# List of top-scoring protein chains for t2k-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 1ji8A 111 5.52e-01 d.203.1.1 66733 1ijbA 202 1.06e+00 c.62.1.1 71229 1xoyA 161 1.13e+00 1k3xA 262 1.43e+00 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1auq 208 1.50e+00 1auq c.62.1.1 34137 1oshA 232 1.86e+00 a.123.1.1 93496 1mugA 168 2.03e+00 1mugA c.18.1.2 31030 1fnsA 196 2.71e+00 1auq c.62.1.1 34136 1ysqA 193 2.92e+00 1sjqA 105 3.58e+00 d.58.7.1 105660 1j93A 353 4.02e+00 c.1.22.1 66454 1bh9A 45 4.30e+00 1bh9A a.22.1.3 16483 1klnA 605 4.46e+00 1xwl c.55.3.5,e.8.1.1 33693,42986 1oakA 196 5.05e+00 1auq c.62.1.1 34138 1b3bA 415 5.24e+00 1hwyA c.2.1.7,c.58.1.1 30244,33892 1oj4A 283 5.25e+00 d.14.1.5,d.58.26.5 93083,93084 2gi3A 476 5.67e+00 2kfnA 605 5.86e+00 1xwl c.55.3.5,e.8.1.1 33682,42975 1d8yA 605 7.05e+00 1xwl c.55.3.5,e.8.1.1 33684,42977 1b26A 416 8.11e+00 1hwyA c.2.1.7,c.58.1.1 30232,33880 4lbd 267 8.94e+00 2lbd a.123.1.1 19289 1kopA 223 9.23e+00 2cba b.74.1.1 27966 1yvoA 172 9.26e+00 1kfd 605 9.37e+00 1xwl c.55.3.5,e.8.1.1 33694,42987 1fcyA 236 9.53e+00 2lbd a.123.1.1 19282 1v1rA 400 9.72e+00 c.36.1.11 108272 1vq0A 302 9.79e+00 1vjpA 394 1.00e+01 c.2.1.3,d.81.1.3 100828,100829 1ae1A 273 1.09e+01 1bdb c.2.1.2 29943 1vhmA 195 1.10e+01 d.110.2.1 100691 2lbd 267 1.12e+01 2lbd a.123.1.1 19287 1souA 194 1.13e+01 c.124.1.6 105858 1ea0A 1479 1.18e+01 b.80.4.1,c.1.4.1,d.153.1.1 64854,64855,64856 1yqdA 366 1.19e+01 1u6zA 513 1.20e+01 1mat 264 1.25e+01 1c24A d.127.1.1 41152 1no7A 604 1.34e+01 e.48.1.1 92016 1lshA 1056 1.35e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 2bduA 297 1.38e+01 2cy0A 263 1.45e+01 1o0xA 262 1.46e+01 d.127.1.1 80755 2g09A 297 1.46e+01 1gmwA 143 1.47e+01 b.107.1.1,d.58.38.1 65347,65348 2matA 264 1.49e+01 1c24A d.127.1.1 41146 1c24A 263 1.52e+01 1c24A d.127.1.1 41148 4matA 278 1.55e+01 1c24A d.127.1.1 41150 1xnzA 264 1.60e+01 2bl1A 172 1.78e+01 1z54A 132 1.79e+01 2bfdA 400 1.79e+01 1wxdA 263 1.85e+01 2d5cA 263 1.91e+01 1mkmA 249 1.93e+01 a.4.5.33,d.110.2.2 79242,79243 1oqjA 97 1.96e+01 d.217.1.1 93417 1x7yA 400 1.97e+01 1dzkA 157 1.97e+01 1obpA b.60.1.1 27096 2ggcA 263 2.00e+01 1gz6A 319 2.02e+01 c.2.1.2 76410 1h6tA 291 2.04e+01 b.1.18.15,c.10.2.1 65686,65687 1s7kA 182 2.05e+01 1gmuA 143 2.09e+01 b.107.1.1,d.58.38.1 