# 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 1s72Z 73 2.23e-01 g.41.8.1 105345 1vqoZ 83 2.58e-01 1kmtA 141 4.17e-01 b.1.18.8 77442 1odhA 174 4.44e-01 d.239.1.1 86850 1vk6A 269 5.16e-01 d.113.1.4,d.113.1.4 100851,100852 1ur6B 52 7.01e-01 g.44.1.1 99812 2cklB 165 9.28e-01 1ww8A 439 9.40e-01 2ct7A 86 9.49e-01 1fsoA 139 1.09e+00 1rhoA b.1.18.8 60007 1wd2A 60 1.34e+00 g.44.1.1 109232 1vckA 115 1.61e+00 2fqpA 97 1.65e+00 1x75A 132 1.77e+00 2a8mA 420 1.92e+00 1jj2Y 73 2.16e+00 1ffkW g.41.8.1 63110 1vd4A 62 2.26e+00 1jm1A 204 2.33e+00 b.33.1.1 71745 2g2kA 170 2.42e+00 1dgfA 497 2.44e+00 1cf9A e.5.1.1 42782 1k7cA 233 3.10e+00 c.23.10.4 68267 1wrvA 308 3.22e+00 1u79A 129 3.32e+00 d.26.1.1 107714 2a8jA 420 3.38e+00 1rlyA 60 3.40e+00 g.41.3.1 104988 1yl35 60 3.44e+00 1dgaA 375 4.17e+00 1yagA 1d4xA 375 4.33e+00 1yagA c.55.1.1,c.55.1.1 59107,59108 1r6lA 239 4.36e+00 d.14.1.4,d.101.1.1 97153,97154 1ee8A 266 4.41e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1rfs 139 4.48e+00 1rfs b.33.1.1 24434 1zxzA 197 4.73e+00 1theA 260 5.22e+00 1theB d.3.1.1 37056 1bq9A 54 5.50e+00 1rb9 g.41.5.1 45238 1vphA 149 5.70e+00 2c1xA 456 5.71e+00 1brfA 53 5.81e+00 1rb9 g.41.5.1 45236 1l7bA 92 6.33e+00 c.15.1.2 91053 2aq6A 147 6.35e+00 1dl6A 58 6.60e+00 1dl6A g.41.3.1 45207 2cjsC 62 6.76e+00 1rmd 116 6.81e+00 1rmd g.37.1.1,g.44.1.1 45025,45322 1pu6A 218 6.86e+00 a.96.1.5 95123 1rb9 53 6.87e+00 1rb9 g.41.5.1 45214 2sak 121 7.09e+00 2sak d.15.5.1 37711 1yk4A 52 7.39e+00 1deoA 233 7.62e+00 1deoA c.23.10.4 31345 2a20A 62 7.69e+00 1q33A 292 7.69e+00 d.113.1.1 95657 1ww9A 392 7.77e+00 1ile 821 7.77e+00 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 2an1A 292 7.84e+00 1k8kA 418 7.96e+00 c.55.1.1,c.55.1.1 68305,68306 2btfA 375 8.12e+00 1yagA c.55.1.1,c.55.1.1 33429,33430 1q35A 320 8.22e+00 c.94.1.1 95661 1l1oC 181 8.28e+00 b.40.4.3 73480 1ptq 50 8.44e+00 1ptq g.49.1.1 45349 1exkA 79 8.64e+00 1exkA g.54.1.1 45384 1hvyA 288 8.95e+00 1bkpA d.117.1.1 41049 1rdg 53 8.96e+00 1rb9 g.41.5.1 45221 1zd9A 188 9.20e+00 1l8dA 112 9.35e+00 h.4.12.1 73687 2d8vA 67 9.53e+00 1mr1C 99 9.73e+00 d.217.1.2 79420 2adoA 196 9.81e+00 1wfeA 86 9.86e+00 1qxfA 66 9.95e+00 g.41.8.4 96527 1xxoA 147 9.97e+00 1zy1B 197 1.00e+01 3daaA 277 1.05e+01 1daaA e.17.1.1 43272 1d0qA 103 1.06e+01 1d0qA g.41.3.2 45208 1m22A 503 1.07e+01 c.117.1.1 78464 2dasA 62 1.09e+01 2a1rA 430 1.10e+01 1ty9A 222 1.12e+01 1ypvA 313 1.14e+01 1w9aA 147 1.15e+01 2aaa 484 1.15e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1zkkA 167 1.16e+01 1wraA 308 1.22e+01 1zu0A 529 1.24e+01 1v87A 114 1.24e+01 g.44.1.1 108422 1twfL 70 1.30e+01 