# List of top-scoring protein chains for t2k-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 1kl9A 182 1.65e-01 1dm5A 315 1.79e-01 1avc a.65.1.1 18186 1ao6A 585 5.79e-01 1bj5 a.126.1.1 19354 a.126.1.1 19355 a.126.1.1 19356 1hyeA 313 6.31e-01 2cmd c.2.1.5 61400 d.162.1.1 61401 1e7aA 585 9.11e-01 1bj5 a.126.1.1 19360 a.126.1.1 19361 a.126.1.1 19362 1cwyA 500 9.30e-01 1cwyA c.1.8.1 28789 1bl0A 129 1.00e+00 1d5yA a.4.1.8 16053 a.4.1.8 16054 1eswA 500 1.06e+00 1cwyA c.1.8.1 59500 1bj5 585 1.13e+00 1bj5 a.126.1.1 19369 a.126.1.1 19370 a.126.1.1 19371 1myt 146 1.21e+00 1a6m a.1.1.2 15207 1ha2A 585 1.43e+00 1bj5 a.126.1.1 60866 a.126.1.1 60867 a.126.1.1 60868 1keaA 221 1.57e+00 a.96.1.2 68491 1h6zA 913 1.58e+00 1g4yR 148 1.97e+00 1cll a.39.1.5 60252 1sknP 92 2.12e+00 1sknP a.37.1.1 17127 1nf1A 333 2.30e+00 1nf1A a.116.1.2 19110 1gc5A 467 2.30e+00 1gc5A c.72.1.3 60429 1k1aA 241 2.73e+00 a.118.2.1 67992 1dl5A 317 2.84e+00 1dl5A c.66.1.7 64720 d.197.1.1 64721 1awcB 153 3.01e+00 1bd8 a.118.2.1 19156 1ecmA 109 3.67e+00 1ecmA a.130.1.1 19492 1qq7A 253 3.69e+00 1qq5A c.108.1.1 43329 1a7j 290 3.97e+00 1a7j c.37.1.6 31952 1qq5A 253 4.04e+00 1qq5A c.108.1.1 43327 1jeqA 609 4.09e+00 1jeqA a.140.2.1 64748 e.31.1.1 64749 1hwyA 501 4.09e+00 1hwyA c.2.1.7 30262 c.58.1.1 33910 1aq6A 253 4.28e+00 1qq5A c.108.1.1 43331 1k32A 1045 4.37e+00 b.36.1.3 68068 b.68.7.1 68069 b.69.9.1 68070 c.14.1.2 68071 1r2fA 319 4.42e+00 1r2fA a.25.1.2 16800 1f8pA 37 4.46e+00 1f8pA j.6.1.1 46091 1ci4A 89 4.57e+00 1qckA a.60.5.1 17970 1b3qA 379 5.32e+00 1b3qA a.30.2.1 16993 b.40.7.1 25454 d.122.1.3 41112 1e79H 146 5.68e+00 1e79H a.2.10.1 15721 b.93.1.1 28438 1qf9A 194 5.69e+00 1zin c.37.1.1 31848 1iqvA 218 5.92e+00 1rss a.75.1.1 62661 1cbuA 180 5.94e+00 1c9kB c.37.1.11 32360 1g5cA 170 6.17e+00 1g5cA c.53.2.1 60264 1fvnA 37 6.24e+00 1fvnA j.6.1.1 46096 1h97A 147 6.26e+00 1h97A a.1.1.2 60812 1b67A 68 6.33e+00 1a7w a.22.1.2 16474 1h9fA 57 6.46e+00 1h9fA a.140.1.1 60826 1b9dA 163 6.64e+00 1b9dA c.55.3.2 33649 1b9gA 57 6.67e+00 2gf1 g.1.1.1 43991 1rec 201 6.74e+00 1rec a.39.1.5 17326 1ron 37 6.75e+00 1ron j.6.1.1 46090 1hwxA 501 7.00e+00 1hwyA c.2.1.7 30250 c.58.1.1 33898 1kgnA 329 7.27e+00 a.25.1.2 68584 1dwtA 153 7.42e+00 1a6m a.1.1.2 15190 1dqwA 267 7.54e+00 1dqwA c.1.2.3 