ie4A 589 2.09e+01 a.118.1.2 137291 2r9zA 463 2.11e+01 2boyA 254 2.13e+01 1fjgT 106 2.15e+01 1fjfT a.7.6.1 16338 1b68A 191 2.18e+01 1nfn a.24.1.1 59076 1mu5A 471 2.20e+01 a.156.1.3,d.14.1.3,d.122.1.2 79472,79473,79474 1zt2B 212 2.24e+01 a.262.1.1 125625 1w2fA 276 2.25e+01 d.143.1.3 109125 3gfvA 303 2.27e+01 1edoA 244 2.33e+01 1ybvA c.2.1.2 29896 2hkjA 469 2.34e+01 a.156.1.3,d.14.1.3,d.122.1.2 136553,136554,136555 1xgwA 176 2.36e+01 3echC 25 2.38e+01 3i0yA 140 2.39e+01 3f2bA 1041 2.41e+01 3eirA 281 2.43e+01 1qcrA 446 2.43e+01 1be3A d.185.1.1,d.185.1.1 59025,59026 1eerA 166 2.45e+01 1eerA a.26.1.2 16846 1std 172 2.61e+01 3stdA 3h5dA 311 2.63e+01 3ltoA 323 2.64e+01 1cii 602 2.81e+01 1cii 1ciiA 602 2.81e+01 f.1.1.1,h.4.3.1 43381,45787 2k37A 59 2.82e+01 2gs8A 317 2.88e+01 1n1jB 97 2.91e+01 a.22.1.3 79814 3m5wA 322 2.91e+01 1fe6C 52 2.92e+01 1fe6C h.1.19.1 45664 1cj3A 392 2.94e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 1tyhA 248 2.95e+01 a.132.1.3 107458 3i0zA 389 2.97e+01 3h0lC 94 3.02e+01 2f6hX 419 3.03e+01 2cb0A 333 3.04e+01 3jqqA 316 3.07e+01 3iuzA 340 3.07e+01 1fe6A 52 3.07e+01 1fe6A h.1.19.1 45662 2nl9A 157 3.12e+01 2chpA 153 3.14e+01 2c1nA 258 3.20e+01 a.118.7.1 129640 1qjbA 245 3.25e+01 1qjaA a.118.7.1 19202 2ax6A 256 3.27e+01 a.123.1.1 127479 1rztA 331 3.29e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1gesA 450 3.31e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30473,30474,40168 1dmgA 225 3.31e+01 1dmgA c.22.1.1 31036 1ybkA 52 3.35e+01 3bhqA 211 3.39e+01 3dbaA 180 3.42e+01 3fgaB 403 3.49e+01 1e52A 63 3.50e+01 1e52A a.2.9.1 59256 3hinA 275 3.54e+01 2gf4A 100 3.57e+01 a.8.10.1 135074 2df8A 325 3.58e+01 3erdA 261 3.59e+01 3erdA a.123.1.1 19293 1b3bA 415 3.59e+01 1hwyA c.2.1.7,c.58.1.1 30244,33892 2qpqA 301 3.61e+01 2fjbA 643 3.63e+01 1jnrA 643 3.65e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1mx4A 168 3.71e+01 d.211.1.1 79640 2jpnA 79 3.72e+01 2bcqA 335 3.78e+01 a.60.6.1,a.60.12.1,d.218.1.2 128304,128305,128306 3jrqA 326 3.80e+01 1f74A 293 3.85e+01 1nal3 c.1.10.1 29079 2jabA 136 3.91e+01 1su0B 159 3.93e+01 d.224.1.2 106015 1ez3A 127 3.94e+01 1dn1B a.47.2.1 17768 1k0iA 394 3.98e+01 c.3.1.2,d.16.1.2 67942,67943 1syyA 