# 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 1pw4A 451 5.84e-38 f.38.1.1 95198 2gfpA 375 1.29e-36 1pv6A 417 3.63e-27 f.38.1.2 95151 2cfqA 417 8.36e-22 1otsA 465 3.73e-03 f.20.1.1 87415 1kplA 473 7.68e-03 f.20.1.1 68782 2a65A 519 3.63e-02 1o7xC 377 3.89e-02 a.103.1.1 81173 1o7xB 377 5.17e-02 a.103.1.1 81172 1o7xD 377 6.13e-02 a.103.1.1 81174 1mznA 240 8.08e-02 a.123.1.1 79704 1jb0A 755 2.36e-01 1jb0A f.29.1.1 62820 2fm9A 215 2.44e-01 1vgmA 378 4.15e-01 1o0wA 252 4.35e-01 a.149.1.1 80751 d.50.1.1 80752 1iomA 377 5.44e-01 a.103.1.1 83698 2bs3C 256 5.48e-01 1qlaC 256 5.85e-01 1qlaC f.21.2.1 43722 1mvcA 240 6.94e-01 a.123.1.1 79499 1kpkA 473 6.95e-01 f.20.1.1 68776 1c3wA 222 7.74e-01 1c3wA f.13.1.1 43405 2at9 247 8.44e-01 1c3wA f.13.1.1 43427 2ng1 293 8.73e-01 1ng1 a.24.13.1 16962 c.37.1.10 32273 2j0wA 449 9.20e-01 2gifA 1057 9.26e-01 1m0kA 262 9.68e-01 f.13.1.1 78344 1rfzA 168 1.00e+00 a.195.1.1 97411 1qkrA 188 1.03e+00 1qkrA a.24.9.1 16628 1i4tB 224 1.04e+00 h.4.7.1 61730 1rxqA 178 1.07e+00 a.213.1.1 105118 1ls1A 295 1.10e+00 a.24.13.1 78170 c.37.1.10 78171 1s35A 214 1.11e+00 a.7.1.1 98420 a.7.1.1 98421 1jpnA 296 1.24e+00 a.24.13.1 67039 c.37.1.10 67040 1i4lA 224 1.33e+00 1i49A h.4.7.1 61718 1ffh 294 1.38e+00 1ng1 a.24.13.1 16960 c.37.1.10 32271 1ng1 294 1.40e+00 1ng1 a.24.13.1 16961 c.37.1.10 32272 1i4dA 224 1.64e+00 h.4.7.1 61682 1xiuA 230 1.78e+00 1lbd 282 1.82e+00 1lbd a.123.1.1 19279 1hkbA 917 1.88e+00 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1wpgA 994 2.02e+00 1aijS 301 2.28e+00 6prcM f.26.1.1 43465 1myo 118 2.30e+00 2myo d.211.1.1 19174 169lA 164 2.39e+00 1l92 d.2.1.3 36963 1aijM 307 2.80e+00 6prcM f.26.1.1 43462 1rzhM 307 2.97e+00 f.26.1.1 98165 1hkcA 917 2.98e+00 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1g5yA 238 3.07e+00 1lbd a.123.1.1 60294 2d5xB 146 3.26e+00 1kgbA 231 3.32e+00 f.13.1.1 68581 1i3dA 146 3.36e+00 a.1.1.2 61587 1czaN 917 3.39e+00 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1s5lA 344 3.52e+00 1a59 378 3.56e+00 1aj8A a.103.1.1 18902 1yucA 255 3.68e+00 1pk5A 248 3.70e+00 a.123.1.1 88139 1uetA 437 3.78e+00 a.160.1.3 99272 d.218.1.7 99273 d.58.16.2 99274 2myo 118 3.81e+00 2myo d.211.1.1 19175 1eulA 994 3.85e+00 1eulA 1y82A 157 3.93e+00 1t9xA 1049 4.23e+00 1iwgA 1053 4.30e+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 1hx1B 114 4.37e+00 1hx1B a.7.7.1 61350 1nw3A 416 4.43e+00 c.66.1.31 86288 1v96A 149 4.46e+00 168lA 164 4.52e+00 1l92 