# 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 1mkiA 330 8.33e-67 e.3.1.2 84994 1bsg 266 8.78e-03 1btl e.3.1.1 42729 1i2sA 282 9.80e-03 e.3.1.1 71104 1iyoA 262 1.21e-02 e.3.1.1 76970 1bza 262 1.21e-02 1btl e.3.1.1 42701 1iysA 262 1.36e-02 e.3.1.1 -11760 1pjjA 271 4.12e-02 1nnjA 271 5.20e-02 a.156.1.2 80669 b.113.1.1 80670 g.39.1.8 80671 4blmA 265 6.28e-02 1btl e.3.1.1 42721 1alq 266 6.55e-02 1btl e.3.1.1 42707 1btl 263 7.75e-02 1btl e.3.1.1 42691 1ei5A 520 7.98e-02 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1n9bA 265 9.33e-02 e.3.1.1 85463 1g6aA 271 1.06e-01 1btl e.3.1.1 42704 1hzoA 271 1.18e-01 e.3.1.1 71092 1ghpA 258 1.19e-01 1btl e.3.1.1 60520 1m40A 263 1.45e-01 e.3.1.1 74437 1is1A 185 1.69e-01 d.67.3.1 83704 1qwlA 505 2.05e-01 e.5.1.1 -11823 1ermA 263 2.26e-01 1btl e.3.1.1 42690 1fqgA 263 2.33e-01 1btl e.3.1.1 42699 1g6wA 261 2.52e-01 1hqoA a.45.1.1 17751 c.47.1.5 33045 1hqoA 258 2.58e-01 1hqoA a.45.1.1 17749 c.47.1.5 33043 1dgfA 497 2.75e-01 1cf9A e.5.1.1 42782 1klxA 138 2.97e-01 a.118.18.1 77440 1m7sA 484 3.15e-01 e.5.1.1 74574 1k82A 268 3.55e-01 a.156.1.2 75866 b.113.1.1 75867 g.39.1.8 75868 1ouvA 273 3.65e-01 a.118.18.1 -1586 7catA 506 4.10e-01 1cf9A e.5.1.1 42781 1pioA 257 5.36e-01 1btl e.3.1.1 42719 1kbuA 349 6.54e-01 a.60.9.1 72284 d.163.1.1 72285 1dghB 498 6.58e-01 1cf9A e.5.1.1 42791 1oshA 232 6.74e-01 a.123.1.1 -1697 1k0dA 260 7.59e-01 a.45.1.1 67930 c.47.1.5 67931 1nrfA 262 8.02e-01 e.3.1.1 -11780 1volA 204 8.43e-01 1tfb a.74.1.2 18370 a.74.1.2 18371 1s3zA 165 8.74e-01 1e25A 282 9.34e-01 1e25A e.3.1.1 42731 1bueA 265 9.55e-01 1btl e.3.1.1 42727 1oktA 211 9.58e-01 a.45.1.1 -942 c.47.1.5 -7467 1cf9A 753 9.93e-01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1fcyA 236 1.13e+00 2lbd a.123.1.1 19282 1n4oA 276 1.15e+00 e.3.1.1 -11764 1j1jA 240 1.19e+00 a.118.16.1 -1637 1o7eA 276 1.23e+00 e.3.1.1 -11766 1p80A 753 1.27e+00 c.23.16.3 -6547 e.5.1.1 -11840 1cby 259 1.32e+00 1cby d.103.1.1 40705 4lbd 267 1.43e+00 2lbd a.123.1.1 19289 1r5qA 102 1.46e+00 unknown_sccs -965 2lbd 267 1.50e+00 2lbd a.123.1.1 19287 3blm 257 1.55e+00 1btl e.3.1.1 42709 3crxA 343 1.58e+00 4crxA a.60.9.1 18101 d.163.1.1 42161 1keyA 235 1.59e+00 a.118.16.1 72389 1a4pA 96 1.60e+00 1b4cA a.39.1.2 17176 2bmhA 455 1.85e+00 1bu7A a.104.1.1 18941 1thfD 253 1.92e+00 1thfD c.1.2.1 28535 1omhA 293 2.04e+00 unknown_sccs -10527 1prgA 270 2.08e+00 2prgA a.123.1.1 19314 1vdkA 466 2.35e+00 a.127.1.1 -1752 1vh7A 265 2.44e+00 c.1.2.1 -5159 1n91A 108 2.51e+00 d.206.1.1 80326 1b87A 181 2.97e+00 1b87A d.108.1.1 40797 1ncx 162 3.10e+00 1ncx a.39.1.5 