# List of top-scoring protein chains for t04-100-30-str2 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 1mrzA 293 4.32e-01 b.43.5.1 -4048 c.26.1.3 -6616 1geqA 248 7.11e-01 2tysA c.1.2.4 28589 1g73C 121 9.34e-01 1g3fA g.52.1.1 45375 1lfpA 249 1.36e+00 e.39.1.1 73885 1scjB 71 1.77e+00 1scjB d.58.3.2 39069 1dmlB 36 1.91e+00 1dmlB 1se0A 116 2.01e+00 g.52.1.1 -12841 1g57A 217 2.09e+00 1g57A d.115.1.2 60253 1id1A 153 2.61e+00 1id1A c.2.1.9 62286 1iirA 415 2.71e+00 1iirA c.87.1.5 62453 1e4yA 214 2.72e+00 1zin c.37.1.1 31901 g.41.2.1 45181 1itwA 741 2.93e+00 c.77.1.2 76793 1ejdA 419 2.98e+00 1uae d.68.2.2 39576 1qopA 268 3.08e+00 2tysA c.1.2.4 28570 1tqnA 486 3.13e+00 1cc8A 73 3.30e+00 1cc8A d.58.17.1 39343 1hk9A 74 3.43e+00 b.38.1.2 83541 1fukA 165 3.45e+00 1fukA c.37.1.19 32409 1o4uA 285 3.45e+00 c.1.17.1 86624 d.41.2.1 86625 1scy 32 3.60e+00 1pnh g.3.7.2 44155 2tysA 268 3.84e+00 2tysA c.1.2.4 28572 1jg5A 83 4.06e+00 d.205.1.1 66666 1odkA 235 4.21e+00 c.56.2.1 86863 1qdeA 224 4.44e+00 1qvaA c.37.1.19 32410 1rvgA 305 4.53e+00 c.1.10.2 -5500 1jqbA 351 4.79e+00 b.35.1.2 77151 c.2.1.1 77152 1h75A 81 4.79e+00 1h75A c.47.1.1 60716 2fokA 579 4.80e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1xyzA 347 4.91e+00 1taxA c.1.8.3 28804 1kevA 351 4.93e+00 1pedA b.35.1.2 24749 c.2.1.1 29765 1dbtA 239 5.02e+00 1dbtA c.1.2.3 28539 1j6oA 268 5.38e+00 c.1.9.12 77088 1jmvA 141 6.15e+00 c.26.2.4 66897 1akz 223 6.29e+00 3eugA c.18.1.1 31007 1mdbA 539 6.62e+00 e.23.1.1 79008 1ptmA 329 6.95e+00 unknown_sccs -8456 1q9uA 130 7.20e+00 unknown_sccs -11025 1mu5A 471 7.34e+00 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 2ak3A 226 7.50e+00 1zin c.37.1.1 31892 g.41.2.1 45193 1sdoA 203 7.62e+00 unknown_sccs -7558 1kwgA 645 7.77e+00 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1p3jA 217 8.02e+00 c.37.1.1 -6996 g.41.2.1 -12769 1b00A 127 8.23e+00 3chy c.23.1.1 31122 1m3uA 264 8.41e+00 c.1.12.8 84784 1cby 259 8.52e+00 1cby d.103.1.1 40705 1i60A 278 8.55e+00 c.1.15.4 71118 1oi7A 288 8.82e+00 c.2.1.8 87049 c.23.4.1 87050 1zrn 232 8.93e+00 1qq5A c.108.1.1 43323 1ni4B 341 9.14e+00 c.36.1.7 85729 c.48.1.2 85730 1vjqA 79 9.52e+00 unknown_sccs -13478 1gca 309 9.75e+00 1gca c.93.1.1 35659 1veaA 148 9.90e+00 1i1kA 309 1.01e+01 1daaA e.17.1.1 61533 1pwhA 327 1.03e+01 c.79.1.1 -8524 1g6sA 427 1.04e+01 1eps d.68.2.2 39584 1r5rA 119 1.06e+01 a.39.2.1 -893 1vhtA 218 1.08e+01 c.37.1.1 -7004 1o6aA 96 1.09e+01 unknown_sccs -4101 1h7sA 365 1.09e+01 d.14.1.3 65705 d.122.1.2 65706 1n3bA 216 1.12e+01 c.37.1.1 79959 1s5aA 150 1.14e+01 unknown_sccs -9300 1nar 290 1.14e+01 1nar c.1.8.5 28988 1f9zA 135 1.16e+01 1qipA d.32.1.1 38484 1hw1A 239 1.19e+01 1e2xA a.4.5.6 16111 a.78.1.1 18441 1r0vA 305 1.20e+01 c.52.2.1 -7572 c.52.2.1 -7573 