d.2.1.3 36975 1dgkN 917 4.54e+00 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 2ghcX 261 4.66e+00 2gnxA 365 4.75e+00 1u19A 349 5.11e+00 1sesA 421 5.20e+00 1sesA a.2.7.1 15710 d.104.1.1 40710 2c5kT 95 5.43e+00 1k87A 669 5.44e+00 a.176.1.1 77286 c.1.23.2 77287 1mmoG 162 5.52e+00 1mtyG a.23.3.1 16512 1qhaA 917 5.53e+00 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1r89A 437 5.58e+00 a.160.1.3 97221 d.218.1.7 97222 d.58.16.2 97223 2h8fB 146 5.74e+00 1oafA 261 5.90e+00 a.93.1.1 86734 1iwhB 146 6.03e+00 a.1.1.2 76883 1kxpD 458 6.08e+00 a.126.1.1 73160 a.126.1.1 73161 a.126.1.1 73162 1h7cA 108 6.10e+00 a.7.5.1 70914 1b33B 161 6.14e+00 1qgwC a.1.1.3 15650 1jdhA 529 6.15e+00 a.118.1.1 66549 1dkfA 233 6.15e+00 3erdA a.123.1.1 19280 1g3jA 532 6.16e+00 3bct a.118.1.1 19114 2gmyA 153 6.25e+00 1mtyG 162 6.52e+00 1mtyG a.23.3.1 16498 1wjtA 103 6.71e+00 1unlD 208 6.75e+00 1zs3A 182 6.80e+00 2f6hX 419 7.14e+00 1y01A 102 7.23e+00 1bmfG 272 7.32e+00 1e1qG c.49.2.1 33160 3mag 307 7.56e+00 3mag c.66.1.25 34205 2csgA 424 7.93e+00 1nbmG 272 8.05e+00 1e1qG c.49.2.1 33161 1bgc 174 8.08e+00 1bgc a.26.1.1 16822 3bct 457 8.25e+00 3bct a.118.1.1 19112 1eijA 80 8.36e+00 1eijA a.5.6.1 16298 1foeA 377 8.66e+00 1foeA a.87.1.1 18517 b.55.1.1 26969 1qq8A 214 8.70e+00 1qq8A 1hz4A 373 9.14e+00 a.118.8.2 65960 1i7wA 538 1.01e+01 3bct a.118.1.1 61909 1b5l 172 1.02e+01 1b5l a.26.1.3 16900 1v74B 87 1.06e+01 a.24.20.1 100443 1lfpA 249 1.07e+01 e.39.1.1 73885 1ibrB 462 1.09e+01 1qgrA a.118.1.1 19120 1b5sA 242 1.11e+01 1eaf c.43.1.1 32626 1n0qA 93 1.12e+01 k.37.1.1 79754 1jb0L 154 1.17e+01 1jb0L f.31.1.1 62829 103l 167 1.18e+01 1l92 d.2.1.3 36870 1z8uA 102 1.21e+01 2gd5A 179 1.21e+01 1e1qG 272 1.21e+01 1e1qG c.49.2.1 33162 1mswD 883 1.22e+01 e.8.1.3 79427 1dm5A 315 1.23e+01 1avc a.65.1.1 18186 1f88A 348 1.27e+01 1f88A f.13.1.2 43429 1wa5B 530 1.29e+01 1av6A 289 1.31e+01 3mag c.66.1.25 34218 2fd5A 180 1.31e+01 1n45A 233 1.34e+01 a.132.1.1 79981 1owcA 427 1.35e+01 a.103.1.1 104039 1agrH 205 1.40e+01 1agrE a.91.1.1 18539 1vkeA 133 1.40e+01 a.152.1.2 108650 1yarO 237 1.41e+01 2h79A 269 1.41e+01 1y9qA 192 1.44e+01 2c2aA 258 1.45e+01 1u7gA 385 1.46e+01 f.44.1.1 107723 2azjA 289 1.46e+01 1h4lD 147 1.46e+01 a.74.1.1 70873 1b8dA 164 1.49e+01 1cpcA a.1.1.3 15665 1jli 112 1.51e+01 1jli a.26.1.2 16884 2avpA 70 1.54e+01 1i49A 224 1.55e+01 1i49A h.4.7.1 61679 1aeiA 315 1.56e+01 1avc a.65.1.1 18180 1i5pA 633 1.60e+01 1i5pA b.18.1.3 61817 b.77.2.1 