# 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.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 1zhvA 134 3.46e-02 1g61A 228 4.31e-02 1g61A d.126.1.1 41126 2g0dA 409 7.34e-02 1kwmA 402 1.48e-01 c.56.5.1,d.58.3.1 73079,73080 1a3yA 149 1.61e-01 1obpA b.60.1.1 27110 1dzkA 157 2.48e-01 1obpA b.60.1.1 27096 2f06A 144 3.51e-01 2g76A 335 5.04e-01 1yj7A 171 6.75e-01 1dc7A 124 1.09e+00 1dbwA c.23.1.1 31093 1ab6A 125 1.17e+00 3chy c.23.1.1 31054 3chy 128 1.26e+00 3chy c.23.1.1 31038 1ab5A 125 1.30e+00 3chy c.23.1.1 31056 2b30A 301 1.55e+00 1wwkA 307 1.73e+00 1cye 129 1.91e+00 3chy c.23.1.1 31077 1kvnA 104 2.03e+00 d.201.1.1 73066 1jbeA 128 2.15e+00 3chy c.23.1.1 62845 1nm2A 317 2.39e+00 c.19.1.1,d.58.23.1 80654,80655 1s9uA 207 2.67e+00 a.184.1.1 105390 1zvpA 133 2.74e+00 1umgA 362 2.79e+00 d.280.1.1 107956 1l3iA 192 2.87e+00 c.66.1.22 77676 1yioA 208 2.91e+00 2atzA 180 3.05e+00 2gukA 120 3.23e+00 1ccwA 137 3.90e+00 1be1 c.23.6.1 31238 1mp1A 111 3.95e+00 a.188.1.1 91382 1rz4A 226 3.95e+00 a.4.5.53,a.118.1.18 105131,105132 1emwA 88 4.23e+00 1emwA d.27.1.1 38448 1vjqA 79 4.30e+00 k.43.1.1 100830 1q1oA 98 4.57e+00 d.15.2.2 95596 1v3rA 116 4.64e+00 1yqhA 109 4.72e+00 1v2xA 194 4.88e+00 c.116.1.1 100274 1a4uA 254 5.00e+00 1b16A c.2.1.2 29878 1ipd 345 5.15e+00 1cnzA c.77.1.1 35038 1lb2B 84 5.52e+00 a.60.3.1 77871 1bsg 266 5.53e+00 1btl e.3.1.1 42729 1vfjA 116 5.55e+00 1wh8A 111 5.55e+00 1lvaA 258 5.64e+00 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1v6sA 390 5.73e+00 c.86.1.1 100424 2ct8A 497 5.75e+00 1pqsA 77 5.93e+00 d.15.2.2 88277 1t3tA 1303 6.01e+00 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1dr8B 344 6.27e+00 1cnzA c.77.1.1 35052 1xaa 345 6.27e+00 1cnzA c.77.1.1 35033 1idm 343 6.32e+00 1cnzA c.77.1.1 35035 2ewrA 170 6.59e+00 1x31C 206 6.62e+00 1b16A 254 6.81e+00 1b16A c.2.1.2 29875 1lngA 87 7.42e+00 d.201.1.1 74045 1cmaA 104 7.69e+00 1cmbA a.43.1.5 17486 1yqzA 438 8.15e+00 1sbyA 254 8.28e+00 1meoA 209 8.39e+00 c.65.1.1 79035 1lrv 244 8.63e+00 1lrv a.118.1.5 19146 1wkrA 340 8.79e+00 b.50.1.2 109395 1fjgP 88 9.08e+00 1emwA d.27.1.1 38444 1xhfA 123 9.14e+00 2b82A 211 9.15e+00 1vbkA 307 9.28e+00 2fclA 169 9.34e+00 1mjoA 104 9.35e+00 1cmbA a.43.1.5 17466 1myn 44 9.41e+00 1gpt g.3.7.4 44172 1fp2A 352 9.56e+00 1fpxA a.4.5.29,c.66.1.12 59941,59942 1rmwA 212 9.64e+00 1fpxA 352 9.69e+00 1fpxA a.4.5.29,c.66.1.12 59950,59951 1wn0A 145 