# List of top-scoring protein chains for t2k-100-30-bys 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 1mkiA 330 2.21e-41 e.3.1.2 84994 1fw9A 164 9.36e-02 1fw9A d.190.1.1 60059 1i2sA 282 1.02e-01 e.3.1.1 71104 1k1zA 78 1.27e-01 b.34.2.1 68026 1bza 262 1.30e-01 1btl e.3.1.1 42701 1ei5A 520 1.45e-01 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1iyoA 262 1.57e-01 e.3.1.1 76970 1k38A 254 1.61e-01 e.3.1.1 84303 1iysA 262 1.64e-01 e.3.1.1 -11760 1klxA 138 2.36e-01 a.118.18.1 77440 4blmA 265 2.73e-01 1btl e.3.1.1 42721 1hzoA 271 5.00e-01 e.3.1.1 71092 1n9bA 265 5.24e-01 e.3.1.1 85463 1gcqC 70 5.82e-01 1gcpA b.34.2.1 60436 1oshA 232 5.96e-01 a.123.1.1 -1697 1qq7A 253 7.00e-01 1qq5A c.108.1.1 43329 1qq5A 253 7.02e-01 1qq5A c.108.1.1 43327 1gcpA 70 7.23e-01 1gcpA b.34.2.1 60430 1rom 403 7.35e-01 1rom a.104.1.1 18963 1ermA 263 7.97e-01 1btl e.3.1.1 42690 1np3A 338 8.00e-01 a.100.1.2 85946 c.2.1.6 85947 1bsg 266 8.18e-01 1btl e.3.1.1 42729 1uch 230 8.69e-01 1uch d.3.1.6 37129 1jfbA 404 8.91e-01 a.104.1.1 66624 1aq6A 253 9.15e-01 1qq5A c.108.1.1 43331 1cmnA 402 1.08e+00 1rom a.104.1.1 18958 1g6aA 271 1.17e+00 1btl e.3.1.1 42704 1uw4B 248 1.21e+00 unknown_sccs -1560 1ghpA 258 1.26e+00 1btl e.3.1.1 60520 1alq 266 1.27e+00 1btl e.3.1.1 42707 3blm 257 1.30e+00 1btl e.3.1.1 42709 1fqgA 263 1.32e+00 1btl e.3.1.1 42699 1j1jA 240 1.37e+00 a.118.16.1 -1637 1f24A 402 1.38e+00 1rom a.104.1.1 18953 1m40A 263 1.39e+00 e.3.1.1 74437 1auiB 169 1.40e+00 1auiB a.39.1.5 17325 1ncx 162 1.47e+00 1ncx a.39.1.5 17222 1regX 122 1.52e+00 1regX d.58.27.1 39406 1top 162 1.54e+00 1ncx a.39.1.5 17223 1fqvJ 149 1.58e+00 1fqvD a.157.1.1 19266 d.42.1.1 38670 1btl 263 1.60e+00 1btl e.3.1.1 42691 1ouvA 273 1.84e+00 a.118.18.1 -1586 1keyA 235 1.97e+00 a.118.16.1 72389 1pioA 257 2.11e+00 1btl e.3.1.1 42719 1i9sA 210 2.20e+00 1i9sA c.45.1.1 62099 1abv 134 2.43e+00 1abv a.70.1.1 18317 1kktA 511 2.46e+00 a.102.2.1 68687 1fqvD 149 2.54e+00 1fqvD a.157.1.1 19263 d.42.1.1 38667 1odoA 408 2.86e+00 a.104.1.1 -1463 1m7gA 211 2.88e+00 c.37.1.4 78724 1fa0A 537 2.97e+00 1fa0B a.160.1.1 75837 d.218.1.3 75838 d.58.16.1 39335 1fa0B 537 2.98e+00 1fa0B a.160.1.1 75839 d.218.1.3 75840 d.58.16.1 39336 1mfqC 129 3.07e+00 a.36.1.1 79046 1b8dA 164 3.14e+00 1cpcA a.1.1.3 15665 1qpaA 345 3.17e+00 1arv a.93.1.1 18585 1d6jA 211 3.32e+00 1d6jA c.37.1.4 31940 1uedA 406 3.34e+00 a.104.1.1 -1459 1omhA 293 3.53e+00 unknown_sccs -10527 1ezvF 125 3.60e+00 1be3F f.27.1.1 59550 1cii 602 4.33e+00 1cii f.1.1.1 43381 h.4.3.1 45787 1jg8A 347 4.49e+00 1jg8A c.67.1.1 62946 1e25A 282 4.52e+00 