# List of top-scoring protein chains for t2k-100-30-str 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 1ivhA 394 4.91e-02 3mdeA a.29.3.1 16608 e.6.1.1 42869 1bpoA 494 1.79e-01 1bpoA a.118.1.4 19143 b.69.6.1 27670 1eb6A 177 3.57e-01 d.92.1.12 64895 1fc6A 388 5.81e-01 1fc6A b.36.1.3 64738 c.14.1.2 64739 1j99A 293 9.40e-01 1g33A 73 9.91e-01 a.39.1.4 65121 1fuoA 467 1.11e+00 1furA a.127.1.1 19411 3vtk 343 1.18e+00 1qhiA c.37.1.1 31884 1k92A 455 1.28e+00 c.26.2.1 68325 d.210.1.1 68326 1chuA 540 1.36e+00 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 1be3J 62 1.44e+00 1be3J f.2.1.8 43671 5pal 109 1.50e+00 1a75A a.39.1.4 17215 1hw6A 278 1.55e+00 1frb c.1.7.1 61296 1a26 361 1.63e+00 1a26 a.41.1.1 17412 d.166.1.2 42274 1gnlA 544 1.86e+00 1avsA 90 1.87e+00 1cll a.39.1.5 17226 1furA 467 1.88e+00 1furA a.127.1.1 19403 1f74A 293 2.02e+00 1nal3 c.1.10.1 29079 1top 162 2.05e+00 1ncx a.39.1.5 17223 1efyA 350 2.06e+00 1a26 a.41.1.1 17413 d.166.1.2 42275 1iatA 557 2.58e+00 1dqrA c.80.1.2 62123 1a80 277 2.65e+00 1frb c.1.7.1 28700 3adk 195 2.78e+00 1zin c.37.1.1 31885 2fokA 579 2.79e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1din 236 2.99e+00 1din c.69.1.9 34682 1ermA 263 3.39e+00 1btl e.3.1.1 42690 1d2zA 108 3.40e+00 1d2zA a.77.1.1 18437 1orc 71 3.61e+00 1orc a.35.1.2 17054 1kfnA 56 3.62e+00 1f5sA 211 3.98e+00 1f5sA c.108.1.4 59656 1j97A 211 3.98e+00 1f5sA c.108.1.4 62753 1l7mA 211 4.08e+00 1ncx 162 4.92e+00 1ncx a.39.1.5 17222 1jceA 344 4.94e+00 c.55.1.1 62876 c.55.1.1 62877 1pah 308 5.29e+00 4pah d.178.1.1 42578 1j8uA 325 5.34e+00 1dmwA 307 5.36e+00 4pah d.178.1.1 42580 4pah 308 5.37e+00 4pah d.178.1.1 42576 1tfe 145 5.54e+00 1tfe d.43.1.1 38680 1derA 547 5.71e+00 1derA a.129.1.1 19459 c.8.5.1 30788 d.56.1.1 38907 1ft5A 211 5.72e+00 1bvb a.138.1.3 19681 1d6mA 653 5.72e+00 1d6mA e.10.1.1 43248 1e4yA 214 5.84e+00 1zin c.37.1.1 31901 g.41.2.1 45181 1itg 166 5.89e+00 1b9dA c.55.3.2 33661 1l1zA 274 6.05e+00 1l7uA 263 6.11e+00 1m40A 263 6.11e+00 1bvb 211 6.14e+00 1bvb a.138.1.3 19683 1dn1A 594 6.15e+00 1dn1A e.25.1.1 43357 1kl1A 419 6.34e+00 1jkoC 52 6.50e+00 a.4.1.2 66809 1jdbB 1073 6.50e+00 a.92.1.1 18574 c.24.1.1 31503 c.30.1.1 31705 c.30.1.1 31706 d.142.1.2 41550 d.142.1.2 41551 1osa 148 6.50e+00 1cll a.39.1.5 17300 1dn1B 267 6.52e+00 1dn1B a.47.2.1 17771 1shbA 104 6.58e+00 1fmk d.93.1.1 40425 1bxrA 