# 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 1mu5A 471 1.27e-01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1q48A 134 3.67e-01 unknown_sccs -9776 1mdl 359 3.76e-01 2mnr c.1.11.2 29247 d.54.1.1 38891 2mnr 357 3.82e-01 2mnr c.1.11.2 29245 d.54.1.1 38889 1wdcB 156 7.48e-01 1wdcB a.39.1.5 17302 1dkzA 219 8.67e-01 1dkzA unknown_sccs -445 unknown_sccs -3060 1kk8B 139 8.95e-01 a.39.1.5 77430 2trcP 217 9.44e-01 1b9yC c.47.1.6 33051 1o08A 221 9.81e-01 c.108.1.6 86525 1jpmA 366 1.03e+00 c.1.11.2 67031 d.54.1.1 67032 1o20A 427 1.12e+00 c.82.1.1 86556 1btl 263 1.37e+00 1btl e.3.1.1 42691 1hf8A 289 1.38e+00 1hg5A unknown_sccs -399 unknown_sccs -1628 1tvxA 75 1.42e+00 1tvxA d.9.1.1 37441 1j09A 468 1.49e+00 a.97.1.1 77025 c.26.1.1 77026 1ermA 263 1.51e+00 1btl e.3.1.1 42690 1rvkA 382 1.64e+00 c.1.11.2 -5568 d.54.1.1 -9826 1ezvB 352 1.87e+00 1ezvB d.185.1.1 59543 d.185.1.1 59544 1kb9B 352 1.93e+00 d.185.1.1 77313 d.185.1.1 77314 1lshB 319 2.14e+00 f.7.1.1 74245 1gln 468 2.17e+00 1gln a.97.1.1 18752 c.26.1.1 31588 1r71A 178 2.18e+00 1i6iA 366 2.25e+00 1bg2 c.37.1.9 61844 1a0rP 245 2.33e+00 1b9yC c.47.1.6 33054 1n9bA 265 2.42e+00 e.3.1.1 85463 1a0p 290 2.74e+00 1a0p a.60.9.1 18105 d.163.1.1 42165 1bj7 156 2.87e+00 1bj7 b.60.1.1 27113 1m40A 263 2.88e+00 e.3.1.1 74437 1viaA 175 3.13e+00 c.37.1.2 -7021 1k1vA 41 3.90e+00 a.37.1.1 71999 1fsz 372 4.11e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1ikpA 613 4.21e+00 b.29.1.7 66182 d.166.1.1 66183 f.1.5.1 66184 1c9kA 180 4.26e+00 1c9kB c.37.1.11 32363 1i0hA 205 4.77e+00 1avmA a.2.11.1 15760 d.44.1.1 38685 1ec7A 446 4.77e+00 1bqg c.1.11.2 29218 d.54.1.1 38862 1k07A 263 5.01e+00 d.157.1.1 77218 1eyvA 156 5.28e+00 1eyvA a.79.1.1 18446 1k3xA 262 5.39e+00 a.156.1.2 77242 b.113.1.1 77243 g.39.1.8 77244 1uesA 191 5.39e+00 1o6dA 163 5.46e+00 c.116.1.3 -6689 1gr0A 367 5.55e+00 c.2.1.3 70379 d.81.1.3 70380 1f32A 149 5.61e+00 1f32A d.62.1.1 39539 1h8pA 109 5.63e+00 g.14.1.2 70916 g.14.1.2 70917 1v9yA 167 5.73e+00 1dozA 309 5.78e+00 1ak1 c.92.1.1 35592 1ix9A 205 5.99e+00 a.2.11.1 76899 d.44.1.1 76900 1f0jA 377 6.07e+00 1f0jA a.125.1.1 19346 1uypA 432 6.17e+00 unknown_sccs -3480 unknown_sccs -4554 1iz5A 249 6.26e+00 d.131.1.2 83834 d.131.1.2 83835 1nt4A 391 6.28e+00 c.60.1.2 -7942 1dqsA 393 6.28e+00 1dqsA e.22.1.1 43347 1itg 166 6.42e+00 1b9dA c.55.3.2 33661 1bia 321 6.70e+00 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1dm5A 315 6.81e+00 1avc a.65.1.1 18186 1s14A 194 6.89e+00 d.122.1.2 -10973 1nu5A 370 6.90e+00 c.1.11.2 -5565 d.54.1.1 -9823 1p3dA 475 6.93e+00 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1c7qA 445 7.03e+00 2pgi c.80.1.2 35307 1yrnB 83 7.11e+00 1akhB a.4.1.1 15986 1iscA 192 7.37e+00 1avmA a.2.11.1 15733 d.44.1.1 38726 1nfp 228 7.54e+00 1nfp c.1.16.2 29555 1kmtA 141 8.04e+00 b.1.18.8 77442 1n62C 288 8.07e+00 d.87.2.1 80094 d.145.1.3 80095 1qnnA 191 8.35e+00 1avmA a.2.11.1 15792 d.44.1.1 38755 1on2A 142 8.62e+00 a.4.5.24 