1.00e+01 1o50A 157 1.03e+01 d.37.1.1,d.37.1.1 92478,92479 1dpe 507 1.03e+01 1dpe c.94.1.1 35799 1dppA 507 1.11e+01 1dpe c.94.1.1 35800 1cmbA 104 1.15e+01 1cmbA a.43.1.5 17460 1oo0A 147 1.18e+01 d.232.1.1 87182 1gnkA 112 1.27e+01 2pii d.58.5.1 39073 1o4sA 389 1.27e+01 c.67.1.1 86620 1r6xA 395 1.29e+01 b.122.1.3,c.26.1.5 97167,97168 1z7mA 344 1.35e+01 1dk8A 147 1.36e+01 1agrE a.91.1.1 18548 1fgs 428 1.38e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 1sbxA 106 1.40e+01 a.6.1.4 105414 1pil 112 1.40e+01 2pii d.58.5.1 39072 1tjyA 316 1.45e+01 c.93.1.1 107062 1jetA 517 1.45e+01 1jevA c.94.1.1 35718 1cmcA 104 1.46e+01 1cmbA a.43.1.5 17462 1jevA 517 1.48e+01 1jevA c.94.1.1 35720 1mejA 223 1.49e+01 c.65.1.1 79029 1jqgA 433 1.53e+01 c.56.5.1,d.58.3.1 71791,71792 1wyzA 242 1.55e+01 1yrrA 382 1.60e+01 2olbA 517 1.60e+01 1jevA c.94.1.1 35721 1jmsA 381 1.62e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1umnA 165 1.64e+01 a.25.1.1 99607 2al6A 375 1.64e+01 1ntr 124 1.65e+01 1dbwA c.23.1.1 31092 1x54A 434 1.65e+01 2g03A 194 1.66e+01 1avqA 228 1.66e+01 1avqA c.52.1.13 33326 1rz3A 201 1.67e+01 c.37.1.6 98132 1wd7A 261 1.67e+01 1h6pA 203 1.68e+01 a.146.1.1 60690 1hdoA 206 1.69e+01 1he2A c.2.1.2 60965 2pii 112 1.74e+01 2pii d.58.5.1 39071 1ve1A 304 1.75e+01 1ble 163 1.79e+01 1ble c.38.1.1 32475 1mioB 458 1.84e+01 1qguB c.92.2.3 35602 1in0A 163 1.89e+01 d.58.49.1,d.58.49.1 83694,83695 1gh9A 71 1.90e+01 1gh9A g.41.6.1 45266 1xriA 151 1.94e+01 1o1xA 155 1.95e+01 c.121.1.1 86553 1vfgA 390 1.95e+01 a.173.1.1,d.218.1.4 108570,108571 1atlA 202 1.96e+01 1atlA d.92.1.9 40322 1wwpA 119 2.06e+01 2fe7A 166 2.06e+01 1qzzA 374 2.07e+01 a.4.5.29,c.66.1.12 96719,96720 1oxkB 134 2.08e+01 c.23.1.1 93691 1w6kA 732 2.08e+01 1n8nA 212 2.09e+01 c.108.1.12 91706 1ys7A 233 2.09e+01 1bed 181 2.10e+01 1fvkA c.47.1.13 90330 2f60K 64 2.11e+01 1aua 296 2.12e+01 1aua a.5.3.1,c.13.1.1 16290,30882 1qbhA 101 2.12e+01 1g3fA g.52.1.1 45374 1jfuA 186 2.13e+01 c.47.1.10 62940 1jt8A 102 2.13e+01 b.40.4.5 63279 2occE 109 2.14e+01 2occE a.118.11.1 19224 1jbwA 428 2.15e+01 c.59.1.2,c.72.2.2 62860,62861 1kkhA 317 2.17e+01 d.14.1.5,d.58.26.3 72645,72646 1g8fA 511 2.21e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1cw0A 155 2.22e+01 1vsrA c.52.1.15 33333 1z6kA 293 2.31e+01 2d28C 149 2.33e+01 1v5xA 203 2.34e+01 c.1.2.4 100377 1cliA 345 2.36e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1he2A 