1q68B 29 1.30e+01 j.108.1.1 95963 1iyeA 309 1.33e+01 e.17.1.1 83786 1rutX 188 1.34e+01 1lvoA 302 1.34e+01 b.47.1.4 74284 1y3nA 490 1.35e+01 1f4lA 551 1.38e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1zip 217 1.39e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1vq0A 302 1.41e+01 1mswD 883 1.44e+01 e.8.1.3 79427 1sur 215 1.45e+01 1sur c.26.2.2 31620 1zin 217 1.45e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1nykA 165 1.45e+01 b.33.1.1 86408 1mea 28 1.45e+01 g.41.1.1 45176 1weoA 93 1.46e+01 1pfvA 551 1.48e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 2csvA 72 1.52e+01 1yovA 537 1.54e+01 1kbeA 49 1.58e+01 g.49.1.1 68380 6rxn 46 1.58e+01 1rb9 g.41.5.1 45222 1lv3A 68 1.65e+01 g.39.1.9 78231 1f1zA 273 1.65e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 2bx9A 53 1.66e+01 2bibA 547 1.71e+01 1inp 400 1.75e+01 1inp e.7.1.1 42972 1nv8A 284 1.76e+01 c.66.1.30 86224 1iro 54 1.76e+01 1rb9 g.41.5.1 45223 1o12A 376 1.79e+01 b.92.1.5,c.1.9.10 80758,80759 1ldjB 90 1.81e+01 g.44.1.1 73850 2cklA 108 1.82e+01 1wjpA 107 1.83e+01 1qqqA 264 1.88e+01 1bkpA d.117.1.1 40931 1s5aA 150 1.94e+01 d.17.4.10 98525 2cszA 76 1.96e+01 1jj2F 119 1.97e+01 1ffkE d.79.3.1 63091 1tqnA 486 1.97e+01 a.104.1.1 107238 1wr8A 231 1.99e+01 1bc8C 93 2.01e+01 1awcA a.4.5.21 16168 1sp1 29 2.01e+01 g.37.1.1 45051 1twfI 122 2.01e+01 1i50I 122 2.01e+01 g.41.3.1,g.41.3.1 61762,61763 2etxA 209 2.07e+01 4eugA 229 2.09e+01 3eugA c.18.1.1 31019 1qtwA 285 2.15e+01 1qumA c.1.15.1 29392 1t0fA 276 2.15e+01 1yopA 83 2.19e+01 1uch 230 2.23e+01 1uch d.3.1.6 37129 1oahA 519 2.23e+01 a.138.1.3 86736 1scuA 288 2.31e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1xd3A 230 2.31e+01 2cx1A 187 2.32e+01 1o7eA 276 2.36e+01 e.3.1.1 92622 1lm5A 214 2.36e+01 d.211.2.1 74029 1n9dA 199 2.38e+01 a.26.1.1 85464 1qz5A 375 2.39e+01 c.55.1.1,c.55.1.1 96614,96615 1nigA 152 2.41e+01 a.25.2.1 85740 1z6uA 150 2.43e+01 1ifqA 138 2.43e+01 1ifqA d.110.4.1 62350 7taa 478 2.46e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1fl2A 310 2.48e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1uslA 170 2.52e+01 c.121.1.1 99871 1l1dA 152 2.53e+01 b.88.1.3 73452 1woyA 500 2.60e+01 1wxiA 275 2.69e+01 1ab4 477 2.69e+01 1ab4 e.11.1.1 43251 1ti6B 274 2.75e+01 b.3.5.1,d.58.1.5 106976,106977 1a78A 134 2.79e+01 1c1lA b.29.1.3 24212 1zu1A 127 2.79e+01 1dxsA 80 2.80e+01 1cokA a.60.1.2 17944 1zs7A 190 2.81e+01 2erxA 172 2.81e+01 1ywmA 200 2.86e+01 1dxgA 36 2.90e+01 1dxgA g.41.5.2 45247 1afp 51 2.97e+01 1afp g.26.1.1 44947 1zyoA 191 2.98e+01 1wjvA 79 3.00e+01 1p6pA 125 3.07e+01 b.60.1.2 87839 1ayfA 105 3.10e+01 1ayfA