# List of top-scoring protein chains for t2k-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 1atg 231 8.70e-04 1atg c.94.1.1 35834 1ispA 181 2.45e-01 c.69.1.18 76778 2dcnA 311 3.29e-01 1zr6A 503 4.13e-01 1uarA 285 5.18e-01 c.46.1.2,c.46.1.2 107762,107763 1amf 233 5.18e-01 1wod c.94.1.1 35833 1zghA 260 5.84e-01 1sc3A 178 8.48e-01 c.17.1.1 105416 1jetA 517 1.11e+00 1jevA c.94.1.1 35718 1k9uA 78 1.24e+00 a.39.1.10 84348 2c2aA 258 1.26e+00 1xocA 520 1.45e+00 2ajrA 331 1.46e+00 2bvfA 459 1.59e+00 1t6nA 220 1.74e+00 c.37.1.19 106576 1c7gA 456 1.76e+00 c.67.1.2 90415 1tib 269 1.89e+00 3tgl c.69.1.17 34738 1kllA 130 2.05e+00 d.32.1.2 72720 1kafA 108 2.14e+00 d.199.1.1 68372 1wy9A 147 2.35e+00 1tqyB 415 2.37e+00 c.95.1.1,c.95.1.1 107247,107248 1jysA 242 2.48e+00 c.56.2.1 77216 1uhnA 189 2.55e+00 a.39.1.5 99399 1ywqA 200 2.69e+00 1t5hX 504 2.85e+00 e.23.1.1 106449 1x9iA 302 3.63e+00 1zavA 180 3.88e+00 1lssA 140 3.96e+00 c.2.1.9 74246 1pyoA 167 4.08e+00 c.17.1.1 95370 1yqgA 263 4.23e+00 1xccA 220 4.40e+00 1q35A 320 5.11e+00 c.94.1.1 95661 1w9hA 427 5.46e+00 1ig3A 263 5.86e+00 1ig3A b.82.6.1,c.100.1.1 62358,62359 2f3yA 148 5.91e+00 1js3A 486 6.48e+00 c.67.1.6 67215 1nrzA 164 6.66e+00 c.38.1.1 86131 1usyA 275 6.70e+00 1aisA 182 6.88e+00 1ytbA d.129.1.1,d.129.1.1 41288,41289 1jq5A 370 7.29e+00 e.22.1.2 67084 1k66A 149 7.29e+00 c.23.1.1 90941 1ys7A 233 7.33e+00 1xzoA 174 7.39e+00 1khbA 625 7.42e+00 c.91.1.1,c.109.1.1 68606,68607 1prxA 224 7.66e+00 1prxA c.47.1.10 33076 1u0sA 86 7.76e+00 d.58.24.1 107565 2bfwA 200 7.81e+00 1uc7A 125 7.84e+00 c.47.1.1 99163 1cydA 244 7.90e+00 1cydA c.2.1.2 29825 1qx2A 76 7.90e+00 a.39.1.1 104622 2f8mA 244 8.03e+00 2f5gA 133 8.21e+00 1wzuA 300 8.39e+00 1v72A 356 9.21e+00 1wmaA 276 9.27e+00 1exrA 148 9.66e+00 1cll a.39.1.5 17299 1lfpA 249 1.05e+01 e.39.1.1 73885 1ly1A 181 1.05e+01 c.37.1.1 74334 1w7jB 151 1.06e+01 2f4iA 197 1.09e+01 1qtqA 553 1.10e+01 1gtrA b.53.1.2,c.26.1.1 26940,31579 1tca 317 1.10e+01 1tca c.69.1.17 34726 1rhs 296 1.13e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 1wekA 217 1.13e+01 1ixcA 294 1.20e+01 a.4.5.37,c.94.1.1 83764,83765 1whvA 100 1.20e+01 1q15A 503 1.21e+01 c.26.2.1,d.153.1.1 95538,95539 1yliA 153 1.23e+01 2fokA 579 1.24e+01 2fokA a.4.5.12,a.4.5.12,a.4.5.12,c.52.1.12 16131,16132,16133,33323 1cqmA 101 1.27e+01 1ris d.58.14.1 39321 1qu9A 128 1.29e+01 1qu9A d.79.1.1 39755 1yw3A 208 1.34e+01 2bjnA 160 1.34e+01 1vetB 125 1.37e+01 d.110.7.1 108554 2bgkA 278 1.37e+01 