# List of top-scoring protein chains for t2k-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.soe.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 2bycA 137 2.02e+00 d.58.10.2 129476 3l9jT 149 2.06e+00 2qa9E 185 2.16e+00 b.47.1.1 150200 2e7aA 157 2.77e+00 3jxsA 174 2.84e+00 1k42A 168 2.88e+00 b.18.1.14 72032 2brjA 188 2.95e+00 b.159.1.1 146213 1iqaA 160 3.13e+00 b.22.1.1 71274 1s55A 156 3.20e+00 b.22.1.1 118865 1z8kA 193 3.21e+00 b.159.1.1 124703 1oqeA 144 3.48e+00 b.22.1.1 87286 3iteA 562 3.50e+00 1onqA 283 3.53e+00 b.1.1.2,d.19.1.1 93365,93366 1b7yB 785 3.57e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,b.153.1.1 16301,16302,25312,39311,40780,41456 4tsvA 150 3.59e+00 2tnfA b.22.1.1 23860 2tnfA 156 4.39e+00 2tnfA b.22.1.1 23880 1sgpE 185 4.60e+00 1qq4A b.47.1.1 25816 1tnfA 158 4.86e+00 2tnfA b.22.1.1 23871 1kxgA 152 6.36e+00 b.22.1.1 73145 1y6kR 214 6.66e+00 b.1.2.1,b.1.2.1 122663,122664 3ivrA 509 7.04e+00 1z47A 355 7.58e+00 1kbvA 327 7.79e+00 b.6.1.3,b.6.1.3 68395,68396 1a8mA 157 8.43e+00 2tnfA b.22.1.1 23868 3g7sA 549 8.64e+00 2vovA 336 8.65e+00 3hrpA 409 9.09e+00 2gk6A 624 9.36e+00 1pysB 785 9.67e+00 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,b.153.1.1 16299,16300,25311,39310,40779,41455 3gxwA 103 9.70e+00 2glzA 153 1.18e+01 d.81.3.1 135348 1qhuA 460 1.19e+01 1qhuA b.66.1.1,b.66.1.1 27530,27531 1aihA 170 1.22e+01 1aihA d.163.1.1 42149 3a21A 614 1.28e+01 2zklA 369 1.31e+01 3fvqA 359 1.39e+01 1sqlA 146 1.41e+01 d.96.1.3 105925 2e2dC 180 1.42e+01 b.40.3.1 131980 3gfzA 413 1.42e+01 2rdkA 109 1.43e+01 1t5hX 504 1.44e+01 e.23.1.1 106449 2ordA 397 1.50e+01 1nb9A 147 1.54e+01 b.43.5.1 85515 3e53A 480 1.62e+01 2v7bA 529 1.63e+01 3kkgA 146 1.65e+01 3i1iA 377 1.70e+01 1c52 131 1.76e+01 1c52 1c52A 131 1.76e+01 a.3.1.1 15810 1kz7A 353 1.80e+01 a.87.1.1,b.55.1.1 73333,73334 3edpA 236 1.81e+01 2icgA 160 1.88e+01 d.369.1.1 147601 1dt9A 437 1.92e+01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 2b0rA 202 1.98e+01 3eo6A 106 2.03e+01 2sfaA 191 2.04e+01 b.47.1.1 25815 2p2eA 128 2.07e+01 b.124.1.1 149171 2fblA 153 2.16e+01 d.63.1.2 133249 2vt8A 153 2.17e+01 1fguA 252 2.20e+01 1jmcA b.40.4.3,b.40.4.3 25296,25297 3dgpA 80 2.27e+01 7odcA 424 2.30e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 2ghvC 203 2.36e+01 d.318.1.1 135214 2jfrA 234 2.43e+01 1wdxA 69 2.45e+01 1dt1A 129 2.56e+01 1c52 a.3.1.1 15811 1jmcA 246 2.57e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1uyjA 296 2.59e+01 f.8.1.2 108143 1ocsA 162 2.62e+01 d.189.1.1 92776 2igvA 173 2.65e+01 b.62.1.1 147667 1vqtA 213 2.72e+01 c.1.2.3 120417 2wzpR 375 2.74e+01 2vn4A 599 2.79e+01 1f5jA 199 2.81e+01 1axkA b.29.1.11 24342 1o7eA 276 2.85e+01 e.3.1.1 92622 2zwnA 339 2.91e+01 2ajfE 180 3.00e+01 d.318.1.1 126884 2avdA 219 3.01e+01 c.66.1.1 127377 1q8rA 120 3.13e+01 d.79.6.1 96225 2oynA 146 3.13e+01 b.43.5.2 149067 1xzzA 