# List of top-scoring protein chains for t04-100-30-o_notor2-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 1s72Z 73 1.55e-01 g.41.8.1 105345 1vqoZ 83 2.83e-01 2fqpA 97 3.30e-01 1theA 260 5.60e-01 1theB d.3.1.1 37056 2ct7A 86 6.36e-01 1hvyA 288 1.41e+00 1bkpA d.117.1.1 41049 1ypvA 313 1.41e+00 1wd2A 60 1.66e+00 g.44.1.1 109232 1ifqA 138 2.06e+00 1ifqA d.110.4.1 62350 1wrvA 308 2.18e+00 1fsoA 139 2.20e+00 1rhoA b.1.18.8 60007 1kmtA 141 2.40e+00 b.1.18.8 77442 1sur 215 2.48e+00 1sur c.26.2.2 31620 1jj2Y 73 2.54e+00 1ffkW g.41.8.1 63110 1odhA 174 2.57e+00 d.239.1.1 86850 1jm1A 204 2.67e+00 b.33.1.1 71745 1dl6A 58 2.81e+00 1dl6A g.41.3.1 45207 1wjvA 79 3.07e+00 1l1oC 181 3.55e+00 b.40.4.3 73480 1k8kA 418 4.14e+00 c.55.1.1,c.55.1.1 68305,68306 1ee8A 266 4.18e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1lvoA 302 4.76e+00 b.47.1.4 74284 2g2kA 170 4.77e+00 1ur6B 52 4.92e+00 g.44.1.1 99812 2ampA 304 5.13e+00 1vk6A 269 5.56e+00 d.113.1.4,d.113.1.4 100851,100852 1k7cA 233 5.57e+00 c.23.10.4 68267 2awpA 198 5.76e+00 1n9dA 199 5.81e+00 a.26.1.1 85464 1rlyA 60 5.86e+00 g.41.3.1 104988 1zd9A 188 5.92e+00 1ww8A 439 6.00e+00 2g8oA 264 6.01e+00 1zxzA 197 6.06e+00 1xk5A 204 6.32e+00 1evfA 264 6.33e+00 1bkpA d.117.1.1 40932 2cklB 165 6.38e+00 1havA 217 6.41e+00 1havA b.47.1.4 26423 2avuE 192 6.46e+00 2btfA 375 6.50e+00 1yagA c.55.1.1,c.55.1.1 33429,33430 1p5vA 235 6.52e+00 b.1.11.1,b.7.2.1 87812,87813 1xtqA 177 6.62e+00 1zy1B 197 6.81e+00 2g8mA 264 6.92e+00 1vd4A 62 6.93e+00 2g8yA 385 6.94e+00 1y9wA 140 7.03e+00 2cxvA 219 7.09e+00 1uk8A 282 7.13e+00 c.69.1.10 107907 1deoA 233 7.14e+00 1deoA c.23.10.4 31345 2bwfA 77 7.48e+00 1zkkA 167 7.83e+00 1vckA 115 8.03e+00 1qqqA 264 8.05e+00 1bkpA d.117.1.1 40931 1iupA 282 8.06e+00 c.69.1.10 76815 1d4xA 375 8.21e+00 1yagA c.55.1.1,c.55.1.1 59107,59108 1inp 400 8.54e+00 1inp e.7.1.1 42972 2ewrA 170 8.57e+00 1qlnA 883 8.65e+00 1cezA e.8.1.3 43111 1y88A 199 8.82e+00 1qxfA 66 9.05e+00 g.41.8.4 96527 1yioA 208 9.20e+00 1gmyA 261 9.26e+00 d.3.1.1 76236 1wfeA 86 9.54e+00 1lv3A 68 9.73e+00 g.39.1.9 78231 1dgaA 375 9.83e+00 1yagA 1zzpA 130 9.97e+00 1lm5A 214 1.04e+01 d.211.2.1 74029 1u69A 163 1.04e+01 d.32.1.7 107699 1xakA 83 1.09e+01 1q35A 320 1.11e+01 c.94.1.1 95661 1ty9A 222 1.12e+01 2as9A 210 1.13e+01 1sp1 29 1.14e+01 g.37.1.1 45051 1z6uA 150 1.14e+01 1yl35 60 1.15e+01 1xxoA 147 1.18e+01 2aq5A 402 1.22e+01 1u79A 129 1.22e+01 d.26.1.1 107714 1dxgA 