1wohA 305 1.38e+01 c.42.1.1 109446 1x6vA 630 1.39e+01 1kk8B 139 1.39e+01 a.39.1.5 77430 1ve3A 227 1.40e+01 1pmzA 86 1.40e+01 a.39.1.10 104195 1zdrA 164 1.40e+01 2c78A 405 1.41e+01 2bkkA 264 1.44e+01 1v25A 541 1.44e+01 e.23.1.1 108275 1j5xA 342 1.44e+01 c.80.1.1 71591 1ztdA 133 1.53e+01 1o4sA 389 1.58e+01 c.67.1.1 86620 1v4pA 157 1.58e+01 1ylqA 96 1.61e+01 1guiA 155 1.64e+01 b.18.1.14 76351 1wdcB 156 1.65e+01 1wdcB a.39.1.5 17302 1sheA 103 1.67e+01 d.274.1.1 105551 1w0mA 226 1.67e+01 c.1.1.1 109027 1bif 469 1.67e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1ixh 321 1.67e+01 1ixh c.94.1.1 35761 1ykiA 217 1.69e+01 1ggzA 148 1.69e+01 a.39.1.5 70176 1wdcC 156 1.71e+01 1wdcC a.39.1.5 17317 1vkpA 383 1.75e+01 d.126.1.6 108686 1tz9A 367 1.77e+01 c.1.15.6 107466 1u5tB 169 1.79e+01 a.4.5.54,a.4.5.54 107686,107687 1m45A 148 1.86e+01 a.39.1.5 78598 2fug1 438 1.89e+01 1a53 247 1.92e+01 1a53 c.1.2.4 28564 2b4vA 468 1.94e+01 2bolA 314 1.95e+01 1i6aA 219 1.97e+01 c.94.1.1 61827 1yovA 537 1.99e+01 1yqdA 366 1.99e+01 2f1fA 164 2.02e+01 2fdrA 229 2.04e+01 1v6zA 228 2.07e+01 1uwcA 261 2.09e+01 c.69.1.17 100101 1iba 101 2.13e+01 1iba d.95.1.1 40567 1wlsA 328 2.16e+01 2g9iA 249 2.16e+01 1ex7A 186 2.17e+01 1gky c.37.1.1 59537 1m1nB 522 2.18e+01 c.92.2.3 78418 1vmbA 140 2.25e+01 1vyiA 112 2.27e+01 1sc6A 404 2.30e+01 1dmlA 319 2.31e+01 1dmlA d.131.1.2,d.131.1.2 41380,41381 1vqoX 92 2.34e+01 1xc1A 309 2.34e+01 c.94.1.1 109543 2fm8A 135 2.36e+01 2fhpA 187 2.39e+01 1d5yA 292 2.41e+01 1d5yA a.4.1.8,a.4.1.8,d.60.1.2 16055,16056,39532 2fb1A 226 2.42e+01 2b1xA 470 2.45e+01 2g40A 224 2.45e+01 1g6eA 87 2.46e+01 1g6eA b.11.1.6 60317 1el5A 389 2.48e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1kgsA 225 2.50e+01 a.4.6.1,c.23.1.1 68596,68597 1dmgA 225 2.53e+01 1dmgA c.22.1.1 31036 1xtyA 120 2.54e+01 1ywfA 296 2.55e+01 1jk7A 323 2.60e+01 1auiA d.159.1.3 63144 1bx4A 345 2.63e+01 1bx4A c.72.1.1 34935 1o65A 246 2.63e+01 b.58.1.2 92544 2bl0B 145 2.64e+01 1zsyA 357 2.64e+01 1jc4A 148 2.64e+01 1jc4A d.32.1.4 62863 1ftrA 296 2.68e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 2a2fX 325 2.71e+01 2bykA 140 2.73e+01 2ak3A 226 2.73e+01 1zin c.37.1.1,g.41.2.1 31892,45193 1qd9A 124 2.75e+01 1qu9A d.79.1.1 39758 1jftA 340 2.78e+01 a.35.1.5,c.93.1.1 66652,66653 2b4lA 268 2.79e+01 1oxkB 134 2.81e+01 c.23.1.1 93691 1xvxA 312 2.83e+01 2f9sA 151 2.83e+01 1t0hB 224 2.84e+01 c.37.1.1 106208 1t6aA 126 2.85e+01 d.129.8.1 106555 1qnaA 200 2.85e+01 1ytbA