# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 2q1zB 195 3.69e-11 1j58A 385 6.55e-08 b.82.1.2 71531 2qdrA 303 7.76e-08 2f4pA 147 1.11e-07 b.82.1.9 132933 1tq5A 242 3.02e-07 b.82.1.12 119311 3ebrA 159 4.20e-07 1vj2A 126 1.06e-06 b.82.1.10 100796 3cjxA 165 1.10e-06 2pfwA 116 2.41e-06 3ht1A 145 2.42e-06 2o1qA 145 7.03e-06 b.82.1.21 148547 1y3tA 337 7.95e-06 b.82.1.5 122600 2h0vA 338 8.25e-06 1lr5A 163 1.28e-05 b.82.1.2 74215 1o4tA 133 2.23e-05 b.82.1.9 86622 3cewA 125 5.95e-05 2vqaA 361 6.69e-05 1sfnA 246 6.89e-05 b.82.1.11 105496 2d40A 354 7.86e-05 b.82.1.23 146454 3h8uA 125 1.02e-04 2q30A 110 2.45e-04 3h7jA 243 2.90e-04 1fi2A 201 3.15e-04 1fi2A b.82.1.2 59845 2et1A 201 3.61e-04 b.82.1.2 132351 2p17A 277 9.82e-04 3d82A 102 1.08e-03 3l2hA 162 1.40e-03 2o8qA 134 1.89e-03 1v70A 105 2.03e-03 b.82.1.9 113555 3lwcA 119 2.57e-03 3i7dA 163 2.67e-03 1yfuA 174 3.29e-03 b.82.1.20 123094 2gm6A 208 3.85e-03 b.82.1.19 147130 2phdA 368 3.88e-03 b.82.1.23 149468 1rc6A 261 4.38e-03 b.82.1.11 97287 3fjsA 114 4.77e-03 1sefA 274 5.35e-03 b.82.1.11 105452 1vr3A 191 6.78e-03 b.82.1.6 120431 3ibmA 167 7.43e-03 1yhfA 115 1.86e-02 b.82.1.9 123176 3es1A 172 2.33e-02 3kgzA 156 2.89e-02 2pytA 133 3.39e-02 b.82.1.24 149957 2vecA 256 3.71e-02 1xjaA 178 3.80e-02 b.82.4.1 115382 3es4A 116 3.97e-02 2i45A 107 5.26e-02 2arcA 164 5.99e-02 2arcA b.82.4.1 28148 2aacA 177 6.08e-02 2arcA b.82.4.1 28150 1zvfA 176 7.75e-02 b.82.1.20 146029 2bnmA 198 1.00e-01 a.35.1.3,b.82.1.10 128835,128836 2ozjA 114 1.00e-01 1j1lA 290 1.02e-01 b.82.1.12 90766 2fqpA 97 1.30e-01 3eqeA 171 1.55e-01 2zklA 369 1.71e-01 1juhA 350 1.97e-01 b.82.1.5 71884 2e9qA 459 2.05e-01 1qwrA 319 2.32e-01 b.82.1.3 96491 2opkA 112 2.69e-01 3dl3A 119 3.20e-01 b.82.2.13 157762 3eo6A 106 3.61e-01 1od5A 492 3.73e-01 b.82.1.2,b.82.1.2 86832,86833 3lagA 98 4.26e-01 2d5fA 493 4.27e-01 1vrbA 342 4.49e-01 b.82.2.11 120450 1y9qA 192 4.60e-01 a.35.1.8,b.82.1.15 116592,116593 2b8mA 117 5.27e-01 b.82.1.18 128092 2oziA 98 5.31e-01 2cavA 445 5.66e-01 1dgwA b.82.1.2,b.82.1.2 28094,28095 1o5uA 101 6.88e-01 b.82.1.8 92518 3bcwA 123 8.25e-01 2qnkA 286 1.08e+00 3hqxA 111 1.28e+00 1fxzA 476 1.45e+00 b.82.1.2,b.82.1.2 65059,65060 1x82A 190 1.58e+00 b.82.1.7 114955 2gc1A 188 1.59e+00 b.82.1.7 134928 1qxrA 189 1.78e+00 b.82.1.7 96552 3gleA 295 1.89e+00 3b2mA 295 1.89e+00 1ep0A 185 2.06e+00 1dzrA b.82.1.1 28080 1jmxB 349 2.06e+00 b.69.2.2 66906 3jv1A 182 2.14e+00 3ei3A 1158 2.44e+00 3f6zB 101 2.58e+00 3gldA 295 2.88e+00 