# 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 1top 162 2.51e-04 1ncx a.39.1.5 17223 1ncx 162 4.54e-04 1ncx a.39.1.5 17222 1s29A 92 3.73e-03 unknown_sccs -315 1gnlA 544 2.68e-02 e.26.1.1 70287 1ggzA 148 5.23e-02 a.39.1.5 70176 1ctdA 36 1.81e-01 1ctdA a.39.1.5 17230 1f4qA 165 2.17e-01 1alvA a.39.1.8 17360 1a26 361 2.28e-01 1a26 a.41.1.1 17412 d.166.1.2 42274 1avsA 90 2.61e-01 1cll a.39.1.5 17226 1mu5A 471 2.82e-01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1wdcC 156 2.87e-01 1wdcC a.39.1.5 17317 1ecxA 384 3.12e-01 1ecxA c.67.1.3 34431 1eg5A 384 3.47e-01 1ecxA c.67.1.3 34429 1q0uA 219 3.85e-01 c.37.1.19 -7205 1auiB 169 3.86e-01 1auiB a.39.1.5 17325 1g8mA 593 3.88e-01 1g8mA c.24.1.3 60371 c.97.2.1 60372 1a7w 69 3.96e-01 1a7w a.22.1.2 16477 2sas 185 4.11e-01 2sas a.39.1.5 17258 1m9nA 613 4.35e-01 c.24.1.3 78870 c.97.2.1 78871 1cll 148 4.97e-01 1cll a.39.1.5 17263 3cln 148 5.08e-01 1cll a.39.1.5 17286 1g4yR 148 5.09e-01 1cll a.39.1.5 60252 1nuuA 252 5.70e-01 c.26.1.3 86209 1efyA 350 5.94e-01 1a26 a.41.1.1 17413 d.166.1.2 42275 1fezA 256 7.94e-01 1fezA c.108.1.3 43343 1ponA 36 8.35e-01 1ponA a.39.1.5 17239 1rqlA 267 8.42e-01 c.108.1.3 -6814 1k94A 165 8.49e-01 a.39.1.8 68333 1nt4A 391 1.01e+00 c.60.1.2 -7942 1a4iA 301 1.05e+00 1a4iA c.2.1.7 30278 c.58.1.2 33926 2mysB 166 1.07e+00 1wdcB a.39.1.5 17308 1j6pA 418 1.09e+00 b.92.1.4 77089 c.1.9.9 77090 1a4iB 301 1.10e+00 1a4iA c.2.1.7 30279 c.58.1.2 33927 1bfmA 69 1.11e+00 1a7w a.22.1.2 16479 1k9uA 78 1.17e+00 a.39.1.10 84348 1scmB 145 1.20e+00 1wdcB a.39.1.5 17304 1p1mA 406 1.21e+00 b.92.1.4 87696 c.1.9.9 87697 1ctaA 36 1.25e+00 1ctdA a.39.1.5 17232 1dqeA 137 1.35e+00 1dqeA a.39.2.1 17388 1ibcB 88 1.57e+00 1pauB 1n25A 368 1.59e+00 c.37.1.20 85264 1wdcB 156 1.69e+00 1wdcB a.39.1.5 17302 1bj4A 470 1.75e+00 1bj4A c.67.1.4 34479 1bmqB 88 1.83e+00 1pauB 1hfoA 113 1.84e+00 d.80.1.3 61006 1hztA 190 1.94e+00 1i9aA d.113.1.2 61459 1f46A 140 1.97e+00 1f46A d.129.4.1 59643 1g7fA 298 1.97e+00 1pty c.45.1.2 60330 1k0sA 151 2.03e+00 b.40.7.1 67969 2liv 344 2.07e+00 2liv c.93.1.1 35708 3cla 213 2.13e+00 3cla c.43.1.1 32610 1mb3A 124 2.14e+00 c.23.1.1 78907 1m45A 148 2.19e+00 a.39.1.5 78598 1hv9A 456 2.20e+00 1fwyA b.81.1.4 28060 c.68.1.5 34518 1i9aA 182 2.22e+00 1i9aA d.113.1.2 62082 1f47B 144 2.22e+00 1f46A d.129.4.1 59645 1fgs 428 2.30e+00 1fgs c.59.1.2 33959 c.72.2.2 34962 1smlA 269 2.46e+00 1smlA d.157.1.1 42053 1diaA 306 2.50e+00 1a4iA c.2.1.7 30280 c.58.1.2 