65335,65336 1b6q 63 2.21e+01 1nkd a.30.1.1 16977 1hwxA 501 2.25e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 1olsA 400 2.25e+01 c.36.1.11 93331 1gtmA 419 2.31e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1dovA 181 2.38e+01 1dovA a.24.9.1 16627 1vl2A 421 2.39e+01 c.26.2.1,d.210.1.1 108708,108709 2es7A 142 2.46e+01 1yq2A 1024 2.56e+01 1zuhA 168 2.60e+01 1ul4A 94 2.60e+01 g.72.1.1 99538 1wkoA 180 2.64e+01 2g38B 198 2.67e+01 1qeyA 31 2.72e+01 1qeyA h.2.1.1 45666 1vrmA 325 2.72e+01 1ryp2 233 2.75e+01 1ryp2 1jfmA 174 2.83e+01 d.19.1.1 66640 2a74B 188 2.84e+01 1wgeA 83 2.88e+01 1wywA 230 2.89e+01 1olrA 224 2.96e+01 b.29.1.11 93330 1s14A 194 2.97e+01 d.122.1.2 98329 1ohgA 282 2.99e+01 d.183.1.1 93018 1uyjA 296 3.00e+01 f.8.1.2 108143 1qynA 153 3.02e+01 d.33.1.1 96597 3grx 82 3.02e+01 1aba c.47.1.1 32769 1ffk1 177 3.08e+01 1ffk1 1t01B 24 3.21e+01 1mc0A 368 3.22e+01 d.110.2.1,d.110.2.1 78937,78938 1q77A 138 3.26e+01 c.26.2.4 96023 2ch4A 320 3.38e+01 1g0u1 266 3.39e+01 1m9sA 605 3.40e+01 b.1.18.15,b.34.11.1,b.34.11.1,b.34.11.1,c.10.2.1 78874,78875,78876,78877,78878 1fit 147 3.43e+01 1fit d.13.1.1 37499 1fx3B 169 3.46e+01 1fx3B d.33.1.1 38525 1b94A 244 3.54e+01 1rvaA c.52.1.2 33250 1lf7A 182 3.55e+01 b.60.1.1 73878 1wl9A 440 3.58e+01 1vrpA 381 3.62e+01 1bccD 241 3.70e+01 1be3D a.3.1.3,f.23.11.1 15959,43698 1ukfA 188 3.75e+01 d.3.1.10 99488 2fs3A 282 3.83e+01 1vprA 374 3.90e+01 1rvaA 244 3.92e+01 1rvaA c.52.1.2 33240 1k2eA 156 4.06e+01 d.113.1.1 72010 1forL 210 4.06e+01 8fabA b.1.1.1,b.1.1.2 19988,21044 2gz4A 207 4.09e+01 1ieaA 192 4.12e+01 1iakA b.1.1.2,d.19.1.1 21631,38205 1qltA 560 4.14e+01 1qltA d.58.32.1,d.145.1.1 39457,41720 1axtL 216 4.15e+01 8fabA b.1.1.1,b.1.1.2 20304,21296 1by5A 714 4.16e+01 1by5A f.4.3.3 43800 2c3vA 102 4.19e+01 1b1gA 75 4.20e+01 1psrA a.39.1.1 17151 1us8A 147 4.26e+01 c.37.1.12 99859 1z0nA 96 4.28e+01 1az9 457 4.29e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1a16 440 4.30e+01 1az9 c.55.2.1,d.127.1.1 33548,41165 1b3qA 379 4.34e+01 1b3qA a.30.2.1,b.40.7.1,d.122.1.3 16993,25454,41112 1wjtA 103 4.36e+01 2exrA 524 4.40e+01 2b8eA 273 4.40e+01 1uujA 88 4.42e+01 a.221.1.1 108046 1v7rA 186 4.48e+01 c.51.4.1 100482 1g5aA 628 4.56e+01 b.71.1.1,c.1.8.1 65152,65153 2bwvA 440 4.61e+01 1g7pB 99 4.61e+01 b.1.1.2 70155 