28551 3cln 148 7.94e+00 1cll a.39.1.5 17286 2ezxA 89 7.99e+00 1qckA a.60.5.1 17978 1j78A 458 9.26e+00 a.126.1.1 66397 a.126.1.1 66398 a.126.1.1 66399 1b0b 142 9.35e+00 2fal a.1.1.2 15010 1icyA 37 9.51e+00 1osa 148 9.66e+00 1cll a.39.1.5 17300 1e9rA 437 9.69e+00 c.37.1.11 64827 1qckA 89 9.70e+00 1qckA a.60.5.1 17976 1bqbA 301 9.75e+00 1hyt d.92.1.2 58962 1d7bA 186 9.75e+00 1d7bA b.1.9.1 22307 1d7cA 190 9.75e+00 1d7bA b.1.9.1 22309 1ib3A 349 9.84e+00 1ib2A a.118.1.8 62142 1hta 69 9.86e+00 1a7w a.22.1.2 16476 1h8eD 482 9.95e+00 1skyE a.69.1.1 60747 b.49.1.1 60748 c.37.1.11 60749 1ib2A 349 1.01e+01 1ib2A a.118.1.8 62141 1lm8B 118 1.04e+01 1go3F 107 1.04e+01 a.60.8.2 65407 1cll 148 1.07e+01 1cll a.39.1.5 17263 1han 297 1.07e+01 1han d.32.1.3 38506 d.32.1.3 38507 5ukdA 194 1.09e+01 1zin c.37.1.1 31851 1c9kB 180 1.09e+01 1c9kB c.37.1.11 32364 1fvkA 189 1.10e+01 1fvkA a.44.1.1 17490 c.47.1.4 32784 1kblA 873 1.11e+01 c.1.12.2 68384 c.8.1.1 68385 d.142.1.5 68386 1exrA 148 1.13e+01 1cll a.39.1.5 17299 1f4qA 165 1.14e+01 1alvA a.39.1.7 17360 1itg 166 1.17e+01 1b9dA c.55.3.2 33661 1c0aA 585 1.22e+01 1c0aA b.40.4.1 25246 d.74.4.1 39731 d.104.1.1 40767 1fxlA 167 1.22e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1clqA 903 1.23e+01 1clqA c.55.3.5 33717 e.8.1.1 43006 1hyvA 166 1.23e+01 1b9dA c.55.3.2 61424 1vcbA 118 1.24e+01 1vcbA d.15.1.1 37603 1ht9A 76 1.24e+01 4icb a.39.1.1 61252 1k8kD 300 1.32e+01 d.198.2.1 68309 d.198.2.1 68310 1avsA 90 1.32e+01 1cll a.39.1.5 17226 1dioG 173 1.35e+01 1dioG a.23.2.1 16496 1aj8A 371 1.35e+01 1aj8A a.103.1.1 18900 1h5uA 842 1.36e+01 1a8i c.87.1.4 60655 2utgA 70 1.37e+01 1utg a.101.1.1 18814 1bl3A 160 1.38e+01 1b9dA c.55.3.2 33655 1jfkA 134 1.39e+01 a.39.1.5 66639 1jjvA 206 1.44e+01 2af8 86 1.46e+01 2af8 a.28.1.1 16933 1ig5A 75 1.46e+01 4icb a.39.1.1 62363 1qhlA 227 1.49e+01 1qhlA c.37.1.12 32382 1dk8A 147 1.50e+01 1agrE a.91.1.1 18548 2frvB 536 1.54e+01 1h2rL e.18.1.1 43291 1sw6A 327 1.56e+01 1sw6A a.118.2.1 19176 1e79D 482 1.57e+01 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 1nsf 273 1.57e+01 1d2nA c.37.1.13 32429 1bax 94 1.59e+01 1bax a.61.1.3 18133 1c9kA 180 1.64e+01 1c9kB c.37.1.11 32363 1kkhA 317 1.66e+01 1e4yA 214 1.67e+01 1zin c.37.1.1 31901 g.41.2.1 45181 1lla 628 1.68e+01 