# List of top-scoring protein chains for t04-100-30-str2-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 1vk6A 269 1.63e-01 d.113.1.4,d.113.1.4 100851,100852 1vqoZ 83 1.80e-01 1s72Z 73 2.16e-01 g.41.8.1 105345 1hvyA 288 2.43e-01 1bkpA d.117.1.1 41049 1ypvA 313 3.19e-01 2ct7A 86 3.51e-01 1vckA 115 4.26e-01 1dl6A 58 8.39e-01 1dl6A g.41.3.1 45207 1odhA 174 1.20e+00 d.239.1.1 86850 1u0tA 307 1.21e+00 e.52.1.1 107567 1jj2Y 73 1.31e+00 1ffkW g.41.8.1 63110 1p32A 209 1.65e+00 1p32A d.25.1.1 38379 2cklB 165 1.71e+00 1ee8A 266 1.81e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1jm1A 204 1.87e+00 b.33.1.1 71745 1qqqA 264 2.11e+00 1bkpA d.117.1.1 40931 1a8h 500 2.26e+00 1a8h a.27.1.1,c.26.1.1 16922,31589 2g8mA 264 2.38e+00 2g8oA 264 2.38e+00 1evfA 264 2.51e+00 1bkpA d.117.1.1 40932 1neeA 138 2.54e+00 d.241.1.1,g.59.1.1 91841,91842 1d0qA 103 2.61e+00 1d0qA g.41.3.2 45208 1yk4A 52 2.70e+00 1pcxA 810 2.74e+00 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 1bc8C 93 2.96e+00 1awcA a.4.5.21 16168 1k82A 268 3.03e+00 a.156.1.2,b.113.1.1,g.39.1.8 75866,75867,75868 1woyA 500 3.86e+00 1l1oC 181 3.97e+00 b.40.4.3 73480 1rlyA 60 4.21e+00 g.41.3.1 104988 1ptq 50 4.26e+00 1ptq g.49.1.1 45349 1rfs 139 4.27e+00 1rfs b.33.1.1 24434 1qwtA 255 4.33e+00 b.26.1.3 96501 1gvjA 146 4.51e+00 a.4.5.21 90525 1oahA 519 4.87e+00 a.138.1.3 86736 1hyeA 313 5.02e+00 2cmd c.2.1.5,d.162.1.1 61400,61401 1rb9 53 5.10e+00 1rb9 g.41.5.1 45214 1rutX 188 5.37e+00 1mswD 883 5.40e+00 e.8.1.3 79427 1k3eA 156 5.55e+00 d.198.1.1 68103 1iro 54 5.76e+00 1rb9 g.41.5.1 45223 1wrvA 308 6.14e+00 1g8kB 133 6.15e+00 1g8jB b.33.1.1 24435 1wd2A 60 6.82e+00 g.44.1.1 109232 2a1rA 430 7.26e+00 1z4rA 168 7.43e+00 1dgfA 497 7.58e+00 1cf9A e.5.1.1 42782 1qxfA 66 7.68e+00 g.41.8.4 96527 1u2xA 474 7.96e+00 c.72.1.3 107622 1dxgA 36 8.30e+00 1dxgA g.41.5.2 45247 1nykA 165 8.36e+00 b.33.1.1 86408 1twfI 122 8.41e+00 1rdg 53 8.50e+00 1rb9 g.41.5.1 45221 1xakA 83 8.93e+00 1dzlA 505 8.98e+00 1dzlA b.121.6.1 23586 1fs7A 485 9.38e+00 1qdbA a.138.1.3 19691 1vqoC 246 9.41e+00 1bq9A 54 9.48e+00 1rb9 g.41.5.1 45238 1brfA 53 9.65e+00 1rb9 g.41.5.1 45236 2fqpA 97 9.72e+00 1i50I 122 9.84e+00 g.41.3.1,g.41.3.1 61762,61763 1jj2C 246 9.88e+00 1ffkC c.22.1.1 63087 6rxn 46 9.98e+00 1rb9 g.41.5.1 45222 1iyeA 309 1.00e+01 e.17.1.1 83786 2cklA 108 1.01e+01 2cy5A 140 1.01e+01 1s72C 246 1.02e+01 c.22.1.1 105321 1vrmA 325 1.02e+01 1of5B 184 1.02e+01 d.17.4.2 86934 1t0bA 252 1.03e+01 c.23.16.6 