# 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 1.69e-02 1ncx a.39.1.5 17223 1f6yA 262 4.65e-02 1f6yA c.1.21.2 29673 1efyA 350 8.97e-02 1a26 a.41.1.1 17413 d.166.1.2 42275 1aerA 205 2.31e-01 1aerA d.166.1.1 42249 1kgdA 180 2.65e-01 c.37.1.1 68582 1s96A 219 3.41e-01 c.37.1.1 -6972 1jhfA 202 4.15e-01 a.4.5.2 63057 b.87.1.1 63058 1nt4A 391 4.63e-01 c.60.1.2 -7942 1ggzA 148 5.86e-01 a.39.1.5 70176 1se0A 116 7.94e-01 g.52.1.1 -12841 2sas 185 9.00e-01 2sas a.39.1.5 17258 1nhkL 144 1.05e+00 1npk d.58.6.1 39142 1wm1A 317 1.11e+00 4pep 326 1.27e+00 1smrA b.50.1.2 26843 1g8mA 593 1.28e+00 1g8mA c.24.1.3 60371 c.97.2.1 60372 1qtrA 317 1.42e+00 1qtrA c.69.1.7 34660 1iyeA 309 1.44e+00 e.17.1.1 83786 1mu5A 471 1.48e+00 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1p9kA 79 1.76e+00 unknown_sccs -10238 1gky 187 1.86e+00 1gky c.37.1.1 31839 1i1kA 309 1.87e+00 1daaA e.17.1.1 61533 1k9uA 78 1.95e+00 a.39.1.10 84348 1g4yR 148 2.05e+00 1cll a.39.1.5 60252 1e2gA 215 2.16e+00 3tmkA c.37.1.1 59165 1tm0A 350 2.17e+00 1auiB 169 2.49e+00 1auiB a.39.1.5 17325 1ikpA 613 2.56e+00 b.29.1.7 66182 d.166.1.1 66183 f.1.5.1 66184 1e0cA 271 2.56e+00 1e0cA c.46.1.2 32717 c.46.1.2 32718 1fxjA 331 2.58e+00 1fwyA b.81.1.4 28062 c.68.1.5 34520 1kl9A 182 2.60e+00 b.40.4.5 72681 2polA 366 2.67e+00 2polA d.131.1.1 41356 d.131.1.1 41357 d.131.1.1 41358 1k4iA 233 2.67e+00 d.115.1.2 72056 1j3wA 163 2.69e+00 unknown_sccs -10870 1s29A 92 2.75e+00 unknown_sccs -315 1p9qC 256 2.78e+00 1ex7A 186 2.84e+00 1gky c.37.1.1 59537 1gd0A 122 2.94e+00 1dptA d.80.1.3 39834 1i8dA 213 3.28e+00 b.43.4.3 61953 b.43.4.3 61954 1cbf 285 3.35e+00 1cbf c.90.1.1 35587 1qh8A 478 3.44e+00 1qguA c.92.2.3 35633 1s4qA 228 3.49e+00 c.37.1.1 -6975 1smlA 269 3.59e+00 1smlA d.157.1.1 42053 1a7w 69 3.63e+00 1a7w a.22.1.2 16477 1nuuA 252 3.72e+00 c.26.1.3 86209 1gnlA 544 3.74e+00 e.26.1.1 70287 1nf2A 268 3.84e+00 c.108.1.10 -6842 1g57A 217 3.90e+00 1g57A d.115.1.2 60253 1gsa 316 3.92e+00 1gsa c.30.1.3 31718 d.142.1.1 41477 1hv9A 456 4.08e+00 1fwyA b.81.1.4 28060 c.68.1.5 34518 1nn5A 215 4.42e+00 c.37.1.1 85892 1exrA 148 4.49e+00 1cll a.39.1.5 17299 3psg 370 4.62e+00 1smrA b.50.1.2 26841 1e2fA 215 4.87e+00 3tmkA c.37.1.1 59164 1g8iA 190 5.00e+00 1rec a.39.1.5 60363 1kwmA 402 5.28e+00 c.56.5.1 73079 d.58.3.1 73080 1ift 263 5.34e+00 1mrj d.165.1.1 42211 1t9kA 347 5.37e+00 1ok7A 366 5.49e+00 1qf9A 194 5.51e+00 1zin c.37.1.1 31848 1uq5A 263 5.59e+00 d.165.1.1 -11555 1i4mA 108 5.72e+00 d.6.1.1 66025 5ukdA 194 5.95e+00 1zin c.37.1.1 31851 1cd8 114 5.98e+00 1cd8 b.1.1.1 19714 1mmiA 