d.129.1.1,d.129.1.1 41226,41227 1ltqA 301 2.86e+01 c.108.1.9,c.37.1.1 78208,78209 1wwhA 119 2.87e+01 1h4vB 421 2.91e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1gky 187 2.94e+01 1gky c.37.1.1 31839 1yixA 265 2.96e+01 1t95A 240 2.98e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1om1A 332 2.99e+01 d.144.1.7 93347 1u02A 239 3.00e+01 c.108.1.15 107538 1i3cA 149 3.01e+01 c.23.1.1 71112 1sd4A 126 3.05e+01 a.4.5.39 105428 1me8A 503 3.05e+01 c.1.5.1 79028 1ksoA 101 3.06e+01 a.39.1.2 72926 1ig5A 75 3.11e+01 4icb a.39.1.1 62363 2g8lA 299 3.12e+01 1hy7A 173 3.15e+01 d.92.1.11 65957 1ulrA 88 3.17e+01 1v4sA 455 3.19e+01 c.55.1.3,c.55.1.3 100309,100310 1bcpB 199 3.23e+01 1bcpB b.40.2.1,d.169.1.2 25120,42429 1aoeA 192 3.23e+01 1aoeA c.71.1.1 34923 1e0cA 271 3.25e+01 1e0cA c.46.1.2,c.46.1.2 32717,32718 1o7nB 194 3.26e+01 d.17.4.4 81164 1hfc 169 3.26e+01 1hfc d.92.1.11 40335 1s4nA 348 3.27e+01 c.68.1.16 98501 1dd9A 338 3.28e+01 1dd9A e.13.1.1 43254 1bgvA 449 3.32e+01 1k89 c.2.1.7,c.58.1.1 30217,33865 1yzfA 195 3.34e+01 1oacA 727 3.34e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 1vb5A 276 3.36e+01 1mdl 359 3.39e+01 2mnr c.1.11.2,d.54.1.1 29247,38891 1mp9A 198 3.40e+01 d.129.1.1,d.129.1.1 91385,91386 1y93A 159 3.41e+01 1k8uA 90 3.43e+01 a.39.1.2 72181 1exbA 332 3.46e+01 1qrqA c.1.7.1 28666 1w9yA 319 3.47e+01 2gf6A 135 3.47e+01 1odfA 290 3.52e+01 c.37.1.6 92782 1us0A 316 3.53e+01 c.1.7.1 99850 2ajtA 500 3.54e+01 1whzA 70 3.63e+01 1nox 205 3.67e+01 1nox d.90.1.1 40242 1qwkA 317 3.68e+01 c.1.7.1 96482 1uekA 275 3.70e+01 d.14.1.5,d.58.26.5 88483,88484 1pvxA 194 3.70e+01 1axkA b.29.1.11 24341 1g57A 217 3.71e+01 1g57A d.115.1.2 60253 1mho 88 3.74e+01 1b4cA a.39.1.2 17171 1ii5A 233 3.75e+01 c.94.1.1 62412 1dxeA 256 3.75e+01 1dxeA c.1.12.5 29310 1v32A 101 3.79e+01 a.42.1.1 100277 2cy2A 174 3.79e+01 1cjcA 460 3.82e+01 1cjcA c.3.1.1,c.4.1.1 30319,30604 1fp1D 372 3.84e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1gyxA 76 3.89e+01 d.80.1.1 76387 1ub3A 220 3.92e+01 c.1.10.1 88395 2bnmA 198 3.94e+01 1eluA 390 3.95e+01 1elqA c.67.1.3 34434 1zrjA 50 3.97e+01 1iwmA 186 3.97e+01 b.125.1.2 83758 1qvcA 145 3.98e+01 3ullA b.40.4.3 25284 1j3mA 129 3.98e+01 d.129.7.1 103836 2c8mA 262 4.11e+01 2a3nA 355 4.12e+01 1dbqA 289 4.14e+01 1qpzA c.93.1.1 35666 1wdjA 187 4.16e+01 1jbeA 128 4.19e+01 3chy c.23.1.1 62845 1ccwA 137 4.19e+01 1be1 c.23.6.1 31238 1o57A 291 4.25e+01 a.4.5.40,c.61.1.1 92483,92484 1knyA 253 4.27e+01 1knyA a.24.16.1,d.218.1.1 