# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1i2sA 282 1.17e-02 1bsg 266 2.83e-02 1btl e.3.1.1 42729 4blmA 265 5.73e-02 1btl e.3.1.1 42721 1ei5A 520 5.90e-02 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1bza 262 7.05e-02 1btl e.3.1.1 42701 1btl 263 7.61e-02 1btl e.3.1.1 42691 1g6aA 271 9.24e-02 1btl e.3.1.1 42704 1l7uA 263 1.66e-01 1m40A 263 1.66e-01 1ermA 263 1.74e-01 1btl e.3.1.1 42690 1fqgA 263 1.79e-01 1btl e.3.1.1 42699 1alq 266 2.10e-01 1btl e.3.1.1 42707 1hzoA 271 4.59e-01 1ghpA 258 5.43e-01 1btl e.3.1.1 60520 1dgfA 497 7.17e-01 1cf9A e.5.1.1 42782 7catA 506 9.82e-01 1cf9A e.5.1.1 42781 1qamA 244 1.19e+00 2ercA c.66.1.9 34220 1cf9A 753 1.50e+00 1cf9A c.23.16.3 31441 e.5.1.1 42815 1ucyE 109 1.50e+00 1ucyE 1a4pA 96 1.75e+00 1b4cA a.39.1.2 17176 2bmhA 455 1.79e+00 1bu7A a.104.1.1 18941 1k82A 268 1.79e+00 1fcyA 236 1.80e+00 2lbd a.123.1.1 19282 2nef 136 1.81e+00 1efnB d.102.1.1 40704 4lbd 267 2.00e+00 2lbd a.123.1.1 19289 2lbd 267 2.13e+00 2lbd a.123.1.1 19287 1pioA 257 2.30e+00 1btl e.3.1.1 42719 1hqoA 258 2.33e+00 1hqoA a.45.1.1 17749 c.47.1.5 33043 3crxA 343 2.74e+00 4crxA a.60.9.1 18101 d.163.1.1 42161 1bueA 265 2.78e+00 1btl e.3.1.1 42727 1abv 134 3.18e+00 1abv a.70.1.1 18317 1prgA 270 3.19e+00 2prgA a.123.1.1 19314 1mtyD 512 3.32e+00 1mhyD a.25.1.2 16742 1efnB 152 3.33e+00 1efnB d.102.1.1 40699 1volA 204 3.36e+00 1tfb a.74.1.2 18370 a.74.1.2 18371 1k0dA 260 3.39e+00 a.45.1.1 67930 c.47.1.5 67931 1qlwA 328 3.88e+00 1qlwA c.69.1.15 34722 1e7uA 961 3.90e+00 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1e2gA 215 3.92e+00 3tmkA c.37.1.1 59165 1e9eA 215 4.17e+00 c.37.1.1 64810 1qf6A 642 4.18e+00 1qf6A c.51.1.1 33210 d.66.1.1 39551 d.67.1.1 39562 d.104.1.1 40759 1mmoD 512 4.27e+00 1mhyD a.25.1.2 16770 1h8dH 260 4.28e+00 5ptp 1gdoB 240 4.33e+00 1gdoA d.153.1.1 41805 3blm 257 4.34e+00 1btl e.3.1.1 42709 1fm9D 272 4.37e+00 2prgA a.123.1.1 19313 1j9yA 385 4.45e+00 1j9yA c.1.8.3 62791 1ikzA 142 4.56e+00 1e2fA 215 4.68e+00 3tmkA c.37.1.1 59164 1qb2A 109 4.74e+00 1qb2A a.36.1.1 17125 1regX 122 5.00e+00 1regX d.58.27.1 39406 1kpsB 171 5.01e+00 a.118.12.1 68787 4crxA 322 5.27e+00 4crxA a.60.9.1 18095 d.163.1.1 42155 1crxA 322 5.30e+00 4crxA a.60.9.1 18097 d.163.1.1 42157 1k8kG 151 5.38e+00 a.118.13.1 68313 1f5mA 180 5.50e+00 1f5mB d.110.2.1 40895 1chkA 238 5.51e+00 1chkA d.2.1.7 36999 2prgA 271 5.64e+00 2prgA a.123.1.1 19311 