346 3.98e+01 a.25.1.2 106126 3ertA 261 4.07e+01 3erdA a.123.1.1 19292 3hz6A 511 4.07e+01 1bs0A 384 4.11e+01 1bs0A c.67.1.4 34490 2purA 292 4.15e+01 2a6lA 292 4.19e+01 c.1.10.1 126285 2atsA 292 4.21e+01 c.1.10.1 127306 2a6nA 292 4.23e+01 c.1.10.1 126289 1a5t 334 4.26e+01 1a5t 1a5tA 334 4.26e+01 a.80.1.1,c.37.1.20 18450,32423 1orsC 132 4.27e+01 f.14.1.1 87353 1moq 368 4.38e+01 1moq 1moqA 368 4.38e+01 c.80.1.1 35302 1ng6A 148 4.39e+01 a.182.1.1 85670 3glrA 285 4.41e+01 3mghA 329 4.45e+01 3ilwA 470 4.46e+01 2mhr 118 4.54e+01 2mhr 2mhrA 118 4.54e+01 a.24.4.1 16581 3kdjB 316 4.57e+01 3epsA 578 4.63e+01 2peqA 134 4.63e+01 a.280.1.1 149443 1jliA 112 4.64e+01 a.26.1.2 16884 3hhyA 280 4.65e+01 1b9yC 246 4.67e+01 1b9yC c.47.1.6 33052 1cn4C 166 4.72e+01 1eerA a.26.1.2 16847 2e5fA 325 4.75e+01 1xpcA 248 4.75e+01 a.123.1.1 115738 3ip4C 100 4.81e+01 2oy9A 98 4.81e+01 a.276.1.1 149063 2bneA 241 4.82e+01 c.73.1.3 128824 3cveA 72 4.84e+01 3kwqB 83 4.85e+01 2fkzA 155 4.87e+01 a.25.1.1 133688 2qk1A 249 4.89e+01 1ykjA 394 4.93e+01 c.3.1.2,d.16.1.2 145914,145915 2f31A 233 4.94e+01 2f86B 143 4.98e+01 d.17.4.7 146998 2zfyA 234 4.98e+01 1nhyA 219 5.07e+01 a.45.1.1,c.47.1.5 80520,80521 2vccA 891 5.10e+01 2nppB 449 5.16e+01 a.118.1.20 138445 1yioA 208 5.18e+01 a.4.6.2,c.23.1.1 123326,123327 3i6aA 222 5.19e+01 1rzhL 281 5.19e+01 f.26.1.1 98164 1qkrA 188 5.22e+01 1qkrA a.24.9.1 16628 2qm1A 326 5.23e+01 1wleA 501 5.24e+01 1maz 221 5.32e+01 1maz 1wixA 164 5.40e+01 a.40.3.1 114683 2o02A 230 5.43e+01 a.118.7.1 148541 1ihbA 162 5.52e+01 1bd8 d.211.1.1 19161 1xdpA 687 5.53e+01 a.7.15.1,d.322.1.2,d.136.1.4,d.136.1.4 121896,121897,121898,121899 1ursA 402 5.54e+01 c.94.1.1 99833 2oexA 351 5.56e+01 2ej5A 257 5.63e+01 1z0kB 69 5.66e+01 a.2.19.1 124322 3a1gB 40 5.68e+01 1z1bA 356 5.70e+01 d.10.1.4,d.163.1.1 124346,124347 2be3A 226 5.71e+01 d.218.1.8 128349 1gkzA 388 5.71e+01 a.29.5.1,d.122.1.4 65268,65269 1dn1B 267 5.72e+01 1dn1B a.47.2.1 17771 1gqeA 365 5.78e+01 e.38.1.1 70351 3ehmA 532 5.81e+01 2d4xA 248 5.84e+01 1dxy 333 5.89e+01 1dxy 1dxyA 333 5.89e+01 c.2.1.4,c.23.12.1 30094,31354 1fxxA 482 5.93e+01 1fxxA c.55.3.5 33726 3cnxA 170 6.03e+01 d.17.4.17 156850 1br0A 120 6.06e+01 a.47.2.1 