# List of top-scoring protein chains for t2k-100-40-40-str2+CB_burial_14_7 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 1tc5A 194 1.69e-01 c.110.1.1 106752 1aayA 90 3.74e-01 1aayA g.37.1.1 45001 g.37.1.1 45002 g.37.1.1 45003 1f75A 249 3.86e-01 1f75A c.101.1.1 59662 1zaaC 87 4.73e-01 1aayA g.37.1.1 45013 g.37.1.1 45014 g.37.1.1 45015 1a1iA 90 7.35e-01 1aayA g.37.1.1 44998 g.37.1.1 44999 g.37.1.1 45000 1rlyA 60 8.55e-01 g.41.3.1 104988 1dl6A 58 8.55e-01 1dl6A g.41.3.1 45207 4rxn 54 9.29e-01 1rb9 g.41.5.1 45226 1jnrB 150 1.31e+00 d.58.1.5 66969 1hn6A 110 1.37e+00 g.61.1.1 76721 1g2fC 90 1.52e+00 k.12.1.1 60222 1g8oA 310 1.66e+00 1g8oA c.68.1.9 60375 1plfA 72 2.09e+00 1tvxA d.9.1.1 37373 2f4lA 297 2.26e+00 1udh 244 2.36e+00 3eugA c.18.1.1 31015 1yc61 154 2.54e+00 1avyA 74 2.77e+00 1avyB h.1.17.1 45656 1wf9A 107 3.31e+00 1uehA 253 3.72e+00 c.101.1.1 99259 1humA 69 3.89e+00 1b3aA d.9.1.1 37397 1jp3A 253 4.53e+00 1f75A c.101.1.1 63221 1lldA 319 4.54e+00 3ldh c.2.1.5 30177 d.162.1.1 42144 1z3eA 132 4.82e+00 1ehkB 168 5.00e+00 2cuaA b.6.1.2 23041 f.17.2.1 43625 1iro 54 5.10e+00 1rb9 g.41.5.1 45223 1xaoA 121 5.22e+00 2a4hA 126 6.01e+00 1avyC 74 6.02e+00 1avyB h.1.17.1 45658 1vcbA 118 6.05e+00 1vcbA d.15.1.1 37603 2anwA 241 6.11e+00 2anyA 241 6.25e+00 1qwtA 255 6.38e+00 b.26.1.3 96501 1ni4A 365 6.45e+00 c.36.1.11 85728 1v5vA 401 7.13e+00 1b5qA 472 7.36e+00 1b37B c.3.1.2 30404 d.16.1.5 37968 1b37A 472 7.51e+00 1b37B c.3.1.2 30389 d.16.1.5 37953 1t3nA 388 7.93e+00 d.240.1.1 106363 e.8.1.7 106364 1a31A 538 7.93e+00 1a36A d.163.1.2 42170 e.15.1.1 43263 1wthD 391 8.22e+00 8acn 754 8.33e+00 1amj c.8.2.1 30724 c.83.1.1 35400 1f7tA 122 8.44e+00 1f7lA d.150.1.2 59667 1mnnA 340 8.65e+00 b.2.5.7 79324 1k4tA 592 9.05e+00 a.2.8.1 77263 d.163.1.2 77264 e.15.1.1 77265 1pv9A 348 9.12e+00 c.55.2.1 95157 d.127.1.1 95158 6acn 754 9.48e+00 1amj c.8.2.1 30721 c.83.1.1 35397 2bsdA 264 9.48e+00 1amj 754 9.61e+00 1amj c.8.2.1 30725 c.83.1.1 35401 7acn 754 9.93e+00 1amj c.8.2.1 30717 c.83.1.1 35393 1qa7B 217 1.05e+01 1havA b.47.1.4 26426 1v87A 114 1.05e+01 g.44.1.1 108422 1r5tA 142 1.10e+01 c.97.1.1 104812 2fftA 84 1.17e+01 1prcC 336 1.18e+01 6prcC a.138.1.2 19674 1a36A 592 1.22e+01 1a36A a.2.8.1 15715 d.163.1.2 42173 e.15.1.1 43266 1f7lA 121 1.31e+01 1f7lA d.150.1.2 59666 1cjsA 219 1.31e+01 1cjsA e.24.1.1 43354 1frrA 95 1.37e+01 1awd d.15.4.1 37674 1c96A 753 