# List of top-scoring protein chains for t04-100-30-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.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 1yfbA 59 1.94e+00 1sk7A 198 2.31e+00 a.132.1.2 105671 1xb4A 202 2.73e+00 1eceA 358 3.46e+00 1eceA c.1.8.3 28813 1kiyA 374 3.50e+00 a.128.1.5 72555 1d9tA 289 3.54e+00 1deaA 1ne7A 289 3.64e+00 c.124.1.1 91833 1oe4A 247 4.05e+00 c.18.1.3 86895 1yyqA 374 4.21e+00 1u5tC 202 4.31e+00 a.4.5.54,a.4.5.54 107688,107689 1z0kB 69 4.64e+00 1exrA 148 4.87e+00 1cll a.39.1.5 17299 2aelA 374 5.12e+00 1iuhA 198 5.14e+00 d.61.1.2 83711 1z0rA 53 5.23e+00 1cf2O 337 5.55e+00 1b7gO c.2.1.3,d.81.1.1 29994,39909 1h6fA 193 5.70e+00 b.2.5.4 70901 1y9kA 157 5.90e+00 1gqvA 135 6.08e+00 d.5.1.1 70376 1yw5A 177 6.63e+00 1cydA 244 6.73e+00 1cydA c.2.1.2 29825 1pv5A 264 6.95e+00 d.251.1.1 95150 1iwmA 186 6.96e+00 b.125.1.2 83758 1nnhA 294 7.69e+00 d.104.1.1 92005 2fhfA 1083 7.92e+00 1ignA 246 8.10e+00 1ignA a.4.1.6,a.4.1.6 16048,16049 1hi2A 135 8.18e+00 7rsa d.5.1.1 61057 1pmzA 86 8.19e+00 a.39.1.10 104195 1mgpA 313 8.82e+00 c.119.1.1 79098 2bivA 243 9.65e+00 1lmzA 187 9.69e+00 a.96.1.4 74037 1agi 125 1.06e+01 7rsa d.5.1.1 37303 1exqA 154 1.06e+01 1b9dA c.55.3.2 33646 1jdlA 121 1.07e+01 a.3.1.1 66557 1zz1A 369 1.09e+01 1auvA 311 1.11e+01 1auvA c.30.1.5,d.142.1.3 31723,41558 2ffjA 300 1.11e+01 1jmxA 494 1.16e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 1qipA 183 1.24e+01 1qipA d.32.1.1 38470 1mkmA 249 1.27e+01 a.4.5.33,d.110.2.2 79242,79243 2bbrA 195 1.29e+01 1wy9A 147 1.30e+01 2f3yA 148 1.31e+01 1jpzA 473 1.35e+01 a.104.1.1 67069 1bu7A 455 1.37e+01 1bu7A a.104.1.1 18937 1ektA 53 1.38e+01 1ektA b.129.1.3 38764 1za0A 275 1.43e+01 1oz2A 331 1.45e+01 b.34.9.3,b.34.9.3,b.34.9.3 93781,93782,93783 1f02T 66 1.49e+01 1f02T j.67.1.1 46360 1tueA 212 1.50e+01 c.37.1.20 107323 1s6yA 450 1.50e+01 c.2.1.5,d.162.1.2 105314,105315 2bnfB 241 1.55e+01 1ylkA 172 1.56e+01 1k9uA 78 1.57e+01 a.39.1.10 84348 1i0dA 332 1.58e+01 1pscA c.1.9.3 61487 1utcA 363 1.61e+01 a.118.1.4,b.69.6.1 99914,99915 1x0rA 249 1.62e+01 1nksA 194 1.63e+01 1nksA c.37.1.1 31886 1hdoA 206 1.64e+01 1he2A c.2.1.2 60965 1k99A 99 1.64e+01 a.21.1.1 68341 1vcbC 160 1.70e+01 1vcbC b.3.3.1 22535 1ls6A 295 1.72e+01 c.37.1.5 91115 1ywfA 296 1.73e+01 1npiA 61 1.75e+01 g.3.7.1 80685 2f6eA 127 1.75e+01 1gppA 237 1.77e+01 b.86.1.2 