# List of top-scoring protein chains for t04-100-30-bys-scores 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 1tffA 234 1.25e-01 d.3.1.11 106854 1wgzA 510 2.26e-01 1srvA 145 3.98e-01 1derA c.8.5.1 30817 1b8zA 90 4.45e-01 1huuA a.55.1.1 17902 1tjoA 182 4.84e-01 1mojA 182 6.54e-01 a.25.1.1 91367 1sheA 103 8.76e-01 d.274.1.1 105551 1tx4A 198 1.19e+00 1tx4A a.116.1.1 19098 1wnfA 328 1.33e+00 1kid 203 1.47e+00 1derA c.8.5.1 30771 1wlsA 328 1.50e+00 2abqA 306 1.56e+00 1qkrA 188 1.57e+00 1qkrA a.24.9.1 16628 3pyp 125 1.74e+00 3pyp d.110.3.1 40897 1jigA 146 1.96e+00 a.25.1.1 71685 1nwzA 125 2.13e+00 d.110.3.1 86370 1dbhA 354 3.00e+00 1awe a.87.1.1,b.55.1.1 18514,26967 2fbwC 141 3.09e+00 1e3aA 260 3.25e+00 1ajqA d.153.1.2 41838 1gk9A 260 3.36e+00 d.153.1.2 65246 2fflA 756 3.53e+00 1wl9A 440 3.78e+00 2bwvA 440 4.00e+00 1tn6A 382 4.04e+00 1az9 457 4.06e+00 1az9 c.55.2.1,d.127.1.1 33547,41164 2ex3B 264 4.14e+00 1ay7B 89 4.69e+00 1ay7B c.9.1.1 30836 1kktA 511 4.89e+00 a.102.2.1 68687 1z4eA 153 5.01e+00 1tufA 434 5.05e+00 b.49.2.3,c.1.6.1 107335,107336 2hpaA 342 6.09e+00 1cviA c.60.1.2 33985 1l9hA 349 6.23e+00 f.13.1.2 73720 1ld8A 382 6.28e+00 a.118.6.1 73838 2fh5A 185 6.46e+00 1q8iA 783 6.53e+00 c.55.3.5,e.8.1.1 96208,96209 1nd6A 354 6.82e+00 c.60.1.2 80407 1twiA 434 7.08e+00 b.49.2.3,c.1.6.1 107399,107400 1xfiA 367 7.26e+00 e.50.1.1 109584 1u19A 349 7.28e+00 4pah 308 7.85e+00 4pah d.178.1.1 42576 2anuA 255 8.28e+00 1ecfA 504 8.51e+00 1ecfB c.61.1.1,d.153.1.1 34053,41820 1evyA 366 8.62e+00 1evyA a.100.1.6,c.2.1.6 18811,30215 1bzpA 153 8.63e+00 1a6m a.1.1.2 15020 2mgg 154 8.64e+00 1a6m a.1.1.2 15069 1v9dA 340 8.86e+00 a.207.1.1 100535 1iq8A 582 8.88e+00 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1j8uA 325 8.90e+00 d.178.1.1 71611 1qtrA 317 9.14e+00 1qtrA c.69.1.7 34660 1n1bA 549 9.21e+00 a.102.4.1,a.128.1.3 79799,79800 1mlg 154 9.53e+00 1a6m a.1.1.2 15104 1rwtA 232 9.68e+00 f.43.1.1 97992 1v6tA 255 9.85e+00 1d8dA 377 9.87e+00 1ft1A a.118.6.1 19185 1a6m 151 1.00e+01 1a6m a.1.1.2 15018 1hzxA 349 1.02e+01 1f88A f.13.1.2 61466 1w33A 181 1.03e+01 1qs1A 462 1.05e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1ywfA 296 1.07e+01 1dmtA 696 1.07e+01 1dmtA d.92.1.4 40296 1mod 154 1.08e+01 1a6m a.1.1.2 15107 103m 154 1.09e+01 1a6m a.1.1.2 15124 1m1zA 513 1.09e+01 c.26.2.1,d.153.1.1 78457,78458 1mlo 