d.75.1.1 -10344 1dfoA 417 1.21e+01 1bj4A c.67.1.4 34480 1fa8A 135 1.22e+01 1qipA d.32.1.1 38486 1fm9D 272 1.24e+01 2prgA a.123.1.1 19313 1havA 217 1.25e+01 1havA b.47.1.4 26423 1oywA 523 1.26e+01 unknown_sccs -270 c.37.1.19 -7209 c.37.1.19 -7210 1qgiA 259 1.28e+01 1qgiA d.2.1.7 37001 1jd5A 124 1.32e+01 g.52.1.1 66544 1dcfA 136 1.32e+01 1dcfA c.23.1.2 31124 1qh3A 260 1.34e+01 1qh5A d.157.1.2 42059 1djnA 729 1.35e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1iyeA 309 1.39e+01 e.17.1.1 83786 1o94A 729 1.40e+01 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1kafA 108 1.44e+01 d.199.1.1 68372 1qh5A 260 1.49e+01 1qh5A d.157.1.2 42057 1gmxA 108 1.49e+01 c.46.1.3 65355 2irfG 113 1.50e+01 2irfG a.4.5.23 16185 1lxa 262 1.53e+01 1lxa b.81.1.1 28052 1pgl1 185 1.55e+01 2tmdA 729 1.61e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1o1zA 234 1.63e+01 c.1.18.3 86555 1o5zA 442 1.64e+01 c.59.1.2 -7939 c.72.2.2 -8418 1nf2A 268 1.65e+01 c.108.1.10 -6842 1hnjA 317 1.66e+01 1hn9A c.95.1.1 35969 c.95.1.1 35970 1fjhA 257 1.68e+01 1fjhB c.2.1.2 29870 1rf6A 427 1.70e+01 d.68.2.2 -10314 1hg7A 66 1.77e+01 1msi b.85.1.1 28280 1zin 217 1.81e+01 1zin c.37.1.1 31915 g.41.2.1 45178 1reqB 637 1.83e+01 1reqB c.1.19.1 29621 c.23.6.1 31248 1qwgA 251 1.83e+01 unknown_sccs -5678 1te2A 226 1.87e+01 1o9gA 250 1.89e+01 c.66.1.29 86692 1psuA 140 1.93e+01 d.38.1.5 88285 1kq3A 376 1.96e+01 e.22.1.2 68790 1m6jA 261 1.97e+01 c.1.1.1 78693 1ne9A 335 1.98e+01 d.108.1.4 -10805 d.108.1.4 -10806 1s4qA 228 1.99e+01 c.37.1.1 -6975 1nbaA 264 1.99e+01 1nbaA unknown_sccs 31753 1lqpA 135 2.04e+01 d.32.1.2 78151 1nkiA 135 2.04e+01 d.32.1.2 -9544 1o66A 275 2.05e+01 c.1.12.8 -5590 1qniA 581 2.06e+01 1qniA b.6.1.4 23042 b.69.3.1 27642 1qtwA 285 2.07e+01 1qumA c.1.15.1 29392 1id2A 106 2.09e+01 1aac b.6.1.1 62288 1l8rA 101 2.09e+01 a.6.1.4 73700 1k1xA 659 2.11e+01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1vicA 262 2.13e+01 c.68.1.13 -8252 1qorA 327 2.14e+01 1qorA b.35.1.2 24766 c.2.1.1 29782 1mj5A 302 2.17e+01 c.69.1.8 -8326 1cv2A 296 2.18e+01 1bn6A c.69.1.8 34680 1j1yA 136 2.22e+01 d.38.1.5 -9671 1gefA 123 2.22e+01 1gefA c.52.1.18 60465 5croA 66 2.27e+01 1orc a.35.1.2 17044 1hnnA 282 2.30e+01 c.66.1.15 65895 1a78A 134 2.36e+01 1c1lA b.29.1.3 24212 1jbkA 195 2.41e+01 c.37.1.20 71631 1iba 101 2.45e+01 1iba d.95.1.1 40567 1ne2A 200 2.47e+01 c.66.1.32 85586 1v7zA 260 2.48e+01 unknown_sccs -6353 1ako 268 2.49e+01 1ako d.151.1.1 41779 1ucsA 64 2.52e+01 b.85.1.1 88466 1gsa 316 2.53e+01 1gsa c.30.1.3 31718 d.142.1.1 41477 1j5yA 187 2.57e+01 a.4.5.1 71592 d.94.2.1 71593 1v2dA 381 2.60e+01 1eu8A 409 2.62e+01 1eu8A c.94.1.1 59502 1gx3A 284 2.62e+01 d.3.1.5 70678 1rl6A 177 2.62e+01 1rl6A d.141.1.1 41473 d.141.1.1 41474 1khvA 516 2.70e+01 e.8.1.4 