36 1.23e+01 1dxgA g.41.5.2 45247 1a78A 134 1.25e+01 1c1lA b.29.1.3 24212 2kfnA 605 1.26e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1w9aA 147 1.28e+01 1uv4A 293 1.30e+01 2aq4A 434 1.31e+01 1xbfA 140 1.37e+01 d.273.1.1 109538 1rdg 53 1.43e+01 1rb9 g.41.5.1 45221 1umwA 237 1.45e+01 d.223.1.2,d.223.1.2 99631,99632 1v87A 114 1.46e+01 g.44.1.1 108422 1e53A 59 1.49e+01 1e53A g.49.1.2 45356 1yk4A 52 1.49e+01 2dasA 62 1.55e+01 1vor2 58 1.67e+01 1wxiA 275 1.68e+01 1qvbA 481 1.69e+01 1qvbA c.1.8.4 28983 1rb9 53 1.69e+01 1rb9 g.41.5.1 45214 1r6lA 239 1.70e+01 d.14.1.4,d.101.1.1 97153,97154 1zu0A 529 1.70e+01 3daaA 277 1.70e+01 1daaA e.17.1.1 43272 1tr9A 341 1.74e+01 1yovA 537 1.74e+01 1yaxA 153 1.75e+01 1weoA 93 1.76e+01 1cojA 212 1.77e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1twfL 70 1.82e+01 1u3aA 189 1.82e+01 1utyA 187 1.82e+01 b.147.1.1 108036 1fvkA 189 1.83e+01 1fvkA c.47.1.13 90351 1ptq 50 1.85e+01 1ptq g.49.1.1 45349 2aq6A 147 1.86e+01 1cv8 174 1.90e+01 1cv8 d.3.1.1 37089 2aaiB 262 1.94e+01 1abrB b.42.2.1,b.42.2.1 25561,25562 2gpyA 233 1.94e+01 2a20A 62 1.94e+01 1r5mA 425 1.96e+01 1q68B 29 2.02e+01 j.108.1.1 95963 1vziA 126 2.03e+01 b.1.13.1,g.41.5.2 108967,108968 1d3bA 75 2.04e+01 1d3bA b.38.1.1 24798 1u8vA 490 2.05e+01 1li4A 432 2.06e+01 c.2.1.4,c.23.12.3 84616,84617 1a88A 275 2.07e+01 1brt c.69.1.12 34707 1wjpA 107 2.09e+01 2bcoA 350 2.17e+01 1bq9A 54 2.19e+01 1rb9 g.41.5.1 45238 1brfA 53 2.20e+01 1rb9 g.41.5.1 45236 1fp0A 88 2.20e+01 1fp0A g.50.1.2 45361 2erxA 172 2.23e+01 1m22A 503 2.24e+01 c.117.1.1 78464 2aw2B 108 2.29e+01 1yopA 83 2.30e+01 1ywzA 175 2.31e+01 2sak 121 2.46e+01 2sak d.15.5.1 37711 1ile 821 2.52e+01 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 1eq2A 310 2.56e+01 1eq2A c.2.1.2 29814 2cy5A 140 2.57e+01 1wijA 140 2.63e+01 1mswD 883 2.67e+01 e.8.1.3 79427 7taa 478 2.67e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1dpgA 485 2.67e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1mea 28 2.77e+01 g.41.1.1 45176 1m4uA 206 2.78e+01 g.17.1.7 78625 1nykA 165 2.80e+01 b.33.1.1 86408 1pfvA 551 2.82e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1rutX 188 2.83e+01 1umgA 362 2.83e+01 d.280.1.1 107956 1bc8C 93 2.84e+01 1awcA a.4.5.21 16168 2fclA 169 2.85e+01 1ldg 316 2.95e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1qtwA 285 2.97e+01 1qumA c.1.15.1 29392 1g4mA 393 3.01e+01 b.1.18.11,b.1.18.11 65143,65144 1qlaB 239 