# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 2gcxA 75 2.01e-08 2h3jA 75 3.24e-08 1bi0 226 1.70e-02 1bi0 1fx7A 230 1.95e-02 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1qw1A 121 5.81e-02 1e0cA 271 1.50e-01 1e0cA c.46.1.2,c.46.1.2 32717,32718 1y8xB 98 2.16e-01 1bymA 97 2.42e-01 1bi0 b.34.1.2 24458 2bpsA 81 4.16e-01 1t0yA 122 4.77e-01 d.15.1.1 99066 1opd 85 7.39e-01 1ptf 1opdA 85 7.63e-01 d.94.1.1 40560 1sphA 88 9.36e-01 1ptf d.94.1.1 40544 2dchX 216 1.31e+00 2nwvA 114 1.53e+00 d.326.1.1 138720 1vqoK 132 2.61e+00 b.39.1.1 120372 1z2mA 155 2.75e+00 d.15.1.1,d.15.1.1 124387,124388 1zx6A 58 2.77e+00 1y8qB 640 2.88e+00 2jg2A 422 2.92e+00 1gatA 60 2.99e+00 1gatA g.39.1.1 45106 1y51A 88 3.50e+00 1whzA 70 3.58e+00 d.50.3.2 114656 1x1mA 107 3.62e+00 d.15.1.1 121592 1vg5A 73 3.65e+00 a.5.2.1 113640 2f1fA 164 3.69e+00 d.58.18.6,d.58.18.6 132760,132761 1knmA 130 4.06e+00 b.42.2.1 72781 1j6oA 268 4.07e+00 c.1.9.12 77088 1gcqA 61 4.27e+00 1ckaA b.34.2.1 60434 2rcfA 91 4.31e+00 1oebA 62 4.36e+00 b.34.2.1 86909 1kafA 108 4.48e+00 d.199.1.1 68372 2z1mA 345 4.60e+00 1v2yA 105 4.71e+00 d.15.1.1 100275 1ah1 129 5.05e+00 1ah1 1aboA 62 5.50e+00 1bbzA b.34.2.1 24474 1dv0A 47 5.51e+00 1dv0A a.5.2.1 16289 2fomB 185 5.53e+00 b.47.1.3 133884 2drmA 58 5.61e+00 1uarA 285 5.81e+00 c.46.1.2,c.46.1.2 107762,107763 1zuyA 58 5.88e+00 1utiA 58 5.88e+00 b.34.2.1 99962 2d1hA 109 6.07e+00 a.4.5.50 131125 1s68A 249 6.09e+00 d.142.2.4 98591 1cbfA 285 6.10e+00 c.90.1.1 35587 1pgyA 47 6.22e+00 a.5.2.1 94696 2qq9A 226 6.29e+00 3c0cA 73 6.75e+00 1zjjA 263 6.78e+00 2o88A 58 7.11e+00 2hcuA 213 7.25e+00 1sz7A 200 7.60e+00 3d33A 108 7.72e+00 2hvqA 335 7.89e+00 2gatA 66 8.10e+00 1gatA g.39.1.1 45102 1bbzA 58 8.19e+00 1bbzA b.34.2.1 24477 2bzyA 67 8.48e+00 1lckA 175 8.51e+00 1lckA b.34.2.1,d.93.1.1 24552,40421 2qmmA 197 8.53e+00 2bwbA 46 8.56e+00 a.5.2.1 129329 1zoiA 276 9.02e+00 2qalM 117 9.37e+00 2cp8A 54 9.52e+00 a.5.2.1 130695 2re3A 194 9.67e+00 1ootA 60 1.01e+01 b.34.2.1 93386 3cjxA 165 1.02e+01 1pch 88 1.03e+01 1ptf 2raqA 97 1.03e+01 2bjnA 160 1.04e+01 1pchA 88 1.04e+01 d.94.1.1 40564 1vr0A 247 1.05e+01 c.148.1.1 120428 2qpqA 301 1.10e+01 2iimA 62 1.12e+01 b.34.2.1 137434 2dklA 85 1.13e+01 a.5.2.1 131555 1rhs 296 1.20e+01 1rhs 2fu4A 83 1.20e+01 1rhsA 296 1.20e+01 c.46.1.2,c.46.1.2 32703,32704 3c24A 286 1.20e+01 1go3F 107 1.21e+01 a.60.8.2 65407 1wr1B 58 1.23e+01 a.5.2.1 121185 1isiA 265 1.29e+01 c.23.14.3 71394 2a28A 54 1.30e+01 3bn1A 373 1.31e+01 1ghpA 258 1.33e+01 