61818 f.1.3.1 61819 1kgnA 329 1.62e+01 a.25.1.2 68584 1xjzA 233 1.62e+01 1a0p 290 1.64e+01 1a0p a.60.9.1 18105 d.163.1.1 42165 2c2nA 339 1.64e+01 1gakA 141 1.64e+01 1gakA a.19.1.1 16415 2cdqA 510 1.65e+01 1spgB 147 1.68e+01 1cg5B a.1.1.2 15588 1r5qA 102 1.75e+01 a.186.1.1 97103 1keyA 235 1.78e+01 a.118.16.1 72389 151l 164 1.81e+01 1l92 d.2.1.3 36944 1adt 356 1.85e+01 1anv a.54.1.1 17887 g.51.1.1 45362 g.51.1.1 45368 2cwyA 94 1.88e+01 1bccE 196 1.88e+01 1rie b.33.1.1 24431 f.23.12.1 43699 2azeA 155 1.88e+01 1rkpA 326 1.90e+01 a.211.1.2 97620 1eztA 166 1.90e+01 1agrE a.91.1.1 18541 1z98A 281 1.91e+01 1nz6A 101 1.93e+01 a.2.3.1 86441 1agrE 205 1.93e+01 1agrE a.91.1.1 18538 156l 164 1.98e+01 1l92 d.2.1.3 36709 2dgzA 113 1.98e+01 1v8gA 329 2.00e+01 a.46.2.1 100505 c.27.1.1 100506 164l 164 2.03e+01 1l92 d.2.1.3 36714 1bf5A 545 2.04e+01 1bg1A a.47.1.1 17766 b.2.5.5 22460 d.93.1.1 40526 1f76A 336 2.04e+01 c.1.4.1 76160 1yeyA 444 2.04e+01 2fb5A 205 2.05e+01 1k7yA 577 2.08e+01 a.46.1.1 68272 c.23.6.1 68273 d.173.1.1 68274 1kpsB 171 2.08e+01 a.118.12.1 68787 1my6A 199 2.10e+01 a.2.11.1 85232 d.44.1.1 85233 1mx4A 168 2.11e+01 d.211.1.1 79640 1oyeA 1049 2.19e+01 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 109l 164 2.20e+01 1l92 d.2.1.3 36781 1esxA 96 2.22e+01 1esxA j.11.1.1 59501 1dlyA 164 2.24e+01 1dlyA a.1.1.1 14983 2i3fA 224 2.26e+01 2go7A 207 2.32e+01 113l 164 2.32e+01 1l92 d.2.1.3 36678 1anv 356 2.32e+01 1anv a.54.1.1 17890 g.51.1.1 45365 g.51.1.1 45371 191l 164 2.33e+01 1l92 d.2.1.3 36826 1pii 452 2.34e+01 1pii c.1.2.4 28559 c.1.2.4 28563 2dfaA 250 2.37e+01 1mla 309 2.38e+01 1mla c.19.1.1 31031 d.58.23.1 39383 1w2yA 229 2.38e+01 a.204.1.1 109140 1pq1A 196 2.45e+01 f.1.4.1 94986 1is2A 661 2.47e+01 a.29.3.2 71382 a.29.3.2 71383 e.6.1.2 71384 1vpt 348 2.48e+01 3mag c.66.1.25 34207 1hzxA 349 2.54e+01 1f88A f.13.1.2 61466 2axtB 510 2.59e+01 1glm 470 2.60e+01 1ayx a.102.1.1 18821 1bmtA 246 2.65e+01 1bmtA a.46.1.1 17757 c.23.6.1 31235 1jtvA 327 2.66e+01 c.2.1.2 84230 1fdt 327 2.70e+01 1fds c.2.1.2 29841 1wn0A 145 2.71e+01 1gai 472 2.71e+01 1ayx a.102.1.1 18819 173l 164 2.72e+01 1l92 d.2.1.3 36728 1lfkA 398 2.72e+01 a.104.1.1 77926 1w0bA 102 2.73e+01 a.7.11.1 108985 1f16A 192 2.75e+01 1f16A f.1.4.1 43400 1z2iA 358 2.77e+01 158l 164 2.79e+01 1l92 d.2.1.3 36747 1xgsA 295 2.85e+01 1bn5 a.4.5.25 16216 d.127.1.1 41153 1l58 164 2.87e+01 1l92 d.2.1.3 36635 1rc9A 221 2.94e+01 1c05A 159 2.97e+01 1c05A d.66.1.2 39559 