366 6.04e+00 d.131.1.1 -11093 d.131.1.1 -11094 d.131.1.1 -11095 1wdcC 156 6.11e+00 1wdcC a.39.1.5 17317 1mkfA 382 6.69e+00 b.116.1.1 79232 1v5xA 203 6.86e+00 c.1.2.4 -5169 1a4iA 301 6.91e+00 1a4iA c.2.1.7 30278 c.58.1.2 33926 1n0wA 243 6.93e+00 c.37.1.11 79772 1f4qA 165 7.44e+00 1alvA a.39.1.8 17360 1f46A 140 7.61e+00 1f46A d.129.4.1 59643 1m1nA 491 7.94e+00 c.92.2.3 78417 1mp4A 292 8.02e+00 c.68.1.6 79376 4icb 76 8.33e+00 4icb a.39.1.1 17145 1lktA 104 8.48e+00 1lktA b.90.1.1 28398 1b8bA 605 8.76e+00 1b8bA 1lf6A 684 8.96e+00 a.102.1.5 77918 b.30.5.5 77919 1m45A 148 9.15e+00 a.39.1.5 78598 1nmoA 247 9.29e+00 unknown_sccs -8746 1ton 235 9.43e+00 5ptp b.47.1.2 26307 1scuA 288 9.60e+00 2scuA c.2.1.8 30307 c.23.4.1 31135 1oi2A 366 9.62e+00 c.32.1.2 87039 d.79.2.2 87040 2if1 126 9.64e+00 2if1 d.64.1.1 39547 1kk8B 139 9.65e+00 a.39.1.5 77430 1bt0A 76 9.69e+00 1ubi d.15.1.1 37607 1g2yA 32 9.78e+00 unknown_sccs 17003 1j4aA 333 9.87e+00 c.2.1.4 71502 c.23.12.1 71503 1bx7 55 9.89e+00 1bx7 g.3.15.1 44355 1ukuA 102 9.90e+00 d.58.5.2 -9992 1t3cA 421 9.94e+00 1kbvA 327 1.01e+01 b.6.1.3 68395 b.6.1.3 68396 1h6lA 353 1.02e+01 b.68.3.1 60687 1hk9A 74 1.08e+01 b.38.1.2 83541 1kjwA 295 1.09e+01 b.34.2.1 68643 c.37.1.1 68644 1apyB 141 1.13e+01 1apyB 1eg5A 384 1.15e+01 1ecxA c.67.1.3 34429 1sedA 117 1.17e+01 1s5pA 235 1.18e+01 c.31.1.5 -6774 1s6cA 183 1.19e+01 a.39.1.5 -858 1sbxA 106 1.21e+01 1pf5A 131 1.24e+01 d.79.1.1 -10368 1q9jA 422 1.25e+01 1vjqA 79 1.25e+01 unknown_sccs -13478 1np6A 174 1.30e+01 c.37.1.10 85954 1o1zA 234 1.31e+01 c.1.18.3 86555 1pg4A 652 1.32e+01 e.23.1.1 88067 1nepA 130 1.34e+01 b.1.18.7 80440 1jf2A 195 1.36e+01 1ej3A a.39.1.5 62930 1sy6A 204 1.37e+01 1fu1A 203 1.38e+01 1fu1B b.59.1.1 27076 h.1.11.1 45630 1qtwA 285 1.38e+01 1qumA c.1.15.1 29392 3htsB 102 1.40e+01 2hts a.4.5.22 16175 1rv3A 483 1.40e+01 1a62 130 1.42e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1bj4A 470 1.42e+01 1bj4A c.67.1.4 34479 1adn 92 1.46e+01 1adn g.48.1.1 45348 1wdcB 156 1.47e+01 1wdcB a.39.1.5 17302 1ik9A 213 1.50e+01 b.59.1.1 66176 h.1.11.1 66177 1kopA 223 1.51e+01 2cba b.74.1.1 27966 1g5hA 454 1.51e+01 1g5hA c.51.1.1 60270 d.104.1.1 60271 1svfB 38 1.51e+01 1svfB h.3.2.1 45764 1j6pA 418 1.53e+01 b.92.1.4 77089 c.1.9.9 77090 2hhmA 276 1.54e+01 1imbA e.7.1.1 42955 3ladA 476 1.55e+01 1lvl c.3.1.5 30573 c.3.1.5 30574 d.87.1.1 40208 1uiuA 502 1.58e+01 c.94.1.1 -8674 1m22A 503 1.59e+01 c.117.1.1 78464 1qv1A 195 1.62e+01 a.39.1.5 -830 2fokA 579 1.66e+01 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1k94A 165 1.66e+01 a.39.1.8 