1btl e.3.1.1 60520 2qsfX 171 1.34e+01 3bhdA 234 1.34e+01 1yixA 265 1.39e+01 c.1.9.12 123371 1k1eA 180 1.44e+01 c.108.1.5 67995 1v30A 124 1.44e+01 d.269.1.1 113496 1zzmA 259 1.44e+01 c.1.9.12 125911 1ptf 88 1.46e+01 1ptf 1ptfA 88 1.46e+01 d.94.1.1 40549 1b4aA 149 1.49e+01 1b4aA a.4.5.3,d.74.2.1 16088,39721 1pht 85 1.54e+01 1ckaA 1phtA 85 1.54e+01 b.34.2.1 24483 1genA 218 1.56e+01 b.66.1.1 27536 1h9sA 140 1.56e+01 1b9mA b.40.6.2,b.40.6.2 60843,60844 1ywyA 74 1.57e+01 b.55.2.1 124166 2ggrA 76 1.62e+01 1f42A 306 1.65e+01 1f42A b.1.1.4,b.1.2.1,b.1.2.1 59636,59637,59638 1vekA 84 1.67e+01 a.5.2.1 113636 1r89A 437 1.69e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 2fyqA 194 1.70e+01 1h80A 464 1.70e+01 b.80.1.8 65714 2jejA 358 1.71e+01 d.240.1.1,e.8.1.7 138284,138285 1befA 181 1.71e+01 1befA b.47.1.3 26419 2iayA 114 1.74e+01 1x6mA 196 1.77e+01 b.88.1.4 114920 1jx4A 352 1.78e+01 d.240.1.1,e.8.1.7 90378,90379 1e0tA 470 1.91e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27064,29292,33146 1bkb 136 1.92e+01 1bkb 1gcqC 70 1.94e+01 1gcpA b.34.2.1 60436 2o31A 67 1.95e+01 1wrbA 253 1.99e+01 c.37.1.19 121192 1rpnA 335 1.99e+01 c.2.1.2 97708 1ulrA 88 2.00e+01 d.58.10.1 113283 1xyfA 436 2.04e+01 1taxA b.42.2.1,c.1.8.3 25577,28909 1fr3A 67 2.05e+01 1fr3A b.40.6.1 25436 1dpeA 507 2.06e+01 c.94.1.1 35799 2glfA 450 2.06e+01 1im4A 221 2.08e+01 e.8.1.7 62581 1bkbA 136 2.09e+01 b.34.5.2,b.40.4.5 24609,25341 1kpeA 126 2.11e+01 1kpf d.13.1.1 37508 1guiA 155 2.14e+01 b.18.1.14 76351 1wdiA 345 2.16e+01 e.53.1.1 114535 2ak5A 64 2.19e+01 1oflA 481 2.20e+01 b.80.1.4 103934 2j3wB 188 2.20e+01 1d2zB 153 2.21e+01 1d2zB a.77.1.2 18439 2nygA 273 2.21e+01 1wiwA 290 2.23e+01 c.80.1.1 114681 1pioA 257 2.24e+01 1btl e.3.1.1 42719 2fbhA 146 2.25e+01 a.4.5.28 133245 2i6vA 87 2.27e+01 1peaA 385 2.30e+01 c.93.1.1 35662 1pea 385 2.30e+01 1pea 1ci4A 89 2.38e+01 1qckA a.60.5.1 17970 1qfrA 89 2.38e+01 1ptf d.94.1.1 40552 1wc9A 169 2.39e+01 d.278.1.2 114507 1y0eA 223 2.45e+01 c.1.2.5 116297 3bpdA 100 2.47e+01 2d1zA 436 2.48e+01 2og5A 357 2.54e+01 1fjgM 126 2.61e+01 1fjfM a.156.1.1 16293 2o9sA 67 2.64e+01 2hjhA 354 2.64e+01 1dboA 506 2.64e+01 1dbgA b.80.1.4 28034 1uheA 97 2.66e+01 1azeA 56 2.66e+01 b.34.2.1 24536 1xfsA 178 2.67e+01 d.129.3.5 109589 1iz6A 138 2.75e+01 b.34.5.2,b.40.4.5 76976,76977 2o8bA 934 2.76e+01 2g5cA 281 2.77e+01 a.100.1.12,c.2.1.6 134646,134647 1fjgJ 105 2.78e+01 1fjfJ d.58.15.1 39330 1eggA 147 2.81e+01 1eggA d.169.1.1 42333 2bjdA 101 2.81e+01 2imlA 199 2.82e+01 