75896,75897 1ga6A 372 4.28e+01 1ga1A c.41.1.2 32556 1r12A 258 4.31e+01 e.4.1.1 96780 1eljA 381 4.33e+01 4mbp c.94.1.1 35791 1ru0A 105 4.33e+01 2d13A 227 4.34e+01 1j98A 157 4.43e+01 1j98A d.185.1.2 62755 1pjcA 361 4.43e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1q0pA 223 4.45e+01 c.62.1.1 95507 1i58A 189 4.47e+01 1b3qA d.122.1.3 61773 2aifA 135 4.47e+01 1xcbA 211 4.50e+01 a.4.5.38,c.2.1.12 109552,109553 1k94A 165 4.50e+01 a.39.1.8 68333 1e6yC 247 4.51e+01 1mroC d.58.31.1 39441 8abp 306 4.54e+01 8abp c.93.1.1 35647 2aqlA 173 4.58e+01 1cjwA 166 4.61e+01 1cjwA d.108.1.1 40818 2ac3A 316 4.62e+01 1ejdA 419 4.67e+01 1uae d.68.2.2 39576 1q7sA 117 4.69e+01 c.131.1.1 96055 1xg5A 279 4.69e+01 1xu9A 286 4.70e+01 1s8nA 205 4.79e+01 c.23.1.1 105374 1l5wA 796 4.81e+01 c.87.1.4 73605 1nnlA 225 4.86e+01 c.108.1.4 85906 1st9A 143 4.86e+01 c.47.1.10 98987 2cxcA 144 4.87e+01 1ii7A 333 4.90e+01 1ii7A d.159.1.4 62415 1nnhA 294 4.90e+01 d.104.1.1 92005 1a4iA 301 4.94e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 2av5A 120 4.96e+01 1j5uA 136 5.00e+01 d.208.1.1 71584 1zzmA 259 5.01e+01 1vqoE 178 5.03e+01 1f06A 320 5.03e+01 1dapA c.2.1.3,d.81.1.3 59556,59557 1vj0A 380 5.08e+01 b.35.1.2,c.2.1.1 100786,100787 1zetA 388 5.16e+01 1ss4A 153 5.17e+01 d.32.1.6 105976 1zsxA 347 5.22e+01 2cvdA 198 5.24e+01 1vjvA 415 5.40e+01 d.3.1.9 108632 1y89A 238 5.42e+01 1x7dA 350 5.43e+01 1xo5A 183 5.51e+01 1r89A 437 5.55e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1iyhA 198 5.56e+01 a.45.1.1,c.47.1.5 83790,83791 1k07A 263 5.58e+01 d.157.1.1 77218 2bx6A 350 5.65e+01 1pg4A 652 5.66e+01 e.23.1.1 88067 1ewkA 490 5.77e+01 1ewkA c.93.1.1 35712 1qh8B 519 5.80e+01 1qguB c.92.2.3 35634 1h2bA 359 5.91e+01 b.35.1.2,c.2.1.1 90543,90544 1o26A 232 5.92e+01 d.207.1.1 86566 2as0A 396 5.94e+01 1v9fA 325 5.96e+01 d.265.1.3 108448 1gtzA 156 5.97e+01 c.23.13.1 70539 1lk5A 229 6.02e+01 c.124.1.4,d.58.40.1 73960,73961 1m1nA 491 6.05e+01 c.92.2.3 78417 1hh1A 143 6.07e+01 1gefA c.52.1.18 61036 1gz2A 142 6.10e+01 d.169.1.1 83392 1mb3A 124 6.22e+01 c.23.1.1 78907 1eybA 471 6.36e+01 1ey2A b.82.1.4 28115 2bmoB 194 6.45e+01 2fztA 79 6.46e+01 1ydyA 356 6.49e+01 2g0wA 296 6.56e+01 1avsA 90 6.59e+01 1cll a.39.1.5 17226 1r6xA 395 6.68e+01 b.122.1.3,c.26.1.5 97167,97168 1b7yB 785 6.73e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1tqgA 105 6.77e+01 a.24.10.3 107224 1yt8A 539 6.77e+01 1i76A 163 6.78e+01 1hfc d.92.1.11 61877 1o98A 511 6.81e+01 c.105.1.1,c.76.1.3 