17222 1n71A 180 3.27e+00 d.108.1.1 85370 1mfqC 129 3.42e+00 a.36.1.1 79046 6gsvA 217 3.43e+00 1b8xA a.45.1.1 17633 c.47.1.5 32925 1l1zA 274 3.76e+00 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1fm9D 272 3.81e+00 2prgA a.123.1.1 19313 1ne9A 335 3.83e+00 d.108.1.4 -10805 d.108.1.4 -10806 2prgA 271 3.95e+00 2prgA a.123.1.1 19311 1b4pA 217 4.34e+00 a.45.1.1 83158 c.47.1.5 83159 4crxA 322 4.36e+00 4crxA a.60.9.1 18095 d.163.1.1 42155 1tafA 68 4.40e+00 1tafA a.22.1.3 16481 1crxA 322 4.44e+00 4crxA a.60.9.1 18097 d.163.1.1 42157 1f9aA 168 4.55e+00 1f9aA c.26.1.3 31602 1top 162 4.65e+00 1ncx a.39.1.5 17223 1iwgA 1053 4.77e+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 1kpkA 473 4.86e+00 f.20.1.1 68776 1e9cA 215 4.90e+00 c.37.1.1 64808 1d6jA 211 5.10e+00 1d6jA c.37.1.4 31940 1e2gA 215 5.21e+00 3tmkA c.37.1.1 59165 1a31A 538 5.29e+00 1a36A d.163.1.2 42170 e.15.1.1 43263 1clc 639 5.31e+00 1clc a.102.1.2 18835 b.1.18.2 21872 1d3uB 201 5.32e+00 1aisB a.74.1.2 18386 a.74.1.2 18387 1ad1A 266 5.34e+00 1aj2 c.1.21.1 29668 1e9eA 215 5.34e+00 c.37.1.1 64810 1k8kG 151 5.42e+00 a.118.13.1 68313 1gwiA 411 5.43e+00 a.104.1.1 76364 1nn5A 215 5.47e+00 c.37.1.1 85892 1r2zA 274 5.74e+00 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 1hy3A 294 5.79e+00 c.37.1.5 71090 1g3mA 294 5.90e+00 c.37.1.5 83268 1odoA 408 5.95e+00 a.104.1.1 -1463 1e2fA 215 6.12e+00 3tmkA c.37.1.1 59164 1v2zA 111 6.13e+00 1abv 134 6.13e+00 1abv a.70.1.1 18317 1uwzA 136 6.29e+00 1regX 122 6.31e+00 1regX d.58.27.1 39406 1gpr 162 6.46e+00 1gpr b.84.3.1 28267 1aquA 297 6.75e+00 1aquA c.37.1.5 31942 1mtyD 512 6.77e+00 1mhyD a.25.1.2 16742 1lmeA 176 6.80e+00 d.167.1.1 84629 1fw9A 164 6.82e+00 1fw9A d.190.1.1 60059 1a36A 592 7.00e+00 1a36A a.2.8.1 15715 d.163.1.2 42173 e.15.1.1 43266 1lghA 56 7.00e+00 1lghA f.3.1.1 43733 1m7gA 211 7.01e+00 c.37.1.4 78724 1pd21 199 7.05e+00 1pd21 1g8pA 350 7.15e+00 1g8pA c.37.1.20 60376 1kpsB 171 7.28e+00 a.118.12.1 68787 1jplA 171 7.44e+00 a.118.9.2 67027 1mmoD 512 7.67e+00 1mhyD a.25.1.2 16770 1epaA 164 7.88e+00 1epaA b.60.1.1 27128 1ci8A 392 8.04e+00 e.3.1.1 64765 2bltA 361 8.06e+00 1gceA e.3.1.1 42739 1epbA 164 8.19e+00 1epaA b.60.1.1 27126 1rgzA 363 8.33e+00 e.3.1.1 -11771 1onhA 364 8.44e+00 e.3.1.1 -11769 1hbzA 498 8.45e+00 1cf9A e.5.1.1 60937 1gweA 503 8.49e+00 e.5.1.1 70667 1e7uA 961 8.58e+00 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1qm4A 396 8.65e+00 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1ga0A 364 8.69e+00 1gceA e.3.1.1 60410 1gceA 364 8.72e+00 1gceA e.3.1.1 42738 1gyxA 76 8.75e+00 d.80.1.1 76387 