1073 6.73e+00 a.92.1.1 18570 c.24.1.1 31499 c.30.1.1 31697 c.30.1.1 31698 d.142.1.2 41542 d.142.1.2 41543 1hy3A 294 7.03e+00 1a7w 69 7.13e+00 1a7w a.22.1.2 16477 1fqvD 149 7.18e+00 1fqvD a.122.1.1 19263 d.42.1.2 38667 1btl 263 7.19e+00 1btl e.3.1.1 42691 1fqvJ 149 7.28e+00 1fqvD a.122.1.1 19266 d.42.1.2 38670 1fqgA 263 7.28e+00 1btl e.3.1.1 42699 1fmjA 351 7.54e+00 c.37.1.5 59879 1epuA 591 7.70e+00 1dn1A e.25.1.1 43358 1keeC 1073 7.71e+00 a.92.1.1 68500 c.24.1.1 68501 c.30.1.1 68502 c.30.1.1 68503 d.142.1.2 68504 d.142.1.2 68505 1fs1B 141 7.79e+00 1vcbB a.122.1.1 19252 d.42.1.2 38664 1hcrA 52 7.81e+00 1hcrA a.4.1.2 16020 1fokA 568 7.81e+00 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1gdtA 183 7.81e+00 2rslA a.4.1.2 16021 c.53.1.1 33348 1keeG 1073 7.90e+00 a.92.1.1 68516 c.24.1.1 68517 c.30.1.1 68518 c.30.1.1 68519 d.142.1.2 68520 d.142.1.2 68521 1jb9A 316 8.51e+00 1fnc b.43.4.2 62840 c.25.1.1 62841 1aj3 110 8.62e+00 1cunA a.7.1.1 16319 1exrA 148 8.86e+00 1cll a.39.1.5 17299 1jvnA 555 9.00e+00 c.1.2.1 67355 c.23.16.1 67356 1znf 27 9.18e+00 g.37.1.1 45036 1e3hA 757 9.39e+00 1e3hA a.4.9.1 16257 d.14.1.4 37572 d.14.1.4 37573 d.52.3.1 38810 d.101.1.1 40695 d.101.1.1 40696 4cpv 109 9.46e+00 1a75A a.39.1.4 17198 1lehA 364 9.66e+00 1bw9A c.2.1.7 30268 c.58.1.1 33916 1tpt 440 9.86e+00 1brwA a.46.2.1 17763 c.27.1.1 31627 d.41.3.1 38625 1k47A 337 9.88e+00 1amuA 563 1.00e+01 1amuA e.23.1.1 43351 1f07A 321 1.10e+01 1ezwA c.1.16.3 59560 1cdp 109 1.10e+01 1a75A a.39.1.4 17197 1mml 265 1.11e+01 1mml e.8.1.2 43015 1hqsA 423 1.11e+01 1iso c.77.1.1 61154 1bg4 302 1.12e+01 1taxA c.1.8.3 28806 1f1eA 154 1.14e+01 a.22.1.2 64927 1bfmA 69 1.14e+01 1a7w a.22.1.2 16479 1shaA 104 1.16e+01 1fmk d.93.1.1 40424 1a1z 91 1.18e+01 1a1z a.77.1.1 18427 1qpaA 345 1.18e+01 1arv a.93.1.1 18585 1ay2 159 1.20e+01 2pil d.24.1.1 38377 1om2A 95 1.22e+01 1om2A a.23.4.1 16520 1aky 221 1.24e+01 1zin c.37.1.1 31896 g.41.2.1 45197 2pth 193 1.26e+01 2pth c.56.3.1 33793 1atg 231 1.28e+01 1atg c.94.1.1 35834 1jcfA 344 1.30e+01 c.55.1.1 62878 c.55.1.1 62879 2ak3A 226 1.31e+01 1zin c.37.1.1 31892 g.41.2.1 45193 1abmA 198 1.39e+01 1avmA a.2.11.1 15748 d.44.1.1 38707 1eudA 311 1.42e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 3pbgA 468 1.48e+01 1e70M c.1.8.4 28951 1gqeA 365 1.48e+01 1pbgA 468 1.49e+01 1e70M c.1.8.4 28946 1jdlA 121 1.51e+01 a.3.1.1 