# 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 2.38e-01 g.41.8.1 105345 1odhA 174 2.51e-01 d.239.1.1 86850 1vqoZ 83 2.84e-01 1ur6B 52 2.91e-01 g.44.1.1 99812 1vk6A 269 3.29e-01 d.113.1.4,d.113.1.4 100851,100852 1kmtA 141 3.72e-01 b.1.18.8 77442 2cklB 165 5.05e-01 1wd2A 60 8.49e-01 g.44.1.1 109232 1fsoA 139 1.06e+00 1rhoA b.1.18.8 60007 1dgfA 497 1.11e+00 1cf9A e.5.1.1 42782 2ct7A 86 1.17e+00 1d4xA 375 1.27e+00 1yagA c.55.1.1,c.55.1.1 59107,59108 2fqpA 97 1.36e+00 1dgaA 375 1.41e+00 1yagA 1vd4A 62 1.46e+00 1jm1A 204 1.48e+00 b.33.1.1 71745 1x75A 132 1.51e+00 1vckA 115 1.57e+00 1jj2Y 73 1.70e+00 1ffkW g.41.8.1 63110 1ww8A 439 1.74e+00 1rlyA 60 1.84e+00 g.41.3.1 104988 2aq6A 147 2.38e+00 2btfA 375 2.38e+00 1yagA c.55.1.1,c.55.1.1 33429,33430 1yl35 60 2.49e+00 2a8mA 420 2.59e+00 1pu6A 218 2.71e+00 a.96.1.5 95123 2a20A 62 2.76e+00 1qxfA 66 3.09e+00 g.41.8.4 96527 1l7bA 92 3.12e+00 c.15.1.2 91053 1ee8A 266 3.25e+00 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1wrvA 308 3.50e+00 1d0qA 103 3.58e+00 1d0qA g.41.3.2 45208 1bq9A 54 3.75e+00 1rb9 g.41.5.1 45238 1brfA 53 3.93e+00 1rb9 g.41.5.1 45236 1xxoA 147 4.07e+00 2sak 121 4.11e+00 2sak d.15.5.1 37711 2a1rA 430 4.14e+00 1r6lA 239 4.28e+00 d.14.1.4,d.101.1.1 97153,97154 1dl6A 58 4.37e+00 1dl6A g.41.3.1 45207 1ile 821 4.45e+00 1ile a.27.1.1,b.51.1.1,c.26.1.1 16924,26889,31591 1rfs 139 4.46e+00 1rfs b.33.1.1 24434 1w9aA 147 4.63e+00 1rb9 53 4.64e+00 1rb9 g.41.5.1 45214 2adoA 196 4.69e+00 1rmd 116 4.72e+00 1rmd g.37.1.1,g.44.1.1 45025,45322 1k7cA 233 4.98e+00 c.23.10.4 68267 1vphA 149 5.14e+00 1zd9A 188 5.21e+00 1yk4A 52 5.22e+00 1u79A 129 5.24e+00 d.26.1.1 107714 2a8jA 420 5.34e+00 2c1xA 456 5.57e+00 1theA 260 6.02e+00 1theB d.3.1.1 37056 1zxzA 197 6.04e+00 1yovA 537 6.21e+00 1q68B 29 6.21e+00 j.108.1.1 95963 1q35A 320 6.48e+00 c.94.1.1 95661 1ww9A 392 6.51e+00 1rutX 188 6.52e+00 1exkA 79 6.65e+00 1exkA g.54.1.1 45384 1mr1C 99 6.81e+00 d.217.1.2 79420 1vq0A 302 6.93e+00 1f4lA 551 7.02e+00 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1wfeA 86 7.05e+00 1rdg 53 7.34e+00 1rb9 g.41.5.1 45221 1qz5A 375 7.35e+00 c.55.1.1,c.55.1.1 96614,96615 1lvoA 302 7.61e+00 b.47.1.4 74284 1pfvA 551 7.78e+00 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1v87A 114 7.99e+00 g.44.1.1 108422 1nykA 165 8.01e+00 b.33.1.1 86408 1w2lA 99 8.44e+00 1hvyA 288 8.83e+00 1bkpA d.117.1.1 41049 1ptq 50 8.92e+00 1ptq g.49.1.1 45349 2csvA 72 9.04e+00 1l1oC 181 9.13e+00 b.40.4.3 73480 1nv8A 284 9.46e+00 c.66.1.30 86224 1wraA 308 9.84e+00 1zyoA 191 1.00e+01 2etxA 209 1.02e+01 2bibA 547 1.02e+01 3daaA 277 1.04e+01 1daaA e.17.1.1 43272 1iyeA 309 1.04e+01 e.17.1.1 83786 1qtwA 285 1.07e+01 1qumA c.1.15.1 29392 1zkkA 167 1.08e+01 1l8dA 112 1.09e+01 