1otsA 465 9.06e+00 f.20.1.1 87415 1cqqA 180 9.11e+00 1cqqA b.47.1.4 26422 3adk 195 9.15e+00 1zin c.37.1.1 31885 1lgr 468 9.17e+00 1lgr d.15.9.1 37837 d.128.1.1 41167 1ezoA 370 9.20e+00 4mbp c.94.1.1 59539 2lgsA 468 9.33e+00 1lgr d.15.9.1 37838 d.128.1.1 41168 1jf0A 195 9.36e+00 1ej3A a.39.1.5 62926 1qf6A 642 9.45e+00 1qf6A c.51.1.1 33210 d.15.10.1 39551 d.67.1.1 39562 d.104.1.1 40759 2blsA 358 9.52e+00 1gceA e.3.1.1 42747 1ci9A 392 9.58e+00 e.3.1.1 64767 1p6xA 334 9.71e+00 c.37.1.1 -6983 1efnB 152 9.83e+00 1efnB d.102.1.1 40699 1d5rA 324 9.94e+00 1d5rA b.7.1.1 23181 c.45.1.1 32697 1pi4A 358 1.01e+01 e.3.1.1 -11774 1na3A 91 1.01e+01 k.38.1.1 85481 1fsyA 358 1.01e+01 1gceA e.3.1.1 60016 1aisB 200 1.02e+01 1aisB a.74.1.2 18384 a.74.1.2 18385 1fs1B 141 1.06e+01 1vcbB a.157.1.1 19252 d.42.1.1 38664 1j1iA 296 1.06e+01 c.69.1.10 83977 1n00A 321 1.07e+01 a.65.1.1 85241 1jtkA 136 1.08e+01 c.97.1.1 71862 1ucyE 109 1.08e+01 1ucyE 1l0wA 580 1.08e+01 b.40.4.1 73426 d.74.4.1 73427 d.104.1.1 73428 1h2sA 225 1.09e+01 f.13.1.1 76578 1o89A 345 1.11e+01 b.35.1.2 -3703 c.2.1.1 -5727 1qb2A 109 1.14e+01 1qb2A a.36.1.1 17125 2nef 136 1.16e+01 1efnB d.102.1.1 40704 1ggzA 148 1.21e+01 a.39.1.5 70176 1f44A 324 1.24e+01 a.60.9.1 64982 d.163.1.1 64983 1q6aA 107 1.25e+01 unknown_sccs -960 1uch 230 1.29e+01 1uch d.3.1.6 37129 1fjcA 96 1.29e+01 1fjcA d.58.7.1 39212 1qguA 478 1.29e+01 1qguA c.92.2.3 35625 1pbv 195 1.30e+01 1pbv a.118.3.1 19179 1h1lA 481 1.35e+01 c.92.2.3 70851 1sr7A 259 1.37e+01 1wdcC 156 1.42e+01 1wdcC a.39.1.5 17317 1bu7A 455 1.43e+01 1bu7A a.104.1.1 18937 1qh8A 478 1.46e+01 1qguA c.92.2.3 35633 1lvfA 110 1.48e+01 a.47.2.1 74280 1np3A 338 1.50e+01 a.100.1.2 85946 c.2.1.6 85947 1nipA 289 1.53e+01 1cp2A c.37.1.10 32263 1gwcA 230 1.54e+01 a.45.1.1 70660 c.47.1.5 70661 1omrA 201 1.57e+01 a.39.1.5 -854 1lshA 1056 1.59e+01 a.118.4.1 74242 f.7.1.1 74243 f.7.1.1 74244 1cx4A 305 1.59e+01 b.82.3.2 59099 b.82.3.2 59100 1jb0A 755 1.61e+01 1jb0A f.29.1.1 62820 1in4A 334 1.61e+01 1hqcA a.4.5.11 62597 c.37.1.20 62598 1l8bA 190 1.61e+01 d.86.1.1 73683 2sqcA 631 1.65e+01 2sqcA a.102.4.2 18854 a.102.4.2 18855 1qamA 244 1.66e+01 2ercA c.66.1.24 34220 1g5pA 289 1.71e+01 1cp2A c.37.1.10 32253 1hce 118 1.71e+01 1hce b.42.5.2 25625 1ax4A 467 1.73e+01 1ax4A c.67.1.2 34391 1nogA 177 1.75e+01 a.25.2.2 85923 2at2A 300 1.79e+01 3csuA c.78.1.1 35196 c.78.1.1 35197 1s6cA 183 1.79e+01 a.39.1.5 -858 2ahjA 206 1.80e+01 2ahjA d.149.1.1 41772 1qv1A 195 1.86e+01 a.39.1.5 -830 1r8sE 203 1.91e+01 a.118.3.1 -1579 1dlyA 164 1.93e+01 1dlyA a.1.1.1 14983 1m7yA 435 1.93e+01 c.67.1.4 