76262 1zs9A 261 1.79e+01 1tfzA 424 1.80e+01 d.32.1.3,d.32.1.3 106886,106887 1fjgK 129 1.84e+01 1fjfK c.55.4.1 33733 1ggzA 148 1.88e+01 a.39.1.5 70176 2abbA 364 1.93e+01 2erfA 209 1.97e+01 1a6m 151 2.01e+01 1a6m a.1.1.2 15018 1g4yR 148 2.01e+01 1cll a.39.1.5 60252 2g0uA 92 2.02e+01 1vypX 364 2.03e+01 c.1.4.1 108905 1wkaA 147 2.07e+01 1qqyA 130 2.08e+01 3lzt d.2.1.2 36586 1b7dA 61 2.10e+01 1aho g.3.7.1 44139 1ob8A 135 2.10e+01 2ew8A 249 2.12e+01 1qkkA 155 2.12e+01 1dbwA c.23.1.1 31104 1orsC 132 2.14e+01 f.14.1.1 87353 2f1sA 186 2.17e+01 1ovlA 271 2.19e+01 a.123.1.1 87455 1bzpA 153 2.19e+01 1a6m a.1.1.2 15020 1o2dA 371 2.21e+01 e.22.1.2 86591 1zklA 353 2.22e+01 1bkdS 439 2.23e+01 1bkdS a.117.1.1 19111 1vyrA 364 2.26e+01 c.1.4.1 108906 1gt1A 159 2.31e+01 b.60.1.1 90515 1k1xA 659 2.31e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 2f6hX 419 2.34e+01 1jq0A 84 2.34e+01 h.3.2.1 71786 1dzkA 157 2.34e+01 1obpA b.60.1.1 27096 1q06A 135 2.37e+01 a.6.1.3 95493 2jdxA 385 2.40e+01 1jdw d.126.1.2 41139 1q6cA 495 2.44e+01 c.1.8.1 95970 1mlg 154 2.49e+01 1a6m a.1.1.2 15104 2b7kA 200 2.49e+01 1obpA 159 2.51e+01 1obpA b.60.1.1 27092 3thiA 371 2.52e+01 2thiA c.94.1.1 35792 1hzyA 332 2.57e+01 1pscA c.1.9.3 61468 1v3hA 495 2.58e+01 c.1.8.1 108303 1jsf 130 2.65e+01 3lzt d.2.1.2 36410 1dqzA 280 2.66e+01 1dqyA c.69.1.3 34638 1gvoA 364 2.69e+01 c.1.4.1 76357 1mpp 361 2.71e+01 2rmpA b.50.1.2 26856 1lz1 130 2.74e+01 3lzt d.2.1.2 36415 1h61A 364 2.74e+01 1oyc c.1.4.1 60657 1w85A 368 2.79e+01 1wdpA 495 2.81e+01 1mym 154 2.83e+01 1a6m a.1.1.2 15054 1xw8A 252 2.89e+01 2abqA 306 2.90e+01 1xzoA 174 2.91e+01 1mlo 154 2.91e+01 1a6m a.1.1.2 15085 1hn2A 159 2.91e+01 b.60.1.1 65890 1mll 154 2.91e+01 1a6m a.1.1.2 15057 2carA 196 2.92e+01 1mod 154 2.92e+01 1a6m a.1.1.2 15107 1j7dA 145 2.94e+01 1jatB d.20.1.1 62680 103m 154 2.94e+01 1a6m a.1.1.2 15124 1geqA 248 2.97e+01 2tysA c.1.2.4 28589 1eiwA 111 3.03e+01 1eiwA c.23.3.1 31130 1b0nA 111 3.04e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1byb 495 3.07e+01 1byb c.1.8.1 28790 1pu1A 94 3.08e+01 d.266.1.1 104307 1mbmA 198 3.10e+01 b.47.1.3 78916 1dseA 292 3.11e+01 1ryc a.93.1.1 59130 1z6oM 191 3.11e+01 1f0nA 285 3.12e+01 1dqyA c.69.1.3 34636 2mgb 154 3.12e+01 1a6m a.1.1.2 15102 2if1 126 3.12e+01 2if1 d.64.1.1 39547 1vchA 175 3.12e+01 1psrA 100 3.16e+01 1psrA a.39.1.2 17180 