# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1bouB 302 1.07e-01 1bouB c.56.6.1 33859 1xxbA 78 1.57e-01 1xxaA d.74.2.1 39706 1xxcA 78 1.64e-01 1xxaA d.74.2.1 39712 1a27 289 2.94e-01 1fds c.2.1.2 29839 1dciA 275 3.42e-01 1dciA c.14.1.3 30918 1fdt 327 3.45e-01 1fds c.2.1.2 29841 1fds 327 4.24e-01 1fds c.2.1.2 29838 1fxkC 133 5.66e-01 1fxkC a.2.5.1 15702 1l2qA 458 7.34e-01 1l2rA 458 7.55e-01 1dysA 348 1.02e+00 1bvwA c.6.1.1 30669 1ek0A 170 1.10e+00 1ctqA c.37.1.8 32076 1ej2A 181 1.36e+00 1f9aA c.26.1.3 59414 1gg1A 350 1.68e+00 1qr7A c.1.10.4 29187 1xxaA 78 1.69e+00 1xxaA d.74.2.1 39700 1c3pA 375 1.98e+00 1c3pA c.42.1.2 32606 1hrdA 449 2.20e+00 1k89 c.2.1.7 30219 c.58.1.1 33867 1k89 449 2.32e+00 1k89 c.2.1.7 30218 c.58.1.1 33866 1g2oA 268 2.76e+00 1b8oA c.56.2.1 60228 1qr7A 350 3.56e+00 1qr7A c.1.10.4 29191 1bgvA 449 3.60e+00 1k89 c.2.1.7 30217 c.58.1.1 33865 1h65A 270 4.44e+00 c.37.1.8 65640 1fsz 372 5.37e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1oatA 439 5.60e+00 2dkb c.67.1.4 34461 2cevA 299 5.74e+00 1d3vA c.42.1.1 32576 1bvwA 360 5.81e+00 1bvwA c.6.1.1 30668 1aihA 170 5.96e+00 1aihA d.163.1.1 42149 1qo7A 394 6.04e+00 1qo7A c.69.1.11 34697 2bvwA 362 6.87e+00 1bvwA c.6.1.1 30666 1mroB 442 7.29e+00 1mroB a.89.1.1 18531 d.58.31.2 39449 1i6wA 181 7.35e+00 1i6wA c.69.1.18 61859 1mgtA 174 7.39e+00 1mgtA a.4.2.1 16078 c.55.7.1 33753 1i60A 278 7.66e+00 2oatA 439 7.99e+00 2dkb c.67.1.4 34452 2tysB 397 8.03e+00 2tysB c.79.1.1 35272 16pk 415 8.22e+00 16pk c.86.1.1 35454 1a6f 119 8.53e+00 1a6f d.14.1.2 37564 1dymA 402 9.06e+00 1celA b.29.1.10 24304 1jgtA 513 9.19e+00 c.26.2.1 66684 d.153.1.1 66685 1g99A 408 9.74e+00 1g99A c.55.1.2 33457 c.55.1.2 33458 1dtdA 303 1.01e+01 1aye c.56.5.1 33823 1cb2A 365 1.08e+01 1bvwA c.6.1.1 30661 1a88A 275 1.10e+01 1brt c.69.1.12 34707 1qrdA 273 1.11e+01 1d4aA c.23.5.3 31217 1tca 317 1.16e+01 1tca c.69.1.17 34726 1hbnB 442 1.19e+01 1mroB a.89.1.1 60900 d.58.31.2 60901 1qjwA 365 1.28e+01 1bvwA c.6.1.1 30657 1dcfA 136 1.31e+01 1dcfA c.23.1.2 31124 1pprM 312 1.34e+01 1pprM a.131.1.1 19502 a.131.1.1 19503 1f2dA 341 1.35e+01 1f2dA c.79.1.1 35298 1qnf 484 1.38e+01 1qnf a.99.1.1 18777 c.28.1.1 31632 1guzA 310 1.41e+01 c.2.1.5 65586 d.162.1.1 65587 1tplA 426 1.44e+01 1ax4A c.67.1.2 34387 1ltm 320 1.44e+01 1ltm d.2.1.6 36992 1af8 86 1.46e+01 2af8 a.28.1.1 16932 1gryA 290 1.50e+01 1jfaA 374 1.53e+01 a.128.1.5 66622 1ei9A 279 1.55e+01 1ei9A c.69.1.13 34713 1brwA 433 1.62e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1qfwM 108 1.62e+01 32c2A b.1.1.1 20436 1hr6A 475 1.64e+01 1hr6A d.185.1.1 61164 d.185.1.1 61165 1ppt 36 1.65e+01 1ppt j.6.1.1 46089 1a8q 274 1.70e+01 1brt c.69.1.12 34702 1bksB 397 1.70e+01 2tysB c.79.1.1 35285 1qusA 322 1.71e+01 1ltm d.2.1.6 36991 1aye 401 1.78e+01 1aye c.56.5.1 33824 d.58.3.1 39065 2af8 86 1.81e+01 2af8 a.28.1.1 16933 1f20A 435 1.88e+01 b.43.4.1 64932 c.25.1.4 64933 2wsyA 268 1.89e+01 2tysA c.1.2.4 28588 1tph1 247 1.89e+01 1amk 1bjnA 360 1.90e+01 1bjnA c.67.1.4 34469 1onrA 316 1.91e+01 1onrA