# 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 1souA 194 2.56e-25 1mk4A 157 7.39e-01 d.108.1.1 84979 1cfr 285 1.12e+00 1cfr c.52.1.7 33312 1ixkA 315 1.22e+00 unknown_sccs -8099 1omzA 293 1.29e+00 c.68.1.15 87093 1w2wB 191 1.54e+00 1g2iA 166 1.54e+00 1g2iA c.23.16.2 31438 1i1nA 226 1.58e+00 c.66.1.7 71102 1i7pA 274 1.63e+00 b.43.4.2 66048 c.25.1.1 66049 1dl5A 317 1.85e+00 1dl5A c.66.1.7 64720 d.197.1.1 64721 1b0uA 262 1.88e+00 1b0uA c.37.1.12 32370 1jeyB 565 1.90e+00 1jeqB unknown_sccs -4431 unknown_sccs -7995 2lbp 346 2.01e+00 2liv c.93.1.1 35709 1q7zA 566 2.08e+00 c.1.21.2 -5638 c.1.26.1 -5666 1kqpA 271 2.13e+00 c.26.2.1 72883 1usgA 346 2.16e+00 c.93.1.1 -8635 1dqwA 267 2.18e+00 1dqwA c.1.2.3 28551 1ih8A 271 2.46e+00 2nsyA c.26.2.1 62377 1jg1A 235 2.75e+00 c.66.1.7 66661 1pujA 282 2.87e+00 c.37.1.8 88294 1ls1A 295 2.87e+00 a.24.13.1 78170 c.37.1.10 78171 1qh8A 478 2.91e+00 1qguA c.92.2.3 35633 1gz6A 319 3.26e+00 c.2.1.2 76410 1ndh 272 3.41e+00 1ndh b.43.4.2 25662 c.25.1.1 31552 1fmcA 255 3.41e+00 1cydA c.2.1.2 29856 1ohvA 472 3.44e+00 c.67.1.4 -8181 1pg4A 652 3.61e+00 e.23.1.1 88067 1bdmA 327 3.82e+00 1bmdA c.2.1.5 30137 d.162.1.1 42104 1v9fA 325 4.09e+00 1i60A 278 4.70e+00 c.1.15.4 71118 1bmdA 327 4.79e+00 1bmdA c.2.1.5 30139 d.162.1.1 42106 3chy 128 5.11e+00 3chy c.23.1.1 31038 1vicA 262 5.47e+00 c.68.1.13 -8252 2ng1 293 5.49e+00 1ng1 a.24.13.1 16962 c.37.1.10 32273 1uedA 406 5.83e+00 a.104.1.1 -1459 1qysA 106 5.84e+00 unknown_sccs -13432 1ehiA 377 6.02e+00 1iow c.30.1.2 31716 d.142.1.1 41484 1dljA 402 6.08e+00 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1jvnA 555 6.28e+00 c.1.2.1 67355 c.23.16.1 67356 8abp 306 6.29e+00 8abp c.93.1.1 35647 1i8kA 107 6.91e+00 b.1.1.1 71130 1jbeA 128 6.93e+00 3chy c.23.1.1 62845 1mr7A 209 7.04e+00 b.81.1.3 -4798 1m65A 245 7.53e+00 c.6.3.1 84847 1h2rL 534 7.56e+00 1h2rL e.18.1.1 43298 1o58A 303 7.73e+00 c.79.1.1 -8503 1ass 159 7.87e+00 1a6dA c.8.5.2 30818 4ubpC 570 7.90e+00 1ubpC b.92.1.1 28431 c.1.9.2 29053 1th8A 145 8.28e+00 1np6A 174 8.32e+00 c.37.1.10 85954 1oxxK 353 8.44e+00 b.40.6.3 -3969 c.37.1.12 -7187 1qk8A 146 8.77e+00 1ewxA c.47.1.10 33061 1aop 497 9.59e+00 2aop d.58.36.1 39501 d.58.36.1 39502 d.134.1.1 41425 d.134.1.1 41426 1korA 400 9.71e+00 c.26.2.1 72824 d.210.1.1 72825 1i6wA 181 1.01e+01 1i6wA c.69.1.18 61859 1jflA 228 1.03e+01 c.78.2.1 71656 c.78.2.1 71657 1hssA 124 1.04e+01 1bea a.52.1.2 17819 2liv 344 1.05e+01 2liv c.93.1.1 35708 1ca1 370 1.08e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1pl8A 356 1.09e+01 b.35.1.2 -3716 c.2.1.1 -5740 1o8xA 146 1.10e+01 c.47.1.10 86681 1to6A 371 1.10e+01 1rpjA 288 1.14e+01 2dri c.93.1.1 35656 1hh1A 143 1.16e+01 1gefA c.52.1.18 61036 1fcjA 322 