17772 1it2A 146 6.10e+01 a.1.1.2 66365 1tdzA 272 6.11e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1yzmA 51 6.16e+01 a.2.19.1 124283 1x1nA 524 6.19e+01 c.1.8.1 121593 2q4pA 170 6.22e+01 a.204.1.2 150041 2f2aC 100 6.25e+01 a.137.12.1 132804 3l1nA 194 6.28e+01 1ppjA 446 6.43e+01 d.185.1.1,d.185.1.1 104252,104253 2p6vA 114 6.44e+01 a.277.1.1 149278 2novA 496 6.49e+01 2qkwA 164 6.50e+01 a.8.8.1 150848 1b8gA 429 6.52e+01 1b8gA c.67.1.4 34499 2o7iA 592 6.56e+01 1dt9A 437 6.57e+01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 2jg6A 186 6.59e+01 1yakA 263 6.60e+01 a.132.1.3 122833 2h88C 140 6.69e+01 2g7lA 243 6.70e+01 a.4.1.9,a.121.1.1 134734,134735 2e2aA 105 6.71e+01 a.7.2.1 88499 1zroA 602 6.72e+01 a.264.1.1,a.264.1.1 125551,125552 1b26A 416 6.73e+01 1hwyA c.2.1.7,c.58.1.1 30232,33880 1qazA 351 6.76e+01 1qazA a.102.3.1 18848 1s9aA 257 6.77e+01 b.3.6.1 105379 3dtrL 281 6.80e+01 1b5tA 275 6.84e+01 1b5tA c.1.23.1 29676 3dsyL 281 6.86e+01 2p06A 114 6.87e+01 a.204.1.3 139452 1siqA 392 6.90e+01 a.29.3.1,e.6.1.1 105585,105586 2iswA 323 6.90e+01 1wfdA 93 6.92e+01 a.7.14.1 114578 3du2L 281 6.95e+01 3f7sA 142 6.96e+01 2ax8A 256 6.99e+01 2hueC 84 6.99e+01 a.22.1.1 136776 2ax9A 256 6.99e+01 a.123.1.1 127481 1u4qA 322 7.01e+01 a.7.1.1,a.7.1.1,a.7.1.1 113024,113025,113026 1o0wA 252 7.03e+01 a.149.1.1,d.50.1.1 80751,80752 3duqL 281 7.06e+01 1sr2A 116 7.10e+01 a.24.10.4 112109 2z6vA 414 7.13e+01 1tzyD 103 7.14e+01 a.22.1.1 107533 2ojpA 292 7.15e+01 1l8dA 112 7.15e+01 h.4.12.1 73687 3cx5F 146 7.26e+01 f.28.1.1 157086 3i00A 120 7.33e+01 1m7yA 435 7.35e+01 c.67.1.4 78761 2qypA 91 7.36e+01 a.64.1.1 151477 1ynuA 473 7.37e+01 c.67.1.4 123762 2r8qA 359 7.42e+01 3hhcA 196 7.43e+01 2qxfA 482 7.43e+01 c.55.3.5 151455 1guxB 152 7.56e+01 1guxB a.74.1.3 18389 3hq1A 644 7.57e+01 2oyoA 196 7.60e+01 a.152.1.3 149068 2vzbA 170 7.67e+01 1g7dA 106 7.70e+01 1g7dA a.71.1.1 18318 3evyA 239 7.73e+01 3mczA 352 7.75e+01 2zdiC 151 7.78e+01 1e2aA 105 7.83e+01 1e2aA a.7.2.1 16322 1dkxA 219 7.90e+01 1dkzA a.8.4.1,b.130.1.1 90339,90340 1i1rB 181 7.91e+01 1i1rB a.26.1.1 61548 1pa2A 306 7.93e+01 1bgp a.93.1.1 18693 3fydA 263 7.95e+01 2phzA 311 7.96e+01 c.92.2.4 149488 3lk41 286 7.97e+01