c.1.10.1 29169 1ag9A 175 1.93e+01 1rcf c.23.5.1 31178 2gsaA 432 1.94e+01 2gsaA c.67.1.4 34446 1ewkA 490 1.96e+01 1ewkA c.93.1.1 35712 1cor 82 1.96e+01 451c a.3.1.1 15903 1k4iA 233 1.98e+01 1bksA 268 2.03e+01 2tysA c.1.2.4 28585 2tysA 268 2.04e+01 2tysA c.1.2.4 28572 1jjuA 489 2.04e+01 a.3.1.7 66774 a.3.1.7 66775 b.1.1.6 66776 b.1.1.6 66777 b.61.4.1 66778 1f60A 458 2.06e+01 1efcA b.43.3.1 25705 b.44.1.1 25745 c.37.1.8 32140 1eo6A 117 2.07e+01 1eo6A d.15.1.3 37609 1igtB 444 2.09e+01 1igtB b.1.1.1 19765 b.1.1.2 20867 b.1.1.2 20868 b.1.1.2 20869 1ceqA 316 2.12e+01 1ceqA c.2.1.5 30163 d.162.1.1 42130 1l7vC 249 2.14e+01 2gsq 202 2.18e+01 1pd21 a.45.1.1 17715 c.47.1.5 33009 1a4mA 349 2.19e+01 1a4mA c.1.9.1 29014 1djnA 729 2.19e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1igtD 444 2.19e+01 1igtB b.1.1.1 19767 b.1.1.2 20871 b.1.1.2 20872 b.1.1.2 20873 1b9zA 516 2.20e+01 1b9zA b.3.1.1 22528 c.1.8.2 28798 1qgpA 77 2.22e+01 1qbjA a.4.5.19 16158 1aoeA 192 2.23e+01 1aoeA c.71.1.1 34923 1qe5A 266 2.28e+01 1b8oA c.56.2.1 33784 5bcaA 516 2.29e+01 1b9zA b.3.1.1 22529 c.1.8.2 28799 3cbh 365 2.29e+01 1bvwA c.6.1.1 30665 1kjqA 391 2.29e+01 2chsA 127 2.33e+01 2chsA d.79.1.2 39764 2cmd 312 2.35e+01 2cmd c.2.1.5 30135 d.162.1.1 42102 1hg3A 225 2.36e+01 1hg3A c.1.1.1 61025 1qopA 268 2.36e+01 2tysA c.1.2.4 28570 1mldA 314 2.37e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1pdo 135 2.39e+01 1pdo c.54.1.1 33376 1klpA 115 2.39e+01 1f0iA 504 2.40e+01 1f0iA d.136.1.2 59566 d.136.1.2 59567 2tmdA 729 2.46e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1gpiA 431 2.46e+01 b.29.1.10 65450 1uok 558 2.46e+01 1uok b.71.1.1 27801 c.1.8.1 28788 1eyzA 392 2.50e+01 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1bi5A 389 2.50e+01 1bi5A c.95.1.2 35985 c.95.1.2 35986 1fwxA 595 2.50e+01 b.6.1.4 60069 b.69.3.1 60070 1vxrA 537 2.50e+01 2bce c.69.1.1 34595 1jeqB 565 2.54e+01 1jeqB e.31.1.2 62922 2fcr 173 2.55e+01 1rcf c.23.5.1 31151 1jeyB 565 2.59e+01 1jeqB e.31.1.2 62925 1dgkN 917 2.59e+01 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1k8kA 418 2.60e+01 c.55.1.1 68305 c.55.1.1 68306 1qe3A 489 2.60e+01 2bce c.69.1.1 34630 1ez1A 392 2.62e+01 1ez1A b.84.2.1 28248 c.30.1.1 31655 d.142.1.2 41500 1hdoA 206 2.62e+01 1he2A c.2.1.2 60965 1dixA 208 2.63e+01 1bk7A d.124.1.1 41122 1f4pA 147 2.63e+01 5nul c.23.5.1 59651 1czaN 917 2.65e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 1b8qA 127 2.66e+01 1qauA b.36.1.1 24781 1kxlA 199 2.66e+01 1jdqA 98 2.68e+01 d.68.3.2 66559 1gnlA 544 2.69e+01 2tmnE 316 2.69e+01 1hyt d.92.1.2 59055 1eumA 165 2.70e+01 1eumA a.25.1.1 59507 1dbfA 127 2.72e+01 2chsA d.79.1.2 39761 1fjhB 257 2.77e+01 1fjhB c.2.1.2 29871 1tyfA 193 2.78e+01 1tyfA c.14.1.1 30885 2wsyB 396 2.78e+01 2tysB c.79.1.1 35288 2fx2 147 2.78e+01 1rcf c.23.5.1 31158 1e39A 571 2.78e+01 1qjdA a.138.1.3 19694 c.3.1.4 30431 d.168.1.1 42314 1lkxA 697 2.83e+01 1akr 147 2.84e+01 1rcf c.23.5.1 31152 1hkcA 917 2.86e+01 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1bu5A 147 2.89e+01 