1e25A e.3.1.1 42731 1m6sA 347 4.54e+00 c.67.1.1 78701 1fs1B 141 4.98e+00 1vcbB a.157.1.1 19252 d.42.1.1 38664 1jf0A 195 5.05e+00 1ej3A a.39.1.5 62926 1cqqA 180 5.26e+00 1cqqA b.47.1.4 26422 1lmzA 187 5.38e+00 a.96.1.4 74037 1hqvA 191 5.42e+00 1hqvA a.39.1.8 61160 2nef 136 5.74e+00 1efnB d.102.1.1 40704 1d5rA 324 5.93e+00 1d5rA b.7.1.1 23181 c.45.1.1 32697 1kyoG 126 5.98e+00 f.27.1.1 73259 1na3A 91 6.00e+00 k.38.1.1 85481 1cbg 490 6.03e+00 1e70M c.1.8.4 28933 1i7xB 151 6.23e+00 1i7xB j.71.1.1 61914 1div 149 6.24e+00 1div d.99.1.1 40692 d.100.1.1 40693 1bueA 265 6.31e+00 1btl e.3.1.1 42727 1qwlA 505 6.32e+00 e.5.1.1 -11823 1o7eA 276 6.35e+00 e.3.1.1 -11766 2bmhA 455 6.87e+00 1bu7A a.104.1.1 18941 1n4oA 276 6.94e+00 e.3.1.1 -11764 1i7wB 151 7.13e+00 1i7wB j.71.1.1 61910 2bltA 361 7.31e+00 1gceA e.3.1.1 42739 1l1zA 274 7.55e+00 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1rgzA 363 7.78e+00 e.3.1.1 -11771 1lmeA 176 7.92e+00 d.167.1.1 84629 1m7sA 484 7.94e+00 e.5.1.1 74574 1ga0A 364 7.97e+00 1gceA e.3.1.1 60410 1ad1A 266 8.05e+00 1aj2 c.1.21.1 29668 1jpzA 473 8.07e+00 a.104.1.1 67069 1as4A 341 8.28e+00 1sek e.1.1.1 42623 1jrrA 382 8.29e+00 e.1.1.1 63256 1onhA 364 8.34e+00 e.3.1.1 -11769 1gceA 364 8.40e+00 1gceA e.3.1.1 42738 1lvfA 110 8.42e+00 a.47.2.1 74280 1uocA 289 8.47e+00 unknown_sccs -7671 1lehA 364 8.60e+00 1bw9A c.2.1.7 30268 c.58.1.1 33916 2sqcA 631 8.68e+00 2sqcA a.102.4.2 18854 a.102.4.2 18855 1jjyA 636 8.75e+00 1jjyA 1vhrA 184 8.97e+00 1vhrA c.45.1.1 32651 1mtyD 512 9.08e+00 1mhyD a.25.1.2 16742 1d3uB 201 9.28e+00 1aisB a.74.1.2 18386 a.74.1.2 18387 1k8kD 300 9.37e+00 d.198.2.1 68309 d.198.2.1 68310 1ci8A 392 9.45e+00 e.3.1.1 64765 1cf9A 753 9.57e+00 1cf9A c.23.16.3 31441 e.5.1.1 42815 1sqc 631 9.69e+00 2sqcA a.102.4.2 18858 a.102.4.2 18859 1ci9A 392 9.80e+00 e.3.1.1 64767 1e7uA 961 9.83e+00 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1dgfA 497 9.92e+00 1cf9A e.5.1.1 42782 1dq3A 454 1.00e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1ggrA 168 1.01e+01 1gpr b.84.3.1 28279 1p80A 753 1.02e+01 c.23.16.3 -6547 e.5.1.1 -11840 1dghB 498 1.05e+01 1cf9A e.5.1.1 42791 1dcs 311 1.07e+01 1dcs b.82.2.1 28124 1f3z 161 1.13e+01 1gpr b.84.3.1 28273 1mkmA 249 1.13e+01 a.4.5.33 79242 d.110.2.2 79243 1jmeA 455 1.13e+01 a.104.1.1 66885 1jtdB 273 1.15e+01 b.69.5.2 67265 1e8yA 966 1.15e+01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1rfmA 344 1.16e+01 c.122.1.1 -8032 1qyaA 307 1.16e+01 1hylA 230 1.17e+01 5ptp b.47.1.2 26076 1epxA 370 1.18e+01 1fbaA c.1.10.1 29150 1qlpA 394 1.21e+01 1ovaA e.1.1.1 