1ahtH 259 5.78e+00 5ptp 1c5lH 259 6.06e+00 5ptp 1d6jA 211 6.08e+00 1d6jA c.37.1.4 31940 1ad1A 266 6.25e+00 1aj2 c.1.21.1 29668 1tafA 68 6.37e+00 1tafA a.22.1.3 16481 1f5mB 180 6.51e+00 1f5mB d.110.2.1 40896 1psrA 100 6.71e+00 1psrA a.39.1.2 17180 1axn 323 6.85e+00 1avc a.65.1.1 18149 2cae 484 6.90e+00 1cf9A e.5.1.1 42810 6gsvA 217 6.95e+00 1b8xA a.45.1.1 17633 c.47.1.5 32925 1lvfA 110 6.98e+00 1qaxA 428 7.08e+00 1qaxA d.58.20.1 39376 d.179.1.1 42597 1ax4A 467 7.79e+00 1ax4A c.67.1.2 34391 1a28A 256 7.93e+00 1a28A a.123.1.1 19290 1a36A 592 8.16e+00 1a36A a.2.8.1 15715 d.163.1.2 42173 e.15.1.1 43266 1que 303 8.51e+00 1fnc b.43.4.2 25647 c.25.1.1 31537 1g5pA 289 8.66e+00 1cp2A c.37.1.10 32253 8kme2 259 8.72e+00 1ucyE 1fw9A 164 8.83e+00 1fw9A d.190.1.1 60059 1ncx 162 8.85e+00 1ncx a.39.1.5 17222 1ci9A 392 8.89e+00 e.3.1.1 64767 1adoA 363 8.90e+00 1fbaA c.1.10.1 29124 2bltA 361 9.28e+00 1gceA e.3.1.1 42739 1ci8A 392 9.42e+00 e.3.1.1 64765 1nipA 289 9.56e+00 1cp2A c.37.1.10 32263 1b87A 181 9.59e+00 1b87A d.108.1.1 40797 1epxA 370 9.67e+00 1fbaA c.1.10.1 29150 2at2A 300 9.85e+00 3csuA c.78.1.1 35196 c.78.1.1 35197 1fjcA 96 1.04e+01 1fjcA d.58.7.1 39212 1hbzA 498 1.05e+01 1cf9A e.5.1.1 60937 1d5rA 324 1.06e+01 1d5rA b.7.1.1 23181 c.45.1.1 32697 1dq3A 454 1.06e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1lghA 56 1.06e+01 1lghA f.3.1.1 43733 1fa0A 537 1.07e+01 1fa0B d.58.16.1 39335 e.9.1.2 43229 1qq2A 199 1.07e+01 1qq2A c.47.1.10 33064 1g8pA 350 1.09e+01 1g8pA c.37.1.13 60376 1fsyA 358 1.09e+01 1gceA e.3.1.1 60016 2ercA 244 1.11e+01 2ercA c.66.1.9 34224 2blsA 358 1.11e+01 1gceA e.3.1.1 42747 1a31A 538 1.14e+01 1a36A d.163.1.2 42170 e.15.1.1 43263 1fs1B 141 1.15e+01 1vcbB a.122.1.1 19252 d.42.1.2 38664 1gmuA 143 1.15e+01 b.107.1.1 65335 d.58.38.1 65336 1e8xA 961 1.15e+01 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1elvA 333 1.16e+01 5ptp b.47.1.2 59454 g.18.1.1 59455 1dd5A 185 1.20e+01 1dd5A d.67.3.1 39564 1f44A 324 1.22e+01 a.60.9.1 64982 d.163.1.1 64983 1rec 201 1.23e+01 1rec a.39.1.5 17326 1top 162 1.24e+01 1ncx a.39.1.5 17223 1qpaA 345 1.28e+01 1arv a.93.1.1 18585 1bu7A 455 1.37e+01 1bu7A a.104.1.1 18937 1ga0A 364 1.37e+01 1gceA e.3.1.1 60410 1gceA 364 1.39e+01 1gceA e.3.1.1 42738 1hce 118 1.42e+01 1hce b.42.5.2 25625 1jgjA 217 1.43e+01 1c3wA f.2.1.1 62952 1l1zA 274 1.46e+01 1jtkA 136 1.47e+01 1f16A 192 1.47e+01 1f16A f.1.4.1 43400 