5nul c.23.5.1 31155 1qbjA 81 2.90e+01 1qbjA a.4.5.19 16155 7timA 247 2.90e+01 1amk c.1.1.1 28457 1d3hA 367 2.93e+01 1d3gA c.1.4.1 28601 1j4nA 271 2.95e+01 1j8fA 323 2.95e+01 1j8fA c.31.1.5 62738 1d3vA 323 3.01e+01 1d3vA c.42.1.1 32559 1a0p 290 3.02e+01 1a0p a.60.9.1 18105 d.163.1.1 42165 1gnwA 211 3.04e+01 1gnwA a.45.1.1 17727 c.47.1.5 33021 1qouA 181 3.05e+01 1qouA b.17.1.1 23707 1hjp 203 3.07e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1kiyA 374 3.10e+01 1ten 90 3.12e+01 1ten b.1.2.1 21990 1hyeA 313 3.12e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1qatB 622 3.12e+01 1djxB a.39.1.7 17355 b.7.1.1 23172 c.1.18.1 29600 1jfgA 374 3.13e+01 a.128.1.5 66636 4crxA 322 3.14e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1crxA 322 3.22e+01 4crxA a.60.9.1 18097 d.163.1.1 42157 1b8aA 438 3.23e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1gnuA 117 3.25e+01 d.15.1.3 65403 1gmeA 151 3.25e+01 b.15.1.1 65305 1i5nA 146 3.26e+01 1i5nA a.24.10.3 61805 3crxA 343 3.28e+01 4crxA a.60.9.1 18101 d.163.1.1 42161 1ep3B 262 3.28e+01 1ep2B b.43.4.2 25664 c.25.1.3 31554 1h7wB 1025 3.30e+01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1h7wD 1025 3.35e+01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 1gx5A 536 3.37e+01 1h7xA 1025 3.37e+01 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1gteA 1025 3.37e+01 1d3gA 367 3.40e+01 1d3gA c.1.4.1 28600 1h5qA 265 3.41e+01 1cydA c.2.1.2 60643 1h7wA 1025 3.42e+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 1e0tA 470 3.42e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1jqeA 292 3.45e+01 1f44A 324 3.47e+01 a.60.9.1 64982 d.163.1.1 64983 1jndA 420 3.57e+01 1quvA 578 3.58e+01 1quvA e.8.1.4 43119 1h7xC 1025 3.60e+01 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1jq3A 296 3.60e+01 c.66.1.17 67079 1gthA 1025 3.62e+01 1inlA 296 3.63e+01 c.66.1.17 66220 1gk8A 475 3.64e+01 c.1.14.1 65234 d.58.9.1 65235 1j6wA 175 3.64e+01 1j98A d.185.1.2 62663 1qidA 537 3.65e+01 2bce c.69.1.1 34593 1gthC 1025 3.65e+01 1go4A 205 3.68e+01 1dulA 69 3.69e+01 1dulA a.36.1.1 17121 1ea5A 537 3.70e+01 2bce c.69.1.1 34592 2gar 212 3.71e+01 2gar c.65.1.1 34161 1fjhA 257 3.73e+01 1fjhB c.2.1.2 29870 1ayl 541 3.74e+01 1ayl c.91.1.1 64718 c.109.1.1 64719 1gthD 1025 3.74e+01 1php 394 3.75e+01 16pk c.86.1.1 35452 1czyC 168 3.75e+01 1d0aB b.8.1.1 23222 h.1.2.1 45429 1gteD 1025 3.76e+01 1bif 469 3.76e+01 1bif c.37.1.7 31961 c.60.1.4 34003 1d0aB 168 3.77e+01 1d0aB b.8.1.1 23224 h.1.2.1 45431 1iexA 605 3.78e+01 c.1.8.7 66127 c.23.11.1 66128 1czyA 168 3.83e+01 1d0aB b.8.1.1 23220 h.1.2.1 45427 1ca4A 168 3.83e+01 1d0aB b.8.1.1 23238 h.1.2.1 45445 1fc2D 224 3.89e+01 1igtB b.1.1.2 21516 b.1.1.2 21517 1kl9A 182 3.91e+01 1hlb 158 3.91e+01 1hlb a.1.1.2 15625 1eyeA 280 3.92e+01 1aj2 c.1.21.1 29672 1ex1A 605 3.93e+01 1ex1A c.1.8.7 29013 c.23.11.1 31347 1h7xB 1025 3.93e+01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1gthB 1025 3.97e+01 1hfoA 113 3.97e+01 d.80.1.3 61006 1jwhA 337 3.98e+01 1rlaA 323 3.99e+01 1d3vA c.42.1.1 32561