42628 1iapA 211 1.22e+01 a.91.1.1 62119 1el4A 195 1.22e+01 1ej3A a.39.1.5 59453 1tfb 208 1.25e+01 1tfb a.74.1.2 18382 a.74.1.2 18383 1m0qA 433 1.26e+01 c.67.1.4 78350 1qi7A 253 1.27e+01 1qi7A d.165.1.1 42210 1hkcA 917 1.30e+01 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1o69A 394 1.30e+01 c.67.1.4 -8209 1rx0A 393 1.31e+01 a.29.3.1 -742 e.6.1.1 -11858 1p9vA 310 1.31e+01 1sdjA 310 1.31e+01 d.21.1.2 -9420 d.21.1.2 -9421 1e8xA 961 1.31e+01 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1mmoD 512 1.33e+01 1mhyD a.25.1.2 16770 7catA 506 1.35e+01 1cf9A e.5.1.1 42781 1jf2A 195 1.36e+01 1ej3A a.39.1.5 62930 1volA 204 1.37e+01 1tfb a.74.1.2 18370 a.74.1.2 18371 1pi4A 358 1.37e+01 e.3.1.1 -11774 1icfI 65 1.37e+01 1icfI g.28.1.1 44958 1fhuA 320 1.38e+01 1fhuA c.1.11.2 29234 d.54.1.1 38878 1fsyA 358 1.39e+01 1gceA e.3.1.1 60016 2ahjC 206 1.41e+01 2ahjA d.149.1.1 41773 1que 303 1.41e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1igwA 434 1.45e+01 c.1.12.7 62370 1aqt 138 1.45e+01 1aqt a.2.10.1 15718 b.93.1.1 28435 1dlyA 164 1.45e+01 1dlyA a.1.1.1 14983 1k4wA 252 1.46e+01 a.123.1.1 72068 1qb2A 109 1.48e+01 1qb2A a.36.1.1 17125 1fhvA 323 1.50e+01 1fhuA c.1.11.2 29235 d.54.1.1 38879 9apiA 347 1.51e+01 1ovaA e.1.1.1 42630 1n00A 321 1.51e+01 a.65.1.1 85241 1pd21 199 1.57e+01 1pd21 2ahjA 206 1.57e+01 2ahjA d.149.1.1 41772 1ewjA 126 1.60e+01 1ecsA d.32.1.2 59526 1b2rA 304 1.61e+01 1fnc b.43.4.2 25648 c.25.1.1 31538 1su8A 636 1.62e+01 e.26.1.2 -12015 1bgeB 175 1.63e+01 1bgc a.26.1.1 16824 1elrA 131 1.66e+01 1a17 a.118.8.1 19209 1lfaA 187 1.67e+01 1ido c.62.1.1 34122 1jlm 192 1.68e+01 1ido c.62.1.1 34140 1go2A 304 1.69e+01 b.43.4.2 76243 c.25.1.1 76244 1mixA 206 1.71e+01 a.11.2.1 79166 b.55.1.5 79167 1i0aA 466 1.72e+01 1auwA a.127.1.1 61479 1kbuA 349 1.72e+01 a.60.9.1 72284 d.163.1.1 72285 1qv1A 195 1.73e+01 a.39.1.5 -830 1teaA 299 1.74e+01 1avsA 90 1.75e+01 1cll a.39.1.5 17226 1fqtA 112 1.75e+01 1fqtA b.33.1.1 24441 1lghA 56 1.75e+01 1lghA f.3.1.1 43733 1rxwA 336 1.79e+01 a.60.7.1 -1041 c.120.1.2 -6680 1dusA 194 1.81e+01 1dusA c.66.1.4 34182 1ogiA 303 1.82e+01 b.43.4.2 -4042 c.25.1.1 -6587 1nq7A 244 1.82e+01 a.123.1.1 -1682 1gikA 261 1.83e+01 d.165.1.1 -11545 2hlcA 230 1.83e+01 5ptp b.47.1.2 26074 1ngvA 534 1.85e+01 c.111.1.2 85698 1oaiA 59 1.87e+01 a.5.2.3 81255 1m5yA 408 1.87e+01 a.167.1.1 78664 d.26.1.1 78665 d.26.1.1 78666 1rgyA 360 1.89e+01 e.3.1.1 -11768 1hce 118 1.92e+01 1hce b.42.5.2 25625 1r6wA 322 1.92e+01 c.1.11.2 -5563 d.54.1.1 -9821 1ksr 100 1.94e+01 1qfhA b.1.18.10 21897 1i6uA 130 1.94e+01 d.140.1.1 61850 