# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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 2.75e-02 3mdeA a.29.3.1 16608 e.6.1.1 42869 1eb6A 177 3.42e-01 d.92.1.12 64895 1fuoA 467 3.88e-01 1furA a.127.1.1 19411 5pal 109 4.78e-01 1a75A a.39.1.4 17215 1bpoA 494 5.51e-01 1bpoA a.118.1.4 19143 b.69.6.1 27670 1f74A 293 7.31e-01 1nal3 c.1.10.1 29079 1a26 361 8.94e-01 1a26 a.41.1.1 17412 d.166.1.2 42274 1efyA 350 9.35e-01 1a26 a.41.1.1 17413 d.166.1.2 42275 1hw6A 278 1.01e+00 1frb c.1.7.1 61296 3vtk 343 1.07e+00 1qhiA c.37.1.1 31884 1furA 467 1.08e+00 1furA a.127.1.1 19403 1avsA 90 1.12e+00 1cll a.39.1.5 17226 1g33A 73 1.14e+00 a.39.1.4 65121 1top 162 1.22e+00 1ncx a.39.1.5 17223 1k92A 455 1.30e+00 c.26.2.1 68325 d.210.1.1 68326 1be3J 62 1.32e+00 1be3J f.2.1.8 43671 1chuA 540 1.42e+00 1chuA a.7.3.1 16325 c.3.1.4 30424 d.168.1.1 42307 1epuA 591 1.46e+00 1dn1A e.25.1.1 43358 1fc6A 388 1.51e+00 1fc6A b.36.1.3 64738 c.14.1.2 64739 1iatA 557 1.61e+00 1dqrA c.80.1.2 62123 1j9bA 141 1.82e+00 c.47.1.12 66459 1j99A 293 1.83e+00 1a80 277 1.97e+00 1frb c.1.7.1 28700 1d2zA 108 2.31e+00 1d2zA a.77.1.1 18437 1dn1A 594 2.46e+00 1dn1A e.25.1.1 43357 1ncx 162 2.62e+00 1ncx a.39.1.5 17222 3adk 195 2.79e+00 1zin c.37.1.1 31885 1gnlA 544 2.86e+00 1shbA 104 2.96e+00 1fmk d.93.1.1 40425 1jceA 344 3.18e+00 c.55.1.1 62876 c.55.1.1 62877 1orc 71 3.40e+00 1orc a.35.1.2 17054 1fs1B 141 3.92e+00 1vcbB a.122.1.1 19252 d.42.1.2 38664 1aj3 110 3.94e+00 1cunA a.7.1.1 16319 1tpt 440 3.97e+00 1brwA a.46.2.1 17763 c.27.1.1 31627 d.41.3.1 38625 1hr6B 443 4.06e+00 1be3A d.185.1.1 61166 d.185.1.1 61167 1f07A 321 4.16e+00 1ezwA c.1.16.3 59560 1e4yA 214 4.62e+00 1zin c.37.1.1 31901 g.41.2.1 45181 1itg 166 4.62e+00 1b9dA c.55.3.2 33661 1osa 148 4.72e+00 1cll a.39.1.5 17300 1exrA 148 4.77e+00 1cll a.39.1.5 17299 1kl1A 419 4.79e+00 1pah 308 4.89e+00 4pah d.178.1.1 42578 1j8uA 325 5.02e+00 4pah 308 5.02e+00 4pah d.178.1.1 42576 1dmwA 307 5.02e+00 4pah d.178.1.1 42580 1qcrJ 59 5.47e+00 1be3J f.2.1.8 43679 1f5sA 211 5.50e+00 1f5sA c.108.1.4 59656 1j97A 211 5.50e+00 1f5sA c.108.1.4 62753 1d6mA 653 5.59e+00 1d6mA e.10.1.1 43248 1l7mA 211 5.65e+00 1ermA 263 5.67e+00 1btl e.3.1.1 42690 1fqvD 149 5.70e+00 1fqvD a.122.1.1 19263 d.42.1.2 38667 1fqvJ 149 5.72e+00 1fqvD a.122.1.1 19266 