# List of top-scoring protein chains for t04-100-30-alpha 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 6.75e-35 e.3.1.2 84994 1i2sA 282 2.08e-03 e.3.1.1 71104 1ghpA 258 2.75e-03 1btl e.3.1.1 60520 4blmA 265 4.09e-03 1btl e.3.1.1 42721 1iysA 262 2.09e-02 e.3.1.1 -11760 1bza 262 4.10e-02 1btl e.3.1.1 42701 1hzoA 271 1.01e-01 e.3.1.1 71092 1np3A 338 1.31e-01 a.100.1.2 85946 c.2.1.6 85947 1ei5A 520 1.38e-01 1ei5A b.61.3.1 27418 b.61.3.1 27419 e.3.1.1 42772 1bsg 266 1.41e-01 1btl e.3.1.1 42729 1auiB 169 1.74e-01 1auiB a.39.1.5 17325 1btl 263 3.02e-01 1btl e.3.1.1 42691 1ermA 263 3.32e-01 1btl e.3.1.1 42690 1n9bA 265 3.41e-01 e.3.1.1 85463 1m40A 263 3.54e-01 e.3.1.1 74437 1fw9A 164 4.43e-01 1fw9A d.190.1.1 60059 2sqcA 631 4.49e-01 2sqcA a.102.4.2 18854 a.102.4.2 18855 1e25A 282 4.61e-01 1e25A e.3.1.1 42731 1klxA 138 4.82e-01 a.118.18.1 77440 1g6aA 271 5.18e-01 1btl e.3.1.1 42704 1omhA 293 6.75e-01 unknown_sccs -10527 1ouvA 273 8.05e-01 a.118.18.1 -1586 1qq7A 253 8.08e-01 1qq5A c.108.1.1 43329 1qq5A 253 8.10e-01 1qq5A c.108.1.1 43327 1regX 122 1.36e+00 1regX d.58.27.1 39406 1gcqC 70 1.43e+00 1gcpA b.34.2.1 60436 1nq7A 244 1.43e+00 a.123.1.1 -1682 1fm9D 272 1.48e+00 2prgA a.123.1.1 19313 1o7eA 276 1.60e+00 e.3.1.1 -11766 1bueA 265 1.63e+00 1btl e.3.1.1 42727 1j1jA 240 1.65e+00 a.118.16.1 -1637 1top 162 1.74e+00 1ncx a.39.1.5 17223 1uedA 406 1.88e+00 a.104.1.1 -1459 1keaA 221 1.93e+00 a.96.1.2 68491 1k38A 254 1.97e+00 e.3.1.1 84303 1qwlA 505 2.07e+00 e.5.1.1 -11823 1qj2B 809 2.15e+00 1qj2B 1qmeA 702 2.17e+00 1pmd d.11.1.1 37487 d.11.1.1 37488 d.175.1.1 42560 e.3.1.1 42769 1vjgA 218 2.26e+00 unknown_sccs -6447 1m6sA 347 2.29e+00 c.67.1.1 78701 1jg8A 347 2.30e+00 1jg8A c.67.1.1 62946 1pmd 675 2.44e+00 1pmd d.11.1.1 37491 d.11.1.1 37492 d.175.1.1 42562 e.3.1.1 42771 1kktA 511 2.60e+00 a.102.2.1 68687 1d5rA 324 2.64e+00 1d5rA b.7.1.1 23181 c.45.1.1 32697 1omrA 201 2.77e+00 a.39.1.5 -854 1rec 201 2.82e+00 1rec a.39.1.5 17326 1dgfA 497 2.83e+00 1cf9A e.5.1.1 42782 1ci9A 392 2.88e+00 e.3.1.1 64767 1ga0A 364 3.11e+00 1gceA e.3.1.1 60410 1oshA 232 3.39e+00 a.123.1.1 -1697 1jfbA 404 3.40e+00 a.104.1.1 66624 1uch 230 3.46e+00 1uch d.3.1.6 37129 1vhrA 184 3.50e+00 1vhrA c.45.1.1 32651 1rcuA 195 3.51e+00 unknown_sccs -7279 1pi4A 358 3.61e+00 e.3.1.1 -11774 1rgzA 363 3.62e+00 e.3.1.1 -11771 1f24A 402 3.70e+00 