d.15.4.1 37684 2g8yA 385 3.13e+01 1t64A 377 3.14e+01 c.42.1.2 106543 2hrvA 142 3.15e+01 2hrvA b.47.1.4 26429 1r5mA 425 3.15e+01 1upiA 225 3.16e+01 b.82.1.1 99757 1i50L 70 3.17e+01 g.41.9.2 61766 1r61A 207 3.27e+01 c.8.8.1 97138 1vhqA 232 3.33e+01 c.23.16.2 100696 1evfA 264 3.34e+01 1bkpA d.117.1.1 40932 1zzpA 130 3.36e+01 1a7i 81 3.37e+01 1b8tA g.39.1.3,g.39.1.3 45143,45144 1puc 105 3.38e+01 1puc d.97.1.1 40675 1w2lA 99 3.45e+01 1fgs 428 3.47e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 1lp9E 194 3.48e+01 b.1.1.1,b.1.1.2 91086,91087 1a7cA 379 3.52e+01 1sek e.1.1.1 42660 1z52A 470 3.56e+01 2fiyA 309 3.57e+01 2cyeA 133 3.59e+01 1g0cA 364 3.63e+01 7a3hA c.1.8.3 60165 1k7hA 476 3.66e+01 c.76.1.1 72101 1e6eB 128 3.84e+01 1ayfA d.15.4.1 59300 1zclA 180 3.84e+01 1c3hA 137 3.86e+01 b.22.1.1 90405 1ji1A 637 4.00e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 2frnA 278 4.04e+01 1lj5A 379 4.05e+01 e.1.1.1 73928 1guiA 155 4.12e+01 b.18.1.14 76351 1yp8A 33 4.20e+01 1jmsA 381 4.24e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 2f6eA 127 4.31e+01 1yuiA 54 4.34e+01 1yuiA g.37.1.1 45073 1vetA 124 4.34e+01 d.110.7.1 108553 1uw2A 61 4.37e+01 g.37.1.4 108064 1oxdA 227 4.38e+01 d.22.1.1 93687 1gp1A 198 4.45e+01 1gp1A c.47.1.10 33059 1mg2D 155 4.47e+01 a.3.1.1 79062 1nrkA 328 4.59e+01 b.44.2.1,d.250.1.1 92089,92090 1am2 199 4.63e+01 1am2 b.86.1.2 28381 1m1qA 91 4.65e+01 a.138.1.3 74419 1ew4A 106 4.65e+01 1ew4A d.82.2.1 40023 1xkwA 665 4.69e+01 1cv8 174 4.69e+01 1cv8 d.3.1.1 37089 2ampA 304 4.75e+01 1jbwA 428 4.76e+01 c.59.1.2,c.72.2.2 62860,62861 1vor2 58 4.80e+01 2g8oA 264 4.81e+01 1sefA 274 4.86e+01 b.82.1.11 105452 2fs3A 282 4.88e+01 1tr9A 341 4.90e+01 1k0mA 241 4.94e+01 a.45.1.1,c.47.1.5 67949,67950 1k3eA 156 5.02e+01 d.198.1.1 68103 1i1kA 309 5.06e+01 1daaA e.17.1.1 61533 1u24A 337 5.13e+01 1uh4A 637 5.14e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1j6zA 376 5.17e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1z8fA 228 5.22e+01 1y5iB 512 5.31e+01 1r8oB 71 5.36e+01 1q16B 512 5.37e+01 d.58.1.5 95548 1zud1 251 5.38e+01 1vfyA 73 5.39e+01 1vfyA g.50.1.1 45357 1omiA 248 5.39e+01 b.82.3.3,a.4.5.4 87079,87080 2sicI 107 5.39e+01 3ssi d.84.1.1 40031 1lw7A 365 5.40e+01 c.26.1.3,c.37.1.1 74295,74296 2aujD 309 5.47e+01 1yt5A 258 5.53e+01 2a8lA 420 5.57e+01 1wgeA 83 5.58e+01 2g8mA 264 5.62e+01 1kdj 102 5.73e+01 1plc b.6.1.1 22864 1dekA 241 5.75e+01 1dekA c.37.1.1 31842 1y9uA 323 5.77e+01 1p5tA 127 5.83e+01 b.55.1.2 94148 1neeA 138 5.83e+01 d.241.1.1,g.59.1.1 91841,91842 1z02A 446 5.84e+01 1plq 258 5.86e+01 1plq d.131.1.2,d.131.1.2 41388,41389 1skoA 143 