2bzuA 181 3.18e+01 2mgg 154 3.19e+01 1a6m a.1.1.2 15069 1u7pA 164 3.20e+01 2eutA 294 3.22e+01 1pii 452 3.23e+01 1pii c.1.2.4,c.1.2.4 28559,28563 1icfI 65 3.24e+01 1icfI g.28.1.1 44958 1jdw 423 3.28e+01 1jdw d.126.1.2 41129 2spl 154 3.30e+01 1a6m a.1.1.2 15047 1vfsA 386 3.35e+01 b.49.2.2,c.1.6.1 108584,108585 1avaA 403 3.37e+01 1jdc b.71.1.1,c.1.8.1 27797,28784 1amy 403 3.40e+01 1jdc b.71.1.1,c.1.8.1 27799,28786 1inlA 296 3.46e+01 c.66.1.17 66220 1vr5A 547 3.50e+01 1bm9A 122 3.51e+01 1bm9A a.4.5.7 16116 3htsB 102 3.52e+01 2hts a.4.5.22 16175 2bn5A 33 3.52e+01 2bzvA 181 3.52e+01 1v25A 541 3.53e+01 e.23.1.1 108275 2a6hE 99 3.56e+01 1nvvS 481 3.58e+01 a.117.1.1 86279 1lm8V 160 3.62e+01 b.3.3.1 74035 1y0nA 78 3.63e+01 1o0pA 104 3.68e+01 d.58.7.1 86535 2bsxA 253 3.68e+01 1cojA 212 3.68e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1wzcA 249 3.68e+01 1y81A 138 3.69e+01 1y4tA 322 3.70e+01 1sv0C 82 3.70e+01 a.60.1.1 106037 1us0A 316 3.81e+01 c.1.7.1 99850 1jdrA 294 3.82e+01 1ryc a.93.1.1 62908 1v93A 296 3.85e+01 c.1.23.1 100532 2frfA 153 3.89e+01 1x3aA 100 3.90e+01 1lrzA 426 3.91e+01 a.2.7.4,d.108.1.4,d.108.1.4 78167,78168,78169 1m65A 245 3.91e+01 c.6.3.1 84847 1top 162 3.97e+01 1ncx a.39.1.5 17223 1fcyA 236 3.99e+01 2lbd a.123.1.1 19282 1lq9A 112 3.99e+01 d.58.4.3 78129 1z53A 294 3.99e+01 1avsA 90 4.01e+01 1cll a.39.1.5 17226 1tp9A 162 4.02e+01 1zbyA 294 4.02e+01 1mlwA 301 4.03e+01 d.178.1.1 79289 2b30A 301 4.04e+01 1pn0A 665 4.05e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 2bneA 241 4.07e+01 1yuzA 202 4.09e+01 1l4dB 122 4.11e+01 d.15.5.1 77684 1v58A 241 4.11e+01 c.47.1.9,d.17.3.1 108371,108372 1ek1A 554 4.13e+01 1cr6B c.69.1.11,c.108.1.2 34685,43335 1oi1A 221 4.13e+01 b.34.9.3,b.34.9.3 87037,87038 1gntA 553 4.14e+01 e.26.1.1 70290 1e2uA 553 4.14e+01 1e1dA e.26.1.1 43362 1gwiA 411 4.18e+01 a.104.1.1 76364 2a65A 519 4.19e+01 1jpc 109 4.19e+01 1b2pA b.78.1.1 27986 2agtA 319 4.20e+01 1tn4 159 4.21e+01 1ncx a.39.1.5 17248 1bjt 793 4.27e+01 1bjt e.11.1.1 43249 1seiA 130 4.28e+01 1seiA d.140.1.1 41463 1wzlA 585 4.29e+01 1oq9A 363 4.30e+01 a.25.1.2 87257 1o6dA 163 4.31e+01 c.116.1.3 92567 1on2A 142 4.32e+01 a.4.5.24,a.76.1.1 87103,87104 1dwtA 153 4.35e+01 1a6m a.1.1.2 15190 1m45A 148 4.37e+01 a.39.1.5 78598 1r8oA 96 4.40e+01 b.42.4.1 104852 1umdA 367 4.42e+01 c.36.1.11 99599 1ug7A 128 4.45e+01 