# List of top-scoring protein chains for t04-100-30-alpha-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 1u5tC 202 9.98e-01 a.4.5.54,a.4.5.54 107688,107689 1yfbA 59 1.50e+00 1z53A 294 3.43e+00 1xb4A 202 3.47e+00 1zbyA 294 3.60e+00 2eutA 294 3.61e+00 1pv5A 264 3.68e+00 d.251.1.1 95150 1dseA 292 3.81e+00 1ryc a.93.1.1 59130 1eceA 358 4.00e+00 1eceA c.1.8.3 28813 1gqvA 135 4.63e+00 d.5.1.1 70376 1hi2A 135 4.85e+00 7rsa d.5.1.1 61057 1ne7A 289 5.33e+00 c.124.1.1 91833 1oz2A 331 5.82e+00 b.34.9.3,b.34.9.3,b.34.9.3 93781,93782,93783 2bivA 243 5.87e+00 1jdrA 294 6.32e+00 1ryc a.93.1.1 62908 1iuhA 198 6.43e+00 d.61.1.2 83711 1mkrA 294 6.64e+00 a.93.1.1 84997 1oe4A 247 6.81e+00 c.18.1.3 86895 1kiyA 374 7.13e+00 a.128.1.5 72555 2aelA 374 7.38e+00 1d9tA 289 7.60e+00 1deaA 1hzyA 332 8.36e+00 1pscA c.1.9.3 61468 1i0dA 332 8.51e+00 1pscA c.1.9.3 61487 1yyqA 374 8.89e+00 1l4dB 122 8.99e+00 d.15.5.1 77684 1auvA 311 9.09e+00 1auvA c.30.1.5,d.142.1.3 31723,41558 2abbA 364 9.95e+00 1y9kA 157 1.00e+01 1qqyA 130 1.01e+01 3lzt d.2.1.2 36586 1r1hA 696 1.02e+01 d.92.1.4 104756 1laxA 370 1.02e+01 c.94.1.1 84576 2bbrA 195 1.06e+01 1bzpA 153 1.12e+01 1a6m a.1.1.2 15020 1mgpA 313 1.13e+01 c.119.1.1 79098 1nnhA 294 1.14e+01 d.104.1.1 92005 1z0rA 53 1.20e+01 1dmtA 696 1.21e+01 1dmtA d.92.1.4 40296 2ew8A 249 1.24e+01 1z0kB 69 1.26e+01 1ls6A 295 1.27e+01 c.37.1.5 91115 1jsf 130 1.27e+01 3lzt d.2.1.2 36410 1zz1A 369 1.28e+01 1lz1 130 1.28e+01 3lzt d.2.1.2 36415 1iwmA 186 1.30e+01 b.125.1.2 83758 1cf2O 337 1.32e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 2frfA 153 1.32e+01 1zs9A 261 1.33e+01 1jdlA 121 1.40e+01 a.3.1.1 66557 1a6m 151 1.41e+01 1a6m a.1.1.2 15018 4mbp 370 1.46e+01 4mbp c.94.1.1 35777 1o0pA 104 1.49e+01 d.58.7.1 86535 1dwtA 153 1.50e+01 1a6m a.1.1.2 15190 1e7wA 291 1.56e+01 c.2.1.2 59373 1mkmA 249 1.61e+01 a.4.5.33,d.110.2.2 79242,79243 2f1sA 186 1.61e+01 1vyrA 364 1.62e+01 c.1.4.1 108906 1q6cA 495 1.62e+01 c.1.8.1 95970 1v3hA 495 1.63e+01 c.1.8.1 108303 1wkaA 147 1.69e+01 1vm8A 534 1.72e+01 103m 154 1.72e+01 1a6m a.1.1.2 15124 1gjnA 153 1.73e+01 a.1.1.2 70191 2bf6A 449 1.73e+01 1exqA 154 1.74e+01 1b9dA c.55.3.2 33646 1f02T 66 1.74e+01 1f02T j.67.1.1 46360 1x0rA 249 1.75e+01 1wdpA 495 1.79e+01 1anf 370 1.80e+01 4mbp c.94.1.1 35776 1byb 495 1.81e+01 1byb c.1.8.1 28790 1mod 154 1.83e+01 1a6m a.1.1.2 15107 2fdbM 164 1.85e+01 1st9A 143 1.86e+01 c.47.1.10 98987 1regX 122 1.88e+01 1regX d.58.27.1 39406 1vypX 364 1.89e+01 c.1.4.1 108905 1u7pA 