68333 1psdA 409 1.67e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1vi2A 300 1.68e+01 c.2.1.7 -5960 c.58.1.5 -6366 2eifA 136 1.69e+01 1bkb b.34.5.2 24607 b.40.4.5 25339 1jfiA 98 1.71e+01 1jfiA a.22.1.3 62936 1el4A 195 1.74e+01 1ej3A a.39.1.5 59453 1geqA 248 1.77e+01 2tysA c.1.2.4 28589 1qjtA 99 1.80e+01 1eh2 a.39.1.6 17335 1p1mA 406 1.82e+01 b.92.1.4 87696 c.1.9.9 87697 1rk6A 496 1.83e+01 b.92.1.6 -5087 b.92.1.6 -5088 c.1.9.11 -5435 1qz9A 416 1.85e+01 c.67.1.3 -8180 1n0xL 215 1.85e+01 b.1.1.1 -2063 b.1.1.2 -2429 1d8cA 723 1.85e+01 1d8cA c.1.13.1 29325 1din 236 1.88e+01 1din c.69.1.9 34682 1fnnA 389 1.91e+01 1fnnA a.4.5.11 16129 c.37.1.20 32426 1s0aA 429 1.91e+01 c.67.1.4 -8201 1f44A 324 1.92e+01 a.60.9.1 64982 d.163.1.1 64983 1mbxC 106 1.93e+01 d.45.1.2 78929 1npyA 271 1.98e+01 c.2.1.7 85995 c.58.1.5 85996 1o2dA 371 1.98e+01 e.22.1.2 86591 1epwA 1290 2.01e+01 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1j2jB 45 2.01e+01 a.7.8.1 84017 1on2A 142 2.02e+01 a.4.5.24 87103 a.76.1.1 87104 1a8s 273 2.05e+01 1brt c.69.1.12 34710 1e5mA 416 2.05e+01 1dd8A c.95.1.1 58973 c.95.1.1 58974 1a8vA 121 2.06e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1mb3A 124 2.10e+01 c.23.1.1 78907 1q1aA 289 2.11e+01 c.31.1.5 -6781 3pmgA 561 2.13e+01 3pmgA c.84.1.1 35408 c.84.1.1 35409 c.84.1.1 35410 d.129.2.1 41301 2pooA 355 2.14e+01 1qlgA b.68.3.1 27626 1l3iA 192 2.15e+01 c.66.1.22 77676 1uhvA 500 2.16e+01 b.71.1.2 -4683 c.1.8.3 -5354 1jli 112 2.19e+01 1jli a.26.1.2 16884 1k6wA 426 2.22e+01 b.92.1.2 68236 c.1.9.5 68237 1fhgA 154 2.23e+01 1tlk b.1.1.4 21706 1f5jA 199 2.23e+01 1axkA b.29.1.11 24342 1srrA 124 2.26e+01 1dz3A c.23.1.1 31110 1avsA 90 2.26e+01 1cll a.39.1.5 17226 1f89A 291 2.27e+01 d.160.1.1 64988 1thfD 253 2.27e+01 1thfD c.1.2.1 28535 1lucB 324 2.28e+01 1lucA c.1.16.1 29548 1bif 469 2.29e+01 1bif c.37.1.7 31961 c.60.1.4 34003 1xyzA 347 2.31e+01 1taxA c.1.8.3 28804 1bo4A 168 2.32e+01 1bo4A d.108.1.1 40798 1bgp 309 2.34e+01 1bgp a.93.1.1 18690 1crzA 403 2.35e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1v54B 227 2.37e+01 b.6.1.2 -2946 f.17.2.1 -12243 1llp 343 2.38e+01 1arv a.93.1.1 18578 1dgyA 363 2.41e+01 1bx4A 1liiA 363 2.43e+01 c.72.1.1 73921 1ig5A 75 2.45e+01 4icb a.39.1.1 62363 1gvnA 90 2.47e+01 a.8.2.1 76353 1htyA 1015 2.48e+01 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 1g6gA 127 2.48e+01 1g6gA b.26.1.2 23916 1s1iF 162 2.49e+01 1p57B 255 2.50e+01 b.47.1.2 -4248 1lzjA 292 2.52e+01 c.68.1.9 74352 1t95A 240 2.55e+01 1imbA 277 2.56e+01 1imbA e.7.1.1 42957 1vhh 162 2.57e+01 1vhh