3cbtA 237 2.95e+00 3exmA 237 2.95e+00 2yu1A 451 2.97e+00 1vp6A 138 3.01e+00 b.82.3.2 113939 1a65A 504 3.27e+00 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 2j3xA 431 3.56e+00 3iteA 562 3.85e+00 1mt6A 280 4.04e+00 b.76.2.1,b.85.7.1 79446,79447 1hfuA 503 4.11e+00 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 3e0cA 1140 4.22e+00 2e26A 725 4.50e+00 2c0zA 216 5.43e+00 b.82.1.1 129615 3a7qA 725 6.03e+00 2xcyA 386 6.30e+00 2jixB 225 6.46e+00 b.1.2.1,b.1.2.1 148107,148108 3eh0A 341 6.88e+00 2p4oA 306 7.14e+00 b.68.6.3 149216 1wkbA 810 7.24e+00 2gu9A 113 7.45e+00 2as9A 210 7.65e+00 3ie4A 107 8.02e+00 1pmi 440 8.46e+00 1pmi 1pmiA 440 8.46e+00 b.82.1.3 28114 1yllA 200 8.57e+00 b.82.1.17 123653 1oi6A 205 8.65e+00 b.82.1.1 103940 3hpeA 164 8.92e+00 2cg7A 90 9.53e+00 g.27.1.1,g.27.1.1 130423,130424 2ea7A 434 1.05e+01 1yjmA 110 1.15e+01 b.26.1.2 123427 3e9tA 114 1.27e+01 2hkdA 320 1.31e+01 1te0A 318 1.36e+01 b.36.1.4,b.47.1.1 112400,112401 2gy5A 423 1.40e+01 1exmA 405 1.41e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1xruA 282 1.42e+01 b.82.1.13 122262 3m46A 666 1.55e+01 2i24N 121 1.55e+01 1cnuA 137 1.58e+01 1cof d.109.1.2 40862 2bwrA 401 1.58e+01 2zu1A 183 1.59e+01 1yqfA 203 1.59e+01 d.25.1.1 123880 3ffjA 666 1.61e+01 2ihoA 293 1.63e+01 b.42.2.1,d.3.1.18 147681,147682 1hcz 252 1.75e+01 1hcz 3mbeD 259 1.80e+01 2a1xA 308 1.81e+01 b.82.2.9 126022 3c6kA 381 1.84e+01 3b5lB 198 1.88e+01 2vpvA 166 1.92e+01 1nltA 248 1.93e+01 b.4.1.1,b.4.1.1,g.54.1.1 91963,91964,91965 1uypA 432 1.98e+01 b.29.1.19,b.67.2.3 100176,100177 2eceA 462 2.01e+01 3fouA 156 2.03e+01 1e5rA 290 2.11e+01 1e5rA b.82.2.4 59276 1qs1A 462 2.13e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 3ckaA 320 2.16e+01 1rgs 288 2.16e+01 1rgs 1ot1A 686 2.21e+01 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 87392,87393,87394,87395 1qs2A 401 2.24e+01 1qs1A d.166.1.1,d.166.1.1 42268,42269 2elfA 370 2.25e+01 2k8qA 134 2.26e+01 2ixkA 184 2.27e+01 2qjvA 270 2.33e+01 1ne6A 283 2.40e+01 b.82.3.2,b.82.3.2 91831,91832 2c12A 439 2.40e+01 a.29.3.1,e.6.1.1 129616,129617 2h5uA 499 2.48e+01 1utcA 363 2.49e+01 a.118.1.4,b.69.6.1 99914,99915 1d2eA 397 2.50e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1eerB 227 2.53e+01 1eerB b.1.2.1,b.1.2.1 22011,22012 1stmA 157 2.59e+01 1stmA b.121.7.1 23281 2brfA 110 2.61e+01 b.26.1.2 128996 3hzaA 174 2.70e+01 1dgwA 178 2.74e+01 1dgwA b.82.1.2 28090 3k3oA 371 2.75e+01 1fnf 368 2.83e+01 1fnf 3frxA 319 2.83e+01 1a1mA 278 2.91e+01 