1gpr 162 1.96e+01 1gpr b.84.3.1 28267 1mroC 247 1.98e+01 1mroC d.58.31.1 39437 1ikzA 142 1.99e+01 1rpxA 230 2.01e+01 1rpxA c.1.2.2 28536 2blsA 358 2.03e+01 1gceA e.3.1.1 42747 1j1qA 261 2.04e+01 d.165.1.1 -11546 1a68 95 2.04e+01 1t1dA d.42.1.2 38639 1qh0A 295 2.07e+01 b.43.4.2 68891 c.25.1.1 68892 1prgA 270 2.08e+01 2prgA a.123.1.1 19314 1lis 136 2.15e+01 1lis a.19.1.1 16406 2lisA 136 2.15e+01 1lis a.19.1.1 16405 1e19A 314 2.18e+01 1b7bA c.73.1.1 34967 1f1eA 154 2.19e+01 a.22.1.2 64927 1ohuA 175 2.24e+01 f.1.4.1 -12058 1n91A 108 2.26e+01 d.206.1.1 80326 1dsxA 87 2.27e+01 1t1dA d.42.1.2 38644 1rec 201 2.28e+01 1rec a.39.1.5 17326 1d7uA 433 2.29e+01 2dkb c.67.1.4 34439 1hqcA 324 2.30e+01 1hqcA a.4.5.11 16127 c.37.1.20 32424 1adoA 363 2.34e+01 1fbaA c.1.10.1 29124 1iwgA 1053 2.34e+01 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 1kb9G 125 2.35e+01 f.27.1.1 77322 1rcuA 195 2.38e+01 unknown_sccs -7279 1kz7A 353 2.38e+01 a.87.1.1 73333 b.55.1.1 73334 1afrA 345 2.40e+01 1afrA a.25.1.2 16805 1hy0A 466 2.41e+01 1auwA a.127.1.1 61392 1a6r 471 2.43e+01 3gcb d.3.1.1 37033 1g60A 260 2.44e+01 c.66.1.11 70151 2dkb 433 2.46e+01 2dkb c.67.1.4 34438 1e3uA 246 2.46e+01 1fofA e.3.1.1 42755 1omrA 201 2.49e+01 a.39.1.5 -854 1tf4A 605 2.51e+01 1tf4A a.102.1.2 18827 b.2.2.2 22393 1cpo 299 2.52e+01 1cpo a.39.3.1 17390 a.39.3.1 17391 1f5aA 513 2.52e+01 1fa0B a.160.1.1 75835 d.218.1.3 75836 d.58.16.1 39337 1vduA 172 2.55e+01 unknown_sccs -1651 1kvkA 395 2.59e+01 d.14.1.5 73060 d.58.26.3 73061 1mf7A 194 2.59e+01 c.62.1.1 84937 1fr1A 361 2.59e+01 1gceA e.3.1.1 42734 1hbnC 248 2.59e+01 1mroC d.58.31.1 60902 1r8sE 203 2.62e+01 a.118.3.1 -1579 1vmoA 163 2.63e+01 1vmoA b.77.1.1 27974 1k8kG 151 2.65e+01 a.118.13.1 68313 1cf7A 76 2.68e+01 1cf7B a.4.5.17 16151 1q7fA 286 2.70e+01 unknown_sccs -4599 1cby 259 2.73e+01 1cby d.103.1.1 40705 1gcb 454 2.76e+01 3gcb d.3.1.1 37034 1g3mA 294 2.78e+01 c.37.1.5 83268 1iwmA 186 2.80e+01 b.125.1.2 83758 1qvjA 292 2.82e+01 d.113.1.1 -10902 2prf 125 2.84e+01 3nul d.110.1.1 40887 1q33A 292 2.84e+01 d.113.1.1 -10901 1ngnA 155 2.85e+01 a.96.1.2 85697 3gcb 470 2.86e+01 3gcb d.3.1.1 37032 1fcyA 236 2.88e+01 2lbd a.123.1.1 19282 1h2sA 225 2.89e+01 f.13.1.1 76578 1s4kA 120 2.91e+01 1oq9A 363 2.92e+01 a.25.1.2 87257 1jtkA 136 2.95e+01 c.97.1.1 71862 1gyxA 76 2.95e+01 d.80.1.1 76387 2gpr 154 2.97e+01 1gpr b.84.3.1 28269 1or3A 165 2.98e+01 1nfn a.24.1.1 16522 3crxA 343 3.01e+01 4crxA a.60.9.1 18101 d.163.1.1 42161 2ae2A 260 3.02e+01 1bdb c.2.1.2 29945 2hp8 68 3.02e+01 1hp8 a.17.1.1 16398 1gweA 503 3.03e+01 e.5.1.1 70667 