164 1.91e+01 1o2dA 371 1.93e+01 e.22.1.2 86591 1g4wR 383 1.97e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1gvoA 364 2.02e+01 c.1.4.1 76357 2f6eA 127 2.03e+01 1dk8A 147 2.08e+01 1agrE a.91.1.1 18548 1mlg 154 2.11e+01 1a6m a.1.1.2 15104 2hts 88 2.12e+01 2hts a.4.5.22 16174 1jpc 109 2.13e+01 1b2pA b.78.1.1 27986 1nksA 194 2.14e+01 1nksA c.37.1.1 31886 1mw9X 592 2.19e+01 e.10.1.1 91480 2mgb 154 2.21e+01 1a6m a.1.1.2 15102 2mgg 154 2.22e+01 1a6m a.1.1.2 15069 1mll 154 2.22e+01 1a6m a.1.1.2 15057 2cmwA 310 2.23e+01 2f9sA 151 2.24e+01 2spl 154 2.25e+01 1a6m a.1.1.2 15047 1mlo 154 2.27e+01 1a6m a.1.1.2 15085 1fjnA 39 2.33e+01 1fjnA g.3.7.3 44171 1qipA 183 2.36e+01 1qipA d.32.1.1 38470 2ghsA 326 2.36e+01 1fohA 664 2.38e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1pii 452 2.41e+01 1pii c.1.2.4,c.1.2.4 28559,28563 1ovlA 271 2.41e+01 a.123.1.1 87455 1mym 154 2.43e+01 1a6m a.1.1.2 15054 1b0nA 111 2.44e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1oi1A 221 2.46e+01 b.34.9.3,b.34.9.3 87037,87038 1lm8V 160 2.49e+01 b.3.3.1 74035 1pn0A 665 2.50e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1za0A 275 2.51e+01 1oshA 232 2.57e+01 a.123.1.1 93496 1cydA 244 2.61e+01 1cydA c.2.1.2 29825 1k99A 99 2.64e+01 a.21.1.1 68341 1fmcA 255 2.70e+01 1cydA c.2.1.2 29856 1yj7A 171 2.70e+01 2h1tA 188 2.70e+01 1xzoA 174 2.71e+01 1omp 370 2.76e+01 4mbp c.94.1.1 35778 1h61A 364 2.76e+01 1oyc c.1.4.1 60657 1yaxA 153 2.77e+01 1npiA 61 2.82e+01 g.3.7.1 80685 2abqA 306 2.87e+01 1seiA 130 2.87e+01 1seiA d.140.1.1 41463 1p5jA 372 2.90e+01 c.79.1.1 104067 1fcyA 236 2.97e+01 2lbd a.123.1.1 19282 2a6hE 99 2.98e+01 2b7kA 200 3.02e+01 1xnfA 275 3.07e+01 1twuA 139 3.07e+01 d.32.1.8 107413 1utcA 363 3.11e+01 a.118.1.4,b.69.6.1 99914,99915 1y4tA 322 3.11e+01 1tdhA 364 3.14e+01 a.156.1.2,b.113.1.1,g.39.1.8 106772,106773,106774 1r8oA 96 3.18e+01 b.42.4.1 104852 1lmzA 187 3.20e+01 a.96.1.4 74037 1jmxA 494 3.20e+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 1m65A 245 3.21e+01 c.6.3.1 84847 1zklA 353 3.21e+01 1pq9A 253 3.22e+01 a.123.1.1 95004 1bjt 793 3.26e+01 1bjt e.11.1.1 43249 1yw5A 177 3.27e+01 1dp4A 435 3.31e+01 1dp4A c.93.1.1 35710 2bcqA 335 3.33e+01 1xw8A 252 3.35e+01 1ob8A 135 3.36e+01 2bneA 241 3.45e+01 1t4wA 196 3.47e+01 b.2.5.2 106427 2gz4A 207 3.48e+01 1oq9A 363 3.52e+01 a.25.1.2 87257 2bsxA 253 3.54e+01 1z2lA 423 3.55e+01 1ff9A 450 3.55e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 2arpA 116 3.55e+01 1q7fA 286 3.65e+01 b.68.9.1 