66557 1qdbA 473 1.52e+01 1qdbA a.138.1.3 19688 2hfh 109 1.54e+01 2hfh a.4.5.14 16145 2itg 163 1.54e+01 1b9dA c.55.3.2 33669 1fx3A 169 1.57e+01 1fx3B d.33.1.1 38524 1ib2A 349 1.57e+01 1ib2A a.118.1.8 62141 1qp6A 35 1.58e+01 1qp6A k.16.1.1 46443 1kr7A 110 1.59e+01 1ib3A 349 1.61e+01 1ib2A a.118.1.8 62142 1hrhA 136 1.62e+01 1rthA c.55.3.1 33577 1qsaA 618 1.63e+01 1qsaA a.118.5.1 19182 d.2.1.6 36988 1cll 148 1.66e+01 1cll a.39.1.5 17263 1mldA 314 1.67e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1copD 66 1.69e+01 1orc a.35.1.2 17058 1yghA 164 1.73e+01 1yghA d.108.1.1 40802 1iq8A 582 1.74e+01 1jigA 146 1.77e+01 2mysB 166 1.77e+01 1wdcB a.39.1.5 17308 1cz1A 394 1.79e+01 1cz1A c.1.8.3 28839 1sly 618 1.80e+01 1qsaA a.118.5.1 19184 d.2.1.6 36990 3pviA 157 1.80e+01 3pviA c.52.1.6 33300 1de5A 426 1.82e+01 1de5A c.1.15.2 29402 3lck 271 1.84e+01 1fmk d.144.1.2 41686 2pvbA 107 1.90e+01 1a75A a.39.1.4 17205 1b93A 152 1.95e+01 1b93A c.24.1.2 31507 1khcA 147 1.95e+01 b.34.9.2 68608 1ctj 89 1.95e+01 1ctj a.3.1.1 15798 1ordA 730 1.99e+01 1ordA c.23.7.1 31274 c.67.1.5 34503 d.125.1.1 41124 1ap6A 198 2.00e+01 1avmA a.2.11.1 15746 d.44.1.1 38705 1d8wA 426 2.02e+01 1de5A c.1.15.2 29394 1c4kA 730 2.03e+01 1ordA c.23.7.1 31273 c.67.1.5 34502 d.125.1.1 41123 1myo 118 2.03e+01 2myo a.118.2.1 19174 1qhiA 366 2.04e+01 1qhiA c.37.1.1 31860 1kimA 366 2.05e+01 1qhiA c.37.1.1 31864 1dqrA 557 2.05e+01 1dqrA c.80.1.2 35305 1ek9A 428 2.05e+01 1ek9A f.5.1.1 43809 1de6A 426 2.06e+01 1de5A c.1.15.2 29398 2ki5A 366 2.06e+01 1qhiA c.37.1.1 31862 1kxlA 199 2.09e+01 1hlvA 131 2.12e+01 a.4.1.7 65854 a.4.1.7 65855 1qpcA 279 2.19e+01 1fgkA d.144.1.2 41685 1ggzA 148 2.19e+01 1ezvI 55 2.20e+01 1be3J f.2.1.8 59553 1hta 69 2.22e+01 1a7w a.22.1.2 16476 1bza 262 2.25e+01 1btl e.3.1.1 42701 1kid 203 2.26e+01 1derA c.8.5.1 30771 1c3oC 1073 2.27e+01 a.92.1.1 18563 c.24.1.1 31492 c.30.1.1 31683 c.30.1.1 31684 d.142.1.2 41528 d.142.1.2 41529 1hyp 80 2.33e+01 1hyp a.52.1.1 17806 1a9xA 1058 2.37e+01 a.92.1.1 18550 c.24.1.1 31479 c.30.1.1 31657 c.30.1.1 31658 d.142.1.2 41502 d.142.1.2 41503 1a75A 108 2.40e+01 1a75A a.39.1.4 17216 1e2kA 331 2.42e+01 1qhiA c.37.1.1 31854 1rro 108 2.45e+01 1a75A a.39.1.4 17195 1hr6B 443 2.46e+01 1be3A d.185.1.1 61166 d.185.1.1 61167 1c3oA 1073 2.52e+01 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1kxu 333 2.56e+01 1jkw