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.1.5 21861 1af8 86 1.69e+01 2af8 a.28.1.1 16932 1jguH 217 1.72e+01 b.1.1.1 66688 b.1.1.2 66689 1dsbA 189 1.73e+01 1fvkA a.44.1.1 17497 c.47.1.4 32791 1axn 323 1.74e+01 1avc a.65.1.1 18149 2ts1 419 1.78e+01 2ts1 c.26.1.1 31564 1ehiA 377 1.81e+01 1iow c.30.1.2 31716 d.142.1.1 41484 1gjnA 153 1.84e+01 1auiB 169 1.87e+01 1auiB a.39.1.5 17325 1flp 142 1.89e+01 1flp a.1.1.2 15011 4icb 76 1.90e+01 4icb a.39.1.1 17145 1f16A 192 1.92e+01 1f16A f.1.4.1 43400 1bfmA 69 1.97e+01 1a7w a.22.1.2 16479 1f1zA 273 1.98e+01 1f1zA a.4.5.27 16081 c.52.1.16 33334 1e8aA 91 2.00e+01 1b4cA a.39.1.2 17188 1wdcC 156 2.01e+01 1wdcC a.39.1.5 17317 1utg 70 2.03e+01 1utg a.101.1.1 18813 1kpsB 171 2.03e+01 a.118.12.1 68787 1e6bA 221 2.04e+01 1e6bA a.45.1.1 59294 c.47.1.5 59295 1exqA 154 2.05e+01 1b9dA c.55.3.2 33646 1k94A 165 2.05e+01 a.39.1.7 68333 2occE 109 2.08e+01 2occE a.118.11.1 19224 1pbv 195 2.08e+01 1pbv a.118.3.1 19179 1kq3A 376 2.10e+01 e.22.1.2 68790 1g8mA 593 2.11e+01 1g8mA c.24.1.3 60371 c.97.2.1 60372 2ng1 293 2.11e+01 1ng1 a.24.13.1 16962 c.37.1.10 32273 2ak3A 226 2.17e+01 1zin c.37.1.1 31892 g.41.2.1 45193 1cf7B 95 2.20e+01 1cf7B a.4.5.17 16152 1mjc 69 2.26e+01 1mjc b.40.4.5 25319 4blmA 265 2.30e+01 1btl e.3.1.1 42721 1vid 221 2.34e+01 1vid c.66.1.1 34178 1l4uA 176 2.36e+01 1is8A 230 2.36e+01 d.96.1.1 66321 1d2fA 390 2.36e+01 1d2fA c.67.1.3 34411 1ddeA 338 2.36e+01 1dd9A e.13.1.1 43255 1a7w 69 2.38e+01 1a7w a.22.1.2 16477 1sek 378 2.39e+01 1sek e.1.1.1 42675 1bpoA 494 2.39e+01 1bpoA a.118.1.4 19143 b.69.6.1 27670 1bd3A 243 2.40e+01 1bd3A c.61.1.1 34098 1ulo 152 2.44e+01 1ulo b.18.1.6 23768 1qghA 156 2.47e+01 1qghA a.25.1.1 16728 1ll1 590 2.48e+01 1lla a.85.1.1 18488 a.86.1.1 18499 b.1.1.5 21864 1g8fA 511 2.50e+01 1g8fA b.58.1.2 60348 c.26.1.5 60349 c.37.1.15 60350 1kzhA 555 2.50e+01 1dguA 183 2.52e+01 1dguA a.39.1.5 17333 1aa6 715 2.52e+01 2napA b.52.2.2 26916 c.81.1.1 35324 2mhr 118 2.53e+01 2mhr a.24.4.1 16581 1vtmP 158 2.54e+01 1rmvA a.24.5.1 16587 1dzrA 183 2.60e+01 1dzrA b.82.1.1 28076 1d2eA 397 2.61e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1jeiA 53 2.62e+01 1jeiA a.140.1.1 62918 1tpt 440 2.63e+01 1brwA a.46.2.1 17763 c.27.1.1 31627 d.41.3.1 38625 1tam 132 2.65e+01 1hiwA a.61.1.1 