3.03e+01 1qlaB a.1.2.1,d.15.4.2 15679,37707 1ubkS 267 3.03e+01 e.19.1.1 88423 1ayoA 130 3.07e+01 1ayoA b.2.4.1 22431 1ti6B 274 3.15e+01 b.3.5.1,d.58.1.5 106976,106977 1qfmA 710 3.19e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1acvA 189 3.20e+01 1fvkA c.47.1.13 90328 1p32A 209 3.22e+01 1p32A d.25.1.1 38379 2bx9A 53 3.23e+01 1h3nA 878 3.26e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1m2kA 249 3.28e+01 c.31.1.5 84754 1vdwA 254 3.30e+01 e.7.1.1 100569 1h4rA 314 3.32e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1x75A 132 3.38e+01 1m2tB 263 3.39e+01 b.42.2.1,b.42.2.1 84762,84763 1nigA 152 3.40e+01 a.25.2.1 85740 1h2wA 710 3.45e+01 b.69.7.1,c.69.1.4 76596,76597 1zyoA 191 3.46e+01 1pm6A 72 3.50e+01 a.6.1.7 94894 6rxn 46 3.51e+01 1rb9 g.41.5.1 45222 1dxsA 80 3.54e+01 1cokA a.60.1.2 17944 1e19A 314 3.58e+01 1b7bA c.73.1.1 34967 1i50L 70 3.59e+01 g.41.9.2 61766 2fs3A 282 3.60e+01 2an1A 292 3.65e+01 1f4lA 551 3.66e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1h2rS 267 3.67e+01 2frvA e.19.1.1 43310 1x31D 99 3.69e+01 1woyA 500 3.70e+01 1rfs 139 3.70e+01 1rfs b.33.1.1 24434 2h3bA 494 3.83e+01 2cwsA 237 3.87e+01 1exkA 79 3.88e+01 1exkA g.54.1.1 45384 2d8vA 67 3.90e+01 1fiqB 350 3.91e+01 1fiqB d.87.2.1,d.145.1.3 40229,41760 1k0mA 241 3.92e+01 a.45.1.1,c.47.1.5 67949,67950 1l1dA 152 3.95e+01 b.88.1.3 73452 1sz6B 263 3.95e+01 1q33A 292 3.97e+01 d.113.1.1 95657 1zin 217 3.98e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1xiwA 105 3.99e+01 1iyeA 309 4.00e+01 e.17.1.1 83786 1tqnA 486 4.03e+01 a.104.1.1 107238 1vphA 149 4.08e+01 2a6hD 1524 4.09e+01 1vmhA 144 4.09e+01 1m3qA 317 4.20e+01 a.96.1.3,d.129.1.2 91184,91185 4eugA 229 4.25e+01 3eugA c.18.1.1 31019 1vq0A 302 4.27e+01 1jfrA 262 4.30e+01 1jfrA c.69.1.16 34724 2f4pA 147 4.35e+01 1th8A 145 4.44e+01 d.122.1.3 106908 2cklA 108 4.45e+01 1sefA 274 4.46e+01 b.82.1.11 105452 8pchA 220 4.50e+01 1cs8A 1k7hA 476 4.56e+01 c.76.1.1 72101 1ihoA 283 4.56e+01 1ihoA c.26.1.4 62390 1l3yA 41 4.57e+01 g.3.11.6 73558 1zboA 210 4.61e+01 1tz9A 367 4.63e+01 c.1.15.6 107466 1z4vA 532 4.70e+01 1uzxA 169 4.71e+01 d.20.1.2 100238 2aaa 484 4.78e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1qz5A 375 4.80e+01 c.55.1.1,c.55.1.1 96614,96615 1jb0F 164 4.83e+01 1jb0F f.23.16.1 62825 1qa7A 217 4.86e+01 1havA b.47.1.4 26425 2bbkL 125 4.88e+01 2bbkL g.21.1.1 44882 1p6pA 125 4.89e+01 b.60.1.2 87839 2adoA 196 4.94e+01 1zip 217 