1toh 343 1.50e+01 4pah d.178.1.1 42573 1kxqE 120 1.51e+01 1gdoA 240 1.53e+01 1gdoA d.153.1.1 41804 1fqvJ 149 1.54e+01 1fqvD a.122.1.1 19266 d.42.1.2 38670 1itm 130 1.56e+01 1rcb a.26.1.2 16858 1thfD 253 1.60e+01 1thfD c.1.2.1 28535 1wdcC 156 1.65e+01 1wdcC a.39.1.5 17317 1rcb 129 1.73e+01 1rcb a.26.1.2 16854 1efyA 350 1.74e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1a16 440 1.74e+01 1az9 c.55.2.1 33548 d.127.1.1 41165 1epaA 164 1.74e+01 1epaA b.60.1.1 27128 1jplA 171 1.75e+01 a.118.9.2 67027 1fqvD 149 1.76e+01 1fqvD a.122.1.1 19263 d.42.1.2 38667 1kpkA 473 1.76e+01 f.2.1.13 68776 2int 129 1.77e+01 1rcb a.26.1.2 16855 1fr1A 361 1.78e+01 1gceA e.3.1.1 42734 1hziA 129 1.80e+01 1rcb a.26.1.2 61449 2sqcA 631 1.80e+01 2sqcA a.102.4.2 18854 a.102.4.2 18855 1lgr 468 1.81e+01 1lgr d.15.9.1 37837 d.128.1.1 41167 2lgsA 468 1.85e+01 1lgr d.15.9.1 37838 d.128.1.1 41168 1fp6A 289 1.88e+01 1cp2A c.37.1.10 32243 1epbA 164 1.89e+01 1epaA b.60.1.1 27126 2gwxA 267 1.93e+01 2prgA a.123.1.1 19323 1jpzA 473 1.94e+01 a.104.1.1 67069 1az9 457 1.95e+01 1az9 c.55.2.1 33547 d.127.1.1 41164 1ezvD 245 1.98e+01 1be3D a.3.1.3 59546 f.2.1.8 59547 1el4A 195 1.99e+01 1ej3A a.39.1.5 59453 1eqfA 280 1.99e+01 1eqfA a.29.2.1 16972 a.29.2.1 16973 1gegA 256 2.02e+01 1ybvA c.2.1.2 29888 1jmrA 249 2.08e+01 1zac 90 2.08e+01 1ncx a.39.1.5 17236 1go3F 107 2.08e+01 a.60.8.2 65407 1jf2A 195 2.15e+01 1ej3A a.39.1.5 62930 1sur 215 2.15e+01 1sur c.26.2.2 31620 1ezm 301 2.17e+01 1hyt d.92.1.2 58980 1hpwA 129 2.20e+01 1hpwA d.24.1.1 61118 1jfrA 262 2.20e+01 1jfrA c.69.1.16 34724 1jb0A 755 2.23e+01 1jb0A f.2.1.12 62820 1dcnA 424 2.23e+01 1auwA a.127.1.1 19420 1jrrA 382 2.23e+01 e.1.1.1 63256 1hs6A 611 2.26e+01 1hs6A a.118.1.7 61233 b.98.1.1 61234 d.92.1.13 61235 1pd21 199 2.28e+01 1pd21 1hm6A 346 2.28e+01 1avc a.65.1.1 18147 3adk 195 2.28e+01 1zin c.37.1.1 31885 2ptd 298 2.29e+01 2plc c.1.18.2 29605 1keaA 221 2.31e+01 a.96.1.2 68491 1qm4A 396 2.31e+01 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1llp 343 2.33e+01 1arv a.93.1.1 18578 1bif 469 2.34e+01 1bif c.37.1.7 31961 c.60.1.4 34003 1f52A 468 2.36e+01 1lgr d.15.9.1 37839 d.128.1.1 41169 1fa0B 537 2.39e+01 1fa0B d.58.16.1 39336 e.9.1.2 43230 1tplA 426 2.42e+01 1ax4A c.67.1.2 34387 1e55A 512 2.43e+01 1e70M c.1.8.4 28934 1fqtA 112 2.44e+01 1fqtA b.33.1.1 24441 1mkp 144 2.48e+01 1vhrA c.45.1.1 32654 1qk9A 92 2.49e+01 1qk9A d.10.1.3 