106199 1pxvA 183 1.08e+01 d.3.1.1 95301 1dgaA 375 1.11e+01 1yagA 1a88A 275 1.12e+01 1brt c.69.1.12 34707 1d4xA 375 1.14e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 1v54F 98 1.15e+01 g.41.5.3 100327 3daaA 277 1.17e+01 1daaA e.17.1.1 43272 1wxiA 275 1.19e+01 1ile 821 1.24e+01 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 1w2lA 99 1.24e+01 1dusA 194 1.26e+01 1dusA c.66.1.4 34182 1g4iA 123 1.27e+01 1poa a.133.1.2 60241 1zgwA 139 1.27e+01 1r5mA 425 1.29e+01 2occF 98 1.32e+01 2occF g.41.5.3 45256 1wuaA 375 1.33e+01 1kssA 571 1.37e+01 a.138.1.3,c.3.1.4,d.168.1.1 72928,72929,72930 1e39A 571 1.38e+01 1qjdA a.138.1.3,c.3.1.4,d.168.1.1 19694,30431,42314 1yc5A 246 1.38e+01 1lj5A 379 1.43e+01 e.1.1.1 73928 1uch 230 1.47e+01 1uch d.3.1.6 37129 1x31D 99 1.47e+01 1ywzA 175 1.48e+01 1y9wA 140 1.50e+01 1mr1C 99 1.51e+01 d.217.1.2 79420 1vd4A 62 1.51e+01 7taa 478 1.52e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1n6zA 105 1.53e+01 d.263.1.1 85369 1e53A 59 1.54e+01 1e53A g.49.1.2 45356 1pvmA 184 1.57e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 1zyoA 191 1.57e+01 1jgsA 138 1.59e+01 a.4.5.28 66683 1i9bA 217 1.63e+01 1i9bA b.96.1.1 62084 2bhvA 246 1.64e+01 1xxsA 122 1.65e+01 1a7cA 379 1.66e+01 1sek e.1.1.1 42660 1xd3A 230 1.68e+01 1qz5A 375 1.69e+01 c.55.1.1,c.55.1.1 96614,96615 1rmd 116 1.71e+01 1rmd g.37.1.1,g.44.1.1 45025,45322 1ur6B 52 1.71e+01 g.44.1.1 99812 1j6zA 376 1.73e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1u8bA 133 1.75e+01 1y0pA 571 1.75e+01 1p2hA 571 1.76e+01 a.138.1.3,c.3.1.4,d.168.1.1 93930,93931,93932 1fp0A 88 1.77e+01 1fp0A g.50.1.2 45361 2sak 121 1.78e+01 2sak d.15.5.1 37711 1wfeA 86 1.78e+01 1q9iA 571 1.82e+01 a.138.1.3,c.3.1.4,d.168.1.1 96273,96274,96275 1bnb 38 1.89e+01 1bnb g.9.1.1 44592 1h3nA 878 1.92e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1zin 217 1.92e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1y4hA 188 1.92e+01 2fxuA 375 1.92e+01 1vggA 161 1.94e+01 1i1kA 309 1.96e+01 1daaA e.17.1.1 61533 1cbs 137 1.96e+01 1hmt b.60.1.2 27201 1vq0A 302 1.98e+01 1b71A 191 2.00e+01 1ryt a.25.1.1,g.41.5.1 16647,45246 1ryt 190 2.00e+01 1ryt a.25.1.1,g.41.5.1 16646,45245 1vhqA 232 2.13e+01 c.23.16.2 100696 1gqpA 221 2.19e+01 b.18.1.9 70372 1k1eA 180 2.26e+01 c.108.1.5 67995 1s3eA 520 2.29e+01 c.3.1.2,d.16.1.5 98426,98427 1inp 400 2.33e+01 1inp e.7.1.1 42972 1sp1 29 2.34e+01 g.37.1.1 45051 2au3A 407 2.34e+01 1y75B 118 2.36e+01 1q1gA 276 2.40e+01 c.56.2.1 95574 1y4lA 