206 2.39e+01 1he2A c.2.1.2 60966 1uxc 65 2.40e+01 1uxc a.35.1.5 17119 1wy2A 351 2.41e+01 1k66A 149 2.44e+01 c.23.1.1 90941 1t1vA 93 2.48e+01 c.47.1.14 106278 1v8fA 276 2.48e+01 c.26.1.4 100503 1tyyA 339 2.49e+01 1j7xA 302 2.51e+01 c.14.1.2 66425 1dthA 203 2.51e+01 1atlA d.92.1.9 40324 2gu3A 136 2.51e+01 1wcwA 261 2.53e+01 1oasA 322 2.53e+01 1oasA c.79.1.1 35293 1o0yA 260 2.55e+01 c.1.10.1 80756 1jg1A 235 2.56e+01 c.66.1.7 66661 1ddeA 338 2.59e+01 1dd9A e.13.1.1 43255 1a2oA 349 2.61e+01 1chd c.23.1.1,c.40.1.1 31120,32479 1vmaA 306 2.67e+01 a.24.13.1,c.37.1.10 108887,108888 1obpA 159 2.68e+01 1obpA b.60.1.1 27092 1vixA 420 2.68e+01 c.56.5.4,d.58.19.1 100777,100778 1a05A 358 2.69e+01 1cnzA c.77.1.1 35059 1v54E 109 2.69e+01 a.118.11.1 100326 1s3zA 165 2.73e+01 d.108.1.1 105250 1yqgA 263 2.81e+01 1han 297 2.86e+01 1han d.32.1.3,d.32.1.3 38506,38507 1u5hA 273 2.86e+01 1wi6A 88 3.00e+01 1mzhA 225 3.05e+01 c.1.10.1 79698 1dlyA 164 3.05e+01 1dlyA a.1.1.1 14983 2c60A 111 3.05e+01 1cxpC 466 3.09e+01 1mhlC 1ir3A 306 3.11e+01 1fmk d.144.1.7 41702 1xt9A 212 3.16e+01 1iyhA 198 3.17e+01 a.45.1.1,c.47.1.5 83790,83791 1ffh 294 3.19e+01 1ng1 a.24.13.1,c.37.1.10 16960,32271 1r1qA 100 3.21e+01 d.93.1.1 104763 1coo 98 3.25e+01 1coo a.60.3.1 17967 1kvkA 395 3.26e+01 d.14.1.5,d.58.26.3 73060,73061 1hxvA 113 3.27e+01 d.26.1.1 71089 1gt1A 159 3.28e+01 b.60.1.1 90515 2ax4A 198 3.28e+01 2eueA 279 3.39e+01 1iseA 185 3.40e+01 d.67.3.1 90691 1hn2A 159 3.42e+01 b.60.1.1 65890 1uxd 65 3.46e+01 1uxc a.35.1.5 17118 1b65A 375 3.48e+01 1b65A d.154.1.1 42020 2csbA 519 3.48e+01 2ci1A 275 3.53e+01 189l 164 3.54e+01 1l92 d.2.1.3 36960 2cvdA 198 3.59e+01 1e6mA 128 3.60e+01 3chy c.23.1.1 31039 1pba 81 3.61e+01 1pytA d.58.3.1 39067 1nw8A 319 3.62e+01 c.66.1.11 86292 2gq1A 332 3.62e+01 1o4vA 183 3.64e+01 c.23.8.1 86628 1iqzA 81 3.66e+01 d.58.1.4 66281 1lgtA 297 3.70e+01 d.32.1.3,d.32.1.3 77956,77957 1ycdA 243 3.76e+01 1ogdA 131 3.77e+01 c.133.1.1 92893 1z3eB 73 3.80e+01 1mwqA 101 3.84e+01 d.58.4.7 91481 3grx 82 3.86e+01 1aba c.47.1.1 32769 1ks8A 433 3.86e+01 a.102.1.2 77519 3ladA 476 3.94e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30573,30574,40208 180lA 164 4.00e+01 1l92 d.2.1.3 36867 1ufkA 254 4.09e+01 c.66.1.39 99340 152l 164 4.09e+01 1l92 d.2.1.3 36904 1ek8A 185 4.14e+01 1ek8A d.67.3.1 59444 1wmwA 330 4.15e+01 2f8lA 344 4.17e+01 1phr 157 4.21e+01 1dg9A c.44.1.1 32635 1wu7A 