86684,86685 2abqA 306 6.83e+01 1e42A 258 6.86e+01 1e42A b.1.10.1,d.105.1.1 22316,40792 1v7rA 186 6.91e+01 c.51.4.1 100482 1wu4A 396 6.92e+01 1seiA 130 6.93e+01 1seiA d.140.1.1 41463 2cygA 312 6.94e+01 1ei6A 406 6.95e+01 c.76.1.4 90443 1yxcA 292 6.98e+01 1r9dA 787 7.03e+01 c.7.1.1 104865 1r9wA 145 7.04e+01 d.89.1.2 97264 1u5tA 233 7.05e+01 a.4.5.54,a.4.5.54 107684,107685 1rg9A 383 7.07e+01 d.130.1.1,d.130.1.1,d.130.1.1 97427,97428,97429 1kq3A 376 7.07e+01 e.22.1.2 68790 1fxkB 109 7.07e+01 1fxkA a.2.5.1 15704 1gnuA 117 7.08e+01 d.15.1.3 65403 1xv2A 237 7.09e+01 1r8eA 278 7.14e+01 a.6.1.3,d.60.1.1 104843,104844 1qlmA 316 7.16e+01 1qlmA d.147.1.1 41765 1f1eA 154 7.23e+01 a.22.1.2 64927 1uasA 362 7.24e+01 b.71.1.1,c.1.8.1 88388,88389 1qy1A 174 7.27e+01 b.60.1.1 96568 1yv4A 104 7.29e+01 1xfkA 336 7.29e+01 1k20A 310 7.29e+01 c.107.1.1 68027 1xd8A 289 7.31e+01 2bkyA 97 7.37e+01 1j55A 95 7.39e+01 a.39.1.2 77078 1jg1A 235 7.42e+01 c.66.1.7 66661 1xneA 113 7.49e+01 1go3F 107 7.52e+01 a.60.8.2 65407 1gnlA 544 7.56e+01 e.26.1.1 70287 1oi7A 288 7.63e+01 c.2.1.8,c.23.4.1 87049,87050 1dcfA 136 7.63e+01 1dcfA c.23.1.2 31124 1g5cA 170 7.68e+01 1g5cA c.53.2.1 60264 1smd 496 7.68e+01 1smd b.71.1.1,c.1.8.1 27768,28755 1pf5A 131 7.70e+01 d.79.1.1 94604 1jbkA 195 7.70e+01 c.37.1.20 71631 1ekgA 127 7.72e+01 1dlxA d.82.2.1 40021 1jb3A 131 7.88e+01 1jc7A b.40.3.2 62833 1vknA 351 7.96e+01 c.2.1.3,d.81.1.1 108676,108677 2a10A 125 8.01e+01 1onrA 316 8.02e+01 1onrA c.1.10.1 29169 1q9uA 130 8.09e+01 d.129.7.1 96314 1oo0B 110 8.11e+01 d.58.7.1 87183 1o0iA 138 8.11e+01 d.38.1.5 86532 2cw6A 298 8.12e+01 1iugA 352 8.14e+01 c.67.1.3 90699 1wr8A 231 8.16e+01 1id0A 152 8.23e+01 d.122.1.3 66111 4tmkA 213 8.25e+01 5tmpA c.37.1.1 31930 1s12A 94 8.26e+01 2b1xB 172 8.30e+01 1jp4A 308 8.36e+01 1jp4A e.7.1.1 63223 1ga8A 311 8.38e+01 1ga8A c.68.1.4 34516 7odcA 424 8.41e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1xezA 721 8.41e+01 1zndA 174 8.44e+01 1n7kA 234 8.45e+01 c.1.10.1 85374 2fs3A 282 8.45e+01 1qysA 106 8.49e+01 k.41.1.1 96603 2bj7A 138 8.53e+01 1v5iB 76 8.53e+01 1r3dA 264 8.54e+01 830cA 168 8.58e+01 1ck7A d.92.1.11 40400 1z2uA 150 8.62e+01 2bs3A 656 8.71e+01 2gaxA 135 8.71e+01 1fehA 574 8.73e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1y1pA 342 8.75e+01 1y4tA 322 8.75e+01 1h70A 255 8.76e+01 1h70A d.126.1.3 60711 2d69A 430 8.86e+01 1rtqA 299 8.86e+01 c.56.5.4 97819 2freA 200 8.89e+01 1v37A 177 8.96e+01 1mqoA 227 9.00e+01 d.157.1.1 103846