h.4.12.1 73687 2cklA 108 1.10e+01 2an1A 292 1.12e+01 1zy1B 197 1.14e+01 2aaa 484 1.20e+01 7taa b.71.1.1,c.1.8.1 27777,28764 1upiA 225 1.21e+01 b.82.1.1 99757 1lv3A 68 1.21e+01 g.39.1.9 78231 2bx9A 53 1.22e+01 1ifqA 138 1.23e+01 1ifqA d.110.4.1 62350 1ypvA 313 1.23e+01 1y3nA 490 1.24e+01 6rxn 46 1.26e+01 1rb9 g.41.5.1 45222 1zin 217 1.26e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1twfL 70 1.26e+01 1mea 28 1.27e+01 g.41.1.1 45176 1sur 215 1.28e+01 1sur c.26.2.2 31620 1zip 217 1.30e+01 1zin c.37.1.1,g.41.2.1 31916,45179 1k8kA 418 1.31e+01 c.55.1.1,c.55.1.1 68305,68306 1deoA 233 1.34e+01 1deoA c.23.10.4 31345 1iro 54 1.40e+01 1rb9 g.41.5.1 45223 2cx1A 187 1.42e+01 1wr8A 231 1.45e+01 1weoA 93 1.48e+01 1o12A 376 1.49e+01 b.92.1.5,c.1.9.10 80758,80759 1m22A 503 1.52e+01 c.117.1.1 78464 1jj2F 119 1.52e+01 1ffkE d.79.3.1 63091 1ldjB 90 1.53e+01 g.44.1.1 73850 1woyA 500 1.59e+01 1twfI 122 1.59e+01 1i50I 122 1.60e+01 g.41.3.1,g.41.3.1 61762,61763 4eugA 229 1.66e+01 3eugA c.18.1.1 31019 1sp1 29 1.70e+01 g.37.1.1 45051 1yopA 83 1.72e+01 1wjpA 107 1.75e+01 1inp 400 1.82e+01 1inp e.7.1.1 42972 1zs7A 190 1.83e+01 1neeA 138 1.86e+01 d.241.1.1,g.59.1.1 91841,91842 1z6uA 150 1.89e+01 1f1zA 273 1.91e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 1ab4 477 1.93e+01 1ab4 e.11.1.1 43251 1tqnA 486 1.96e+01 a.104.1.1 107238 1ti6B 274 1.99e+01 b.3.5.1,d.58.1.5 106976,106977 1x31D 99 2.00e+01 1j6zA 376 2.05e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1guiA 155 2.06e+01 b.18.1.14 76351 1kbeA 49 2.06e+01 g.49.1.1 68380 1jmsA 381 2.07e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1ty9A 222 2.07e+01 1bc8C 93 2.07e+01 1awcA a.4.5.21 16168 1c3hA 137 2.09e+01 b.22.1.1 90405 1uch 230 2.12e+01 1uch d.3.1.6 37129 1r5mA 425 2.12e+01 1fl2A 310 2.13e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1puc 105 2.13e+01 1puc d.97.1.1 40675 1xd3A 230 2.14e+01 1wxiA 275 2.15e+01 1fgs 428 2.16e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 1tr9A 341 2.17e+01 1t64A 377 2.26e+01 c.42.1.2 106543 2cszA 76 2.31e+01 7taa 478 2.31e+01 7taa b.71.1.1,c.1.8.1 27778,28765 1dxgA 36 2.35e+01 1dxgA g.41.5.2 45247 1q33A 292 2.37e+01 d.113.1.1 95657 1a7i 81 2.43e+01 1b8tA g.39.1.3,g.39.1.3 45143,45144 1afp 51 2.45e+01 1afp g.26.1.1 44947 1t0fA 276 2.45e+01 1vhqA 232 2.51e+01 c.23.16.2 100696 2g8yA 385 2.53e+01 1n9dA 199 2.55e+01 a.26.1.1 85464 2ampA 304 2.63e+01 1zu1A 127 2.75e+01 1ayfA 105 2.76e+01 1ayfA d.15.4.1 37684 1dxsA 80 2.77e+01 1cokA a.60.1.2 17944 2fiyA 309 2.80e+01 1scuA 288 2.83e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 2erxA 172 2.87e+01 1k0iA 394 2.90e+01 c.3.1.2,d.16.1.2 67942,67943 1jbwA 428 2.90e+01 c.59.1.2,c.72.2.2 62860,62861 1i50L 70 2.98e+01 g.41.9.2 61766 1ykjA 