1fngA 192 4.62e+01 1iakA b.1.1.2,d.19.1.1 59904,59905 1bssA 244 4.73e+01 1rvaA c.52.1.2 33256 2h4uA 145 4.75e+01 1o0pA 104 4.77e+01 d.58.7.1 86535 1h7sA 365 4.77e+01 d.14.1.3,d.122.1.2 65705,65706 1ht9A 76 4.77e+01 4icb a.39.1.1 61252 1mg7A 417 4.85e+01 d.14.1.6,d.58.26.6 84954,84955 1z0mA 96 4.89e+01 1jj2E 177 4.91e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1fneA 192 4.92e+01 1iakA b.1.1.2,d.19.1.1 59896,59897 1bdmA 327 5.02e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1s1eA 224 5.04e+01 1s72E 178 5.06e+01 d.141.1.1,d.141.1.1 105323,105324 1w1kA 560 5.07e+01 d.58.32.1,d.145.1.1 109059,109060 1eteA 134 5.12e+01 1eteA a.26.1.2 16869 1mkyA 439 5.14e+01 c.37.1.8,c.37.1.8,d.52.5.1 79250,79251,79252 1i58A 189 5.16e+01 1b3qA d.122.1.3 61773 1t1jA 125 5.18e+01 c.137.1.1 106249 1phk 298 5.37e+01 1cdkA d.144.1.7 41635 1vaoA 560 5.54e+01 1qltA d.58.32.1,d.145.1.1 39461,41724 4icb 76 5.56e+01 4icb a.39.1.1 17145 1mioA 534 5.68e+01 1qguA c.92.2.3 35601 1e9lA 377 5.69e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1u8vA 490 5.73e+01 1b97A 244 5.73e+01 1rvaA c.52.1.2 33252 1n67A 359 5.73e+01 b.2.3.4,b.2.3.4 85354,85355 1b96A 244 5.73e+01 1rvaA c.52.1.2 33268 1h2xA 710 5.73e+01 b.69.7.1,c.69.1.4 76598,76599 1bdmB 327 5.99e+01 1bmdA c.2.1.5,d.162.1.1 30138,42105 3fisA 98 6.01e+01 1fipA a.4.1.12 18994 1zpyA 95 6.01e+01 1bmdA 327 6.04e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 1csbB 205 6.07e+01 1theB 1dysA 348 6.07e+01 1bvwA c.6.1.1 30669 1x31D 99 6.10e+01 1jk7A 323 6.14e+01 1auiA d.159.1.3 63144 1u32A 293 6.15e+01 d.159.1.3 107631 1vqoE 178 6.17e+01 1ex2A 189 6.18e+01 1ex2A c.51.4.2 33225 1vp4A 425 6.22e+01 1fr2B 134 6.25e+01 d.4.1.1 83257 1sx5A 244 6.26e+01 c.52.1.2 99023 1vf6A 83 6.32e+01 a.194.1.1 100600 1fzoB 99 6.33e+01 1agdB b.1.1.2 60157 1lssA 140 6.42e+01 c.2.1.9 74246 1vf8A 377 6.53e+01 1qfmA 710 6.53e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 2ethA 154 6.59e+01 2d8aA 348 6.61e+01 1lk2B 99 6.61e+01 b.1.1.2 91058 2f1lA 187 6.61e+01 1e8gA 560 6.61e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1cb2A 365 6.61e+01 1bvwA c.6.1.1 30661 1u3aA 189 6.73e+01 1qjwA 365 6.75e+01 1bvwA c.6.1.1 30657 1dqnA 230 6.77e+01 1dqnA c.61.1.1 34067 1ax4A 467 6.77e+01 1ax4A c.67.1.2 34391 2fa8A 105 6.80e+01 1bdb 277 6.82e+01 