68627 4eugA 229 2.70e+01 3eugA c.18.1.1 31019 1f35A 162 2.71e+01 1f35A b.94.1.1 59628 1o63A 219 2.72e+01 c.94.1.1 -8691 1miwA 404 2.72e+01 a.173.1.1 79162 d.218.1.4 79163 1eyzA 392 2.72e+01 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1l4uA 176 2.73e+01 c.37.1.2 73568 1cv8 174 2.74e+01 1cv8 d.3.1.1 37089 1lf6A 684 2.75e+01 a.102.1.5 77918 b.30.5.5 77919 1pnh 31 2.77e+01 1pnh g.3.7.2 44162 3gcb 470 2.82e+01 3gcb d.3.1.1 37032 1i12A 160 2.83e+01 1i21A d.108.1.1 61515 1dfeA 37 2.84e+01 1dfeA g.42.1.1 45318 1l0qA 391 2.90e+01 b.1.3.1 77644 b.69.2.3 77645 1p2fA 220 2.91e+01 a.4.6.1 87720 c.23.1.1 87721 1kgsA 225 2.91e+01 a.4.6.1 68596 c.23.1.1 68597 1ixkA 315 2.97e+01 unknown_sccs -8099 1ia9A 280 2.97e+01 1ia9A d.144.1.5 62113 2gwxA 267 2.98e+01 2prgA a.123.1.1 19323 1gcb 454 2.99e+01 3gcb d.3.1.1 37034 1vkfA 188 2.99e+01 1mkmA 249 3.06e+01 a.4.5.33 79242 d.110.2.2 79243 1svsA 353 3.07e+01 1sheA 103 3.10e+01 1bmv1 198 3.11e+01 1bmv1 1d4fA 431 3.14e+01 1b3rA c.2.1.4 30110 c.23.12.3 31370 1cipA 353 3.15e+01 1cipA a.66.1.1 18210 c.37.1.8 32093 1dy9A 187 3.15e+01 1jxpA b.47.1.3 26400 1wod 233 3.19e+01 1wod c.94.1.1 35832 1b7yB 785 3.20e+01 1pysB a.6.1.1 16301 a.6.1.1 16302 b.40.4.4 25312 d.58.13.1 39311 d.104.1.1 40780 d.138.1.1 41456 1iqrA 420 3.20e+01 a.99.1.1 66275 c.28.1.1 66276 1gx1A 160 3.23e+01 d.79.5.1 70675 1fmjA 351 3.23e+01 c.37.1.5 59879 1e9rA 437 3.24e+01 c.37.1.11 64827 1amf 233 3.25e+01 1wod c.94.1.1 35833 1oxnA 140 3.26e+01 g.52.1.1 -12844 5eau 548 3.27e+01 5eat a.102.4.1 18851 a.128.1.3 19443 1e8yA 966 3.32e+01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1mb3A 124 3.38e+01 c.23.1.1 78907 1okrA 123 3.42e+01 unknown_sccs -235 1iqqA 200 3.43e+01 d.124.1.1 66274 1h1dA 221 3.43e+01 c.66.1.1 83452 1gs5A 258 3.47e+01 c.73.1.2 70395 3rubS 123 3.47e+01 1rboC d.73.1.1 39616 1c8zA 265 3.51e+01 1c8zA d.23.1.1 38375 1m2dA 110 3.54e+01 c.47.1.11 78476 1qavA 90 3.55e+01 1qauA b.36.1.1 24777 1po5A 476 3.56e+01 a.104.1.1 -1467 1qjvA 342 3.62e+01 1qjvA b.80.1.5 28035 1o0iA 138 3.63e+01 d.38.1.5 86532 1oyc 400 3.66e+01 1oyc c.1.4.1 28603 1buoA 121 3.66e+01 1buoA d.42.1.1 38631 1ub0A 258 3.68e+01 c.72.1.2 88394 1fyhB 229 3.70e+01 1jrhI b.1.2.1 22055 b.1.2.1 22056 1vhsA 175 3.71e+01 d.108.1.1 -10794 1gyxA 76 3.73e+01 d.80.1.1 76387 1j5uA 136 3.73e+01 d.208.1.1 71584 1hyhA 309 3.78e+01 1hyhA c.2.1.5 30150 d.162.1.1 42117 1fjsL 52 3.78e+01 1hcgB g.3.11.1 44226 1kjqA 391 3.78e+01 b.84.2.1 72616 c.30.1.1 72617 d.142.1.2 72618 1s5dA 240 3.81e+01 d.166.1.1 -11563 1egaA 301 3.82e+01 1egaA c.37.1.8 32150 d.52.3.1 38836 1aq0A 306 3.87e+01 1aq0A c.1.8.3 28842 1igs 248 3.90e+01 1a53 c.1.2.4 28565 1a53 247 3.95e+01 1a53 c.1.2.4 28564 1iso 416 3.96e+01 1iso c.77.1.1 35065 1q0uA 219 3.96e+01 c.37.1.19 -7205