87103 a.76.1.1 87104 1bl3A 160 8.80e+00 1b9dA c.55.3.2 33655 1fsoA 139 9.16e+00 1rhoA b.1.18.8 60007 1exqA 154 9.26e+00 1b9dA c.55.3.2 33646 1eu3A 210 9.37e+00 1an8 b.40.2.2 25206 d.15.6.1 37795 1gqpA 221 9.78e+00 b.18.1.9 70372 1k61A 60 9.93e+00 a.4.1.1 77270 1n9lA 109 1.07e+01 d.110.3.6 85468 1qydA 313 1.15e+01 c.2.1.2 -5786 1dqiA 124 1.17e+01 1do6A b.1.13.1 22357 1ur5A 309 1.23e+01 c.2.1.5 -5910 d.162.1.1 -11477 1iw0A 215 1.26e+01 a.132.1.1 83720 1cpcA 162 1.27e+01 1cpcA a.1.1.3 15643 1o7zA 77 1.30e+01 d.9.1.1 86660 1f00I 282 1.30e+01 1f00I b.1.14.1 22368 b.1.14.1 22369 d.169.1.3 42439 1rypC 244 1.30e+01 1rypC d.153.1.4 41934 1khiA 176 1.31e+01 b.34.5.2 77408 b.40.4.5 77409 1ew0A 130 1.35e+01 1drmA d.110.3.2 40905 1n0wA 243 1.37e+01 c.37.1.11 79772 1ofuA 320 1.41e+01 c.32.1.1 86972 d.79.2.1 86973 1a0cA 438 1.44e+01 1a0cA c.1.15.3 29529 1oltA 457 1.44e+01 unknown_sccs -5688 1r4vA 171 1.44e+01 unknown_sccs -1221 1t0yA 122 1.44e+01 d.15.1.1 -9151 1j54A 186 1.48e+01 c.55.3.5 77077 1dvoA 152 1.50e+01 1dvoA a.136.1.1 19623 1bxeA 113 1.51e+01 1bxeA d.55.1.1 38898 1ubi 76 1.54e+01 1ubi d.15.1.1 37584 5eau 548 1.55e+01 5eat a.102.4.1 18851 a.128.1.3 19443 1h1oA 183 1.56e+01 a.3.1.4 83454 a.3.1.4 83455 1q2wA 308 1.57e+01 b.47.1.4 88355 1e9gA 286 1.59e+01 1wgjA b.40.5.1 59393 1h0pA 182 1.60e+01 b.62.1.1 76450 1kay 381 1.62e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1b8oA 284 1.62e+01 1b8oA c.56.2.1 33762 1iz0A 302 1.63e+01 b.35.1.2 83821 c.2.1.1 83822 1b7yA 350 1.65e+01 1pysA d.104.1.1 40776 1d2eA 397 1.66e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1ezwA 349 1.67e+01 1ezwA c.1.16.3 29558 1sw6A 327 1.69e+01 1sw6A d.211.1.1 19176 1qycA 308 1.73e+01 c.2.1.2 -5782 1hm6A 346 1.76e+01 1avc a.65.1.1 18147 1ogwA 76 1.78e+01 d.15.1.1 87001 1dgwX 79 1.78e+01 1caxB b.82.1.2 28091 1huxA 270 1.82e+01 1huxA c.55.1.5 61278 1f44A 324 1.82e+01 a.60.9.1 64982 d.163.1.1 64983 1kf6C 130 1.83e+01 f.21.2.2 72399 1i4jA 110 1.90e+01 d.55.1.1 76734 1sbxA 106 1.92e+01 1bupA 386 1.94e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1okrA 123 1.95e+01 unknown_sccs -235 1m3qA 317 1.96e+01 a.96.1.3 -1288 d.129.1.2 -11006 1kte 105 1.97e+01 1kte c.47.1.1 32771 1dgwA 178 1.98e+01 1dgwA b.82.1.2 28090 1zymA 258 1.99e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 1d2zB 153 2.02e+01 1d2zB a.77.1.2 18439 1ad3A 452 2.04e+01 1ad3A c.82.1.1 35335 1lswA 131 2.05e+01 d.110.3.2 78181 1ujnA 348 2.05e+01 e.22.1.1 -11998 1q1hA 110 2.11e+01 unknown_sccs -262 1pysA 350 2.11e+01 1pysA d.104.1.1 40775 1do6A 124 2.12e+01 1do6A b.1.13.1 22361 1a62 130 2.12e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1quqA 129 2.12e+01 1quqA b.40.4.3 25303 1m2dA 110 2.15e+01 c.47.1.11 78476 1b7yB 785 2.16e+01 1pysB a.6.1.1 16301 a.6.1.1 16302 b.40.4.4 25312 d.58.13.1 39311 d.104.1.1 40780 d.138.1.1 41456 2kinA 238 2.16e+01 1bg2 c.37.1.9 32190 1kit 757 2.20e+01 1kit b.29.1.8 24272 b.29.1.8 24273 b.68.1.1 27616 1squA 155 2.22e+01 