1rom a.104.1.1 18953 1cqqA 180 3.73e+00 1cqqA b.47.1.4 26422 1fsyA 358 3.77e+00 1gceA e.3.1.1 60016 1ornA 226 3.81e+00 a.96.1.1 87342 1mp1A 111 3.88e+00 unknown_sccs -996 2bltA 361 4.13e+00 1gceA e.3.1.1 42739 1efnB 152 4.43e+00 1efnB d.102.1.1 40699 1n62B 809 4.45e+00 d.41.1.1 80092 d.133.1.1 80093 1ad4A 266 4.50e+00 1aj2 c.1.21.1 29670 1bu7A 455 4.53e+00 1bu7A a.104.1.1 18937 1kkhA 317 4.81e+00 d.14.1.5 72645 d.58.26.3 72646 1uocA 289 4.87e+00 unknown_sccs -7671 1ad1A 266 4.94e+00 1aj2 c.1.21.1 29668 1m7sA 484 4.99e+00 e.5.1.1 74574 1s4kA 120 5.02e+00 1h2sA 225 5.08e+00 f.13.1.1 76578 1abv 134 5.18e+00 1abv a.70.1.1 18317 1mtyD 512 5.23e+00 1mhyD a.25.1.2 16742 1vduA 172 5.38e+00 unknown_sccs -1651 1bf6A 291 5.39e+00 1pscA c.1.9.3 29065 1n91A 108 5.46e+00 d.206.1.1 80326 1repC 251 5.63e+00 1repC a.4.5.10 16125 a.4.5.10 16126 2ae2A 260 5.68e+00 1bdb c.2.1.2 29945 1odoA 408 5.85e+00 a.104.1.1 -1463 1uw4B 248 6.02e+00 unknown_sccs -1560 1mun 225 6.24e+00 1mun a.96.1.2 18744 1pjjA 271 6.36e+00 1jnrA 643 6.41e+00 a.7.3.1 66966 c.3.1.4 66967 d.168.1.1 66968 1q5dA 419 6.42e+00 a.104.1.1 -1454 1tvfA 369 6.55e+00 2ahjA 206 6.63e+00 2ahjA d.149.1.1 41772 1e7uA 961 6.76e+00 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1na3A 91 6.94e+00 k.38.1.1 85481 1fqtA 112 6.98e+00 1fqtA b.33.1.1 24441 1qb2A 109 7.06e+00 1qb2A a.36.1.1 17125 1gpr 162 7.14e+00 1gpr b.84.3.1 28267 1n83A 270 7.15e+00 a.123.1.1 80276 1k78A 149 7.55e+00 a.4.1.5 68255 a.4.1.5 68256 1dq3A 454 7.56e+00 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1rgyA 360 7.83e+00 e.3.1.1 -11768 1jpzA 473 7.84e+00 a.104.1.1 67069 1v74A 107 8.00e+00 unknown_sccs -9319 1e8yA 966 8.17e+00 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1k3yA 221 8.18e+00 a.45.1.1 77245 c.47.1.5 77246 1c3yA 108 8.30e+00 1c3yA a.39.2.1 17387 1eswA 500 8.44e+00 1cwyA c.1.8.1 59500 1i9sA 210 8.63e+00 1i9sA c.45.1.1 62099 1rx0A 393 9.28e+00 a.29.3.1 -742 e.6.1.1 -11858 1nnjA 271 9.66e+00 a.156.1.2 80669 b.113.1.1 80670 g.39.1.8 80671 1gd0A 122 9.69e+00 1dptA d.80.1.3 39834 1cpo 299 1.01e+01 1cpo a.39.3.1 17390 a.39.3.1 17391 1cf9A 753 1.01e+01 1cf9A c.23.16.3 31441 e.5.1.1 42815 1n1bA 549 1.01e+01 a.102.4.1 79799 a.128.1.3 79800 1lmzA 187 1.03e+01 a.96.1.4 74037 1mpgA 282 1.07e+01 1mpgA a.96.1.3 18747 d.129.1.2 41296 1nzoA 363 1.07e+01 b.105.1.1 -2933 e.3.1.1 -11784 1fs0E 138 1.09e+01 1aqt a.2.10.1 59997 b.93.1.1 59998 1k8kD 300 1.11e+01 d.198.2.1 68309 d.198.2.1 68310 1wdcB 156 1.12e+01 1wdcB a.39.1.5 17302 1lmeA 176 1.14e+01 d.167.1.1 84629 1n00A 321 1.16e+01 a.65.1.1 85241 1l0gA 358 1.16e+01 e.3.1.1 73400 1l1zA 274 1.16e+01 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1que 303 1.19e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1pd21 199 1.20e+01 1pd21 4crxA 322 1.20e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1n4qB 377 1.21e+01 a.102.4.3 -1424 1dm5A 315 1.31e+01 1avc a.65.1.1 18186 1p5sA 203 1.31e+01 a.40.1.1 -900 1mwxA 646 1.32e+01 d.17.4.5 79610 d.175.1.1 79611 e.3.1.1 79612 1knwA 425 1.33e+01 b.49.2.3 -4274 c.1.6.1 -5229 1i4wA 353 1.34e+01 c.66.1.24 66028 1cpt 412 1.34e+01 1cpt a.104.1.1 18968 1pfvA 551 1.35e+01 a.27.1.1 -727 c.26.1.1 -6603 g.41.1.1 -12765 1p80A 753 1.36e+01 c.23.16.3 -6547 e.5.1.1 -11840 1oaiA 59 1.40e+01 a.5.2.3 81255 1qv1A 195 1.42e+01 a.39.1.5 -830 1o69A 394 1.44e+01 c.67.1.4 -8209 1lvfA 110 1.47e+01 a.47.2.1 74280 1j0aA 325 1.48e+01 c.79.1.1 83871 1hw1A 239 1.48e+01 1e2xA a.4.5.6 16111 a.78.1.1 18441 1p3wA 404 1.49e+01 c.67.1.3 87752 1hm6A 346 1.50e+01 1avc a.65.1.1 18147 1jgjA 217 1.51e+01 1c3wA f.13.1.1 62952 1pprM 312 1.52e+01 1pprM a.131.1.1 19502 a.131.1.1 19503 1icfI 65 1.52e+01 1icfI g.28.1.1 44958 1i7wB 151 1.53e+01 1i7wB j.71.1.1 61910 1rztA 331 1.57e+01 a.60.6.1 -1023 a.60.12.1 -1030 d.218.1.2 -9807 1fcyA 236 1.58e+01 2lbd a.123.1.1 19282 1adoA 363 1.59e+01 1fbaA c.1.10.1 29124 1go2A 304 1.59e+01 b.43.4.2 76243 c.25.1.1 76244 1nowA 507 1.60e+01 c.1.8.6 85936 d.92.2.1 85937 1f4lA 551 1.61e+01 1qqtA a.27.1.1 59648 c.26.1.1 59649 g.41.1.1 59650 1j1qA 261 1.62e+01 d.165.1.1 -11546 1oq9A 363 1.64e+01 a.25.1.2 87257 1s9uA 207 1.64e+01 1o7fA 469 1.66e+01 a.4.5.31 81131 b.82.3.2 81132 b.82.3.2 81133 1lghA 56 1.66e+01 1lghA f.3.1.1 43733 1korA 400 1.66e+01 c.26.2.1 72824 d.210.1.1 72825 1sig 339 1.68e+01 1sig a.177.1.1 19068 1fiy 883 1.70e+01 1fiy c.1.12.3 29307 1ne9A 335 1.72e+01 d.108.1.4 -10805 d.108.1.4 -10806 1o0wA 252 1.73e+01 a.149.1.1 80751 d.50.1.1 80752 1rzhL 281 1.73e+01 f.26.1.1 -12215 1g6sA 427 1.74e+01 1eps d.68.2.2 39584 1r5qA 102 1.74e+01 unknown_sccs -965 1qi7A 253 1.76e+01 1qi7A d.165.1.1 42210 1ogiA 303 1.77e+01 b.43.4.2 -4042 c.25.1.1 -6587 1ku1A 230 1.79e+01 a.118.3.1 72996 