154 1.10e+01 1a6m a.1.1.2 15085 1mll 154 1.12e+01 1a6m a.1.1.2 15057 2c31A 568 1.21e+01 1u2kA 309 1.22e+01 1wm1A 317 1.22e+01 c.69.1.7 109405 1z5zA 271 1.24e+01 1wmiA 90 1.27e+01 1vgmA 378 1.29e+01 2end 138 1.31e+01 2end a.18.1.1 16400 1rcwA 231 1.34e+01 a.132.1.4 97299 2be4A 272 1.39e+01 1fmhB 33 1.41e+01 1fmhB k.6.1.1 46410 2mgb 154 1.42e+01 1a6m a.1.1.2 15102 1k8kA 418 1.48e+01 c.55.1.1,c.55.1.1 68305,68306 2c2aA 258 1.57e+01 1kz7A 353 1.63e+01 a.87.1.1,b.55.1.1 73333,73334 2b7oA 464 1.66e+01 1j34A 129 1.67e+01 d.169.1.1 84048 1rw6A 210 1.69e+01 a.47.4.1 105113 1r1hA 696 1.72e+01 d.92.1.4 104756 1colA 204 1.78e+01 1a87 f.1.1.1 43378 1xbtA 193 1.79e+01 1yqgA 263 1.80e+01 1mym 154 1.80e+01 1a6m a.1.1.2 15054 1qojA 63 1.82e+01 1qojA a.2.9.1 15716 1kl1A 419 1.85e+01 c.67.1.4 72663 1mtzA 293 1.87e+01 c.69.1.7 79467 1q0pA 223 1.89e+01 c.62.1.1 95507 2spl 154 1.89e+01 1a6m a.1.1.2 15047 1qghA 156 1.90e+01 1qghA a.25.1.1 16728 1nox 205 1.95e+01 1nox d.90.1.1 40242 1w4rA 195 1.96e+01 1chuA 540 1.99e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1ydhA 216 1.99e+01 1yjsA 419 2.02e+01 2eboA 74 2.03e+01 2eboA h.3.2.1 45754 1gx3A 284 2.07e+01 d.3.1.5 70678 1ne2A 200 2.08e+01 c.66.1.32 85586 1csn 298 2.17e+01 1csn d.144.1.7 41664 1jmsA 381 2.22e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 2g7lA 243 2.23e+01 1w5rA 278 2.23e+01 1g5aA 628 2.27e+01 b.71.1.1,c.1.8.1 65152,65153 1urvA 190 2.28e+01 1ut0A 190 2.28e+01 a.1.1.2 108012 1d2zB 153 2.29e+01 1d2zB a.77.1.2 18439 2es4D 332 2.30e+01 1ymqA 261 2.30e+01 1lq7A 67 2.34e+01 k.9.1.1 74183 1nh1A 330 2.42e+01 e.45.1.1 91871 1n35A 1267 2.45e+01 e.8.1.4 79935 1x3mA 415 2.49e+01 1tk9A 188 2.51e+01 c.80.1.3 107082 2fvhA 120 2.56e+01 1xmkA 79 2.56e+01 1t9kA 347 2.61e+01 c.124.1.5 106721 1wd7A 261 2.70e+01 1em9A 154 2.74e+01 1d1dA a.73.1.1 18333 1euhA 475 2.82e+01 1euhA c.82.1.1 35369 2aamA 309 2.84e+01 2ts1 419 2.99e+01 2ts1 c.26.1.1 31564 1khoA 370 3.01e+01 a.124.1.1,b.12.1.3 72489,72490 1qrvA 73 3.05e+01 1cktA a.21.1.1 16425 1kf6C 130 3.06e+01 f.21.2.2 72399 1yc9A 442 3.08e+01 1tq8A 163 3.09e+01 c.26.2.4 107204 1qz5A 375 3.12e+01 c.55.1.1,c.55.1.1 96614,96615 1qddA 144 3.18e+01 1qddA d.169.1.1 42324 1rfyA 102 3.21e+01 1dwtA 153 3.22e+01 1a6m a.1.1.2 15190 1gjnA 153 3.22e+01 a.1.1.2 70191 1qjbA 245 3.23e+01 1qjaA a.118.7.1 19202 1v64A 108 3.26e+01 