96036 1fjgK 129 3.66e+01 1fjfK c.55.4.1 33733 1b7dA 61 3.67e+01 1aho g.3.7.1 44139 1xvxA 312 3.68e+01 1nvvS 481 3.70e+01 a.117.1.1 86279 1ucnA 152 3.70e+01 d.58.6.1 99183 1ylkA 172 3.72e+01 1tueA 212 3.78e+01 c.37.1.20 107323 1bkdS 439 3.81e+01 1bkdS a.117.1.1 19111 1tfzA 424 3.81e+01 d.32.1.3,d.32.1.3 106886,106887 2b30A 301 3.84e+01 1gt1A 159 3.84e+01 b.60.1.1 90515 1uw4A 91 3.85e+01 d.58.7.4 100071 1hdoA 206 3.87e+01 1he2A c.2.1.2 60965 1px5A 349 3.90e+01 a.160.1.2,d.218.1.6 95277,95278 2es7A 142 3.92e+01 3ertA 261 3.93e+01 3erdA a.123.1.1 19292 1xpcA 248 3.94e+01 1vcc 77 3.95e+01 1vcc d.121.1.1 41092 1hyoA 421 3.96e+01 1qcnA b.34.8.1,d.177.1.1 59001,59002 1wnyA 186 3.97e+01 1vr5A 547 3.98e+01 1obpA 159 3.98e+01 1obpA b.60.1.1 27092 2d1yA 256 4.00e+01 1s2oA 244 4.00e+01 1eiwA 111 4.02e+01 1eiwA c.23.3.1 31130 1dmgA 225 4.07e+01 1dmgA c.22.1.1 31036 1s9uA 207 4.07e+01 a.184.1.1 105390 1hn2A 159 4.14e+01 b.60.1.1 65890 1xtlA 175 4.19e+01 1gqzA 274 4.22e+01 d.21.1.1,d.21.1.1 83311,83312 1x84A 189 4.27e+01 1wlgA 299 4.33e+01 1ja9A 274 4.35e+01 c.2.1.2 62817 1jug 125 4.36e+01 3lzt d.2.1.2 36587 2bgzA 299 4.38e+01 1h8gA 95 4.45e+01 b.109.1.1 65735 1vfsA 386 4.46e+01 b.49.2.2,c.1.6.1 108584,108585 2bnfB 241 4.47e+01 1ywfA 296 4.51e+01 1wjvA 79 4.59e+01 1lktA 104 4.60e+01 1lktA b.90.1.1 28398 1uc7A 125 4.61e+01 c.47.1.1 99163 1mzgA 146 4.62e+01 d.224.1.1 79696 2erfA 209 4.64e+01 1ug7A 128 4.67e+01 a.24.24.1 107824 1o5iA 249 4.71e+01 c.2.1.2 92499 2gaiA 633 4.71e+01 2fwhA 134 4.72e+01 1ois 223 4.74e+01 1a36A e.15.1.1 43267 1wi9A 72 4.75e+01 1j8bA 112 4.76e+01 d.222.1.1 77101 1w9yA 319 4.79e+01 1xqoA 256 4.84e+01 1vcbC 160 4.85e+01 1vcbC b.3.3.1 22535 1vl8A 267 4.86e+01 c.2.1.2 108733 1j7dA 145 4.87e+01 1jatB d.20.1.1 62680 1whzA 70 4.91e+01 1cojA 212 4.93e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 3htsB 102 4.95e+01 2hts a.4.5.22 16175 1wk8A 194 4.98e+01 1sv0C 82 4.98e+01 a.60.1.1 106037 1atiA 505 5.00e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 1t0tV 248 5.03e+01 d.58.4.10 106229 1orsC 132 5.05e+01 f.14.1.1 87353 1wkqA 164 5.05e+01 c.97.1.2 109393 1nzjA 298 5.10e+01 c.26.1.1 92377 1lmq 129 5.13e+01 3lzt d.2.1.2 36588 2aaxA 275 5.15e+01 1top 162 5.16e+01 1ncx a.39.1.5 17223 1vp4A 425 5.18e+01 1vcdA 126 5.20e+01 1r6xA 395 5.23e+01 b.122.1.3,c.26.1.5 97167,97168 1fc4A 401 5.25e+01 1bs0A c.67.1.4 59760 1yqgA 263 5.29e+01 1icpA 376 5.29e+01 1oyc c.1.4.1 62270 1i8oA 114 5.32e+01 1ycc a.3.1.1 61979 1sk7A 198 5.33e+01 a.132.1.2 