4.94e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1z4xA 532 4.96e+01 1bs0A 384 5.07e+01 1bs0A c.67.1.4 34490 1llmC 88 5.07e+01 g.37.1.1,g.37.1.1 91059,91060 1o9iA 266 5.11e+01 a.25.1.3 92671 1wnfA 328 5.12e+01 1dgfA 497 5.12e+01 1cf9A e.5.1.1 42782 1gp1A 198 5.18e+01 1gp1A c.47.1.10 33059 1rc6A 261 5.20e+01 b.82.1.11 97287 1suuA 312 5.22e+01 b.68.10.1 99006 1oxxK 353 5.23e+01 b.40.6.3,c.37.1.12 93715,93716 1dl0A 37 5.24e+01 1dl0A g.3.6.2 44112 1ogdA 131 5.36e+01 c.133.1.1 92893 1t2dA 322 5.39e+01 c.2.1.5,d.162.1.1 99084,99085 2b5iD 217 5.51e+01 1iro 54 5.58e+01 1rb9 g.41.5.1 45223 1oxdA 227 5.60e+01 d.22.1.1 93687 1xfkA 336 5.60e+01 1xhcA 367 5.61e+01 1kyqA 274 5.66e+01 c.2.1.11,e.37.1.1 73281,73282 2cxkA 95 5.67e+01 2bwkA 121 5.68e+01 2etxA 209 5.70e+01 1oxsC 353 5.70e+01 b.40.6.3,c.37.1.12 87519,87520 1b33N 67 5.78e+01 1b33N d.30.1.1 38459 2fxuA 375 5.78e+01 1hyuA 521 5.83e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1cqxA 403 5.88e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1w8kA 447 5.89e+01 1gpr 162 5.91e+01 1gpr b.84.3.1 28267 1nox 205 6.04e+01 1nox d.90.1.1 40242 1hdlA 55 6.10e+01 g.68.1.2 65808 1q48A 134 6.11e+01 d.224.1.2 95783 1jkvA 266 6.15e+01 a.25.1.3 71719 1afp 51 6.15e+01 1afp g.26.1.1 44947 1un3A 123 6.18e+01 d.5.1.1 99646 1cqmA 101 6.18e+01 1ris d.58.14.1 39321 1hl2A 297 6.19e+01 c.1.10.1 83581 1ng0A 253 6.20e+01 b.121.4.7 80475 1guiA 155 6.21e+01 b.18.1.14 76351 1ew4A 106 6.23e+01 1ew4A d.82.2.1 40023 2eu8A 216 6.23e+01 1nx8A 273 6.23e+01 b.82.2.8 86374 1u00A 227 6.25e+01 1o12A 376 6.26e+01 b.92.1.5,c.1.9.10 80758,80759 2a1rA 430 6.28e+01 1m07A 111 6.30e+01 d.5.1.1 78328 1eybA 471 6.33e+01 1ey2A b.82.1.4 28115 1ofnA 205 6.42e+01 b.82.1.1 92830 1oi6A 205 6.45e+01 b.82.1.1 103940 1p6oA 161 6.47e+01 c.97.1.2 94185 1f83A 425 6.53e+01 1f82A d.92.1.7 40306 1g2fC 90 6.55e+01 k.12.1.1 60222 1wuiS 267 6.56e+01 2fiyA 309 6.69e+01 1q18A 332 6.71e+01 c.55.1.7,c.55.1.7 104470,104471 1l8dA 112 6.78e+01 h.4.12.1 73687 1l4iA 206 6.85e+01 b.1.11.1,b.7.2.1 73564,73565 1oyjA 231 6.86e+01 a.45.1.1,c.47.1.5 87597,87598 1itbB 315 6.86e+01 1itbB b.1.1.4,b.1.1.4,b.1.1.4 21720,21721,21722 1lwdA 413 6.88e+01 c.77.1.1 78265 1nal1 297 6.94e+01 1nal3 2h58A 330 6.99e+01 1p3jA 217 7.00e+01 c.37.1.1,g.41.2.1 94022,94023 1euvB 86 7.00e+01 1a5r d.15.1.1 37598 2a0jA 149 7.01e+01 1bu7A 455 7.01e+01 1bu7A a.104.1.1 18937 1wuaA 375 7.06e+01 1r0uA 148 7.11e+01 b.60.1.5 96741 