246 3.15e+01 2jngA 105 3.26e+01 b.34.9.4 148150 2wgoA 98 3.27e+01 1d7kA 421 3.35e+01 7odcA b.49.2.3,c.1.6.1 26486,28648 1olzA 663 3.53e+01 b.1.1.4,b.69.12.1,g.16.2.1 93341,93342,93343 3bc9A 599 3.54e+01 1x99A 145 3.54e+01 b.97.1.2 114978 3hfiA 170 3.66e+01 2amuA 143 3.67e+01 1h8vA 218 3.73e+01 2nlrA b.29.1.11 60795 1u9tA 354 3.80e+01 e.62.1.1 119651 1oa2A 218 3.96e+01 b.29.1.11 86721 3bpqA 52 4.05e+01 1h4gA 207 4.09e+01 b.29.1.11 70863 1xynA 178 4.15e+01 b.29.1.11 24322 2be1A 339 4.17e+01 1qr4A 186 4.27e+01 1qr4B b.1.2.1,b.1.2.1 21986,21987 2hrvA 142 4.32e+01 2hrvA b.47.1.4 26429 2eayA 233 4.34e+01 2zooA 442 4.38e+01 3ge2A 130 4.43e+01 2zplA 97 4.45e+01 3kpkA 434 4.49e+01 1khdA 345 4.50e+01 a.46.2.1,c.27.1.1 77400,77401 3loeA 30 4.51e+01 1cqxA 403 4.63e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 3hxsA 141 4.71e+01 1dfnA 30 4.73e+01 g.9.1.1 44570 2ibpA 409 4.74e+01 1siqA 392 4.78e+01 a.29.3.1,e.6.1.1 105585,105586 2ckkA 127 4.85e+01 2ebdA 309 4.90e+01 2g8sA 353 4.90e+01 3ldtA 169 4.96e+01 1o97C 264 5.10e+01 c.26.2.3 81232 3i5dA 356 5.13e+01 2vnuD 760 5.13e+01 b.40.4.5,b.40.4.5,b.40.4.5,b.40.4.16 153344,153345,153346,153347 2qkiB 188 5.33e+01 1xwvA 129 5.35e+01 b.1.18.7 116134 1vc3B 97 5.36e+01 3ic3A 101 5.41e+01 2e7dA 131 5.45e+01 1tzzA 392 5.65e+01 c.1.11.2,d.54.1.1 112896,112897 1lci 550 5.67e+01 1lci 1umkA 275 5.70e+01 b.43.4.2,c.25.1.1 113312,113313 2vbuA 136 5.83e+01 b.43.5.2 152911 3lo4A 30 5.86e+01 2pt7A 330 5.87e+01 c.37.1.11 149834 3ib7A 330 5.90e+01 2qsqA 111 5.92e+01 3fgqA 397 5.92e+01 3mhsA 476 5.93e+01 1z4vA 532 5.93e+01 1fna 93 5.99e+01 1fnf 2qo4A 126 6.00e+01 1fnaA 91 6.00e+01 b.1.2.1 21971 3glaA 100 6.01e+01 3jx8A 250 6.01e+01 2pjzA 263 6.05e+01 3kpiA 434 6.11e+01 1tuc 63 6.15e+01 1tuc 2h29A 189 6.15e+01 1vfsA 386 6.17e+01 b.49.2.2,c.1.6.1 108584,108585 1iz6A 138 6.29e+01 b.34.5.2,b.40.4.5 76976,76977 3lo1A 30 6.37e+01 2h8eA 120 6.44e+01 3ftjA 226 6.44e+01 3bpuA 88 6.45e+01 2dd8S 202 6.53e+01 d.318.1.1 131393 1ktjA 129 6.66e+01 b.1.18.7 72974 2ztgA 739 6.72e+01 1h4aX 173 6.73e+01 b.11.1.1,b.11.1.1 83479,83480 1gutA 68 6.80e+01 b.40.6.1 65576 1ndh 272 6.82e+01 1ndh 3lvxA 30 6.83e+01 1p9qC 256 6.87e+01 a.5.8.1,d.235.1.2,d.58.11.3 104093,104094,104095 1u79A 129 6.90e+01 d.26.1.1 107714 1usrA 454 7.04e+01 b.68.1.1 99881 1e3pA 757 7.14e+01 1e3hA a.4.9.1,b.40.4.5,d.14.1.4,d.14.1.4,d.52.3.1,d.101.1.1,d.101.1.1 16258,25328,37574,37575,38811,40697,40698 3lwdA 226 7.16e+01 2fuqA 747 7.17e+01 1f3uB 171 7.22e+01 1f3uB b.65.1.1 27525 3e1yA 451 7.26e+01 3cwxA 176 7.27e+01 3hzhB 172 7.36e+01 2ougA 162 7.55e+01 2b5oA 402 7.57e+01 3m05A 114 7.59e+01 1ltlA 279 7.60e+01 b.40.4.11 84701 3e7wA 511 7.62e+01 2bmzA 141 7.69e+01 1g6q2 328 7.74e+01 1g6q2 1ca1 370 7.78e+01 1ca1 1ca1A 370 7.78e+01 a.124.1.1,b.12.1.3 19340,23648 1wjuA 100 7.84e+01 d.15.1.1 114712 2oojA 141 7.95e+01 b.159.2.1 148928