1bdb c.2.1.2 29874 2aqjA 538 6.82e+01 1s0yA 76 6.93e+01 d.80.1.1 98314 2gf6A 135 6.93e+01 1pf4A 582 6.97e+01 c.37.1.12,f.37.1.1 88052,88053 2bhvA 246 7.00e+01 1kpuB 99 7.03e+01 b.1.1.2 84458 1fzkB 99 7.08e+01 1agdB b.1.1.2 60151 1ttwA 138 7.16e+01 d.198.1.1 107308 1vhcA 224 7.23e+01 c.1.10.1 100661 1fs7A 485 7.23e+01 1qdbA a.138.1.3 19691 2ad9A 119 7.24e+01 1odkA 235 7.25e+01 c.56.2.1 86863 1emvB 134 7.36e+01 1bxiB d.4.1.1 37135 1khbA 625 7.38e+01 c.91.1.1,c.109.1.1 68606,68607 1b04A 318 7.39e+01 1b04A d.142.2.2 41579 1w0bA 102 7.41e+01 a.7.11.1 108985 1s69A 124 7.42e+01 a.1.1.1 105305 1zfd 32 7.42e+01 1zfd g.37.1.1 45039 1ee8A 266 7.45e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1u9iA 519 7.52e+01 1a5t 334 7.57e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1kjvB 100 7.60e+01 b.1.1.2 77423 1w6uA 302 7.64e+01 1e8nA 710 7.65e+01 1qfmA b.69.7.1,c.69.1.4 27675,34643 1eonA 245 7.72e+01 1rvaA c.52.1.2 33238 1uuqA 440 7.75e+01 c.1.8.3 100015 1iw2A 182 7.75e+01 b.60.1.1 71468 1ym5A 300 7.76e+01 1y7tA 327 7.78e+01 1ztxL 212 7.78e+01 1iakB 185 7.79e+01 1iakB b.1.1.2,d.19.1.1 21626,38200 1bxiB 134 7.83e+01 1bxiB d.4.1.1 37136 1g0sA 209 7.89e+01 1g0sA d.113.1.1 60187 1a05A 358 7.92e+01 1cnzA c.77.1.1 35059 1dowA 205 7.94e+01 1dovA a.24.9.1 16626 2fhi 147 8.05e+01 1fit d.13.1.1 37505 1snzA 344 8.06e+01 b.30.5.4 98930 1theB 260 8.08e+01 1theB d.3.1.1 37057 1a3rL 220 8.08e+01 8fabA b.1.1.1,b.1.1.2 19780,20890 1x0tA 120 8.12e+01 1jenB 67 8.12e+01 1jenB d.156.1.1 42029 1y01A 102 8.15e+01 2c6cA 707 8.20e+01 1ey2A 471 8.22e+01 1ey2A b.82.1.4 28116 2d9rA 104 8.22e+01 1a6tA 210 8.22e+01 8fabA b.1.1.1,b.1.1.2 20248,21258 1v8dA 235 8.23e+01 c.140.1.1 108425 1o6zA 303 8.32e+01 c.2.1.5,d.162.1.1 81107,81108 1sctB 151 8.34e+01 3sdhA a.1.1.2 15003 2g30A 258 8.35e+01 1gyxA 76 8.40e+01 d.80.1.1 76387 1o5iA 249 8.43e+01 c.2.1.2 92499 1owfA 99 8.62e+01 a.55.1.1 87487 1rtxA 123 8.63e+01 a.1.1.1 97827 1ac1A 189 8.63e+01 1fvkA c.47.1.13 90326 1r2zA 274 8.69e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1z8uA 102 8.76e+01 1itxA 419 8.79e+01 c.1.8.5,d.26.3.1 71425,71426 1m4jA 142 8.81e+01 d.109.1.2 78602 3icb 75 8.83e+01 4icb a.39.1.1 17147 2fxqA 264 8.92e+01 1dqpA 230 8.95e+01 1dqnA c.61.1.1 34069 1jjoC 261 8.98e+01 1ihfA 99 8.99e+01 1huuA a.55.1.1 17893