a.24.24.1 107824 1gjnA 153 4.52e+01 a.1.1.2 70191 1kcbA 340 4.64e+01 b.6.1.3,b.6.1.3 90951,90952 2fnaA 357 4.68e+01 1vdeA 454 4.69e+01 1vdeA b.86.1.2,d.95.2.2,d.95.2.2 28378,40581,40582 2fbqA 235 4.80e+01 2aqaA 63 4.87e+01 1ht6A 405 4.91e+01 b.71.1.1,c.1.8.1 83629,83630 2bw4A 340 4.92e+01 1wtaA 275 4.94e+01 1t5oA 351 4.97e+01 c.124.1.5 106459 1rovA 857 4.99e+01 a.119.1.1,b.12.1.1 97674,97675 1nw1A 429 4.99e+01 d.144.1.8 86286 1nzjA 298 4.99e+01 c.26.1.1 92377 1fohA 664 5.00e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1gqzA 274 5.07e+01 d.21.1.1,d.21.1.1 83311,83312 1nif 340 5.07e+01 1nif b.6.1.3,b.6.1.3 23048,23049 1s9uA 207 5.09e+01 a.184.1.1 105390 1wz3A 96 5.12e+01 1y0vH 146 5.19e+01 1dmgA 225 5.23e+01 1dmgA c.22.1.1 31036 1yewC 289 5.29e+01 1xbrA 184 5.35e+01 1xbrA b.2.5.4 22458 1bwzA 274 5.36e+01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1a8vA 121 5.37e+01 1a62 a.140.3.1,b.40.4.5 64712,64713 1mw9X 592 5.39e+01 e.10.1.1 91480 1iujA 106 5.43e+01 d.58.4.5 90701 2a2pA 129 5.47e+01 1mvcA 240 5.51e+01 a.123.1.1 79499 1zvtA 256 5.61e+01 1cy5A 97 5.62e+01 1cy5A a.77.1.3 18430 1iw7E 99 5.64e+01 a.143.1.1 71476 1dxsA 80 5.68e+01 1cokA a.60.1.2 17944 1n7kA 234 5.79e+01 c.1.10.1 85374 1whzA 70 5.80e+01 1djtA 64 5.81e+01 1aho g.3.7.1 44132 1pwmA 316 5.82e+01 c.1.7.1 95231 2a4dA 160 5.84e+01 1regX 122 5.85e+01 1regX d.58.27.1 39406 1dvpA 220 5.89e+01 1dvpA a.118.9.2,g.50.1.1 19216,45358 1f3mC 297 5.91e+01 1hcl d.144.1.7 41677 2bgkA 278 5.96e+01 1rxqA 178 5.97e+01 a.213.1.1 105118 1u24A 337 6.02e+01 1fp2A 352 6.05e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1z64A 26 6.10e+01 1mzgA 146 6.10e+01 d.224.1.1 79696 1m0kA 262 6.13e+01 f.13.1.1 78344 1vpmA 169 6.14e+01 1c3wA 222 6.21e+01 1c3wA f.13.1.1 43405 1lktA 104 6.21e+01 1lktA b.90.1.1 28398 1fjnA 39 6.26e+01 1fjnA g.3.7.3 44171 1cs1A 386 6.28e+01 1ibjA c.67.1.3 34399 1dmtA 696 6.31e+01 1dmtA d.92.1.4 40296 1wzzA 334 6.31e+01 2a6sA 84 6.34e+01 1ub1A 133 6.42e+01 d.10.1.3 99140 1dp4A 435 6.45e+01 1dp4A c.93.1.1 35710 2gkeA 274 6.45e+01 2pil 159 6.51e+01 2pil d.24.1.1 38376 2fdbM 164 6.53e+01 2ceyA 306 6.54e+01 1j8bA 112 6.55e+01 d.222.1.1 77101 1xseA 295 6.56e+01 1hhsA 664 6.59e+01 1hi0P e.8.1.6 61045 1s2oA 244 6.60e+01 1f1uA 323 6.61e+01 d.32.1.3,d.32.1.3 83200,83201 1xvsA 126 6.62e+01 1dk8A 147 6.63e+01 1agrE a.91.1.1 18548 1uvjA 664 