33928 1exrA 148 2.80e+00 1cll a.39.1.5 17299 1rv3A 483 2.82e+00 2hnp 321 2.87e+00 1pty c.45.1.2 32678 1kk8B 139 2.90e+00 a.39.1.5 77430 1hzfA 367 3.03e+00 a.102.4.4 76731 1wm1A 317 3.10e+00 1nxiA 132 3.17e+00 d.58.47.1 86381 1p9qC 256 3.25e+00 1ig5A 75 3.25e+00 4icb a.39.1.1 62363 1osa 148 3.30e+00 1cll a.39.1.5 17300 1ls8A 142 3.30e+00 a.39.2.1 78176 1sedA 117 3.39e+00 1fwyA 331 3.55e+00 1fwyA b.81.1.4 28064 c.68.1.5 34522 1m7xA 617 3.56e+00 b.1.18.2 78749 b.71.1.1 78750 c.1.8.1 78751 1npdA 288 3.70e+00 c.2.1.7 80681 c.58.1.5 80682 1rwyA 109 3.80e+00 a.39.1.4 -825 1ht9A 76 3.80e+00 4icb a.39.1.1 61252 1g57A 217 3.83e+00 1g57A d.115.1.2 60253 1edqA 540 3.99e+00 1ctn b.1.18.2 21873 c.1.8.5 29002 d.26.3.1 38436 1a75A 108 3.99e+00 1a75A a.39.1.4 17216 1vi2A 300 4.01e+00 c.2.1.7 -5960 c.58.1.5 -6366 1brlB 324 4.18e+00 1lucA c.1.16.1 29554 1ctn 540 4.25e+00 1ctn b.1.18.2 21876 c.1.8.5 29005 d.26.3.1 38439 1jx2B 315 4.32e+00 c.37.1.8 67404 1dmaA 214 4.40e+00 1aerA d.166.1.1 42251 1k9tA 540 4.45e+00 b.1.18.2 77298 c.1.8.5 77299 d.26.3.1 77300 1m46A 148 4.50e+00 a.39.1.5 78599 1aerA 205 4.66e+00 1aerA d.166.1.1 42249 1qtrA 317 4.86e+00 1qtrA c.69.1.7 34660 1fxjA 331 4.86e+00 1fwyA b.81.1.4 28062 c.68.1.5 34520 1i2aA 219 5.19e+00 e.24.1.1 -12012 1lucB 324 5.20e+00 1lucA c.1.16.1 29548 1cjsA 219 5.38e+00 1cjsA e.24.1.1 43354 1auiA 521 5.67e+00 1auiA d.159.1.3 42085 1a99A 344 5.69e+00 1pot c.94.1.1 35812 1qtoA 122 5.74e+00 1bylA d.32.1.2 38494 1fsz 372 5.97e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1djnA 729 6.14e+00 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1hfuA 503 6.27e+00 b.6.1.3 65827 b.6.1.3 65828 b.6.1.3 65829 1zac 90 6.28e+00 1ncx a.39.1.5 17236 1jwyB 315 6.55e+00 c.37.1.8 67401 1abrA 251 6.79e+00 1mrj d.165.1.1 42196 1gntA 553 6.89e+00 e.26.1.1 70290 1a65A 504 6.94e+00 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1e2uA 553 6.95e+00 1e1dA e.26.1.1 43362 1nzoA 363 7.09e+00 b.105.1.1 -2933 e.3.1.1 -11784 1nf2A 268 7.10e+00 c.108.1.10 -6842 1otgA 125 7.23e+00 1otgA d.80.1.2 39831 3htsB 102 7.31e+00 2hts a.4.5.22 16175 2fokA 579 7.33e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1din 236 7.36e+00 1din c.69.1.9 34682 1npyA 271 7.37e+00 c.2.1.7 85995 c.58.1.5 85996 1ggvA 232 7.45e+00 1din c.69.1.9 34683 1qwnA 1045 7.53e+00 a.8.3.1 -414 b.30.5.6 -3517 c.6.2.1 -6058 1j2gA 319 7.80e+00 1mwwA 128 7.85e+00 unknown_sccs -10451 1eq9A 222 7.94e+00 5ptp b.47.1.2 26068 1k4iA 233 8.08e+00 