1ne9A 335 3.04e+01 d.108.1.4 -10805 d.108.1.4 -10806 1gtmA 419 3.04e+01 1hwyA c.2.1.7 30223 c.58.1.1 33871 1pjjA 271 3.06e+01 1pylA 97 3.07e+01 1mbyA 88 3.08e+01 d.223.1.1 78931 1iexA 605 3.09e+01 c.1.8.7 66127 c.23.11.1 66128 1kp0A 402 3.10e+01 c.55.2.1 72834 d.127.1.1 72835 1dpjA 329 3.12e+01 1smrA b.50.1.2 26828 1ex1A 605 3.20e+01 1ex1A c.1.8.7 29013 c.23.11.1 31347 1k7wA 468 3.20e+01 a.127.1.1 72130 1bu7A 455 3.24e+01 1bu7A a.104.1.1 18937 1hcqA 84 3.25e+01 2nllB g.39.1.2 45117 1dcnD 436 3.26e+01 1auwA a.127.1.1 19423 1zrn 232 3.30e+01 1qq5A c.108.1.1 43323 1knwA 425 3.32e+01 b.49.2.3 -4274 c.1.6.1 -5229 1ecsA 126 3.32e+01 1ecsA d.32.1.2 59407 1ornA 226 3.32e+01 a.96.1.1 87342 1qo7A 394 3.33e+01 1qo7A c.69.1.11 34697 1auwA 468 3.35e+01 1auwA a.127.1.1 19416 3eipA 84 3.35e+01 3eipA d.26.2.1 38434 1on2A 142 3.36e+01 a.4.5.24 87103 a.76.1.1 87104 1repC 251 3.36e+01 1repC a.4.5.10 16125 a.4.5.10 16126 1korA 400 3.39e+01 c.26.2.1 72824 d.210.1.1 72825 1dcnA 424 3.40e+01 1auwA a.127.1.1 19420 1r2zA 274 3.42e+01 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 1p5sA 203 3.43e+01 a.40.1.1 -900 1p9bA 442 3.43e+01 c.37.1.10 -7115 1t1dA 100 3.46e+01 1t1dA d.42.1.2 38637 1jy5A 212 3.46e+01 d.124.1.1 71940 1mun 225 3.47e+01 1mun a.96.1.2 18744 1fs0E 138 3.47e+01 1aqt a.2.10.1 59997 b.93.1.1 59998 1ax4A 467 3.49e+01 1ax4A c.67.1.2 34391 1vsd 152 3.52e+01 1cxqA c.55.3.2 33625 1c3yA 108 3.52e+01 1c3yA a.39.2.1 17387 6prcL 273 3.53e+01 6prcL f.26.1.1 43434 1q0rA 298 3.54e+01 unknown_sccs -8330 1qhaA 917 3.57e+01 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1p35A 299 3.57e+01 1p35A b.28.1.1 23925 1dcuA 357 3.62e+01 1frpA e.7.1.1 42943 1s98A 107 3.64e+01 1a8p 258 3.65e+01 1fdr b.43.4.2 25654 c.25.1.1 31544 2gdm 153 3.65e+01 2gdm a.1.1.2 15212 1mrg 263 3.70e+01 1mrj d.165.1.1 42183 1ogsA 497 3.70e+01 b.71.1.2 86997 c.1.8.3 86998 1mjnA 179 3.71e+01 c.62.1.1 79210 1eg5A 384 3.72e+01 1ecxA c.67.1.3 34429 1f1uA 323 3.73e+01 d.32.1.3 83200 d.32.1.3 83201 1nekC 129 3.74e+01 f.21.2.2 80431 1d6aB 262 3.75e+01 1qi7A d.165.1.1 42198 1dbiA 280 3.76e+01 1gci c.41.1.1 32543 1uwzA 136 3.76e+01 1fuoA 467 3.79e+01 1furA a.127.1.1 19411 1jz8A 1023 3.81e+01 b.1.4.1 67830 b.1.4.1 67831 b.18.1.5 67832 b.30.5.1 67833 c.1.8.3 67834 1th8A 145 3.81e+01 1nogA 177 3.86e+01 a.25.2.2 85923 1n87A 56 3.89e+01 g.44.1.2 85390 1n1bA 549 3.89e+01 a.102.4.1 79799 a.128.1.3 79800 1k78A 149 3.91e+01 a.4.1.5 68255 a.4.1.5 68256 1m0uA 249 3.91e+01 a.45.1.1 78359 c.47.1.5 78360 1ecxA 384 3.97e+01 1ecxA c.67.1.3 34431 1fchA 368 3.98e+01 1fchA a.118.8.1 19212