1agdA b.1.1.2,d.19.1.1 20753,38266 1dmhA 311 2.94e+01 1dmhA b.3.6.1 22633 1lk2A 274 2.98e+01 b.1.1.2,d.19.1.1 91056,91057 3e5zA 296 3.03e+01 1fzkA 274 3.05e+01 1agdA b.1.1.2,d.19.1.1 60149,60150 1ujxA 119 3.07e+01 b.26.1.2 99473 1ajkA 214 3.11e+01 1axkA b.29.1.2 24176 3c3vA 510 3.16e+01 1cxlA 686 3.23e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21829,22498,27736,28723 1h3iA 293 3.24e+01 b.76.2.1,b.85.7.1 76635,76636 2oa2A 148 3.29e+01 3ef2A 293 3.31e+01 2qf3A 243 3.33e+01 b.47.1.1 150724 2vveA 254 3.40e+01 2ux0A 143 3.42e+01 d.17.4.7 152231 2do3A 69 3.43e+01 b.34.5.5 131596 1wt9B 123 3.45e+01 d.169.1.1 121255 2hqsA 415 3.45e+01 b.68.4.1,c.51.2.1 136662,136663 2ggoA 401 3.51e+01 1vdzA 588 3.58e+01 1iz6A 138 3.61e+01 b.34.5.2,b.40.4.5 76976,76977 3kl9A 355 3.64e+01 3gkeA 349 3.68e+01 1ev7A 317 3.70e+01 1ev7B c.52.1.9 33315 3ikjA 588 3.75e+01 1d3cA 686 3.77e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 3d0jA 140 3.81e+01 1c4rA 182 3.82e+01 1c4rA b.29.1.4 24229 1ospO 257 3.83e+01 1ospO b.76.1.1 27971 1x8mA 288 3.85e+01 b.82.1.13 109516 2wwuA 371 3.88e+01 2pn0A 141 3.93e+01 1lcl 142 3.97e+01 1lcl 1aipA 405 3.98e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1s0uA 408 4.02e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 2gc7A 386 4.03e+01 b.69.2.1 134954 3ia8A 163 4.06e+01 2c78A 405 4.08e+01 b.43.3.1,b.44.1.1,c.37.1.8 130037,130038,130039 2atfA 200 4.10e+01 b.82.1.19 127290 2b5hA 200 4.10e+01 b.82.1.19 127894 3e1yA 451 4.13e+01 1j1tA 233 4.14e+01 b.29.1.18 90771 2wvvA 450 4.18e+01 3e91A 306 4.23e+01 1bec 238 4.26e+01 1bec 1becA 238 4.26e+01 b.1.1.1,b.1.1.2 20627,21561 3k1qI 639 4.30e+01 3fw6A 534 4.30e+01 1neu 124 4.39e+01 1neu 1neuA 124 4.39e+01 b.1.1.1 19704 1v8qA 85 4.40e+01 b.84.4.1 108428 1ixxB 123 4.42e+01 1ixxB d.169.1.1 42336 1ebaA 215 4.42e+01 1eerB b.1.2.1,b.1.2.1 22015,22016 1lci 550 4.43e+01 1lci 2vq5A 201 4.45e+01 2digA 68 4.47e+01 b.34.9.1 131529 1j34B 123 4.48e+01 d.169.1.1 84049 1p35A 299 4.53e+01 1p35A b.28.1.1 23925 1hocA 272 4.54e+01 1agdA b.1.1.2,d.19.1.1 20815,38297 2bbkH 355 4.56e+01 2bbkH b.69.2.1 27634 2nv0A 196 4.58e+01 c.23.16.1 138625 1hdkA 141 4.61e+01 b.29.1.3 65807 3ea8A 306 4.62e+01 2aujD 309 4.63e+01 1ywkA 289 4.72e+01 b.82.1.13 124155 1zrrA 179 4.78e+01 b.82.1.6 125555 1sixA 174 4.81e+01 b.85.4.1 98892 1i9gA 280 4.81e+01 c.66.1.13 62090 1axkA 394 4.83e+01 1axkA b.29.1.2,b.29.1.11 24181,24315 1agdA 276 4.86e+01 1agdA b.1.1.2,d.19.1.1 20741,38260 1dueA 242 4.86e+01 b.47.1.1 