105671 1p0zA 131 5.34e+01 d.110.6.1 93882 1o26A 232 5.37e+01 d.207.1.1 86566 1xseA 295 5.38e+01 3thiA 371 5.40e+01 2thiA c.94.1.1 35792 1g8fA 511 5.43e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1wz3A 96 5.43e+01 1umdA 367 5.46e+01 c.36.1.11 99599 2b95A 106 5.47e+01 1q7bA 244 5.47e+01 c.2.1.2 96026 1icfI 65 5.54e+01 1icfI g.28.1.1 44958 1lq9A 112 5.56e+01 d.58.4.3 78129 1pvmA 184 5.59e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1sqnA 261 5.63e+01 a.123.1.1 105944 1t5oA 351 5.66e+01 c.124.1.5 106459 1cs1A 386 5.66e+01 1ibjA c.67.1.3 34399 1q1uA 144 5.67e+01 b.42.1.1 95608 2aclB 244 5.71e+01 1udzA 182 5.73e+01 b.51.1.1 99239 1vd2A 89 5.76e+01 d.15.2.2 108517 1xsnA 335 5.77e+01 2bt6A 108 5.78e+01 1yn8A 59 5.82e+01 1zkrA 153 5.83e+01 1wy9A 147 5.84e+01 1g5aA 628 5.84e+01 b.71.1.1,c.1.8.1 65152,65153 2fiyA 309 5.86e+01 2f06A 144 5.87e+01 1jf3A 147 5.92e+01 a.1.1.2 71642 1ignA 246 5.93e+01 1ignA a.4.1.6,a.4.1.6 16048,16049 1v93A 296 5.95e+01 c.1.23.1 100532 1x3aA 100 5.96e+01 1y81A 138 5.98e+01 1dp0A 1023 5.99e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 22073,22074,23722,24346,28845 2arzA 247 5.99e+01 1qtnA 164 6.05e+01 1pauA c.17.1.1 30999 1a79A 171 6.05e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1dzkA 157 6.05e+01 1obpA b.60.1.1 27096 1emvB 134 6.05e+01 1bxiB d.4.1.1 37135 1vr0A 247 6.05e+01 1xtmA 175 6.06e+01 1jmmA 377 6.06e+01 b.30.6.1 71749 2bn5A 33 6.08e+01 1iw7E 99 6.10e+01 a.143.1.1 71476 1okrA 123 6.18e+01 a.4.5.39 93269 2a65A 519 6.20e+01 1jv1A 505 6.24e+01 c.68.1.5 71892 1jz8A 1023 6.25e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 67830,67831,67832,67833,67834 1zvtA 256 6.28e+01 2cwaA 263 6.28e+01 1x9mA 698 6.29e+01 1ub1A 133 6.34e+01 d.10.1.3 99140 2aukA 190 6.35e+01 1rztA 331 6.35e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 1wp5A 323 6.36e+01 1x7yA 400 6.40e+01 1b25A 619 6.41e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 2afaA 425 6.44e+01 1b4pA 217 6.49e+01 a.45.1.1,c.47.1.5 83158,83159 1w94A 156 6.49e+01 1jq0A 84 6.53e+01 h.3.2.1 71786 1eaiC 61 6.53e+01 1eaiC g.22.1.1 44894 2ffjA 300 6.55e+01 1sr7A 259 6.59e+01 a.123.1.1 105957 1gpr 162 6.61e+01 1gpr b.84.3.1 28267 1fr2B 134 6.64e+01 d.4.1.1 83257 2cvxA 888 6.65e+01 1tif 78 6.66e+01 1tif d.15.8.1 37836 1vlmA 219 6.70e+01 c.66.1.41 108836 1bwzA 274 6.70e+01 1bwzA d.21.1.1,d.21.1.1 38337,38338 1mbmA 198 6.73e+01 b.47.1.3 78916 1xvsA 126 6.77e+01 1k9uA 78 6.78e+01 a.39.1.10 84348 1afrA 345 6.79e+01 1afrA a.25.1.2 