1.19e+01 1oasA c.79.1.1 35289 1vjnA 220 1.19e+01 unknown_sccs -11458 1efdN 266 1.21e+01 1efdN c.92.2.1 35597 1lfpA 249 1.24e+01 e.39.1.1 73885 1egwA 77 1.24e+01 1mnmA d.88.1.1 40234 1m1nA 491 1.24e+01 c.92.2.3 78417 1gcoA 261 1.26e+01 1ybvA c.2.1.2 29884 1uunA 184 1.32e+01 unknown_sccs -12370 1mzhA 225 1.33e+01 c.1.10.1 79698 1ujpA 271 1.35e+01 c.1.2.4 -5177 1mdoA 393 1.40e+01 c.67.1.4 79013 1ep3B 262 1.43e+01 1ep2B b.43.4.2 25664 c.25.1.3 31554 1srrA 124 1.43e+01 1dz3A c.23.1.1 31110 1ofuA 320 1.44e+01 c.32.1.1 86972 d.79.2.1 86973 1oxsC 353 1.45e+01 b.40.6.3 87519 c.37.1.12 87520 1sv6A 269 1.52e+01 1geeA 261 1.52e+01 c.2.1.2 -5814 1jyhA 157 1.54e+01 d.60.1.3 71956 1ejxC 567 1.55e+01 b.92.1.1 83184 c.1.9.2 83185 1dmhA 311 1.57e+01 1dmhA b.3.6.1 22633 1o5iA 249 1.59e+01 c.2.1.2 -5833 1r2zA 274 1.61e+01 a.156.1.2 -370 b.113.1.1 -5094 g.39.1.8 -12748 1p5dX 463 1.63e+01 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1vh7A 265 1.63e+01 c.1.2.1 -5159 1vhtA 218 1.64e+01 c.37.1.1 -7004 1hgxA 183 1.65e+01 1tc1A c.61.1.1 34027 1g63A 181 1.65e+01 1g5qA c.34.1.1 60299 1rwiA 270 1.66e+01 unknown_sccs -4603 1kr4A 125 1.70e+01 d.58.5.2 72889 1ubkL 534 1.72e+01 e.18.1.1 88422 1dgwA 178 1.73e+01 1dgwA b.82.1.2 28090 4xis 387 1.73e+01 4xis c.1.15.3 29421 1rjdA 334 1.74e+01 unknown_sccs -8079 1oaa 259 1.75e+01 1oaa c.2.1.2 29829 1lyp 32 1.75e+01 1lyp j.17.1.1 46169 3xis 387 1.77e+01 4xis c.1.15.3 29423 1e8aA 91 1.78e+01 1b4cA a.39.1.2 17188 1thfD 253 1.78e+01 1thfD c.1.2.1 28535 1qh8B 519 1.79e+01 1qguB c.92.2.3 35634 1m1nB 522 1.80e+01 c.92.2.3 78418 1jnrB 150 1.80e+01 d.58.1.5 66969 1cruA 454 1.81e+01 1c9uA b.68.2.1 27617 1gmiA 136 1.83e+01 b.7.1.1 65309 1mrzA 293 1.83e+01 b.43.5.1 -4048 c.26.1.3 -6616 1l2tA 235 1.85e+01 c.37.1.12 73514 1e3dB 542 1.85e+01 1h2rL e.18.1.1 59189 1vhoA 346 1.87e+01 unknown_sccs -4283 c.56.5.4 -7893 1li4A 432 1.91e+01 c.2.1.4 84616 c.23.12.3 84617 1j6pA 418 1.92e+01 b.92.1.4 77089 c.1.9.9 77090 1of4A 179 1.95e+01 b.18.1.18 86932 1eudB 396 1.96e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1oh4A 179 1.96e+01 b.18.1.18 -3123 1jyeA 349 2.00e+01 c.93.1.1 67455 1n45A 233 2.00e+01 a.132.1.1 79981 1kqzA 273 2.01e+01 c.1.8.5 68844 1htqA 477 2.01e+01 d.15.9.1 71035 d.128.1.1 71036 1umdA 367 2.02e+01 c.36.1.11 -6969 1k2yX 463 2.02e+01 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1h4vB 421 2.04e+01 1adjA c.51.1.1 60624 d.104.1.1 60625 1n7kA 234 2.06e+01 c.1.10.1 85374 1qq8A 214 2.06e+01 1qq8A 1nowA 507 2.07e+01 c.1.8.6 85936 d.92.2.1 85937 1po5A 476 2.19e+01 a.104.1.1 -1467 1mc0A 368 2.21e+01 d.110.2.1 78937 d.110.2.1 78938 1f5mA 180 2.23e+01 1f5mB d.110.2.1 40895 1nox 205 2.24e+01 1nox d.90.1.1 40242 1qstA 160 2.24e+01 1yghA