6.66e+01 e.8.1.6 100045 1cby 259 6.70e+01 1cby d.103.1.1 40705 1b79A 119 6.71e+01 1b79A a.81.1.1 18451 1xqoA 256 6.73e+01 1wa8B 95 6.78e+01 2aaxA 275 6.79e+01 1f9zA 135 6.81e+01 1qipA d.32.1.1 38484 2ct9A 208 6.82e+01 1wybA 392 6.84e+01 1g6oA 330 6.91e+01 1g6oA c.37.1.11 32430 1xi7A 61 6.95e+01 1oshA 232 7.04e+01 a.123.1.1 93496 1ucnA 152 7.08e+01 d.58.6.1 99183 1wmhA 89 7.13e+01 1pq9A 253 7.14e+01 a.123.1.1 95004 1uw4A 91 7.18e+01 d.58.7.4 100071 1jmmA 377 7.18e+01 b.30.6.1 71749 1vp4A 425 7.24e+01 1oyeA 1049 7.24e+01 d.58.44.1,d.58.44.1,d.58.44.1,d.58.44.1,d.225.1.1,d.225.1.1,f.35.1.1,f.35.1.1 87587,87588,87589,87590,87591,87592,87593,87594 1qd9A 124 7.28e+01 1qu9A d.79.1.1 39758 1lxiA 139 7.33e+01 g.17.1.2 84735 1ryt 190 7.34e+01 1ryt a.25.1.1,g.41.5.1 16646,45245 1lkoA 191 7.42e+01 a.25.1.1,g.41.5.1 78063,78064 2cz1A 206 7.52e+01 1i50B 1224 7.53e+01 e.29.1.1 61755 1a62 130 7.59e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1y6zA 263 7.60e+01 1mkrA 294 7.61e+01 a.93.1.1 84997 2a8yA 270 7.65e+01 1yhvA 297 7.66e+01 2arzA 247 7.70e+01 1snrA 341 7.72e+01 b.6.1.3,b.6.1.3 105823,105824 1yhuB 144 7.80e+01 1apxA 249 7.82e+01 1ryc a.93.1.1 18669 2booA 247 7.84e+01 2gs5A 198 7.86e+01 1twuA 139 7.93e+01 d.32.1.8 107413 2cwaA 263 7.93e+01 1aerA 205 7.96e+01 1aerA d.166.1.1 42249 1yemA 179 8.07e+01 1q7fA 286 8.08e+01 b.68.9.1 96036 1u55A 188 8.09e+01 d.278.1.1 107677 1ff9A 450 8.12e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1xtmA 175 8.18e+01 1st9A 143 8.21e+01 c.47.1.10 98987 2afaA 425 8.22e+01 1j9qA 341 8.23e+01 1nif b.6.1.3,b.6.1.3 62765,62766 1xyiA 66 8.23e+01 1ngnA 155 8.31e+01 a.96.1.2 85697 1r8eA 278 8.33e+01 a.6.1.3,d.60.1.1 104843,104844 1r1hA 696 8.34e+01 d.92.1.4 104756 1f20A 435 8.35e+01 b.43.4.1,c.25.1.4 64932,64933 1dbwA 126 8.38e+01 1dbwA c.23.1.1 31095 2cmwA 310 8.45e+01 2etgA 296 8.45e+01 2ftwA 521 8.47e+01 2bduA 297 8.47e+01 1gmeA 151 8.49e+01 b.15.1.1 65305 1tu1A 148 8.50e+01 d.107.1.3 107316 1bn7A 294 8.50e+01 1bn6A c.69.1.8 34677 1tc5A 194 8.53e+01 c.110.1.1 106752 1vm8A 534 8.56e+01 1xdpA 687 8.59e+01 1woyA 500 8.68e+01 1mkiA 330 8.73e+01 e.3.1.2 84994 2boqA 331 8.73e+01 2ahjA 206 8.82e+01 2ahjA d.149.1.1 41772 1kepA 348 8.83e+01 c.2.1.2 68536 2cb5A 453 8.86e+01 3gcb d.3.1.1 37035 1zsqA 528 8.91e+01 1oc2A 348 8.95e+01 c.2.1.2 92765 1wnyA 186 8.97e+01 2aclB 244 8.99e+01