1ibzA 112 2.84e+01 1ibzA b.6.1.4 62237 1q2kA 31 2.86e+01 g.3.7.2 95630 2cr5A 109 2.87e+01 d.15.1.2 130733 2g6fX 59 2.89e+01 1z96A 40 2.90e+01 2p2uA 171 2.91e+01 2i7rA 118 2.92e+01 d.32.1.2 137102 1egiA 147 2.93e+01 1eggA d.169.1.1 42331 1dppA 507 2.95e+01 1dpe c.94.1.1 35800 1oe4A 247 2.96e+01 c.18.1.3 86895 2yyvA 227 2.98e+01 2cwlA 302 2.99e+01 a.25.1.3 130927 1nthA 458 2.99e+01 c.1.25.1 80730 2ckwA 515 3.03e+01 2a08A 60 3.03e+01 1dbgA 506 3.11e+01 1dbgA b.80.1.4 28033 1xu6A 80 3.11e+01 g.16.3.1 116047 1qg0A 308 3.15e+01 1fnc b.43.4.2,c.25.1.1 25639,31529 1umuA 116 3.15e+01 1umuA b.87.1.1 28382 2okfA 140 3.18e+01 1b9hA 388 3.27e+01 1b9hA c.67.1.4 34488 2mcmA 112 3.32e+01 b.1.7.1 22207 1rk8A 165 3.32e+01 d.58.7.1 97603 1jxgA 100 3.34e+01 b.6.1.1 67413 1cskA 71 3.37e+01 1ckaA b.34.2.1 24513 1griA 217 3.38e+01 1griA b.34.2.1,b.34.2.1,d.93.1.1 24531,24532,40473 1b4qA 105 3.40e+01 1kte c.47.1.1 32773 2gh1A 301 3.43e+01 c.66.1.49 135170 1kpf 126 3.44e+01 1kpf 2qbuA 232 3.45e+01 1s5jA 847 3.51e+01 c.55.3.5,e.8.1.1 112040,112041 2vqeM 126 3.51e+01 2eo2A 71 3.63e+01 1xv5A 401 3.68e+01 1gcpA 70 3.80e+01 1gcpA b.34.2.1 60430 1prs 173 3.84e+01 1prs 2otuA 115 3.85e+01 1skyE 473 3.98e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18314,26479,32359 1ew4A 106 4.01e+01 1ew4A d.82.2.1 40023 1ibyA 112 4.02e+01 1ibzA b.6.1.4 62233 2dclA 127 4.05e+01 1efnA 59 4.06e+01 1bbzA b.34.2.1 24465 1npsA 88 4.07e+01 1prs b.11.1.1 23622 1ktbA 405 4.08e+01 b.71.1.1,c.1.8.1 72960,72961 1vl4A 447 4.15e+01 d.283.1.1 108718 1qvbA 481 4.19e+01 1qvbA c.1.8.4 28983 2jc4A 256 4.19e+01 1vd6A 224 4.20e+01 c.1.18.3 119991 1zpvA 91 4.22e+01 d.58.18.7 125475 2gw8A 114 4.23e+01 2op5A 117 4.23e+01 3cp0A 82 4.30e+01 3bhnA 236 4.30e+01 1b9mA 265 4.33e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1kpfA 125 4.34e+01 d.13.1.1 37507 1gutA 68 4.36e+01 b.40.6.1 65576 2vqeQ 105 4.38e+01 2b0jA 358 4.41e+01 a.100.1.11,c.2.1.6 127639,127640 2dxcA 126 4.44e+01 1y0nA 78 4.45e+01 d.291.1.1 116305 1fjgI 128 4.45e+01 1fjfI d.14.1.1 37559 2hi1A 330 4.56e+01 1zlmA 58 4.65e+01 2eifA 136 4.66e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1mo1A 87 4.67e+01 d.94.1.1 91363 1noaA 113 4.69e+01 b.1.7.1 22208 1d2mA 665 4.73e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 2o95A 187 4.75e+01 1b7yB 785 4.78e+01 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 2qdyB 212 4.79e+01 1x2kA 68 4.87e+01 2mcm 112 4.88e+01 2mcm 2vknA 70 4.88e+01 3mag 307 4.89e+01 3mag 1el6A 219 4.98e+01 1el6B