37485 1dz4A 414 2.52e+01 1phd a.104.1.1 18903 1l0wA 580 2.54e+01 1ilk 151 2.60e+01 2ilk a.26.1.3 16886 1hy0A 466 2.61e+01 1auwA a.127.1.1 61392 1sqc 631 2.62e+01 2sqcA a.102.4.2 18858 a.102.4.2 18859 1fmcA 255 2.66e+01 1cydA c.2.1.2 29856 1jnxX 214 2.71e+01 c.15.1.3 63201 c.15.1.3 63202 1avsA 90 2.71e+01 1cll a.39.1.5 17226 1mfiA 114 2.73e+01 1dptA d.80.1.3 39856 2ilk 160 2.74e+01 2ilk a.26.1.3 16885 1rlr 761 2.78e+01 1rlr a.98.1.1 18753 c.7.1.2 30679 1jk0A 419 2.86e+01 a.25.1.2 63142 1pbv 195 2.86e+01 1pbv a.118.3.1 19179 1f1zA 273 2.88e+01 1f1zA a.4.5.27 16081 c.52.1.16 33334 1k28A 584 2.91e+01 b.40.8.1 68049 b.108.1.2 68050 d.2.1.3 68051 1bb9 115 2.93e+01 1bb9 b.34.2.1 24554 1i7gA 287 2.94e+01 1k47A 337 2.96e+01 1avc 673 3.01e+01 1avc a.65.1.1 18178 a.65.1.1 18179 2ahjA 206 3.02e+01 2ahjA d.149.1.1 41772 1esl 162 3.11e+01 1esl d.169.1.1 42353 g.3.11.1 44225 1phd 414 3.20e+01 1phd a.104.1.1 18913 1npsA 88 3.21e+01 1prs b.11.1.1 23622 1g1tA 157 3.21e+01 d.169.1.1 65104 g.3.11.1 65105 1dcnD 436 3.24e+01 1auwA a.127.1.1 19423 1phb 414 3.26e+01 1phd a.104.1.1 18906 1aijL 281 3.29e+01 6prcL f.2.1.2 43461 1a26 361 3.31e+01 1a26 a.41.1.1 17412 d.166.1.2 42274 1dlyA 164 3.33e+01 1dlyA a.1.1.1 14983 1jb0L 154 3.34e+01 1jb0L f.2.1.12 62829 2cbp 96 3.38e+01 2cbp b.6.1.1 22895 2fua 215 3.40e+01 2fua c.74.1.1 34977 1qa9A 102 3.40e+01 1qa9A b.1.1.1 19742 1gks 78 3.44e+01 1cc5 a.3.1.1 15909 1elrA 131 3.45e+01 1a17 a.118.8.1 19209 1d8bA 81 3.47e+01 1d8bA a.60.8.1 18094 1h68A 239 3.48e+01 f.2.1.1 60664 1qq7A 253 3.49e+01 1qq5A c.108.1.1 43329 1qq5A 253 3.51e+01 1qq5A c.108.1.1 43327 1ctt 294 3.54e+01 1ctt c.97.1.1 36022 c.97.1.1 36023 1dtoA 221 3.54e+01 1dtoA b.91.1.1 28405 1ek8A 185 3.65e+01 1ek8A d.67.3.1 59444 1gh2A 107 3.69e+01 1erv c.47.1.1 60515 1erjA 393 3.73e+01 1erjA b.69.4.1 27660 1k4wA 252 3.74e+01 1phg 414 3.74e+01 1phd a.104.1.1 18910 1aq6A 253 3.76e+01 1qq5A c.108.1.1 43331 2baa 243 3.76e+01 1cnsA d.2.1.1 36243 1nsyA 271 3.77e+01 2nsyA c.26.2.1 31614 1uby 367 3.78e+01 1uby a.128.1.1 19435 1qqvA 67 3.80e+01 1qqvA a.14.1.1 16379 2nsyA 271 3.82e+01 2nsyA c.26.2.1 31612 1e8yA 966 3.82e+01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1h6gA 256 3.84e+01 1h6gA a.24.9.1 60669 a.24.9.1 60670 1qazA 351 3.85e+01 1qazA a.102.3.1 18848 2ligA 164 3.92e+01 1vls a.24.2.1 16530 1fhuA 320 3.98e+01 1fhuA c.1.11.2 29234 d.54.1.1 38878 1kqpA 271 3.98e+01