d.42.1.2 38670 1hqsA 423 5.83e+00 1iso c.77.1.1 61154 1dqrA 557 5.97e+00 1dqrA c.80.1.2 35305 1jkoC 52 6.07e+00 a.4.1.2 66809 3lck 271 6.28e+00 1fmk d.144.1.2 41686 1jb9A 316 6.28e+00 1fnc b.43.4.2 62840 c.25.1.1 62841 6prcM 323 6.38e+00 6prcM f.2.1.2 43435 1b37B 472 6.48e+00 1b37B c.3.1.2 30390 d.16.1.5 37954 1derA 547 6.73e+00 1derA a.129.1.1 19459 c.8.5.1 30788 d.56.1.1 38907 1hcrA 52 6.91e+00 1hcrA a.4.1.2 16020 1kfnA 56 7.05e+00 1qpcA 279 7.11e+00 1fgkA d.144.1.2 41685 1e7uA 961 7.11e+00 1e8xA a.118.1.6 19147 b.7.1.1 23182 d.15.1.5 37630 d.144.1.4 41710 1a1z 91 7.31e+00 1a1z a.77.1.1 18427 1e3hA 757 7.49e+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 1f61A 429 7.72e+00 1dquA c.1.12.6 29319 1jcfA 344 7.75e+00 c.55.1.1 62878 c.55.1.1 62879 1ib2A 349 7.77e+00 1ib2A a.118.1.8 62141 1tfe 145 7.87e+00 1tfe d.43.1.1 38680 1ib3A 349 8.09e+00 1ib2A a.118.1.8 62142 1din 236 8.25e+00 1din c.69.1.9 34682 1mldA 314 8.50e+00 2cmd c.2.1.5 30122 d.162.1.1 42089 2fokA 579 8.85e+00 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1shaA 104 8.94e+00 1fmk d.93.1.1 40424 1qp6A 35 8.95e+00 1qp6A k.16.1.1 46443 1f8mA 429 9.30e+00 1dquA c.1.12.6 29315 1ctj 89 9.33e+00 1ctj a.3.1.1 15798 1l7uA 263 9.40e+00 1m40A 263 9.40e+00 1b5qA 472 1.01e+01 1b37B c.3.1.2 30404 d.16.1.5 37968 2ak3A 226 1.01e+01 1zin c.37.1.1 31892 g.41.2.1 45193 1jvnA 555 1.02e+01 c.1.2.1 67355 c.23.16.1 67356 1keeC 1073 1.02e+01 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 1cll 148 1.03e+01 1cll a.39.1.5 17263 1jdbB 1073 1.05e+01 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 1jdlA 121 1.05e+01 a.3.1.1 66557 1dxrM 323 1.06e+01 6prcM f.2.1.2 43432 1znf 27 1.07e+01 g.37.1.1 45036 1k47A 337 1.08e+01 1fmjA 351 1.13e+01 c.37.1.5 59879 1f8rA 498 1.17e+01 1f8rA c.3.1.2 30410 d.16.1.5 37974 2itg 163 1.18e+01 1b9dA c.55.3.2 33669 1kr7A 110 1.18e+01 1btl 263 1.19e+01 1btl e.3.1.1 42691 1fqgA 263 1.20e+01 1btl e.3.1.1 42699 1ek9A 428 1.21e+01 1ek9A f.5.1.1 43809 1fjgM 126 1.22e+01 1fjfM a.5.5.1 16293 1hy3A 294 1.25e+01 1l1zA 274 1.25e+01 1irk 306 1.25e+01 1fmk d.144.1.2 41703 1keeG 1073 1.26e+01 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 1amuA 563 1.26e+01 1amuA e.23.1.1 43351 1ordA 730 1.27e+01 1ordA c.23.7.1 31274 c.67.1.5 34503 d.125.1.1 41124 1qhiA 366 1.28e+01 