16pk 415 1.82e+01 16pk c.86.1.1 35454 1epxA 370 1.84e+01 1fbaA c.1.10.1 29150 1kb9D 246 1.85e+01 a.3.1.3 77317 f.23.11.1 77318 1lvaA 258 1.85e+01 a.4.5.35 74276 a.4.5.35 74277 a.4.5.35 74278 a.4.5.35 74279 1ezvF 125 1.86e+01 1be3F f.27.1.1 59550 1kb9G 125 1.86e+01 f.27.1.1 77322 5pal 109 1.88e+01 1a75A a.39.1.4 17215 1g60A 260 1.88e+01 c.66.1.11 70151 1a59 378 1.88e+01 1aj8A a.103.1.1 18902 1q1hA 110 1.92e+01 unknown_sccs -262 1g8kA 825 1.92e+01 1g8jA b.52.2.2 26920 c.81.1.1 35328 1q0rA 298 1.92e+01 unknown_sccs -8330 1spgA 144 1.97e+01 1abwA a.1.1.2 15409 1t6aA 126 1.99e+01 1uufA 369 2.02e+01 b.35.1.2 -3706 c.2.1.1 -5730 1iapA 211 2.03e+01 a.91.1.1 62119 1zrn 232 2.04e+01 1qq5A c.108.1.1 43323 3eipA 84 2.08e+01 3eipA d.26.2.1 38434 2dkb 433 2.08e+01 2dkb c.67.1.4 34438 1dlyA 164 2.09e+01 1dlyA a.1.1.1 14983 1q7fA 286 2.13e+01 unknown_sccs -4599 1gtmA 419 2.14e+01 1hwyA c.2.1.7 30223 c.58.1.1 33871 5eau 548 2.14e+01 5eat a.102.4.1 18851 a.128.1.3 19443 1fsgA 233 2.18e+01 1qk3A c.61.1.1 34029 1bcpD 110 2.20e+01 1bcpD b.40.2.1 25132 1aa7A 158 2.24e+01 1aa7A a.95.1.1 18741 1j5vA 351 2.24e+01 c.72.1.1 71585 1n3kA 130 2.27e+01 a.77.1.4 79965 1hbzA 498 2.27e+01 1cf9A e.5.1.1 60937 1nekC 129 2.29e+01 f.21.2.2 80431 1nj4A 363 2.30e+01 b.105.1.1 80545 e.3.1.1 80546 1hy0A 466 2.34e+01 1auwA a.127.1.1 61392 1mkmA 249 2.38e+01 a.4.5.33 79242 d.110.2.2 79243 1a4pA 96 2.43e+01 1b4cA a.39.1.2 17176 1jf2A 195 2.43e+01 1ej3A a.39.1.5 62930 1v9mA 323 2.45e+01 unknown_sccs -12292 1f44A 324 2.45e+01 a.60.9.1 64982 d.163.1.1 64983 1lddA 74 2.45e+01 a.4.5.34 73841 2ahjB 212 2.46e+01 2ahjB b.34.4.4 24599 1m3qA 317 2.48e+01 a.96.1.3 -1288 d.129.1.2 -11006 1afrA 345 2.49e+01 1afrA a.25.1.2 16805 1div 149 2.52e+01 1div d.99.1.1 40692 d.100.1.1 40693 1a7w 69 2.53e+01 1a7w a.22.1.2 16477 1oalA 151 2.59e+01 b.1.8.1 86739 2dtr 226 2.61e+01 1bi0 a.4.5.24 16193 a.76.1.1 18399 b.34.1.2 24450 1j1iA 296 2.63e+01 c.69.1.10 83977 1elrA 131 2.64e+01 1a17 a.118.8.1 19209 1oyeA 1049 2.69e+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 1gweA 503 2.69e+01 e.5.1.1 70667 2ran 316 2.71e+01 1avc a.65.1.1 18170 1uwzA 136 2.74e+01 1ebmA 317 2.74e+01 1ebmA a.96.1.3 18751 d.129.1.2 41300 1p2xA 159 2.77e+01 1el4A 195 2.80e+01 1ej3A a.39.1.5 59453 1ezvD 245 2.81e+01 1be3D a.3.1.3 59546 f.23.11.1 59547 1g0cA 364 2.83e+01 7a3hA c.1.8.3 60165 