d.115.1.2 72056 1e32A 458 8.09e+00 1e32A b.52.2.3 59183 c.37.1.20 59184 d.31.1.1 59185 1jbgA 109 8.31e+00 a.6.1.3 66480 1hxkA 1015 8.31e+00 a.8.3.1 83070 b.30.5.6 83071 c.6.2.1 83072 1brt 277 8.34e+00 1brt c.69.1.12 34699 1htyA 1015 8.53e+00 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 1ku1A 230 8.58e+00 a.118.3.1 72996 1hwwA 1015 8.65e+00 a.8.3.1 83067 b.30.5.6 83068 c.6.2.1 83069 1ja9A 274 8.73e+00 c.2.1.2 62817 1e1dA 553 8.95e+00 1e1dA e.26.1.1 43363 1fp4A 492 9.15e+00 c.92.2.3 76187 2tmdA 729 9.19e+00 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1broA 277 9.27e+00 1brt c.69.1.12 34700 1o94A 729 9.34e+00 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1uzxA 169 9.45e+00 d.20.1.2 -9409 1rfzA 168 9.57e+00 unknown_sccs -1206 1s6cA 183 9.59e+00 a.39.1.5 -858 1j6uA 469 9.63e+00 c.5.1.1 77094 c.59.1.1 77095 c.72.2.1 77096 1p9kA 79 1.02e+01 unknown_sccs -10238 1qapA 296 1.03e+01 1qpoA c.1.17.1 29559 d.41.2.1 38595 4pep 326 1.05e+01 1smrA b.50.1.2 26843 1uiqA 351 1.07e+01 1v7cA 351 1.07e+01 c.79.1.1 -8512 1klaA 112 1.07e+01 2tgi g.17.1.2 44779 1esxA 96 1.12e+01 1esxA j.11.1.1 59501 5pal 109 1.12e+01 1a75A a.39.1.4 17215 1pdo 135 1.15e+01 1pdo c.54.1.1 33376 1kgdA 180 1.17e+01 c.37.1.1 68582 1o1fC 147 1.18e+01 i.15.1.1 80997 1g33A 73 1.19e+01 a.39.1.4 65121 1lvfA 110 1.19e+01 a.47.2.1 74280 1bgp 309 1.20e+01 1bgp a.93.1.1 18690 1bvyF 191 1.22e+01 1bvyF c.23.5.1 31207 1qdeA 224 1.24e+01 1qvaA c.37.1.19 32410 1m5tA 124 1.25e+01 c.23.1.1 78660 1t3cA 421 1.25e+01 1el4A 195 1.26e+01 1ej3A a.39.1.5 59453 1kwmA 402 1.31e+01 c.56.5.1 73079 d.58.3.1 73080 1b4aA 149 1.33e+01 1b4aA a.4.5.3 16088 d.74.2.1 39721 1fokA 568 1.33e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1b9hA 388 1.34e+01 1b9hA c.67.1.4 34488 1jakA 512 1.35e+01 c.1.8.6 66472 d.92.2.1 66473 1h97A 147 1.36e+01 1h97A a.1.1.2 60812 1cv8 174 1.40e+01 1cv8 d.3.1.1 37089 1l1qA 186 1.41e+01 c.61.1.1 77653 1mil 104 1.45e+01 1d4tA d.93.1.1 40496 1twdA 256 1.48e+01 1wdnA 226 1.48e+01 1lst c.94.1.1 35816 1o66A 275 1.51e+01 c.1.12.8 -5590 1fdr 248 1.54e+01 1fdr b.43.4.2 25653 c.25.1.1 31543 1nrzA 164 1.55e+01 c.38.1.1 86131 1e8cA 498 1.57e+01 c.98.1.1 59377 c.59.1.1 59378 c.72.2.1 59379 1br1B 150 1.58e+01 1wdcC a.39.1.5 17309 1itzA 675 1.59e+01 c.36.1.6 76798 c.36.1.10 76797 c.48.1.1 76799 1kkuA 279 1.59e+01 c.26.1.3 72661 1hta 69 1.61e+01 1a7w a.22.1.2 16476 1igwA 434 1.63e+01 c.1.12.7 62370 2lbp 346 1.66e+01 2liv c.93.1.1 35709 1ogsA 497 