76140 1w4sA 174 4.89e+01 1gytA 503 4.97e+01 c.50.1.1,c.56.5.3 70765,70766 1pmjX 185 4.98e+01 b.18.1.18 104194 1agjA 242 5.02e+01 1agjA b.47.1.1 25827 1jtdB 273 5.03e+01 b.69.5.2 67265 3holA 509 5.04e+01 1r9gA 216 5.06e+01 c.23.16.1 97258 1reqB 637 5.09e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 3gneA 252 5.12e+01 1fzoA 274 5.17e+01 1agdA b.1.1.2,d.19.1.1 60155,60156 2qtwB 546 5.21e+01 1ci3M 249 5.21e+01 1hcz b.2.6.1,b.84.2.2 22480,28266 2w7sA 200 5.22e+01 2b9uA 176 5.36e+01 3hhyA 280 5.36e+01 1upiA 225 5.43e+01 b.82.1.1 99757 1qhoA 686 5.44e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 3l4mC 137 5.48e+01 3fpxA 499 5.53e+01 1ebpA 211 5.53e+01 1eerB b.1.2.1,b.1.2.1 22023,22024 1we0A 187 5.57e+01 c.47.1.10 120930 3pcgA 200 5.59e+01 3pchA b.3.6.1 22647 2cwrA 103 5.67e+01 3g7gA 158 5.67e+01 1qr4B 186 5.80e+01 1qr4B b.1.2.1,b.1.2.1 21988,21989 3esmA 152 5.95e+01 3gyrA 612 5.99e+01 2f68X 313 6.00e+01 1a9eA 277 6.03e+01 1agdA b.1.1.2,d.19.1.1 20757,38268 3ktxA 499 6.03e+01 3lhnA 126 6.04e+01 3hxjA 330 6.07e+01 2gefA 217 6.10e+01 1ub1A 133 6.10e+01 d.10.1.3 99140 3btxA 204 6.12e+01 1extA 162 6.18e+01 1extA g.24.1.1,g.24.1.1,g.24.1.1 44900,44901,44902 1cpnA 208 6.21e+01 b.29.1.2 24175 3fq3A 197 6.33e+01 3lvmA 423 6.38e+01 3ea9A 306 6.39e+01 2in5A 207 6.39e+01 b.177.1.1 147736 2h2zA 306 6.40e+01 1cauA 181 6.42e+01 1dgwA b.82.1.2 28102 1kz7A 353 6.46e+01 a.87.1.1,b.55.1.1 73333,73334 1bpoA 494 6.46e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 2oy7A 320 6.48e+01 1sotA 320 6.48e+01 b.36.1.4,b.47.1.1 105852,105853 1l7lA 121 6.56e+01 b.18.1.16 77790 2cqsA 842 6.56e+01 2z0tA 109 6.64e+01 2qv8A 159 6.68e+01 3eadA 137 6.76e+01 3b3qE 197 6.83e+01 b.29.1.4 154813 2g6yA 217 6.83e+01 1cqqA 180 6.84e+01 1cqqA b.47.1.4 26422 2dq6A 870 6.97e+01 3elnA 200 7.07e+01 b.82.1.19 158185 3pchA 200 7.12e+01 3pchA b.3.6.1 22653 1efuA 385 7.17e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1ep2B 261 7.28e+01 1ep2B b.43.4.2,c.25.1.3 25666,31556 1k28A 584 7.30e+01 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 1p3wA 404 7.37e+01 c.67.1.3 87752 1a1oA 276 7.61e+01 1agdA b.1.1.2,d.19.1.1 20751,38265 2zu2A 302 7.66e+01 1hlcA 129 7.66e+01 1c1lA b.29.1.3 24208 2nmmA 135 7.68e+01 d.322.1.1 138372 1p9sA 300 7.68e+01 b.47.1.4 87999 2bibA 547 7.69e+01 b.109.1.1,d.157.1.8 128581,128582 3bb6A 127 7.70e+01 b.82.2.13 155045 3bzhA 194 7.81e+01 1crzA 403 7.84e+01 1crzA b.68.4.1,c.51.2.1 27629,33211 2agcA 162 7.94e+01 2v72A 143 7.97e+01