1gdoA 240 2.84e+01 1gdoA d.153.1.1 41804 1mw9X 592 2.87e+01 e.10.1.1 -11986 1cy9A 264 2.90e+01 1ecl e.10.1.1 43236 1rcwA 231 2.90e+01 unknown_sccs -1921 2sas 185 2.94e+01 2sas a.39.1.5 17258 1jrrA 382 2.94e+01 e.1.1.1 63256 1q44A 326 2.97e+01 c.37.1.5 -7037 1k7wA 468 3.00e+01 a.127.1.1 72130 1seiA 130 3.00e+01 1seiA d.140.1.1 41463 1uf2A 1019 3.00e+01 unknown_sccs -12036 1psrA 100 3.05e+01 1psrA a.39.1.2 17180 1uc8A 280 3.05e+01 unknown_sccs -6718 unknown_sccs -11230 1rdr 461 3.05e+01 1rdr e.8.1.4 43116 2gwxA 267 3.06e+01 2prgA a.123.1.1 19323 1cqxA 403 3.07e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 2utgA 70 3.08e+01 1utg a.101.1.1 18814 1ido 192 3.12e+01 1ido c.62.1.1 34139 1d7uA 433 3.15e+01 2dkb c.67.1.4 34439 1b67A 68 3.16e+01 1a7w a.22.1.2 16474 1avsA 90 3.18e+01 1cll a.39.1.5 17226 1a8b 318 3.19e+01 1avc a.65.1.1 18171 1o6aA 96 3.19e+01 unknown_sccs -4101 1dusA 194 3.21e+01 1dusA c.66.1.4 34182 1m93C 41 3.22e+01 1or3A 165 3.23e+01 1nfn a.24.1.1 16522 1i0aA 466 3.25e+01 1auwA a.127.1.1 61479 1bhdA 118 3.31e+01 1bkrA a.40.1.1 17398 1m7gA 211 3.33e+01 c.37.1.4 78724 4pep 326 3.33e+01 1smrA b.50.1.2 26843 1mkp 144 3.34e+01 1vhrA c.45.1.1 32654 1k47A 337 3.35e+01 d.14.1.5 72040 d.58.26.4 72041 1k8tA 510 3.37e+01 e.41.1.1 68316 6paxA 133 3.38e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1ek8A 185 3.44e+01 1ek8A d.67.3.1 59444 1hp8 68 3.44e+01 1hp8 a.17.1.1 16399 1c3cA 429 3.49e+01 1c3cA a.127.1.1 19425 1p9bA 442 3.50e+01 c.37.1.10 -7115 1uldA 150 3.51e+01 b.29.1.3 -3423 1ijgA 309 3.52e+01 1fouA e.27.1.1 62493 1acf 125 3.56e+01 3nul d.110.1.1 40882 1ox0A 430 3.59e+01 c.95.1.1 87495 c.95.1.1 87496 1ex1A 605 3.59e+01 1ex1A c.1.8.7 29013 c.23.11.1 31347 1r8sE 203 3.66e+01 a.118.3.1 -1579 1utg 70 3.70e+01 1utg a.101.1.1 18813 1r7aA 504 3.75e+01 b.71.1.1 -4664 c.1.8.1 -5283 1eexA 554 3.75e+01 1dioA c.1.19.3 29650 1rpxA 230 3.75e+01 1rpxA c.1.2.2 28536 1np7A 489 3.79e+01 a.99.1.1 80677 c.28.1.1 80678 1s48A 609 3.80e+01 e.8.1.4 -11955 1jadA 251 3.88e+01 h.4.10.1 66461 1qyaA 307 3.89e+01 1f1eA 154 3.93e+01 a.22.1.2 64927 1bo1A 416 3.94e+01 1bo1A d.143.1.2 41591 1ukkA 142 3.94e+01 d.227.1.1 -11206 1uouA 474 3.95e+01 a.46.2.1 -951 c.27.1.1 -6642 d.41.3.1 -9715 1kiyA 374 3.96e+01 a.128.1.5 72555 1c0pA 363 3.98e+01 1an9A c.4.1.2 30647 d.16.1.3 37934 3pte 349 4.00e+01 3pte e.3.1.1 42687