1gqvA 135 7.21e+01 d.5.1.1 70376 2dexX 671 7.26e+01 1ldjB 90 7.26e+01 g.44.1.1 73850 1zaaC 87 7.28e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45013,45014,45015 1hn6A 110 7.28e+01 g.61.1.1 76721 2trxA 108 7.34e+01 1thx c.47.1.1 32719 2aheA 267 7.34e+01 1sz2A 332 7.35e+01 1z60A 59 7.36e+01 1t1jA 125 7.36e+01 c.137.1.1 106249 1plq 258 7.37e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1d0qA 103 7.38e+01 1d0qA g.41.3.2 45208 1wc2A 181 7.40e+01 1t0bA 252 7.41e+01 c.23.16.6 106199 1i1kA 309 7.42e+01 1daaA e.17.1.1 61533 1a8h 500 7.45e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1fl2A 310 7.49e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1n0nA 199 7.59e+01 a.2.11.1,d.44.1.1 79750,79751 1cl4A 60 7.59e+01 1cl4A g.40.1.1 45171 1hi2A 135 7.60e+01 7rsa d.5.1.1 61057 1m0gA 30 7.61e+01 g.46.1.1 84743 1nepA 130 7.62e+01 b.1.18.7 80440 1cy5A 97 7.68e+01 1cy5A a.77.1.3 18430 1ifc 132 7.69e+01 b.60.1.2 27173 2a97A 439 7.69e+01 2fqaA 27 7.72e+01 1q6oA 216 7.73e+01 c.1.2.3 95986 1sy6A 204 7.77e+01 b.1.1.4,b.1.1.4 106111,106112 1qd1A 325 7.79e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1g9pA 45 7.87e+01 g.3.6.2 65171 1qnnA 191 7.87e+01 1avmA a.2.11.1,d.44.1.1 15792,38755 1uch 230 7.89e+01 1uch d.3.1.6 37129 3pmgA 561 7.99e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 2a9kA 187 8.00e+01 1uby 367 8.02e+01 1uby a.128.1.1 19435 1azwA 313 8.03e+01 1qtrA c.69.1.7 34658 1kv8A 216 8.05e+01 c.1.2.3 73054 1wdaA 670 8.05e+01 b.2.9.1,b.6.1.6,d.126.1.5 109243,109244,109245 1u8zA 168 8.08e+01 1m65A 245 8.10e+01 c.6.3.1 84847 1n67A 359 8.10e+01 b.2.3.4,b.2.3.4 85354,85355 1wlsA 328 8.12e+01 1aayA 90 8.16e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45001,45002,45003 2a6mA 155 8.19e+01 1v4pA 157 8.21e+01 1c3hA 137 8.22e+01 b.22.1.1 90405 1vcaA 202 8.22e+01 1vcaA b.1.1.3,b.1.1.4 21649,21685 2a8aA 439 8.25e+01 2f8aA 208 8.33e+01 1r8nA 185 8.38e+01 b.42.4.1 104851 1m3vA 122 8.38e+01 g.39.1.3,g.39.1.3 84794,84795 1c28A 135 8.39e+01 1c28A b.22.1.1 23857 1m1qA 91 8.42e+01 a.138.1.3 74419 1a1iA 90 8.58e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 44998,44999,45000 1f3lA 321 8.69e+01 1g6q2 c.66.1.6 59630 1b8oA 284 8.72e+01 1b8oA c.56.2.1 33762 1o7eA 276 8.84e+01 e.3.1.1 92622 1neeA 138 8.88e+01 d.241.1.1,g.59.1.1 91841,91842 1qjpA 171 8.93e+01 1bxwA f.4.1.1 43742 1ywsA 82 8.97e+01 1qo3C 137 8.98e+01 1qo3C d.169.1.1 42350 1jofA 365 8.98e+01 b.69.10.1 71775