d.182.1.1 42606 1pexA 207 4.99e+01 b.66.1.1 27540 1z3eB 73 5.00e+01 a.60.3.1 124401 2vqeI 128 5.03e+01 1yezA 68 5.03e+01 b.40.4.12 123026 1dklA 410 5.04e+01 1dklA c.60.1.2 33996 1s69A 124 5.07e+01 a.1.1.1 105305 2ogeA 399 5.17e+01 1pt1A 143 5.18e+01 b.52.2.1 95084 1cz4A 185 5.26e+01 1cz4A b.52.2.3,d.31.1.1 26934,38468 1qqyA 130 5.35e+01 3lzt d.2.1.2 36586 1ruwA 69 5.37e+01 2i4iA 417 5.37e+01 1ay9A 108 5.40e+01 1umuA b.87.1.1 28384 1xbyA 216 5.40e+01 c.1.2.3 121846 2cw5A 255 5.41e+01 1j6wA 175 5.46e+01 1j98A d.185.1.2 62663 2zayA 147 5.50e+01 2g7uA 257 5.51e+01 1kcvL 214 5.55e+01 b.1.1.1,b.1.1.2 72317,72318 1se8A 301 5.56e+01 b.40.4.3 105448 1fjgQ 105 5.60e+01 1fjfQ b.40.4.5 25352 2o11A 407 5.67e+01 2hpsA 186 5.67e+01 1pqhA 143 5.68e+01 b.52.2.1 95017 2uubI 128 5.75e+01 2z5wA 136 5.87e+01 1avaC 181 5.89e+01 1avaC b.42.4.1 25604 1h9jA 145 5.89e+01 1h9jA b.40.6.2,b.40.6.2 60829,60830 2p0pA 126 5.93e+01 1zc1A 208 5.95e+01 1g3fA 117 5.98e+01 1g3fA g.52.1.1 45378 1eqnA 321 6.03e+01 1dd9A e.13.1.1 43256 1x54A 434 6.04e+01 1vjrA 271 6.06e+01 c.108.1.14 100832 1o2dA 371 6.08e+01 e.22.1.2 86591 1db3A 372 6.12e+01 1db3A c.2.1.2 29813 1mdoA 393 6.14e+01 c.67.1.4 79013 2inbA 140 6.14e+01 1pn2A 280 6.16e+01 d.38.1.4,d.38.1.4 94930,94931 1fnoA 417 6.18e+01 d.58.19.1,c.56.5.4 70145,75841 2amuA 143 6.24e+01 2ahjB 212 6.29e+01 2ahjB b.34.4.4 24599 1q6oA 216 6.29e+01 c.1.2.3 95986 1avzC 57 6.43e+01 1bbzA b.34.2.1 24467 2gu2A 312 6.43e+01 1h3oA 75 6.45e+01 a.22.1.3 76644 1aw8B 91 6.47e+01 1aw8B 2h09A 155 6.48e+01 2jheA 190 6.49e+01 1ahjB 212 6.55e+01 2ahjB b.34.4.4 24601 2yysA 286 6.66e+01 2pg4A 95 6.66e+01 2vgeA 229 6.70e+01 1j48A 110 6.82e+01 b.1.7.1 84112 2v1qA 60 6.82e+01 1yarH 217 6.83e+01 d.153.1.4 122844 1jnyA 435 6.87e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2hldD 478 6.87e+01 2q9vA 90 6.97e+01 1ujnA 348 6.99e+01 e.22.1.1 99460 1hl9A 449 7.06e+01 b.71.1.3,c.1.8.11 90650,90651 1j24A 143 7.07e+01 c.52.1.20 84008 1zelA 298 7.08e+01 1wlpB 138 7.09e+01 b.34.2.1 121010 1h9mA 145 7.17e+01 1h9jA b.40.6.2,b.40.6.2 60833,60834 2dtrA 226 7.18e+01 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1ylhA 560 7.25e+01 1r4pA 297 7.40e+01 d.165.1.2 97025 1a0nB 69 7.49e+01 1bbzA b.34.2.1 24469 1h9fA 57 7.51e+01 1h9fA a.140.1.1 60826 1tg0A 68 7.63e+01 2glwA 92 7.66e+01 3cpkA 150 7.71e+01 1wlfA 179 7.75e+01 d.31.1.1,b.52.2.3 109396,109397 2qghA 425 7.83e+01 1ifyA 49 7.86e+01 a.5.2.1 71207 2eq6A 464 7.88e+01 2yziA 138 7.89e+01 2uubQ 105 7.95e+01 b.40.4.5 139948