1.69e+01 b.71.1.2 86997 c.1.8.3 86998 1hp4A 512 1.71e+01 1hp4A c.1.8.6 61111 d.92.2.1 61112 1f7wA 144 1.72e+01 1f46A d.129.4.1 59679 1j75A 67 1.73e+01 a.4.5.19 62673 1ubpA 101 1.73e+01 1ubpA d.8.1.1 37353 1kl9A 182 1.75e+01 b.40.4.5 72681 1hp5A 512 1.79e+01 1hp4A c.1.8.6 61113 d.92.2.1 61114 1cc1S 283 1.80e+01 2frvA e.19.1.1 43313 1rtxA 123 1.80e+01 a.1.1.1 -3 4ubpA 101 1.82e+01 1ubpA d.8.1.1 37352 1f9zA 135 1.83e+01 1qipA d.32.1.1 38484 2polA 366 1.89e+01 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1e0cA 271 1.92e+01 1e0cA c.46.1.2 32717 c.46.1.2 32718 3ullA 132 1.98e+01 3ullA b.40.4.3 25282 1m1nA 491 1.99e+01 c.92.2.3 78417 1pal 108 2.00e+01 1a75A a.39.1.4 17209 1ok7A 366 2.03e+01 1s96A 219 2.04e+01 c.37.1.1 -6972 1e12A 253 2.07e+01 1c3wA f.13.1.1 43428 1ej3A 191 2.08e+01 1ej3A a.39.1.5 17259 1fp2A 352 2.09e+01 1fpxA a.4.5.29 59941 c.66.1.12 59942 1g8iA 190 2.16e+01 1rec a.39.1.5 60363 3icb 75 2.19e+01 4icb a.39.1.1 17147 1jh3A 107 2.21e+01 d.66.1.4 71661 1d2iA 223 2.22e+01 1d2iA c.52.1.5 33297 1i6pA 220 2.22e+01 1ddzA c.53.2.1 61848 1pa4A 116 2.25e+01 d.52.7.1 -9780 1on2A 142 2.26e+01 a.4.5.24 87103 a.76.1.1 87104 1cqxA 403 2.28e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1dfmA 223 2.28e+01 1d2iA c.52.1.5 33295 1agx 331 2.30e+01 4pgaA c.88.1.1 35564 1n1jB 97 2.31e+01 a.22.1.3 79814 1ggwA 140 2.31e+01 1ggwA a.39.1.5 60490 1mdc 133 2.31e+01 1hmt b.60.1.2 27198 1nmeB 92 2.34e+01 1tlqA 189 2.38e+01 1efm 393 2.38e+01 1efcA c.37.1.8 64732 1ddgA 374 2.38e+01 1amoA b.43.4.1 25671 c.25.1.4 31559 1mg7A 417 2.39e+01 d.14.1.6 84954 d.58.26.6 84955 1c7gA 456 2.41e+01 c.67.1.2 -8153 1b4cA 92 2.44e+01 1b4cA a.39.1.2 17169 1pvaA 110 2.44e+01 1a75A a.39.1.4 17207 1jhfA 202 2.48e+01 a.4.5.2 63057 b.87.1.1 63058 1v2xA 194 2.48e+01 c.116.1.1 -6704 1qx2A 76 2.50e+01 1olsA 400 2.50e+01 c.36.1.11 -6959 1svfB 38 2.51e+01 1svfB h.3.2.1 45764 1mx4A 168 2.53e+01 d.211.1.1 79640 1f60B 94 2.57e+01 1b64 d.58.12.1 39307 1ixmB 192 2.64e+01 1ixmA d.123.1.1 41115 1j0mA 752 2.72e+01 a.102.3.2 83910 b.24.1.1 83911 b.30.5.2 83912 1kn1A 160 2.72e+01 a.1.1.3 77455 1lvhA 221 2.74e+01 c.108.1.6 74282 1h65A 270 2.74e+01 c.37.1.8 65640 1j2jB 45 2.75e+01 a.7.8.1 84017 1gutA 68 2.81e+01 b.40.6.1 65576 1dxrH 258 2.83e+01 6prcH b.41.1.1 25456 f.23.10.1 43433 1jug 125 2.84e+01 3lzt d.2.1.2 36587 1kxqE 120 2.85e+01 b.1.1.1 73171 1rliA 184 2.86e+01 unknown_sccs -6438 1xyzA 347 2.87e+01 1taxA c.1.8.3 28804 1b6rA 355 2.90e+01 1b6rA b.84.2.1 