a.21.1.1 108392 1nrjB 218 3.28e+01 c.37.1.8 86125 1gnwA 211 3.31e+01 1gnwA a.45.1.1,c.47.1.5 17727,33021 1qc7A 101 3.41e+01 1qc7A a.118.14.1 18456 1yq7A 374 3.43e+01 1owfA 99 3.44e+01 a.55.1.1 87487 1pbgA 468 3.46e+01 1e70M c.1.8.4 28946 1wdiA 345 3.50e+01 1ki1B 352 3.53e+01 a.87.1.1,b.55.1.1 72497,72498 1a05A 358 3.63e+01 1cnzA c.77.1.1 35059 1brwA 433 3.66e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1sz9A 144 3.66e+01 a.118.9.4 106139 1v7pB 128 3.72e+01 d.169.1.1 108407 2dh4A 340 3.76e+01 1ukmB 128 3.78e+01 d.169.1.1 99500 2c1vA 338 3.79e+01 1iynA 295 3.82e+01 a.93.1.1 90722 1huuA 90 3.91e+01 1huuA a.55.1.1 17897 1yewB 247 3.96e+01 2cwyA 94 3.96e+01 1e94F 449 3.98e+01 1do0A c.37.1.20 32443 1qsdA 106 4.08e+01 1qsdA a.7.5.1 16335 1lghA 56 4.08e+01 1lghA f.3.1.1 43733 2fxuA 375 4.09e+01 1uxjA 309 4.11e+01 c.2.1.5,d.162.1.1 108112,108113 1gqeA 365 4.12e+01 e.38.1.1 70351 1z6aA 500 4.13e+01 2a0iA 330 4.23e+01 2d0iA 333 4.25e+01 2aeeA 211 4.31e+01 1jq0A 84 4.31e+01 h.3.2.1 71786 1hlvA 131 4.34e+01 a.4.1.7,a.4.1.7 65854,65855 2f94F 350 4.34e+01 2br9A 234 4.35e+01 1ni3A 392 4.37e+01 c.37.1.8,d.15.10.2 80531,80532 1or4A 178 4.40e+01 a.1.1.2 93447 1azwA 313 4.42e+01 1qtrA c.69.1.7 34658 1r7cA 31 4.46e+01 j.35.1.1 104831 2fhzA 109 4.48e+01 2ax6A 256 4.48e+01 1wcwA 261 4.49e+01 1k4mA 213 4.53e+01 c.26.1.3 77258 1ir6A 424 4.54e+01 c.107.1.2 71342 1r6oC 106 4.55e+01 1pieA 419 4.58e+01 d.14.1.5,d.58.26.7 94706,94707 1mkp 144 4.59e+01 1vhrA c.45.1.1 32654 1nbaA 264 4.66e+01 1nbaA c.33.1.3 31753 1rqjA 299 4.67e+01 a.128.1.1 97744 1b0uA 262 4.78e+01 1b0uA c.37.1.12 32370 1uvjA 664 4.78e+01 e.8.1.6 100045 1tuzA 118 4.79e+01 1w9cA 321 4.80e+01 1v8fA 276 4.80e+01 c.26.1.4 100503 1hhsA 664 4.82e+01 1hi0P e.8.1.6 61045 1yv5A 374 4.89e+01 1pi1A 185 4.89e+01 a.29.7.1 94699 1wvfA 520 4.93e+01 1j6zA 376 4.94e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 2fd5A 180 4.96e+01 2ah5A 210 5.04e+01 1mngA 203 5.09e+01 1avmA a.2.11.1,d.44.1.1 15776,38701 1s2xA 206 5.14e+01 a.47.3.1 105229 1pxvA 183 5.16e+01 d.3.1.1 95301 1oyeA 1049 5.24e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 87587,87588,87589,87590,87591,87592,87593,87594 1txgA 335 5.35e+01 2fkiA 126 5.39e+01 1ka2A 499 5.39e+01 d.92.1.5 77305 1w2yA 229 5.40e+01 a.204.1.1 109140 1m1nA 491 5.42e+01 c.92.2.3 78417 1ufaA 520 5.43e+01 a.8.3.3,c.6.2.4 