d.65.1.2 39550 1qd9A 124 2.58e+01 1qu9A d.79.1.1 39758 1tlk 154 2.59e+01 1tlk b.1.1.4 21707 1m4tA 392 2.61e+01 c.95.1.1 78617 c.95.1.1 78618 1qauA 112 2.61e+01 1qauA b.36.1.1 24779 2pvbA 107 2.64e+01 1a75A a.39.1.4 17205 1uasA 362 2.68e+01 b.71.1.1 88388 c.1.8.1 88389 1pea 385 2.68e+01 1pea c.93.1.1 35662 1tafB 70 2.69e+01 1tafB a.22.1.3 16482 1l8aA 886 2.69e+01 c.36.1.6 73678 c.36.1.10 73677 c.48.1.1 73679 1qj5A 429 2.72e+01 1dtyA c.67.1.4 34493 2liv 344 2.78e+01 2liv c.93.1.1 35708 1j30A 144 2.79e+01 a.25.1.1 -650 1dfoA 417 2.80e+01 1bj4A c.67.1.4 34480 1h9sA 140 2.82e+01 1b9mA b.40.6.2 60843 b.40.6.2 60844 1m7jA 484 2.82e+01 b.92.1.6 78732 b.92.1.6 78733 c.1.9.11 78734 1o4sA 389 2.82e+01 c.67.1.1 86620 1bjaA 95 2.86e+01 1bjaA a.4.5.9 16122 1cr5A 189 2.86e+01 1cr5A b.52.2.3 26931 d.31.1.1 38465 1qwnA 1045 2.86e+01 a.8.3.1 -414 b.30.5.6 -3517 c.6.2.1 -6058 1lci 550 2.93e+01 1lci e.23.1.1 43349 1ogdA 131 2.93e+01 unknown_sccs -8007 1mxgA 435 2.99e+01 b.71.1.1 85193 c.1.8.1 85194 1d3vA 323 3.07e+01 1d3vA c.42.1.1 32559 1nddA 76 3.10e+01 1ubi d.15.1.1 37599 1p5fA 189 3.10e+01 c.23.16.2 -6508 1ursA 402 3.11e+01 c.94.1.1 -8651 1xxaA 78 3.15e+01 1xxaA d.74.2.1 39700 1b5fA 239 3.23e+01 1smrA b.50.1.2 26836 1bmqB 88 3.26e+01 1pauB 1a99A 344 3.29e+01 1pot c.94.1.1 35812 1gmxA 108 3.36e+01 c.46.1.3 65355 1ltsA 185 3.36e+01 1lt3A d.166.1.1 42229 1gdhA 320 3.38e+01 1gdhA c.2.1.4 30095 c.23.12.1 31355 1ppt 36 3.40e+01 1ppt j.6.1.1 46089 1eaiC 61 3.42e+01 1eaiC g.22.1.1 44894 1omhA 293 3.44e+01 unknown_sccs -10527 1r72A 211 3.45e+01 unknown_sccs -215 unknown_sccs -5981 1broA 277 3.47e+01 1brt c.69.1.12 34700 1s5dA 240 3.47e+01 d.166.1.1 -11563 1aw7A 194 3.49e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 4crxA 322 3.55e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1cf2O 337 3.55e+01 1b7gO c.2.1.3 29994 d.81.1.1 39909 1hd2A 161 3.57e+01 c.47.1.10 60962 1ugmA 125 3.57e+01 1b67A 68 3.61e+01 1a7w a.22.1.2 16474 1k0sA 151 3.65e+01 b.40.7.1 67969 1hztA 190 3.67e+01 1i9aA d.113.1.2 61459 1g7fA 298 3.71e+01 1pty c.45.1.2 60330 1avyA 74 3.71e+01 1avyB h.1.17.1 45656 1fzrA 138 3.73e+01 1fzrA c.52.1.17 33336 1ubi 76 3.77e+01 1ubi d.15.1.1 37584 1f7dA 136 3.85e+01 1dun b.85.4.1 28353 1b9hA 388 3.86e+01 1b9hA c.67.1.4 34488 1nrvA 105 3.86e+01 d.93.1.1 86126 1jl3A 139 3.87e+01 c.44.1.1 66826 1or7C 90 3.88e+01 a.180.1.1 87336 1lg7A 182 3.95e+01 d.213.1.1 73888 1dqeA 137 3.97e+01 1dqeA a.39.2.1 17388 1q1hA 110 3.97e+01 unknown_sccs -262 1lvwA 295 3.97e+01 c.68.1.6 84723 1gg6C 97 3.97e+01 5ptp 1psuA 140 3.99e+01 d.38.1.5 88285