121 2.45e+01 1k0mA 241 2.46e+01 a.45.1.1,c.47.1.5 67949,67950 1l8dA 112 2.46e+01 h.4.12.1 73687 2bx9A 53 2.46e+01 2g8yA 385 2.51e+01 1mea 28 2.56e+01 g.41.1.1 45176 2airB 153 2.57e+01 1r2zA 274 2.62e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1ojaA 520 2.62e+01 c.3.1.2,d.16.1.5 93096,93097 2fiyA 309 2.68e+01 1l1zA 274 2.68e+01 a.156.1.2,b.113.1.1,g.39.1.8 75911,75912,75913 2ghsA 326 2.69e+01 1yovA 537 2.69e+01 1z6uA 150 2.74e+01 1m2kA 249 2.79e+01 c.31.1.5 84754 1zip 217 2.86e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1lkoA 191 2.90e+01 a.25.1.1,g.41.5.1 78063,78064 1erjA 393 2.92e+01 1erjA b.69.4.1 27660 2fclA 169 2.99e+01 2ewrA 170 3.00e+01 1al3 324 3.06e+01 1al3 c.94.1.1 35835 1vziA 126 3.11e+01 b.1.13.1,g.41.5.2 108967,108968 1vor2 58 3.11e+01 1w9aA 147 3.16e+01 1od5A 492 3.18e+01 b.82.1.2,b.82.1.2 86832,86833 2c43A 323 3.20e+01 2fm8A 135 3.21e+01 2aq6A 147 3.23e+01 1whvA 100 3.23e+01 1o7eA 276 3.24e+01 e.3.1.1 92622 1exkA 79 3.29e+01 1exkA g.54.1.1 45384 1jltA 122 3.29e+01 a.133.1.2 66867 1tqyB 415 3.30e+01 c.95.1.1,c.95.1.1 107247,107248 2an1A 292 3.32e+01 1iv8A 720 3.34e+01 b.71.1.1,c.1.8.1 76842,76843 1n9dA 199 3.36e+01 a.26.1.1 85464 1yh6A 179 3.39e+01 1vpi 122 3.40e+01 1poa a.133.1.2 19559 1pfvA 551 3.43e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1v87A 114 3.44e+01 g.44.1.1 108422 1qtwA 285 3.46e+01 1qumA c.1.15.1 29392 2bydA 323 3.48e+01 1ew4A 106 3.48e+01 1ew4A d.82.2.1 40023 1pueE 89 3.48e+01 1awcA a.4.5.21 16165 1jg5A 83 3.51e+01 d.205.1.1 66666 1se0A 116 3.51e+01 g.52.1.1 98814 1j5uA 136 3.52e+01 d.208.1.1 71584 2aaa 484 3.53e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1k8kA 418 3.54e+01 c.55.1.1,c.55.1.1 68305,68306 1zd9A 188 3.57e+01 1r6lA 239 3.57e+01 d.14.1.4,d.101.1.1 97153,97154 1yl35 60 3.58e+01 1f4lA 551 3.59e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1gv3A 248 3.65e+01 a.2.11.1,d.44.1.1 70585,70586 1p3jA 217 3.68e+01 c.37.1.1,g.41.2.1 94022,94023 1tp6A 128 3.69e+01 d.17.4.12 107184 1nwwA 149 3.69e+01 d.17.4.8 86306 1q35A 320 3.71e+01 c.94.1.1 95661 1sur 215 3.73e+01 1sur c.26.2.2 31620 1ht6A 405 3.76e+01 b.71.1.1,c.1.8.1 83629,83630 1rc6A 261 3.81e+01 b.82.1.11 97287 1cojA 212 3.83e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1yfnA 118 3.85e+01 1sz6B 263 3.91e+01 1wjpA 107 3.93e+01 1s5aA 150 3.98e+01 d.17.4.10 98525 1zwpA 121 4.00e+01 2g58A 121 4.03e+01 1adn 92 4.04e+01 1adn g.48.1.1 45348 1vfyA 73 4.04e+01 1vfyA g.50.1.1 45357 1ykdA 