99329,99330 1on2A 142 5.45e+01 a.4.5.24,a.76.1.1 87103,87104 1jr8A 117 5.45e+01 a.24.15.1 67115 1ej5A 107 5.49e+01 1ej5A a.68.1.1 18268 1dzoA 123 5.52e+01 1dzoA d.24.1.1 38378 1t5jA 313 5.52e+01 a.209.1.1 99125 1a4sA 503 5.59e+01 1bpwA c.82.1.1 35361 2fx0A 201 5.62e+01 1rro 108 5.62e+01 1a75A a.39.1.4 17195 1qu1A 155 5.65e+01 1qu1A h.3.1.1 45670 1q5yA 85 5.69e+01 d.58.18.4 95950 2aplA 157 5.70e+01 1tfuA 157 5.72e+01 c.26.1.3 106859 1gnkA 112 5.74e+01 2pii d.58.5.1 39073 1gk8A 475 5.74e+01 c.1.14.1,d.58.9.1 65234,65235 1gkzA 388 5.78e+01 a.29.5.1,d.122.1.4 65268,65269 1tph1 247 5.85e+01 1amk 1u0fA 564 5.85e+01 1swvA 267 5.88e+01 2g39A 497 5.89e+01 1a9xB 379 5.90e+01 1c3oB c.8.3.1,c.23.16.1 30732,31409 1wuaA 375 5.95e+01 1yeyA 444 5.95e+01 1a8h 500 6.02e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1wwpA 119 6.03e+01 1jq5A 370 6.14e+01 e.22.1.2 67084 1z8oA 404 6.14e+01 1d4xA 375 6.16e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 1c30B 382 6.17e+01 c.8.3.1,c.23.16.1 30736,31413 1a48 306 6.20e+01 1a48 d.143.1.1 41590 1woyA 500 6.30e+01 2btfA 375 6.31e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 1rtwA 220 6.33e+01 a.132.1.3 97823 2a2dA 478 6.38e+01 1n2aA 201 6.41e+01 a.45.1.1,c.47.1.5 91553,91554 1vgwA 231 6.42e+01 c.68.1.13 100612 1sv6A 269 6.43e+01 d.177.1.1 106043 1peqA 714 6.44e+01 a.98.1.1,c.7.1.2 104131,104132 1nnwA 252 6.51e+01 d.159.1.5 80674 1of9A 77 6.57e+01 a.64.1.4 92821 1zoyC 140 6.58e+01 1akhA 61 6.62e+01 1akhA a.4.1.1 15980 2axtT 32 6.63e+01 1dytA 133 6.64e+01 7rsa d.5.1.1 37288 1obdA 306 6.65e+01 d.143.1.1 86767 2bodX 286 6.68e+01 1vqrA 297 6.68e+01 1xo1A 291 6.71e+01 1exnA a.60.7.1,c.120.1.2 18086,33356 1qpaA 345 6.73e+01 1arv a.93.1.1 18585 1irqA 71 6.75e+01 a.43.1.4 66297 1s5lT 32 6.75e+01 1ezvF 125 6.76e+01 1be3F f.27.1.1 59550 1ei5A 520 6.76e+01 1ei5A b.61.3.1,b.61.3.1,e.3.1.1 27418,27419,42772 1qh8A 478 6.77e+01 1qguA c.92.2.3 35633 2gdzA 267 6.79e+01 1h99A 224 6.81e+01 a.142.1.1,a.142.1.1 60814,60815 1x6zA 123 6.85e+01 1ahxA 396 6.86e+01 1ajsA c.67.1.1 34293 1gheA 177 6.92e+01 d.108.1.1 76222 1na3A 91 6.93e+01 k.38.1.1 85481 1ejxA 100 6.97e+01 d.8.1.1 83182 1jwiB 125 6.98e+01 d.169.1.1 67384 1rp4A 389 7.02e+01 a.227.1.1 105027 1iz0A 302 7.02e+01 b.35.1.2,c.2.1.1 83821,83822 1x9dA 538 7.04e+01 1qy5A 269 7.07e+01 d.122.1.1 96573 1ca1 370 