d.108.1.1 40804 1burS 123 2.28e+01 1rboC 1vimA 200 2.33e+01 c.80.1.3 -8532 1tidB 119 2.35e+01 1poiB 260 2.37e+01 1poiB unknown_sccs 34155 1ev7A 317 2.40e+01 1ev7B c.52.1.9 33315 1gqpA 221 2.46e+01 b.18.1.9 70372 1aisA 182 2.47e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1a8rA 221 2.49e+01 1a8rA d.96.1.1 40587 1kk1A 410 2.50e+01 b.43.3.1 72634 b.44.1.1 72635 c.37.1.8 72636 1f8yA 157 2.50e+01 1f8xA c.23.14.1 31395 1p1mA 406 2.50e+01 b.92.1.4 87696 c.1.9.9 87697 1tlfA 301 2.52e+01 1tlfA c.93.1.1 35687 1lk5A 229 2.52e+01 unknown_sccs 73960 d.58.40.1 73961 1qdeA 224 2.56e+01 1qvaA c.37.1.19 32410 1iukA 140 2.57e+01 c.2.1.8 83712 1jmxB 349 2.58e+01 b.69.2.2 66906 1spgB 147 2.58e+01 1cg5B a.1.1.2 15588 1o69A 394 2.58e+01 c.67.1.4 -8209 1d6jA 211 2.60e+01 1d6jA c.37.1.4 31940 1s14A 194 2.64e+01 d.122.1.2 -10973 1gudA 288 2.71e+01 c.93.1.1 83326 1hbkA 94 2.74e+01 1aca a.11.1.1 60887 2hvm 273 2.77e+01 1cnv c.1.8.5 28985 1adjA 421 2.79e+01 1adjA c.51.1.1 33188 d.104.1.1 40737 1i0dA 332 2.80e+01 1pscA c.1.9.3 61487 1a4iA 301 2.87e+01 1a4iA c.2.1.7 30278 c.58.1.2 33926 1dozA 309 2.93e+01 1ak1 c.92.1.1 35592 1brwA 433 2.93e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1l1zA 274 2.95e+01 a.156.1.2 75911 b.113.1.1 75912 g.39.1.8 75913 1owfB 94 2.98e+01 a.55.1.1 87488 1h7wA 1025 2.99e+01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1k07A 263 3.02e+01 d.157.1.1 77218 1dec 39 3.08e+01 1dec g.3.15.2 44376 1d4fA 431 3.10e+01 1b3rA c.2.1.4 30110 c.23.12.3 31370 1nkd 65 3.15e+01 1nkd a.30.1.1 16974 1r5qA 102 3.15e+01 unknown_sccs -965 1kjnA 157 3.19e+01 c.115.1.1 72614 1bo4A 168 3.21e+01 1bo4A d.108.1.1 40798 1gca 309 3.21e+01 1gca c.93.1.1 35659 1aj2 282 3.25e+01 1aj2 c.1.21.1 29665 1bxkA 355 3.34e+01 1bxkA c.2.1.2 29803 1ci3M 249 3.45e+01 1hcz b.2.6.1 22480 b.84.2.2 28266 1tiqA 180 3.45e+01 1ivnA 190 3.51e+01 c.23.10.5 83719 1iw0A 215 3.52e+01 a.132.1.1 83720 1efvB 255 3.55e+01 1efvB c.26.2.3 31634 1a04A 215 3.57e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1ekeA 230 3.59e+01 1ekeA c.55.3.1 33572 1lx7A 253 3.60e+01 c.56.2.1 74329 1auoA 218 3.63e+01 1auoA c.69.1.14 34716 1rxyA 253 3.63e+01 c.56.2.1 -7834 1ispA 181 3.64e+01 c.69.1.18 76778 1rocA 155 3.67e+01 unknown_sccs -2866 1fre 42 3.74e+01 1fre g.43.1.1 45320 1muwA 386 3.74e+01 c.1.15.3 79495 1ga0A 364 3.74e+01 1gceA e.3.1.1 60410 1l6sA 323 3.77e+01 c.1.10.3 73627 1gteA 1025 3.77e+01 a.1.2.2 70440 c.1.4.1 70441 c.3.1.1 70442 c.4.1.1 70443 d.58.1.5 70444 1mslA 109 3.81e+01 1mslA f.16.1.1 43660 1fsz 372 3.84e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1rfmA 344 3.85e+01 c.122.1.1 -8032 1hr6A 475 3.90e+01 1hr6A d.185.1.1 61164 d.185.1.1 61165 1li5A 461 3.97e+01 a.27.1.1 73912 c.26.1.1 73913