# List of top-scoring protein chains for t04-100-30-alpha 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 1top 162 1.58e-01 1ncx a.39.1.5 17223 2sas 185 8.72e-01 2sas a.39.1.5 17258 1efyA 350 9.68e-01 1a26 a.41.1.1 17413 d.166.1.2 42275 1kgdA 180 1.03e+00 c.37.1.1 68582 1ggzA 148 1.28e+00 a.39.1.5 70176 1aerA 205 1.33e+00 1aerA d.166.1.1 42249 1e0cA 271 1.52e+00 1e0cA c.46.1.2 32717 c.46.1.2 32718 1gnlA 544 1.83e+00 e.26.1.1 70287 1nt4A 391 1.95e+00 c.60.1.2 -7942 1wm1A 317 1.99e+00 1p9kA 79 2.18e+00 unknown_sccs -10238 1nhkL 144 2.35e+00 1npk d.58.6.1 39142 1qtrA 317 2.49e+00 1qtrA c.69.1.7 34660 1cbf 285 2.69e+00 1cbf c.90.1.1 35587 1rl6A 177 3.06e+00 1rl6A d.141.1.1 41473 d.141.1.1 41474 1f5jA 199 3.25e+00 1axkA b.29.1.11 24342 1i1kA 309 3.29e+00 1daaA e.17.1.1 61533 1iyeA 309 3.35e+00 e.17.1.1 83786 1j3wA 163 3.36e+00 unknown_sccs -10870 1auiB 169 3.56e+00 1auiB a.39.1.5 17325 1f6yA 262 3.64e+00 1f6yA c.1.21.2 29673 1f4qA 165 3.82e+00 1alvA a.39.1.8 17360 1qy1A 174 3.99e+00 b.60.1.1 -4445 1tm0A 350 4.00e+00 1s96A 219 4.24e+00 c.37.1.1 -6972 1smlA 269 4.43e+00 1smlA d.157.1.1 42053 1g57A 217 5.06e+00 1g57A d.115.1.2 60253 1qjtA 99 5.07e+00 1eh2 a.39.1.6 17335 1i06A 180 5.10e+00 1mup b.60.1.1 27131 1din 236 5.12e+00 1din c.69.1.9 34682 1n0wA 243 5.23e+00 c.37.1.11 79772 1mup 166 5.61e+00 1mup b.60.1.1 27133 1g4yR 148 6.04e+00 1cll a.39.1.5 60252 1vk1A 242 6.61e+00 1wdcC 156 6.72e+00 1wdcC a.39.1.5 17317 1k94A 165 6.99e+00 a.39.1.8 68333 1m45A 148 7.05e+00 a.39.1.5 78598 1exrA 148 7.16e+00 1cll a.39.1.5 17299 1jv4A 162 7.21e+00 b.60.1.1 67343 1k4iA 233 7.22e+00 d.115.1.2 72056 1f46A 140 7.36e+00 1f46A d.129.4.1 59643 1g8iA 190 7.37e+00 1rec a.39.1.5 60363 1k9uA 78 7.53e+00 a.39.1.10 84348 1c7gA 456 7.73e+00 c.67.1.2 -8153 1s29A 92 7.76e+00 unknown_sccs -315 1lf6A 684 7.80e+00 a.102.1.5 77918 b.30.5.5 77919 1fw9A 164 8.22e+00 1fw9A d.190.1.1 60059 1q9jA 422 8.37e+00 1g8mA 593 8.44e+00 1g8mA c.24.1.3 60371 c.97.2.1 60372 1i05A 180 8.92e+00 1mup b.60.1.1 27130 2if1 126 9.37e+00 2if1 d.64.1.1 39547 1cr5A 189 9.80e+00 1cr5A b.52.2.3 26931 d.31.1.1 38465 1lktA 104 1.02e+01 1lktA b.90.1.1 28398 1ss4A 153 1.02e+01 1s6cA 183 1.05e+01 a.39.1.5 -858 4pep 326 1.10e+01 1smrA b.50.1.2 26843 1kk8B 139 1.11e+01 a.39.1.5 77430 1mmiA 366 1.13e+01 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1cf2O 337 1.16e+01 1b7gO c.2.1.3 29994 d.81.1.1 