434 4.27e+01 173l 164 4.27e+01 1l92 d.2.1.3 36728 1b8bA 605 4.37e+01 1b8bA 1d2zB 153 4.39e+01 1d2zB a.77.1.2 18439 1yzhA 214 4.43e+01 1th8A 145 4.44e+01 d.122.1.3 106908 1ewsA 32 4.45e+01 1ewsA g.9.1.1 59534 1v92A 46 4.52e+01 a.5.2.3 100531 1c3pA 375 4.53e+01 1c3pA c.42.1.2 32606 1ub0A 258 4.54e+01 c.72.1.2 88394 1kzhA 555 4.54e+01 c.89.1.1 73361 1m7yA 435 4.57e+01 c.67.1.4 78761 1q7zA 566 4.58e+01 c.1.21.2,c.1.26.1 96090,96091 1jqhA 308 4.60e+01 d.144.1.7 71793 1zk7A 467 4.61e+01 1b0uA 262 4.63e+01 1b0uA c.37.1.12 32370 1dp4A 435 4.63e+01 1dp4A c.93.1.1 35710 1dlwA 116 4.65e+01 1dlyA a.1.1.1 14982 1y0hA 105 4.74e+01 1tl9A 339 4.75e+01 1ospO 257 4.76e+01 1ospO b.76.1.1 27971 174lA 164 4.76e+01 1l92 d.2.1.3 36956 170l 164 4.77e+01 1l92 d.2.1.3 36968 1w8iA 156 4.79e+01 1mfmA 153 4.84e+01 1mfmA b.1.8.1 22246 1yi8A 351 4.89e+01 1ichA 112 4.92e+01 a.77.1.2 71182 1wdyA 285 4.93e+01 1c0eA 157 5.00e+01 1dg9A c.44.1.1 32638 1wj7A 104 5.02e+01 1vj1A 363 5.07e+01 b.35.1.2,c.2.1.1 100794,100795 2adbA 148 5.10e+01 1xmpA 170 5.20e+01 1rtxA 123 5.21e+01 a.1.1.1 97827 1h3fA 432 5.25e+01 c.26.1.1,d.66.1.4 76631,76632 1ctf 74 5.32e+01 1ctf d.45.1.1 38759 192l 164 5.37e+01 1l92 d.2.1.3 36815 1v7rA 186 5.43e+01 c.51.4.1 100482 1xcbA 211 5.43e+01 a.4.5.38,c.2.1.12 109552,109553 1u11A 182 5.45e+01 c.23.8.1 107576 1o2dA 371 5.55e+01 e.22.1.2 86591 1tsg 98 5.61e+01 1tsg 1ffkB 338 5.64e+01 1ffkB b.43.3.2 25719 1eudB 396 5.66e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1lkdA 297 5.67e+01 d.32.1.3,d.32.1.3 78059,78060 1wy5A 317 5.76e+01 1ugmA 125 5.76e+01 d.15.1.3 107827 1vg5A 73 5.78e+01 2cbzA 237 5.79e+01 1d2vC 466 5.85e+01 1mhlC 113l 164 5.86e+01 1l92 d.2.1.3 36678 1yg2A 179 5.86e+01 1dv1A 449 5.90e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 191l 164 5.91e+01 1l92 d.2.1.3 36826 1j0fA 100 5.93e+01 c.47.1.14 90739 1whtA 256 5.94e+01 1ivyA c.69.1.5 34646 1f7uA 607 5.97e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 1pv9A 348 5.97e+01 c.55.2.1,d.127.1.1 95157,95158 1dv2A 452 6.04e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28238,31645,41490 1dd9A 338 6.04e+01 1dd9A e.13.1.1 43254 1g6hA 257 6.07e+01 1gajA c.37.1.12 60318 2f8mA 244 6.12e+01 1x46A 150 6.25e+01 1lx8A 55 6.28e+01 a.6.1.7 84734 2a8lA 420 6.30e+01 1gmwA 143 6.31e+01 b.107.1.1,d.58.38.1 65347,65348 1bu8A 452 6.34e+01 1gpl b.12.1.2,c.69.1.19 23647,34795 1ba9 153 6.35e+01 1mfmA b.1.8.1 