78761 1fa0A 537 1.98e+01 1fa0B a.160.1.1 75837 d.218.1.3 75838 d.58.16.1 39335 1uw4B 248 2.03e+01 unknown_sccs -1560 1cf7A 76 2.06e+01 1cf7B a.4.5.17 16151 1f16A 192 2.07e+01 1f16A f.1.4.1 43400 1psrA 100 2.11e+01 1psrA a.39.1.2 17180 1fjeB 175 2.15e+01 1fj7A d.58.7.1 39210 d.58.7.1 39211 1nrgA 261 2.18e+01 b.45.1.1 80694 1axn 323 2.18e+01 1avc a.65.1.1 18149 1jpzA 473 2.18e+01 a.104.1.1 67069 8ohm 435 2.19e+01 1heiA c.37.1.14 32469 c.37.1.14 32470 1cpt 412 2.20e+01 1cpt a.104.1.1 18968 1q5dA 419 2.23e+01 a.104.1.1 -1454 1bbn 133 2.23e+01 1rcb a.26.1.2 16861 1keaA 221 2.23e+01 a.96.1.2 68491 1adoA 363 2.27e+01 1fbaA c.1.10.1 29124 1a16 440 2.27e+01 1az9 c.55.2.1 33548 d.127.1.1 41165 1lfkA 398 2.27e+01 a.104.1.1 77926 1g1tA 157 2.28e+01 d.169.1.1 65104 g.3.11.1 65105 1k1zA 78 2.31e+01 b.34.2.1 68026 1d2eA 397 2.34e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1fr1A 361 2.34e+01 1gceA e.3.1.1 42734 1esl 162 2.36e+01 1esl d.169.1.1 42353 g.3.11.1 44225 1a28A 256 2.39e+01 1a28A a.123.1.1 19290 1apa 266 2.39e+01 1qi7A d.165.1.1 42205 1qayA 428 2.41e+01 1qaxA d.58.20.1 39378 d.179.1.1 42599 1e8xA 961 2.44e+01 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1gqaA 130 2.46e+01 a.24.3.2 76275 1aq6A 253 2.47e+01 1qq5A c.108.1.1 43331 1br1B 150 2.52e+01 1wdcC a.39.1.5 17309 1nowA 507 2.55e+01 c.1.8.6 85936 d.92.2.1 85937 1m45A 148 2.56e+01 a.39.1.5 78598 1fqvJ 149 2.58e+01 1fqvD a.157.1.1 19266 d.42.1.1 38670 1az9 457 2.62e+01 1az9 c.55.2.1 33547 d.127.1.1 41164 1qq7A 253 2.62e+01 1qq5A c.108.1.1 43329 1qlwA 328 2.65e+01 1qlwA c.69.1.15 34722 1nouA 507 2.65e+01 c.1.8.6 85932 d.92.2.1 85933 1qq5A 253 2.65e+01 1qq5A c.108.1.1 43327 1rom 403 2.68e+01 1rom a.104.1.1 18963 1itm 130 2.69e+01 1rcb a.26.1.2 16858 1bf6A 291 2.73e+01 1pscA c.1.9.3 29065 1dcqA 278 2.74e+01 1dcqA d.211.1.1 19178 g.45.1.1 45326 4tmkA 213 2.75e+01 5tmpA c.37.1.1 31930 1m4rA 151 2.78e+01 a.26.1.3 84799 1rec 201 2.79e+01 1rec a.39.1.5 17326 1pk5A 248 2.82e+01 a.123.1.1 88139 1m6nA 802 2.85e+01 a.162.1.1 78697 a.172.1.1 78698 c.37.1.19 78699 c.37.1.19 78700 1ofdA 1520 2.85e+01 b.80.4.1 86935 c.1.4.1 86936 d.153.1.1 86937 1i39A 225 2.91e+01 1ekeA c.55.3.1 61585 1uby 367 2.92e+01 1uby a.128.1.1 19435 1fmcA 255 2.93e+01 1cydA c.2.1.2 29856 1gh2A 107 2.93e+01 1erv c.47.1.1 60515 1ejhA 190 2.93e+01 1ejhA d.86.1.1 40147 2bifA 469 2.94e+01 1bif c.37.1.7 31963 c.60.1.4 34009 1rgyA 360 2.96e+01 e.3.1.1 -11768 1ldjA 760 2.97e+01 a.4.5.34 73847 a.118.17.1 73848 e.40.1.1 73849 5tmpA 213 2.98e+01 5tmpA c.37.1.1 31931 1gmuA 143 3.01e+01 b.107.1.1 65335 d.58.38.1 65336 1v92A 