398 4.10e+01 2a20A 62 4.14e+01 1t2dA 322 4.15e+01 c.2.1.5,d.162.1.1 99084,99085 1d09B 153 4.15e+01 8atcB d.58.2.1,g.41.7.1 39015,45267 1plq 258 4.15e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1upiA 225 4.18e+01 b.82.1.1 99757 1tk4A 121 4.27e+01 a.133.1.2 107073 1vyiA 112 4.27e+01 1u3eM 174 4.31e+01 d.4.1.3,d.285.1.1 107640,107641 1w66A 232 4.32e+01 1dxsA 80 4.34e+01 1cokA a.60.1.2 17944 1z60A 59 4.35e+01 1ldg 316 4.36e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1uw6A 211 4.39e+01 b.96.1.1 100079 1yt5A 258 4.41e+01 1s1dA 331 4.43e+01 b.67.3.1 98344 1xxoA 147 4.49e+01 2c31A 568 4.52e+01 1ti6B 274 4.55e+01 b.3.5.1,d.58.1.5 106976,106977 1fd3A 41 4.57e+01 1fd3A g.9.1.1 44572 2btfA 375 4.60e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 1tj9A 121 4.61e+01 a.133.1.2 107015 2evrA 246 4.76e+01 1yv4A 104 4.80e+01 1p5vA 235 4.82e+01 b.1.11.1,b.7.2.1 87812,87813 1dpgA 485 4.91e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1s6bA 119 4.92e+01 a.133.1.2 98592 1y75A 118 4.96e+01 1eajA 126 4.97e+01 1f5wA b.1.1.1 59401 1ww8A 439 5.01e+01 1ww9A 392 5.03e+01 1uh4A 637 5.07e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1uesA 191 5.07e+01 a.2.11.1,d.44.1.1 107798,107799 1ji1A 637 5.07e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1wjvA 79 5.07e+01 1cb8A 678 5.09e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1u6mA 199 5.18e+01 1l9xA 315 5.27e+01 c.23.16.1 73762 1y13A 181 5.28e+01 1onc 104 5.29e+01 1onc d.5.1.1 37278 1qstA 160 5.30e+01 1yghA d.108.1.1 40804 2adoA 196 5.37e+01 2bwkA 121 5.37e+01 1hn4A 131 5.37e+01 a.133.1.2 65893 1g4wR 383 5.48e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1x75A 132 5.49e+01 2aheA 267 5.52e+01 2eifA 136 5.56e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1kq1A 77 5.61e+01 b.38.1.2 72848 1wpkA 146 5.61e+01 1p6pA 125 5.63e+01 b.60.1.2 87839 1iab 200 5.64e+01 1iae d.92.1.8 40312 1yfbA 59 5.65e+01 1c28A 135 5.67e+01 1c28A b.22.1.1 23857 1kmtA 141 5.69e+01 b.1.18.8 77442 1yxlA 119 5.69e+01 1zlbA 122 5.70e+01 1hl9A 449 5.71e+01 b.71.1.3,c.1.8.11 90650,90651 1umvX 122 5.72e+01 a.133.1.2 99630 2bsxA 253 5.81e+01 1r8oB 71 5.87e+01 1ifc 132 5.93e+01 b.60.1.2 27173 1vm9A 111 6.00e+01 b.33.1.1 108886 1mc2A 122 6.04e+01 a.133.1.2 74622 1qnnA 191 6.05e+01 1avmA a.2.11.1,d.44.1.1 15792,38755 1s8iA 121 6.07e+01 a.133.1.2 98735 1cqmA 101 6.09e+01 1ris d.58.14.1 39321 1mtyD 512 6.09e+01 1mhyD a.25.1.2 16742 1qvbA 481 6.16e+01 1qvbA c.1.8.4 28983 2csvA 72 