22272 1pbgA 468 6.35e+01 1e70M c.1.8.4 28946 2b61A 377 6.39e+01 1whsA 255 6.40e+01 1ivyA c.69.1.5 34649 1jhdA 396 6.42e+01 b.122.1.3,c.26.1.5 66712,66713 2aqjA 538 6.57e+01 156l 164 6.60e+01 1l92 d.2.1.3 36709 1ufzA 83 6.62e+01 a.5.9.1 107821 1vpqA 273 6.65e+01 1rypL 212 6.66e+01 d.153.1.4 41880 1j6oA 268 6.68e+01 c.1.9.12 77088 1b9hA 388 6.74e+01 1b9hA c.67.1.4 34488 176lA 164 6.75e+01 1l92 d.2.1.3 36942 1s69A 124 6.79e+01 a.1.1.1 105305 1guuA 52 6.81e+01 a.4.1.3 83332 1gsoA 431 6.85e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1aeiA 315 6.86e+01 1avc a.65.1.1 18180 1rkd 309 6.90e+01 1rkd c.72.1.1 34928 1iv0A 98 6.93e+01 c.55.3.8 90706 1k8bA 52 7.11e+01 d.241.1.1 72171 1e3dA 266 7.20e+01 2frvA e.19.1.1 59188 1hra 81 7.20e+01 2nllB g.39.1.2 45130 1s98A 107 7.29e+01 b.124.1.1 105377 1h32B 138 7.32e+01 a.3.1.1 76620 1jnyA 435 7.33e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 137lA 164 7.34e+01 1l92 d.2.1.3 36791 2bkrA 212 7.36e+01 1ls1A 295 7.40e+01 a.24.13.1,c.37.1.10 78170,78171 2ceyA 306 7.55e+01 2dcnA 311 7.57e+01 1b79A 119 7.58e+01 1b79A a.81.1.1 18451 3grs 478 7.63e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30441,30442,40152 1qhhA 167 7.65e+01 1pjr c.37.1.19 32393 2tct 207 7.70e+01 2tct a.4.1.9,a.121.1.1 16063,19240 1jpnA 296 7.72e+01 a.24.13.1,c.37.1.10 67039,67040 2liv 344 7.80e+01 2liv c.93.1.1 35708 2gd9A 189 7.87e+01 1iow 306 7.88e+01 1iow c.30.1.2,d.142.1.1 31713,41481 1j6wA 175 7.95e+01 1j98A d.185.1.2 62663 1ug3A 339 8.01e+01 2aehA 369 8.02e+01 1irk 306 8.03e+01 1fmk d.144.1.7 41703 1gajA 257 8.05e+01 1gajA c.37.1.12 60416 1g65K 211 8.12e+01 d.153.1.4 41907 1ijtA 128 8.12e+01 1bfg b.42.1.1 62510 1bcsA 263 8.22e+01 1ivyA c.69.1.5 34647 1bxsA 501 8.24e+01 1bpwA c.82.1.1 35357 1k1xA 659 8.25e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1ynuA 473 8.29e+01 1ykjA 394 8.30e+01 131l 164 8.30e+01 1l92 d.2.1.3 36685 2ffjA 300 8.31e+01 1ae1A 273 8.35e+01 1bdb c.2.1.2 29943 1swyA 164 8.43e+01 1sgwA 214 8.49e+01 c.37.1.12 105541 1o7bT 98 8.53e+01 d.169.1.4 92620 1mr3F 181 8.61e+01 c.37.1.8 79422 118l 164 8.64e+01 1l92 d.2.1.3 36642 1z5oA 242 8.68e+01 164l 164 8.69e+01 1l92 d.2.1.3 36714 1pm6A 72 8.81e+01 a.6.1.7 94894 111l 164 8.84e+01 1l92 d.2.1.3 36661 1mbe 53 8.84e+01 1mbe a.4.1.3 16038 167lA 164 8.85e+01 1l92 d.2.1.3 36937 1bncA 449 8.90e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28236,31643,41488