39909 3cla 213 1.17e+01 3cla c.43.1.1 32610 1bt0A 76 1.19e+01 1ubi d.15.1.1 37607 1ok7A 366 1.20e+01 1ex7A 186 1.20e+01 1gky c.37.1.1 59537 2polA 366 1.21e+01 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1wdkC 390 1.21e+01 1mp4A 292 1.25e+01 c.68.1.6 79376 1o1zA 234 1.27e+01 c.1.18.3 86555 1p4kA 295 1.28e+01 d.153.1.5 87772 1gky 187 1.30e+01 1gky c.37.1.1 31839 1sznA 417 1.31e+01 4icb 76 1.33e+01 4icb a.39.1.1 17145 1et0A 269 1.34e+01 1et0A e.17.1.1 43289 1jf2A 195 1.36e+01 1ej3A a.39.1.5 62930 1qv1A 195 1.38e+01 a.39.1.5 -830 1qh8A 478 1.40e+01 1qguA c.92.2.3 35633 1gw0A 559 1.41e+01 b.6.1.3 70623 b.6.1.3 70624 b.6.1.3 70625 1f89A 291 1.42e+01 d.160.1.1 64988 1mu5A 471 1.43e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1uasA 362 1.45e+01 b.71.1.1 88388 c.1.8.1 88389 1b5fA 239 1.53e+01 1smrA b.50.1.2 26836 1avsA 90 1.59e+01 1cll a.39.1.5 17226 1a4iA 301 1.60e+01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1dqeA 137 1.61e+01 1dqeA a.39.2.1 17388 1m1nA 491 1.62e+01 c.92.2.3 78417 1eg5A 384 1.62e+01 1ecxA c.67.1.3 34429 1i2kA 269 1.63e+01 e.17.1.1 -11995 1pg4A 652 1.68e+01 e.23.1.1 88067 9gafA 295 1.74e+01 1apyA d.153.1.5 42008 1p57B 255 1.94e+01 b.47.1.2 -4248 1epwA 1290 1.95e+01 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 3psg 370 2.03e+01 1smrA b.50.1.2 26841 1kbvA 327 2.04e+01 b.6.1.3 68395 b.6.1.3 68396 1i4mA 108 2.07e+01 d.6.1.1 66025 1aozA 552 2.10e+01 1aozA b.6.1.3 23124 b.6.1.3 23125 b.6.1.3 23126 1el4A 195 2.12e+01 1ej3A a.39.1.5 59453 1wdcB 156 2.13e+01 1wdcB a.39.1.5 17302 1e8pA 46 2.14e+01 g.55.1.1 59385 1ixkA 315 2.16e+01 unknown_sccs -8099 1l8aA 886 2.17e+01 c.36.1.6 73678 c.36.1.10 73677 c.48.1.1 73679 1uurA 473 2.19e+01 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1vi2A 300 2.26e+01 c.2.1.7 -5960 c.58.1.5 -6366 1t3cA 421 2.34e+01 1r9cA 139 2.34e+01 d.32.1.2 -9557 1iirA 415 2.35e+01 1iirA c.87.1.5 62453 1ubi 76 2.36e+01 1ubi d.15.1.1 37584 1h4gA 207 2.38e+01 b.29.1.11 70863 1fjmA 330 2.42e+01 1auiA d.159.1.3 42082 1jl3A 139 2.48e+01 c.44.1.1 66826 1ogwA 76 2.51e+01 d.15.1.1 87001 1ursA 402 2.51e+01 c.94.1.1 -8651 1czaN 917 2.52e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1k77A 260 2.53e+01 c.1.15.5 72096 1go7P 462 2.53e+01 unknown_sccs 76245 d.92.1.6 76246 1lucB 324 2.54e+01 1lucA c.1.16.1 29548 3ladA 476 2.54e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1k6wA 426 