unknown_sccs -10229 1ns5A 155 2.23e+01 c.116.1.3 80705 3chbD 104 2.29e+01 3chbD b.40.2.1 24970 1ki1B 352 2.30e+01 a.87.1.1 72497 b.55.1.1 72498 1hyvA 166 2.31e+01 1b9dA c.55.3.2 61424 1ekgA 127 2.34e+01 1dlxA d.82.2.1 40021 1q4rA 112 2.37e+01 d.58.4.4 -9943 1nxuA 333 2.40e+01 c.122.1.1 86389 1af3 196 2.43e+01 1maz f.1.4.1 43397 1ucrA 78 2.43e+01 unknown_sccs -308 1c24A 263 2.45e+01 1c24A d.127.1.1 41148 1lb2B 84 2.46e+01 a.60.3.1 77871 1djrD 103 2.47e+01 3chbD b.40.2.1 24865 1hn2A 159 2.48e+01 b.60.1.1 65890 2phlA 397 2.49e+01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1ew2A 513 2.60e+01 1b8jA c.76.1.1 59525 1louA 101 2.62e+01 1ris d.58.14.1 39323 1j5yA 187 2.64e+01 a.4.5.1 71592 d.94.2.1 71593 1ofcX 304 2.67e+01 a.4.1.3 -195 unknown_sccs -199 unknown_sccs -978 1dazC 99 2.67e+01 1hvc b.50.1.1 26501 2ran 316 2.69e+01 1avc a.65.1.1 18170 1hyeA 313 2.69e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1qusA 322 2.70e+01 1ltm d.2.1.6 36991 1g2oA 268 2.71e+01 1b8oA c.56.2.1 60228 1mldA 314 2.75e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1k4zA 159 2.85e+01 b.80.5.1 72070 1lt5D 103 2.85e+01 3chbD b.40.2.1 24875 1obpA 159 2.87e+01 1obpA b.60.1.1 27092 1fkmA 396 2.90e+01 1fkmA a.69.2.1 18315 a.69.2.1 18316 1bt0A 76 2.92e+01 1ubi d.15.1.1 37607 6paxA 133 2.93e+01 6paxA a.4.1.5 64758 a.4.1.5 64759 1dd9A 338 2.95e+01 1dd9A e.13.1.1 43254 1q6hA 224 3.03e+01 d.26.1.1 -9487 1ebmA 317 3.03e+01 1ebmA a.96.1.3 18751 d.129.1.2 41300 1ecmA 109 3.04e+01 1ecmA a.130.1.1 19492 1j9bA 141 3.08e+01 c.47.1.12 66459 1gt1A 159 3.10e+01 b.60.1.1 -4436 1r1dA 247 3.11e+01 unknown_sccs -8335 1p9oA 313 3.11e+01 unknown_sccs -8423 1bh9B 89 3.14e+01 1bh9B a.22.1.3 16485 1ekeA 230 3.22e+01 1ekeA c.55.3.1 33572 1i7oA 429 3.28e+01 1i7oA d.177.1.1 61893 d.177.1.1 61894 1vmoA 163 3.41e+01 1vmoA b.77.1.1 27974 1ka1A 357 3.41e+01 e.7.1.1 68369 1vi9A 299 3.41e+01 c.72.1.5 -8393 1ib8A 164 3.44e+01 b.38.2.1 71168 d.52.4.1 71169 1q25A 432 3.45e+01 1oz9A 150 3.46e+01 unknown_sccs -10588 1qsdA 106 3.46e+01 1qsdA a.7.5.1 16335 1fxkC 133 3.48e+01 1fxkC a.2.5.1 15702 1iwlA 182 3.49e+01 b.125.1.1 83757 1ud9A 245 3.56e+01 1omrA 201 3.57e+01 a.39.1.5 -854 1a4sA 503 3.57e+01 1bpwA c.82.1.1 35361 1nddA 76 3.57e+01 1ubi d.15.1.1 37599 1a8b 318 3.58e+01 1avc a.65.1.1 18171 1oeyA 83 3.65e+01 d.15.2.2 -9162 1ois 223 3.65e+01 1a36A e.15.1.1 43267 1qv9A 283 3.67e+01 unknown_sccs -6888 1fiuA 286 3.74e+01 1fiuA c.52.1.10 33317 1pguA 615 3.78e+01 b.69.4.1 88069 b.69.4.1 88070 1gw0A 559 3.81e+01 b.6.1.3 70623 b.6.1.3 70624 b.6.1.3 70625 1deeG 54 3.84e+01 1fc2C a.8.1.1 16343 1eg5A 384 3.88e+01 1ecxA c.67.1.3 34429 1ka2A 499 3.89e+01 d.92.1.5 77305 1kkoA 413 3.90e+01 c.1.11.2 68675 d.54.1.1 68676 1rec 201 3.91e+01 1rec a.39.1.5 17326 1amy 403 3.91e+01 1jdc b.71.1.1 27799 c.1.8.1 28786 1kyqA 274 3.92e+01 c.2.1.11 73281 e.37.1.1 73282 1n81A 186 3.92e+01 a.185.1.1 85388 1qj2C 285 3.95e+01 1qj2C 1f2tB 148 4.00e+01 1f2tB 1sy3A 184 4.00e+01