6.23e+01 2bbkL 125 6.25e+01 2bbkL g.21.1.1 44882 2cxkA 95 6.29e+01 1juvA 193 6.38e+01 c.71.1.1 90912 1wijA 140 6.48e+01 1fc6A 388 6.50e+01 1fc6A b.36.1.3,c.14.1.2 64738,64739 1sqzA 121 6.50e+01 a.133.1.2 98975 1zy1B 197 6.55e+01 1i50L 70 6.57e+01 g.41.9.2 61766 1h9dA 134 6.57e+01 1cmoA b.2.5.6 60821 1m2tB 263 6.65e+01 b.42.2.1,b.42.2.1 84762,84763 1lv3A 68 6.65e+01 g.39.1.9 78231 2fpeA 62 6.66e+01 1yxhA 126 6.70e+01 1qbjA 81 6.76e+01 1qbjA a.4.5.19 16155 1gqvA 135 6.78e+01 d.5.1.1 70376 1g73C 121 6.81e+01 1g3fA g.52.1.1 45375 1vphA 149 6.88e+01 1t0fC 54 6.90e+01 1a78A 134 6.90e+01 1c1lA b.29.1.3 24212 1kvoA 124 7.00e+01 1poa a.133.1.2 19564 1weoA 93 7.01e+01 1ltlA 279 7.10e+01 b.40.4.11 84701 1zgmA 248 7.10e+01 2fnoA 248 7.10e+01 1zs7A 190 7.11e+01 2cx1A 187 7.14e+01 1a70 97 7.16e+01 1awd d.15.4.1 37678 1c3hA 137 7.16e+01 b.22.1.1 90405 1dl0A 37 7.17e+01 1dl0A g.3.6.2 44112 2etxA 209 7.19e+01 1ryqA 69 7.20e+01 g.41.9.3 105126 1cv8 174 7.22e+01 1cv8 d.3.1.1 37089 1k7hA 476 7.30e+01 c.76.1.1 72101 1u5kA 244 7.31e+01 1h12A 405 7.38e+01 a.102.1.2 83447 1tt0A 623 7.39e+01 1ywsA 82 7.43e+01 2fe5A 94 7.43e+01 2aq5A 402 7.44e+01 1ri6A 343 7.44e+01 b.69.11.1 97503 1rgxA 114 7.47e+01 g.77.1.1 104932 1fsoA 139 7.50e+01 1rhoA b.1.18.8 60007 1tuaA 191 7.55e+01 d.51.1.1,d.51.1.1 107321,107322 1tpm 50 7.58e+01 1tpg g.27.1.1 44957 1gz8A 299 7.59e+01 d.144.1.7 83405 1b77A 228 7.60e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 1hcl 298 7.61e+01 1hcl d.144.1.7 41593 1vljA 407 7.67e+01 e.22.1.2 108832 1zzpA 130 7.79e+01 1j5pA 253 7.81e+01 d.81.1.3,c.2.1.3 71577,83092 1rjoA 646 7.91e+01 1l7bA 92 7.92e+01 c.15.1.2 91053 1siiA 646 8.00e+01 b.30.2.1,d.17.2.1,d.17.2.1 105578,105579,105580 2gq1A 332 8.07e+01 1uby 367 8.10e+01 1uby a.128.1.1 19435 1se7A 83 8.11e+01 1ux2A 212 8.16e+01 b.96.1.1 100132 1t82A 155 8.20e+01 d.38.1.5 106639 1xedA 117 8.21e+01 1dvpA 220 8.22e+01 1dvpA a.118.9.2,g.50.1.1 19216,45358 1ky3A 182 8.30e+01 c.37.1.8 73193 1tzlA 622 8.33e+01 1ho1A 242 8.48e+01 1ho1A c.1.24.1 61097 1z84A 351 8.48e+01 1qysA 106 8.50e+01 k.41.1.1 96603 1yuiA 54 8.61e+01 1yuiA g.37.1.1 45073 1iae 200 8.62e+01 1iae d.92.1.8 40311 1iqyA 638 8.63e+01 b.30.2.1,d.17.2.1,d.17.2.1 76763,76764,76765 1ayoA 130 8.68e+01 1ayoA b.2.4.1 22431 1v6pA 62 8.69e+01 1gl4A 285 8.73e+01 d.22.1.2,g.3.11.5 65286,65287 2b5iD 217 8.78e+01 1ekgA 127 8.78e+01 1dlxA d.82.2.1 40021 1wvkA 86 8.81e+01 1z0rA 53 8.84e+01 1z92B 219 8.92e+01 1s7jA 262 8.95e+01 d.21.1.2 98647