46 3.01e+01 a.5.2.3 -357 1h49A 512 3.03e+01 c.1.8.4 83477 1fqvD 149 3.03e+01 1fqvD a.157.1.1 19263 d.42.1.1 38667 1auiB 169 3.04e+01 1auiB a.39.1.5 17325 1jb0L 154 3.05e+01 1jb0L f.31.1.1 62829 1h8dH 260 3.06e+01 5ptp 1sur 215 3.07e+01 1sur c.26.2.2 31620 1hm6A 346 3.10e+01 1avc a.65.1.1 18147 1cmnA 402 3.11e+01 1rom a.104.1.1 18958 1dfoA 417 3.11e+01 1bj4A c.67.1.4 34480 1jk0A 419 3.12e+01 a.25.1.2 63142 1qqvA 67 3.13e+01 1qqvA a.14.1.1 16379 1efyA 350 3.17e+01 1a26 a.41.1.1 17413 d.166.1.2 42275 1tvfA 369 3.19e+01 1bshA 138 3.19e+01 1aqt a.2.10.1 15720 b.93.1.1 28437 1jgjA 217 3.24e+01 1c3wA f.13.1.1 62952 1r8iA 213 3.24e+01 unknown_sccs -411 1gkxA 388 3.25e+01 a.29.5.1 65266 d.122.1.4 65267 2ahjC 206 3.28e+01 2ahjA d.149.1.1 41773 3bifA 468 3.28e+01 1bif c.37.1.7 31962 c.60.1.4 34008 2olbA 517 3.30e+01 1jevA c.94.1.1 35721 2dkb 433 3.31e+01 2dkb c.67.1.4 34438 1dz4A 414 3.32e+01 1phd a.104.1.1 18903 1n1cA 217 3.32e+01 a.184.1.1 85254 1sqc 631 3.33e+01 2sqcA a.102.4.2 18858 a.102.4.2 18859 1cwwA 102 3.34e+01 1cy5A a.77.1.3 18434 1ls6A 295 3.34e+01 c.37.1.5 -7026 1hp5A 512 3.37e+01 1hp4A c.1.8.6 61113 d.92.2.1 61114 1fp6A 289 3.38e+01 1cp2A c.37.1.10 32243 1lj8A 493 3.40e+01 a.100.1.9 78033 c.2.1.6 78034 1qpaA 345 3.40e+01 1arv a.93.1.1 18585 1in6A 334 3.43e+01 1hqcA a.4.5.11 62601 c.37.1.20 62602 1ek8A 185 3.43e+01 1ek8A d.67.3.1 59444 1epxA 370 3.44e+01 1fbaA c.1.10.1 29150 1osa 148 3.46e+01 1cll a.39.1.5 17300 1jlvA 209 3.48e+01 a.45.1.1 71729 c.47.1.5 71730 2gwxA 267 3.52e+01 2prgA a.123.1.1 19323 2gsq 202 3.55e+01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1c3yA 108 3.57e+01 1c3yA a.39.2.1 17387 1hp4A 512 3.58e+01 1hp4A c.1.8.6 61111 d.92.2.1 61112 1jakA 512 3.58e+01 c.1.8.6 66472 d.92.2.1 66473 1yghA 164 3.60e+01 1yghA d.108.1.1 40802 1gmwA 143 3.63e+01 b.107.1.1 65347 d.58.38.1 65348 1fa0B 537 3.70e+01 1fa0B a.160.1.1 75839 d.218.1.3 75840 d.58.16.1 39336 1ipcA 217 3.71e+01 d.86.1.1 71257 1igwA 434 3.72e+01 c.1.12.7 62370 1l0gA 358 3.72e+01 e.3.1.1 73400 1vnc 609 3.73e+01 1vns a.111.1.3 19065 1el4A 195 3.75e+01 1ej3A a.39.1.5 59453 1lvhA 221 3.78e+01 c.108.1.6 74282 1iu4A 331 3.85e+01 d.3.1.8 71430 1ej1A 190 3.86e+01 1ejhA d.86.1.1 40144 1jevA 517 3.86e+01 1jevA c.94.1.1 35720 1r6wA 322 3.87e+01 c.1.11.2 -5563 d.54.1.1 -9821 1mh0A 287 3.88e+01 b.47.1.2 79110 1kl1A 419 3.92e+01 c.67.1.4 72663 1kkjA 419 3.92e+01 c.67.1.4 72647 1fnmA 691 3.92e+01 1dar b.43.3.1 25709 c.37.1.8 32144 d.14.1.1 37546 d.58.11.1 39302 d.58.11.1 39303 1aqt 138 3.99e+01 1aqt a.2.10.1 15718 b.93.1.1 28435 2fua 215 3.99e+01 2fua c.74.1.1 34977