394 3.01e+01 1nigA 152 3.01e+01 a.25.2.1 85740 1wjvA 79 3.06e+01 2hrvA 142 3.15e+01 2hrvA b.47.1.4 26429 1vfyA 73 3.33e+01 1vfyA g.50.1.1 45357 1ywmA 200 3.38e+01 1uc8A 280 3.42e+01 c.30.1.6,d.142.1.7 99165,99166 1oahA 519 3.42e+01 a.138.1.3 86736 1qqqA 264 3.55e+01 1bkpA d.117.1.1 40931 1vetA 124 3.59e+01 d.110.7.1 108553 1e6eB 128 3.61e+01 1ayfA d.15.4.1 59300 1c4kA 730 3.61e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1k7hA 476 3.62e+01 c.76.1.1 72101 1vor2 58 3.65e+01 1m5wA 243 3.77e+01 c.1.24.1 84836 1plq 258 3.80e+01 1plq d.131.1.2,d.131.1.2 41388,41389 2b9dA 52 3.82e+01 1dekA 241 3.87e+01 1dekA c.37.1.1 31842 1xmxA 385 3.98e+01 1yuiA 54 3.99e+01 1yuiA g.37.1.1 45073 1nrkA 328 4.00e+01 b.44.2.1,d.250.1.1 92089,92090 1d09B 153 4.01e+01 8atcB d.58.2.1,g.41.7.1 39015,45267 2ewrA 170 4.01e+01 1g38A 393 4.02e+01 2admA c.66.1.27 60235 1j3mA 129 4.03e+01 d.129.7.1 103836 1trb 320 4.11e+01 1trb c.3.1.5,c.3.1.5 30529,30530 1ji1A 637 4.11e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1s5aA 150 4.16e+01 d.17.4.10 98525 1uw2A 61 4.17e+01 g.37.1.4 108064 1o7eA 276 4.23e+01 e.3.1.1 92622 1xtqA 177 4.25e+01 1u24A 337 4.28e+01 1oqjA 97 4.30e+01 d.217.1.1 93417 1wuaA 375 4.30e+01 1i1kA 309 4.31e+01 1daaA e.17.1.1 61533 1yc5A 246 4.33e+01 1zud1 251 4.40e+01 1zclA 180 4.44e+01 1mswD 883 4.46e+01 e.8.1.3 79427 1lp9E 194 4.48e+01 b.1.1.1,b.1.1.2 91086,91087 1lm5A 214 4.53e+01 d.211.2.1 74029 1m1qA 91 4.56e+01 a.138.1.3 74419 1a78A 134 4.57e+01 1c1lA b.29.1.3 24212 1wgeA 83 4.58e+01 830cA 168 4.59e+01 1ck7A d.92.1.11 40400 1xkwA 665 4.60e+01 1k0mA 241 4.60e+01 a.45.1.1,c.47.1.5 67949,67950 1ho1A 242 4.61e+01 1ho1A c.1.24.1 61097 1zzpA 130 4.62e+01 1cxqA 162 4.63e+01 1cxqA c.55.3.2 33621 1p3jA 217 4.64e+01 c.37.1.1,g.41.2.1 94022,94023 1y5iB 512 4.71e+01 1q16B 512 4.73e+01 d.58.1.5 95548 1u5kA 244 4.73e+01 1cwvA 492 4.74e+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 1am2 199 4.74e+01 1am2 b.86.1.2 28381 1r61A 207 4.76e+01 c.8.8.1 97138 1z94A 147 4.77e+01 1d4oA 184 4.78e+01 1d4oA c.31.1.4 31748 1lw7A 365 4.88e+01 c.26.1.3,c.37.1.1 74295,74296 1ep0A 185 4.89e+01 1dzrA b.82.1.1 28080 2sicI 107 4.90e+01 3ssi d.84.1.1 40031 1oi6A 205 4.92e+01 b.82.1.1 103940 1v54F 98 4.95e+01 g.41.5.3 100327 2frnA 278 4.97e+01 1z8fA 228 5.02e+01 1ovxA 67 5.06e+01 g.39.1.11 93622 2fg1A 158 5.07e+01 1pbe 394 5.09e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 1yp8A 33 5.10e+01 1yt5A 258 5.10e+01 1a7cA 379 5.17e+01 1sek e.1.1.1 42660 1o9iA 266 5.22e+01 a.25.1.3 92671 1zaaC 87 5.25e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45013,45014,45015 1ht6A 405 5.28e+01 b.71.1.1,c.1.8.1 83629,83630 1uq5A 263 5.30e+01 d.165.1.1 99778 1ofnA 205 5.33e+01 b.82.1.1 92830 1z52A 470 5.36e+01 