18128 1ks9A 291 2.66e+01 a.100.1.7 68857 c.2.1.6 68858 1bxiB 134 2.70e+01 1bxiB d.4.1.1 37136 1c8kA 842 2.71e+01 1a8i c.87.1.4 35491 1iknD 236 2.74e+01 1iknD a.118.2.1 19171 3icb 75 2.75e+01 4icb a.39.1.1 17147 1rpjA 288 2.76e+01 2dri c.93.1.1 35656 1hm6A 346 2.78e+01 1avc a.65.1.1 18147 1d2nA 272 2.82e+01 1d2nA c.37.1.13 32428 1pd21 199 2.88e+01 1pd21 1bgc 174 2.88e+01 1bgc a.26.1.1 16822 3mefA 69 2.92e+01 1mjc b.40.4.5 25320 1rss 151 2.96e+01 1rss a.75.1.1 18392 1ba5 53 2.97e+01 1ba5 a.4.1.4 16045 1f1eA 154 3.00e+01 a.22.1.2 64927 1a8i 842 3.01e+01 1a8i c.87.1.4 35490 1om2A 95 3.03e+01 1om2A a.23.4.1 16520 1ak4C 145 3.05e+01 1ak4C a.73.1.1 18321 1ggzA 148 3.15e+01 1h99A 224 3.16e+01 a.142.1.1 60814 a.142.1.1 60815 2gf1 70 3.17e+01 2gf1 g.1.1.1 43990 1spgB 147 3.18e+01 1cg5B a.1.1.2 15588 1nfiE 215 3.21e+01 1iknD a.118.2.1 19172 1a87 321 3.21e+01 1a87 f.1.1.1 43380 1pbwA 216 3.24e+01 1pbwA a.116.1.1 19103 2dhqA 146 3.25e+01 2dhqA c.23.13.1 31382 1i2tA 61 3.28e+01 1i2tA a.144.1.1 61582 1bn8A 420 3.28e+01 1pcl b.80.1.1 28022 1ev0A 58 3.31e+01 1ev0A d.71.1.1 39594 1jr3E 334 3.33e+01 a.80.1.1 63253 c.37.1.13 63254 1k8kA 418 3.40e+01 c.55.1.1 68305 c.55.1.1 68306 1b72A 97 3.40e+01 2hddA a.4.1.1 16000 1c53 79 3.44e+01 1c53 a.3.1.1 15801 1ez3A 127 3.44e+01 1dn1B a.47.2.1 17768 1yrnA 61 3.45e+01 1akhA a.4.1.1 15981 1c3yA 108 3.48e+01 1c3yA a.39.2.1 17387 1abv 134 3.51e+01 1abv a.70.1.1 18317 1esiA 262 3.51e+01 1skf e.3.1.1 42682 2scpA 174 3.52e+01 2scpA a.39.1.5 17256 1repC 251 3.56e+01 1repC a.4.5.10 16125 a.4.5.10 16126 1l3yA 41 3.59e+01 1qhhA 167 3.65e+01 1pjr c.37.1.13 32393 1qqeA 292 3.67e+01 1qqeA a.118.8.1 19210 1hjp 203 3.68e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1gmlA 178 3.69e+01 1eqfA 280 3.73e+01 1eqfA a.29.2.1 16972 a.29.2.1 16973 1apmE 350 3.73e+01 1cdkA d.144.1.1 41628 1fqvJ 149 3.76e+01 1fqvD a.122.1.1 19266 d.42.1.2 38670 1f81A 88 3.77e+01 1f81A g.53.1.1 45383 1akhA 61 3.82e+01 1akhA a.4.1.1 15980 1fqvD 149 3.86e+01 1fqvD a.122.1.1 19263 d.42.1.2 38667 2mysB 166 3.88e+01 1wdcB a.39.1.5 17308 2nmbA 160 3.88e+01 2nmbA b.55.1.2 26994 1dk5A 322 3.91e+01 1dk5A a.65.1.1 18192 1eexG 173 3.94e+01 1dioG a.23.2.1 16490 1i9sA 210 3.95e+01 1i9sA c.45.1.1 62099 1bed 181 4.00e+01 1fvkA a.44.1.1 17514 c.47.1.4 32808