7.12e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1dp3A 55 7.19e+01 1dp3A a.55.1.2 59128 1j08A 226 7.19e+01 c.47.1.2,c.47.1.2 83855,83856 1bx4A 345 7.19e+01 1bx4A c.72.1.1 34935 1g99A 408 7.24e+01 1g99A c.55.1.2,c.55.1.2 33457,33458 2a33A 215 7.26e+01 1y4hA 188 7.28e+01 1zbtA 371 7.32e+01 1ur5A 309 7.32e+01 c.2.1.5,d.162.1.1 99807,99808 1q3eA 207 7.33e+01 b.82.3.2 95669 2eshA 118 7.34e+01 2f6hX 419 7.37e+01 1tuoA 464 7.38e+01 1qh8B 519 7.41e+01 1qguB c.92.2.3 35634 1a8l 226 7.44e+01 1a8l c.47.1.2,c.47.1.2 32777,32778 2bgiA 272 7.45e+01 2a1dD 329 7.49e+01 1ntyA 311 7.52e+01 a.87.1.1,b.55.1.1 103873,103874 1v63A 101 7.57e+01 a.21.1.1 108391 1vin 268 7.59e+01 1vin a.74.1.1,a.74.1.1 18354,18355 1odfA 290 7.60e+01 c.37.1.6 92782 1y3nA 490 7.71e+01 1xa1A 255 7.73e+01 e.3.1.1 109529 1vpqA 273 7.74e+01 1tdzA 272 7.78e+01 a.156.1.2,b.113.1.1,g.39.1.8 106787,106788,106789 1rpa 342 7.78e+01 1cviA c.60.1.2 33983 1q1hA 110 7.78e+01 a.4.5.41 95580 1jl5A 454 7.80e+01 c.10.2.6 66830 1vprA 374 7.85e+01 1yt3A 375 7.94e+01 2g9iA 249 7.95e+01 2gl5A 410 7.99e+01 1nnjA 271 8.01e+01 a.156.1.2,b.113.1.1,g.39.1.8 80669,80670,80671 1z7aA 308 8.03e+01 1h6dA 433 8.10e+01 c.2.1.3,d.81.1.5 65656,65657 5abp 306 8.11e+01 8abp c.93.1.1 35651 1ey4A 149 8.12e+01 1snc b.40.1.1 24815 2a2cA 478 8.12e+01 1obbA 480 8.16e+01 c.2.1.5,d.162.1.2 86760,86761 1z63A 500 8.21e+01 1omwA 689 8.25e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 1rcuA 195 8.32e+01 c.129.1.1 97295 1nofA 383 8.34e+01 b.71.1.2,c.1.8.3 92020,92021 1wkvA 389 8.34e+01 1dgaA 375 8.35e+01 1yagA 1mbxC 106 8.35e+01 d.45.1.2 78929 1poiA 317 8.39e+01 1poiA c.124.1.2 34153 2b8wA 328 8.40e+01 1xqwA 293 8.46e+01 1mgtA 174 8.50e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1uxy 340 8.53e+01 2mbr d.145.1.2,d.146.1.1 41748,41761 1kgnA 329 8.57e+01 a.25.1.2 68584 1jyhA 157 8.61e+01 d.60.1.3 71956 1dxeA 256 8.63e+01 1dxeA c.1.12.5 29310 1vl5A 260 8.65e+01 c.66.1.41 108720 1lla 628 8.66e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1jhsA 188 8.70e+01 d.107.1.1 84172 1f0iA 504 8.79e+01 1f0iA d.136.1.2,d.136.1.2 59566,59567 1ofgA 381 8.81e+01 1ofgA c.2.1.3,d.81.1.5 30064,39979 1ars 396 8.95e+01 1ajsA c.67.1.1 34287 1v54A 514 8.96e+01 f.24.1.1 100321 1zowA 313 8.96e+01 1qisA 396 8.96e+01 1ajsA c.67.1.1 34284 1r2zA 274 8.98e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894