28241 c.30.1.1 31648 d.142.1.2 41493 1lvl 458 2.90e+01 1lvl c.3.1.5 30567 c.3.1.5 30568 d.87.1.1 40205 2minA 491 2.95e+01 1qguA c.92.2.3 35609 1qv1A 195 2.98e+01 a.39.1.5 -830 1dcfA 136 2.99e+01 1dcfA c.23.1.2 31124 2pvbA 107 3.00e+01 1a75A a.39.1.4 17205 1lqc 56 3.04e+01 1pru a.35.1.5 17109 1lccA 51 3.07e+01 1pru a.35.1.5 17110 1mxa 383 3.08e+01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1jli 112 3.08e+01 1jli a.26.1.2 16884 1b67A 68 3.15e+01 1a7w a.22.1.2 16474 1e8aA 91 3.17e+01 1b4cA a.39.1.2 17188 1mmiA 366 3.24e+01 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1lfwA 470 3.25e+01 c.56.5.4 77942 d.58.19.1 77943 1lcdA 51 3.26e+01 1pru a.35.1.5 17111 1b5fA 239 3.33e+01 1smrA b.50.1.2 26836 1b6sA 355 3.37e+01 1b6rA b.84.2.1 28242 c.30.1.1 31649 d.142.1.2 41494 1xxaA 78 3.39e+01 1xxaA d.74.2.1 39700 1jf0A 195 3.40e+01 1ej3A a.39.1.5 62926 1sxjE 354 3.41e+01 1v5xA 203 3.42e+01 c.1.2.4 -5169 1jf2A 195 3.42e+01 1ej3A a.39.1.5 62930 1nrvA 105 3.42e+01 d.93.1.1 86126 1rg9A 383 3.43e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1kyaA 499 3.46e+01 b.6.1.3 73203 b.6.1.3 73204 b.6.1.3 73205 6prcH 258 3.46e+01 6prcH b.41.1.1 25457 f.23.10.1 43436 1qm4A 396 3.47e+01 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1o6eA 235 3.47e+01 b.57.1.1 81083 1pauB 102 3.50e+01 1pauB 1c24A 263 3.51e+01 1c24A d.127.1.1 41148 1fzrA 138 3.52e+01 1fzrA c.52.1.17 33336 2matA 264 3.52e+01 1c24A d.127.1.1 41146 1hfx 123 3.56e+01 3lzt d.2.1.2 36600 1oi2A 366 3.58e+01 c.32.1.2 87039 d.79.2.2 87040 1fpxA 352 3.59e+01 1fpxA a.4.5.29 59950 c.66.1.12 59951 1ptvA 321 3.59e+01 1pty c.45.1.2 32665 1dp4A 435 3.62e+01 1dp4A c.93.1.1 35710 3minC 491 3.62e+01 1qguA c.92.2.3 35607 1jl3A 139 3.63e+01 c.44.1.1 66826 1bywA 110 3.64e+01 1bywA d.110.3.6 40912 1eaiC 61 3.72e+01 1eaiC g.22.1.1 44894 1jbwA 428 3.78e+01 c.59.1.2 62860 c.72.2.2 62861 4gr1 478 3.78e+01 3grs c.3.1.5 30461 c.3.1.5 30462 d.87.1.1 40162 3psg 370 3.79e+01 1smrA b.50.1.2 26841 1fa8A 135 3.81e+01 1qipA d.32.1.1 38486 1cb7B 483 3.83e+01 1cb7B c.1.19.2 29648 1ep2B 261 3.84e+01 1ep2B b.43.4.2 25666 c.25.1.3 31556 1qhbA 596 3.89e+01 1qhbA a.111.1.2 19055 1ep3B 262 3.90e+01 1ep2B b.43.4.2 25664 c.25.1.3 31554 1kqnA 279 3.92e+01 c.26.1.3 77492 1p57B 255 3.92e+01 b.47.1.2 -4248 1cseE 274 3.93e+01 1gci c.41.1.1 32481 3grs 478 3.94e+01 3grs c.3.1.5 30441 c.3.1.5 30442 d.87.1.1 40152 1qfjA 232 3.96e+01 1qfjA b.43.4.2 25655 c.25.1.1 31545 1gs5A 258 3.97e+01 c.73.1.2 70395