a.74.1.1 18358 a.74.1.1 18359 1b93B 152 2.57e+01 1b93A c.24.1.2 31508 2pil 159 2.58e+01 2pil d.24.1.1 38376 1ef4A 55 2.60e+01 1ef4A a.4.11.1 16272 1ako 268 2.61e+01 1ako d.151.1.1 41779 1f1zA 273 2.62e+01 1f1zA a.4.5.27 16081 c.52.1.16 33334 1qhlA 227 2.63e+01 1qhlA c.37.1.12 32382 1keeE 1073 2.63e+01 a.92.1.1 68508 c.24.1.1 68509 c.30.1.1 68510 c.30.1.1 68511 d.142.1.2 68512 d.142.1.2 68513 1pvaA 110 2.68e+01 1a75A a.39.1.4 17207 2pviA 157 2.75e+01 3pviA c.52.1.6 33302 1fseA 74 2.78e+01 1fseA a.4.6.2 60000 3cln 148 2.80e+01 1cll a.39.1.5 17286 1zymA 258 2.81e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 1mn1 357 2.82e+01 1arv a.93.1.1 18667 1a48 306 2.82e+01 1a48 d.143.1.1 41590 8rucA 475 2.85e+01 1burA c.1.14.1 29339 d.58.9.1 39245 1a04A 215 2.88e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1c4oA 664 2.90e+01 1d2mA c.37.1.13 32415 c.37.1.13 32416 1gp8A 40 2.93e+01 2gp8A j.58.1.1 46342 1keeA 1073 2.95e+01 a.92.1.1 68492 c.24.1.1 68493 c.30.1.1 68494 c.30.1.1 68495 d.142.1.2 68496 d.142.1.2 68497 1k8kC 372 2.99e+01 b.69.4.1 68308 1fpoA 171 3.08e+01 1fpoA a.2.3.1 15693 a.23.1.1 16487 3mdeA 385 3.08e+01 3mdeA a.29.3.1 16594 e.6.1.1 42855 1i4yA 114 3.11e+01 2mhr a.24.4.1 61738 3mddA 385 3.12e+01 3mdeA a.29.3.1 16592 e.6.1.1 42853 1c3oE 1073 3.12e+01 a.92.1.1 18564 c.24.1.1 31493 c.30.1.1 31685 c.30.1.1 31686 d.142.1.2 41530 d.142.1.2 41531 1g8iA 190 3.15e+01 1rec a.39.1.5 60363 1i7dA 659 3.20e+01 1d6mA e.10.1.1 61886 1fwxA 595 3.22e+01 b.6.1.4 60069 b.69.3.1 60070 2kauA 100 3.23e+01 1ubpA d.8.1.1 37335 1fwcA 100 3.24e+01 1ubpA d.8.1.1 37331 1c3oG 1073 3.28e+01 a.92.1.1 18565 c.24.1.1 31494 c.30.1.1 31687 c.30.1.1 31688 d.142.1.2 41532 d.142.1.2 41533 1oacA 727 3.30e+01 1oacA b.30.2.1 24390 d.17.2.1 38007 d.17.2.1 38008 d.82.1.1 40003 2myo 118 3.31e+01 2myo a.118.2.1 19175 1awcB 153 3.32e+01 1bd8 a.118.2.1 19156 1d6zA 727 3.37e+01 1oacA b.30.2.1 24394 d.17.2.1 38015 d.17.2.1 38016 d.82.1.1 40007 1ck9A 104 3.42e+01 1ck9A d.79.3.1 39806 1cs0C 1073 3.50e+01 a.92.1.1 18559 c.24.1.1 31488 c.30.1.1 31675 c.30.1.1 31676 d.142.1.2 41520 d.142.1.2 41521 1iso 416 3.72e+01 1iso c.77.1.1 35065 1e7uA 961 3.72e+01 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1crn 46 3.80e+01 1cbn g.13.1.1 44622 1dik 874 3.81e+01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 256bA 106 3.85e+01 256bA a.24.3.1 16539