1aayA 90 5.39e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 45001,45002,45003 1ihoA 283 5.40e+01 1ihoA c.26.1.4 62390 1skoA 143 5.43e+01 d.110.7.1 105676 1uh4A 637 5.45e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 2fqaA 27 5.45e+01 1a8h 500 5.46e+01 1a8h a.27.1.1,c.26.1.1 16922,31589 1zxuA 217 5.49e+01 1njqA 39 5.51e+01 g.37.1.3 85822 1g2fC 90 5.53e+01 k.12.1.1 60222 2airB 153 5.58e+01 1uslA 170 5.66e+01 c.121.1.1 99871 2f4mA 295 5.66e+01 1p5tA 127 5.68e+01 b.55.1.2 94148 1lj5A 379 5.68e+01 e.1.1.1 73928 1p6pA 125 5.70e+01 b.60.1.2 87839 2apoB 60 5.77e+01 1l1dA 152 5.83e+01 b.88.1.3 73452 1wimA 94 5.87e+01 1abrA 251 5.92e+01 1mrj d.165.1.1 42196 2bt6A 108 5.92e+01 1g8aA 227 6.00e+01 c.66.1.3 90506 1omiA 248 6.14e+01 b.82.3.3,a.4.5.4 87079,87080 1u69A 163 6.18e+01 d.32.1.7 107699 1jkvA 266 6.27e+01 a.25.1.3 71719 1tfuA 157 6.37e+01 c.26.1.3 106859 1kkeA 210 6.40e+01 b.21.1.2,b.83.1.2 68669,68670 1evfA 264 6.42e+01 1bkpA d.117.1.1 40932 1v8eA 224 6.43e+01 2f6eA 127 6.46e+01 2occF 98 6.49e+01 2occF g.41.5.3 45256 1v0jA 399 6.60e+01 1mg2D 155 6.71e+01 a.3.1.1 79062 1vd6A 224 6.85e+01 1y9uA 323 6.89e+01 2fxuA 375 6.94e+01 2ahuA 531 6.95e+01 1h3nA 878 7.02e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 2afgA 140 7.06e+01 1bfg b.42.1.1 25514 1oxdA 227 7.11e+01 d.22.1.1 93687 2fn4A 181 7.12e+01 2fs3A 282 7.20e+01 1oi7A 288 7.22e+01 c.2.1.8,c.23.4.1 87049,87050 1d2vA 104 7.30e+01 1d2vA a.93.1.2 18697 1clvI 32 7.36e+01 1qfdA g.3.2.1 44075 2avuE 192 7.44e+01 1e4yA 214 7.45e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1mxgA 435 7.47e+01 b.71.1.1,c.1.8.1 85193,85194 2au3A 407 7.67e+01 1vrmA 325 7.71e+01 1bu7A 455 7.73e+01 1bu7A a.104.1.1 18937 1cv8 174 7.76e+01 1cv8 d.3.1.1 37089 1t0bA 252 7.77e+01 c.23.16.6 106199 1z60A 59 7.83e+01 1e0eA 55 7.84e+01 1wjcA a.4.10.1 59147 1ej1A 190 7.86e+01 1ejhA d.86.1.1 40144 1jpzA 473 7.88e+01 a.104.1.1 67069 1e53A 59 7.91e+01 1e53A g.49.1.2 45356 1jb0F 164 7.99e+01 1jb0F f.23.16.1 62825 2gatA 66 7.99e+01 1gatA g.39.1.1 45102 2cfuA 658 8.01e+01 1g0cA 364 8.04e+01 7a3hA c.1.8.3 60165 1cxpA 104 8.05e+01 1d2vA a.93.1.2 18695 1qciA 262 8.07e+01 1qi7A d.165.1.1 42201 1sefA 274 8.07e+01 b.82.1.11 105452 1xtzA 264 8.15e+01 1i76A 163 8.26e+01 1hfc d.92.1.11 61877 1xakA 83 8.32e+01 1z02A 446 8.35e+01 1l6wA 220 8.37e+01 c.1.10.1 73632 1u4gA 301 8.41e+01 d.92.1.2 107670 1kz1A 159 8.46e+01 c.16.1.1 73318 1gp1A 198 8.59e+01 1gp1A c.47.1.10 33059 2bhvA 246 8.60e+01 1c7qA 445 8.61e+01 2pgi c.80.1.2 35307 1rie 129 8.68e+01 1rie b.33.1.1 24427 1g66A 207 8.69e+01 1bs9 c.69.1.30 31329 1a1iA 90 8.70e+01 1aayA g.37.1.1,g.37.1.1,g.37.1.1 44998,44999,45000 1jovA 270 8.76e+01 b.30.5.7 84192 1zsqA 528 8.81e+01 1eyeA 280 8.89e+01 1aj2 c.1.21.1 29672