2.64e+01 b.92.1.2 68236 c.1.9.5 68237 1dhr 241 2.68e+01 1dhr c.2.1.2 29832 1mbxC 106 2.69e+01 d.45.1.2 78929 2pvbA 107 2.70e+01 1a75A a.39.1.4 17205 1m22A 503 2.71e+01 c.117.1.1 78464 1kl9A 182 2.72e+01 b.40.4.5 72681 1br1B 150 2.75e+01 1wdcC a.39.1.5 17309 1oi2A 366 2.76e+01 c.32.1.2 87039 d.79.2.2 87040 1ayoA 130 2.78e+01 1ayoA b.2.4.1 22431 1lfwA 470 2.79e+01 c.56.5.4 77942 d.58.19.1 77943 1k7iA 479 2.79e+01 unknown_sccs 77281 d.92.1.6 77282 1a7w 69 2.83e+01 1a7w a.22.1.2 16477 1rewC 135 2.83e+01 g.7.1.3 -12531 1hn2A 159 2.85e+01 b.60.1.1 65890 1f02T 66 2.86e+01 1f02T j.67.1.1 46360 1cwpA 190 2.89e+01 1cwpA b.121.4.5 23305 1bx7 55 2.91e+01 1bx7 g.3.15.1 44355 1jhfA 202 2.91e+01 a.4.5.2 63057 b.87.1.1 63058 1rv3A 483 2.91e+01 1fdr 248 2.92e+01 1fdr b.43.4.2 25653 c.25.1.1 31543 1gt1A 159 2.96e+01 b.60.1.1 -4436 1n25A 368 2.97e+01 c.37.1.20 85264 1efdN 266 2.98e+01 1efdN c.92.2.1 35597 1shsA 147 3.00e+01 1shsA b.15.1.1 23675 1g2yA 32 3.01e+01 unknown_sccs 17003 1cc1S 283 3.02e+01 2frvA e.19.1.1 43313 1kjwA 295 3.04e+01 b.34.2.1 68643 c.37.1.1 68644 1fnnA 389 3.10e+01 1fnnA a.4.5.11 16129 c.37.1.20 32426 1fgs 428 3.11e+01 1fgs c.59.1.2 33959 c.72.2.2 34962 1jk7A 323 3.11e+01 1auiA d.159.1.3 63144 1dfoA 417 3.16e+01 1bj4A c.67.1.4 34480 1j9lA 247 3.18e+01 c.106.1.1 62762 1obpA 159 3.18e+01 1obpA b.60.1.1 27092 3htsB 102 3.20e+01 2hts a.4.5.22 16175 1nif 340 3.23e+01 1nif b.6.1.3 23048 b.6.1.3 23049 1qh7A 207 3.25e+01 1axkA b.29.1.11 24317 1kcbA 340 3.26e+01 b.6.1.3 -2950 b.6.1.3 -2951 1dfmA 223 3.27e+01 1d2iA c.52.1.5 33295 1jbiA 100 3.28e+01 d.209.1.1 66481 1ojaA 520 3.30e+01 c.3.1.2 -6000 d.16.1.5 -9220 1n0xL 215 3.39e+01 b.1.1.1 -2063 b.1.1.2 -2429 1iybA 208 3.44e+01 d.124.1.1 -10977 1bj4A 470 3.48e+01 1bj4A c.67.1.4 34479 1jd1A 129 3.50e+01 1qu9A d.79.1.1 62890 1nddA 76 3.52e+01 1ubi d.15.1.1 37599 1e5mA 416 3.53e+01 1dd8A c.95.1.1 58973 c.95.1.1 58974 1q44A 326 3.53e+01 c.37.1.5 -7037 1hmt 132 3.59e+01 1hmt b.60.1.2 27169 1l5pA 93 3.72e+01 d.15.4.1 73598 1mzbA 136 3.74e+01 unknown_sccs -266 4dpvZ 584 3.75e+01 2cas b.121.5.2 23377 1tj9A 121 3.78e+01 1i60A 278 3.78e+01 c.1.15.4 71118 1snrA 341 3.78e+01 1nuuA 252 3.79e+01 c.26.1.3 86209 1im3D 95 3.81e+01 1im3D b.1.18.5 62568 1bw0A 416 3.87e+01 1bw0A c.67.1.1 34385 1s1iF 162 3.88e+01 1lvwA 295 3.93e+01 c.68.1.6 84723 2fokA 579 3.98e+01 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323