1.39e+01 1amj c.8.2.1 30727 c.83.1.1 35403 1rwjA 82 1.50e+01 a.138.1.1 105114 1xgyL 216 1.59e+01 1bxeA 113 1.60e+01 1bxeA d.55.1.1 38898 1vr7A 142 1.62e+01 1qlpA 394 1.62e+01 1ovaA e.1.1.1 42628 1tzpA 255 1.65e+01 d.65.1.3 107520 1vkbA 161 1.66e+01 d.269.1.1 108643 1b37B 472 1.83e+01 1b37B c.3.1.2 30390 d.16.1.5 37954 1i2aA 219 1.95e+01 e.24.1.1 90660 1xxsA 122 1.98e+01 1na6A 404 1.98e+01 b.142.1.1 91748 c.52.1.22 91749 1b0jA 754 2.04e+01 1amj c.8.2.1 30719 c.83.1.1 35395 1taq 832 2.10e+01 1taq a.60.7.1 18082 c.120.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1havA 217 2.15e+01 1havA b.47.1.4 26423 2occG 84 2.16e+01 2occG f.23.2.1 43522 1dwkA 156 2.19e+01 1dw9A a.35.1.4 17075 d.72.1.1 39606 1dw9A 156 2.19e+01 1dw9A a.35.1.4 17065 d.72.1.1 39596 2aw4Z 70 2.21e+01 1niyA 36 2.23e+01 g.3.6.2 80542 2b1xA 470 2.26e+01 2sniI 83 2.26e+01 2sniI d.40.1.1 38573 1i7nA 309 2.44e+01 c.30.1.5 83681 d.142.1.3 83682 1lm8B 118 2.46e+01 d.15.1.1 74033 1sfe 180 2.50e+01 1sfe a.4.2.1 16073 c.55.7.1 33748 1v54G 85 2.56e+01 f.23.2.1 100328 1brfA 53 2.64e+01 1rb9 g.41.5.1 45236 1vqvA 306 2.68e+01 1a0hA 159 2.75e+01 1a0hA b.47.1.2 26229 g.14.1.1 44655 1lylA 504 2.75e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1pdkB 157 2.75e+01 1pdkB b.2.3.2 22427 1cqxA 403 2.76e+01 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1jlxA 304 2.77e+01 1jlyA b.42.3.1 25583 b.42.3.1 25584 1uoyA 64 2.78e+01 g.3.19.1 99709 1udg 244 2.82e+01 3eugA c.18.1.1 31016 1vajA 214 2.83e+01 1zbdB 134 2.90e+01 1zbdB g.50.1.1 45359 2cszA 76 2.92e+01 1ml0D 76 2.95e+01 d.9.1.1 79254 1cm9A 74 3.09e+01 1b3aA d.9.1.1 37405 2aw4R 103 3.13e+01 1nyoA 163 3.14e+01 b.118.1.1 92345 1auyA 189 3.15e+01 1auyA b.121.4.6 23311 2occF 98 3.22e+01 2occF g.41.5.3 45256 1y4lA 121 3.35e+01 1pvuA 154 3.36e+01 3pviA c.52.1.6 33306 1v54F 98 3.37e+01 g.41.5.3 100327 1nepA 130 3.37e+01 b.1.18.7 80440 1e1oA 504 3.46e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1fc1A 224 3.54e+01 1igtB b.1.1.2 21520 b.1.1.2 21521 1i81A 83 3.54e+01 1d3bB b.38.1.1 61930 1jlyA 304 3.62e+01 1jlyA b.42.3.1 25587 b.42.3.1 25588 1bq9A 54 3.66e+01 1rb9 g.41.5.1 45238 1ff4A 65 3.72e+01 g.7.1.1 83251 1h8eI 50 3.72e+01 1e79I a.137.8.1 60758 1mcpL 220 3.76e+01 8fabA b.1.1.1 19858 b.1.1.2 20958 1s48A 609 3.80e+01 e.8.1.4 98475 1m3sA 186 3.97e+01 c.80.1.3 78573 1mxmA 254 3.97e+01 b.38.1.3 79647 d.58.43.1 79648 f.34.1.1 79649