1t5oA 351 2.98e+01 c.124.1.5 106459 1yewB 247 2.99e+01 114l 164 3.00e+01 1l92 d.2.1.3 36663 1wgzA 510 3.01e+01 1swxA 209 3.01e+01 a.224.1.1 106075 1uuzA 137 3.04e+01 d.233.1.1 100024 1dozA 309 3.05e+01 1ak1 c.92.1.1 35592 2ac4A 309 3.05e+01 1apxA 249 3.06e+01 1ryc a.93.1.1 18669 2ac2A 309 3.08e+01 2i0mA 216 3.08e+01 2hneA 436 3.10e+01 1go4E 100 3.10e+01 h.1.22.1 70296 1jr3D 343 3.12e+01 a.80.1.1 63251 c.37.1.20 63252 2bn5A 33 3.12e+01 2fupA 168 3.16e+01 1gqeA 365 3.16e+01 e.38.1.1 70351 1myt 146 3.17e+01 1a6m a.1.1.2 15207 1i6zA 135 3.17e+01 a.7.7.1 61861 1i5rA 327 3.20e+01 c.2.1.2 83668 1mqvA 125 3.22e+01 a.24.3.2 79415 1paqA 189 3.23e+01 a.118.1.14 94413 1dquA 538 3.24e+01 1dquA c.1.12.7 29314 2ga9A 297 3.28e+01 6cts 433 3.29e+01 1csh a.103.1.1 18891 2avkA 136 3.29e+01 177l 164 3.32e+01 1l92 d.2.1.3 36958 1eca 136 3.32e+01 1flp a.1.1.2 15209 1ecd 136 3.32e+01 1flp a.1.1.2 15211 1jk0A 419 3.35e+01 a.25.1.2 63142 1ak1 310 3.35e+01 1ak1 c.92.1.1 35594 1b6iA 164 3.36e+01 1l92 d.2.1.3 36945 2i7aA 174 3.38e+01 2hyjA 200 3.39e+01 1aa7A 158 3.41e+01 1aa7A a.95.1.1 18741 130l 164 3.42e+01 1l92 d.2.1.3 36638 1d8cA 723 3.48e+01 1d8cA c.1.13.1 29325 1i1gA 141 3.49e+01 a.4.5.32 65982 d.58.4.2 65983 1aj8A 371 3.49e+01 1aj8A a.103.1.1 18900 1l7mA 211 3.52e+01 c.108.1.4 73664 2iu1A 208 3.52e+01 1j7yB 146 3.54e+01 a.1.1.2 66427 1x46A 150 3.54e+01 138l 164 3.54e+01 1l92 d.2.1.3 36679 1phnA 162 3.55e+01 1cpcA a.1.1.3 15641 1t0qA 498 3.56e+01 a.25.1.2 106220 1dl5A 317 3.57e+01 1dl5A c.66.1.7 64720 d.197.1.1 64721 1i1rB 181 3.58e+01 1i1rB a.26.1.1 61548 1a00B 146 3.58e+01 1abwA a.1.1.2 15469 1v39 322 3.61e+01 3mag c.66.1.25 34206 1vp9 322 3.61e+01 3mag c.66.1.25 34210 1wkbA 810 3.62e+01 126l 164 3.62e+01 1l92 d.2.1.3 36699 1vns 609 3.62e+01 1vns a.111.1.3 19061 1oglA 283 3.63e+01 a.204.1.1 92922 1a9cA 221 3.64e+01 1a8rA d.96.1.1 40602 2a1jB 91 3.69e+01 2ganA 190 3.69e+01 1irdB 146 3.74e+01 a.1.1.2 66287 2bcqA 335 3.83e+01 2hyiD 77 3.85e+01 1y74B 50 3.88e+01 1dvpA 220 3.88e+01 1dvpA a.118.9.2 19216 g.50.1.1 45358 1f5sA 211 3.90e+01 1f5sA c.108.1.4 59656 1j97A 211 3.90e+01 1f5sA c.108.1.4 62753 1ew6A 137 3.90e+01 1ewaA a.1.1.2 15637 1ewaA 137 3.90e+01 1ewaA a.1.1.2 15639 1b04A 318 3.91e+01 1b04A d.142.2.2 41579 172l 164 3.97e+01 1l92 d.2.1.3 36905 2gpyA 233 3.98e+01 1h38B 883 3.99e+01 e.8.1.3 76626 1h38D 883 3.99e+01 e.8.1.3 76628 1h38C 883 3.99e+01 e.8.1.3 76627 1g2nA 264 3.99e+01 1lbd a.123.1.1 60227 2f23A 156 3.99e+01