16805 2frnA 278 6.83e+01 1s9pA 227 6.88e+01 a.123.1.1 105384 1vchA 175 6.89e+01 1byi 224 6.93e+01 1byi c.37.1.10 32199 2aqaA 63 6.95e+01 1pmzA 86 6.99e+01 a.39.1.10 104195 2bfdA 400 7.07e+01 1ayfA 105 7.08e+01 1ayfA d.15.4.1 37684 1mwmA 320 7.08e+01 c.55.1.1,c.55.1.1 79580,79581 1q06A 135 7.12e+01 a.6.1.3 95493 2gs5A 198 7.12e+01 1o50A 157 7.14e+01 d.37.1.1,d.37.1.1 92478,92479 1dxsA 80 7.14e+01 1cokA a.60.1.2 17944 1ytvA 366 7.23e+01 1bm9A 122 7.25e+01 1bm9A a.4.5.7 16116 1t7pA 698 7.32e+01 1t7pA c.55.3.5,e.8.1.1 33712,43005 1k1xA 659 7.34e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1wmhA 89 7.35e+01 1lm8C 96 7.36e+01 d.42.1.1 74034 1i7nA 309 7.39e+01 c.30.1.5,d.142.1.3 83681,83682 2gkeA 274 7.39e+01 1wybA 392 7.40e+01 1mkiA 330 7.41e+01 e.3.1.2 84994 2g09A 297 7.41e+01 1lxiA 139 7.44e+01 g.17.1.2 84735 1zrn 232 7.49e+01 1qq5A c.108.1.1 43323 1wzoA 246 7.62e+01 1wycA 392 7.64e+01 1v58A 241 7.64e+01 c.47.1.9,d.17.3.1 108371,108372 1s8nA 205 7.69e+01 c.23.1.1 105374 2bduA 297 7.71e+01 1ihkA 174 7.72e+01 1bfg b.42.1.1 62384 1zu4A 320 7.73e+01 1mroB 442 7.78e+01 1mroB a.89.1.1,d.58.31.2 18531,39449 1hbnB 442 7.78e+01 1mroB a.89.1.1,d.58.31.2 60900,60901 1kb0A 677 7.79e+01 a.3.1.6,b.70.1.1 68378,68379 1owcA 427 7.86e+01 a.103.1.1 104039 1j9qA 341 7.87e+01 1nif b.6.1.3,b.6.1.3 62765,62766 1j96A 323 7.88e+01 c.1.7.1 71616 1mvcA 240 7.88e+01 a.123.1.1 79499 1dleA 298 7.95e+01 1dleA b.47.1.2 26312 1r8eA 278 7.96e+01 a.6.1.3,d.60.1.1 104843,104844 1gefA 123 7.98e+01 1gefA c.52.1.18 60465 1ngnA 155 8.07e+01 a.96.1.2 85697 1nkiA 135 8.08e+01 d.32.1.2 91941 1lqpA 135 8.10e+01 d.32.1.2 78151 1oahA 519 8.12e+01 a.138.1.3 86736 1yewC 289 8.13e+01 1upvA 257 8.16e+01 1inlA 296 8.22e+01 c.66.1.17 66220 1snrA 341 8.22e+01 b.6.1.3,b.6.1.3 105823,105824 1vjfA 180 8.25e+01 d.116.1.1 100809 1zv9A 172 8.26e+01 1wzcA 249 8.33e+01 1f1uA 323 8.33e+01 d.32.1.3,d.32.1.3 83200,83201 1kcbA 340 8.34e+01 b.6.1.3,b.6.1.3 90951,90952 1gmeA 151 8.43e+01 b.15.1.1 65305 2occC 261 8.46e+01 1ocrC f.25.1.1 43520 1ur4A 399 8.47e+01 1xkpA 246 8.56e+01 1f06A 320 8.58e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1j99A 293 8.58e+01 c.37.1.5 71618 1w6uA 302 8.63e+01 1rkuA 206 8.68e+01 c.108.1.11 97627 1uasA 362 8.69e+01 b.71.1.1,c.1.8.1 88388,88389 1avwB 171 8.71e+01 1wba b.42.4.1 25599 1xi7A 61 8.72e+01 1wzlA 585 8.72e+01 1xc1A 309 8.92e+01 c.94.1.1 109543 1pu1A 94 8.92e+01 d.266.1.1 104307 1yuzA 202 8.94e+01 1vpmA 169 8.95e+01 1gvnB 287 8.98e+01 c.37.1.21 76354