5.93e+01 d.110.7.1 105676 1ohgA 282 6.03e+01 d.183.1.1 93018 2bt6A 108 6.03e+01 1d09B 153 6.04e+01 8atcB d.58.2.1,g.41.7.1 39015,45267 1gpr 162 6.11e+01 1gpr b.84.3.1 28267 1p3jA 217 6.12e+01 c.37.1.1,g.41.2.1 94022,94023 2pspA 106 6.23e+01 2pspA g.16.1.1,g.16.1.1 44730,44731 2b9dA 52 6.31e+01 1preA 470 6.31e+01 1preA d.169.1.2,f.8.1.1 42437,43824 1e0eA 55 6.32e+01 1wjcA a.4.10.1 59147 1zx5A 300 6.38e+01 1vrmA 325 6.39e+01 2eu8A 216 6.45e+01 1qlnA 883 6.46e+01 1cezA e.8.1.3 43111 1uq5A 263 6.54e+01 d.165.1.1 99778 1ktjA 129 6.55e+01 b.1.18.7 72974 1zaaC 87 6.57e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45013,45014,45015 1fn9A 365 6.57e+01 1fn9A d.196.1.1 59894 1u0kA 288 6.58e+01 d.21.1.2,d.21.1.2 107547,107548 2fqaA 27 6.60e+01 1kz1A 159 6.62e+01 c.16.1.1 73318 1o9iA 266 6.65e+01 a.25.1.3 92671 1njqA 39 6.67e+01 g.37.1.3 85822 1g2fC 90 6.74e+01 k.12.1.1 60222 1dl0A 37 6.76e+01 1dl0A g.3.6.2 44112 1k0iA 394 6.89e+01 c.3.1.2,d.16.1.2 67942,67943 1nepA 130 6.93e+01 b.1.18.7 80440 1aayA 90 6.96e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45001,45002,45003 1v54F 98 6.98e+01 g.41.5.3 100327 2ewrA 170 7.01e+01 2f8aA 208 7.02e+01 1abrA 251 7.08e+01 1mrj d.165.1.1 42196 1jbbA 153 7.09e+01 1u9aA d.20.1.1 62842 1u2xA 474 7.18e+01 c.72.1.3 107622 1x31D 99 7.20e+01 1y75B 118 7.20e+01 1ywzA 175 7.20e+01 1erd 40 7.21e+01 1erd a.10.1.1 16362 1v0jA 399 7.24e+01 1jatA 155 7.25e+01 1u9aA d.20.1.1 62818 1j3mA 129 7.27e+01 d.129.7.1 103836 1tfuA 157 7.33e+01 c.26.1.3 106859 1xakA 83 7.35e+01 1ykjA 394 7.43e+01 1zsqA 528 7.43e+01 1oi7A 288 7.55e+01 c.2.1.8,c.23.4.1 87049,87050 2fn4A 181 7.56e+01 1wimA 94 7.60e+01 1d4oA 184 7.62e+01 1d4oA c.31.1.4 31748 1c7qA 445 7.63e+01 2pgi c.80.1.2 35307 2airB 153 7.64e+01 1rgyA 360 7.72e+01 e.3.1.1 97456 1wuaA 375 7.77e+01 1ze3C 205 7.82e+01 1bu7A 455 7.90e+01 1bu7A a.104.1.1 18937 1z94A 147 7.93e+01 1v8eA 224 7.96e+01 1cxqA 162 7.98e+01 1cxqA c.55.3.2 33621 1jb0F 164 8.04e+01 1jb0F f.23.16.1 62825 1ep0A 185 8.23e+01 1dzrA b.82.1.1 28080 1ema 236 8.24e+01 1ema d.22.1.1 38339 1ht6A 405 8.31e+01 b.71.1.1,c.1.8.1 83629,83630 1cwvA 492 8.36e+01 1cwvA b.1.14.1,b.1.14.1,b.1.14.1,b.1.14.1,d.169.1.3 22373,22374,22375,22376,42442 1jkvA 266 8.42e+01 a.25.1.3 71719 1vd6A 224 8.44e+01 1qciA 262 8.44e+01 1qi7A d.165.1.1 42201 1iugA 352 8.44e+01 c.67.1.3 90699 1pwxA 254 8.45e+01 c.2.1.2 95262 2apoB 60 8.46e+01 1kkeA 210 8.49e+01 b.21.1.2,b.83.1.2 68669,68670 2fa8A 105 8.74e+01 1h3nA 878 8.78e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 2fo3A 125 8.84e+01 2occF 98 8.91e+01 2occF g.41.5.3 45256 1z60A 59 8.96e+01 1zxuA 217 8.96e+01