1qhiA c.37.1.1 31860 1bjaA 95 1.28e+01 1bjaA a.4.5.9 16122 1kimA 366 1.28e+01 1qhiA c.37.1.1 31864 2ki5A 366 1.29e+01 1qhiA c.37.1.1 31862 1eudA 311 1.29e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1yghA 164 1.37e+01 1yghA d.108.1.1 40802 1bxrA 1073 1.38e+01 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 1ir3A 306 1.38e+01 1fmk d.144.1.2 41702 1sly 618 1.39e+01 1qsaA a.118.5.1 19184 d.2.1.6 36990 1fx3A 169 1.40e+01 1fx3B d.33.1.1 38524 1om2A 95 1.43e+01 1om2A a.23.4.1 16520 1de6A 426 1.51e+01 1de5A c.1.15.2 29398 1abmA 198 1.56e+01 1avmA a.2.11.1 15748 d.44.1.1 38707 1a7w 69 1.56e+01 1a7w a.22.1.2 16477 1ay2 159 1.57e+01 2pil d.24.1.1 38377 1aky 221 1.58e+01 1zin c.37.1.1 31896 g.41.2.1 45197 1d8wA 426 1.59e+01 1de5A c.1.15.2 29394 1ggzA 148 1.60e+01 1gqeA 365 1.60e+01 1atg 231 1.60e+01 1atg c.94.1.1 35834 1zymA 258 1.61e+01 1zymA a.60.10.1 18110 c.8.1.2 30705 3pbgA 468 1.62e+01 1e70M c.1.8.4 28951 1broA 277 1.64e+01 1brt c.69.1.12 34700 1e2kA 331 1.66e+01 1qhiA c.37.1.1 31854 1c4kA 730 1.67e+01 1ordA c.23.7.1 31273 c.67.1.5 34502 d.125.1.1 41123 1de5A 426 1.67e+01 1de5A c.1.15.2 29402 1gw9A 388 1.70e+01 1fseA 74 1.70e+01 1fseA a.4.6.2 60000 1g8iA 190 1.71e+01 1rec a.39.1.5 60363 1lehA 364 1.74e+01 1bw9A c.2.1.7 30268 c.58.1.1 33916 1qhlA 227 1.75e+01 1qhlA c.37.1.12 32382 1bfmA 69 1.75e+01 1a7w a.22.1.2 16479 1cdp 109 1.76e+01 1a75A a.39.1.4 17197 2hfh 109 1.80e+01 2hfh a.4.5.14 16145 1copD 66 1.80e+01 1orc a.35.1.2 17058 1gdtA 183 1.82e+01 2rslA a.4.1.2 16021 c.53.1.1 33348 1f45B 197 1.82e+01 1f45B a.26.1.1 59642 1mml 265 1.83e+01 1mml e.8.1.2 43015 1i7dA 659 1.83e+01 1d6mA e.10.1.1 61886 1a04A 215 1.85e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 4cpv 109 1.86e+01 1a75A a.39.1.4 17198 1kxlA 199 1.89e+01 1iq8A 582 1.90e+01 4xis 387 1.91e+01 4xis c.1.15.3 29421 3xis 387 1.92e+01 4xis c.1.15.3 29423 1hrhA 136 1.94e+01 1rthA c.55.3.1 33577 1e3mA 800 1.95e+01 1ewqA a.113.1.1 19075 c.37.1.12 32389 c.55.6.1 33746 d.75.2.1 39747 1bza 262 2.02e+01 1btl e.3.1.1 42701 1kid 203 2.07e+01 1derA c.8.5.1 30771 1qsaA 618 2.08e+01 1qsaA a.118.5.1 19182 d.2.1.6 36988 3cln 148 2.09e+01 1cll a.39.1.5 17286 1ezwA 349 2.10e+01 1ezwA c.1.16.3 29558 3pviA 157 2.11e+01 3pviA c.52.1.6 33300 3mddA 385 2.15e+01 3mdeA a.29.3.1 16592 e.6.1.1 42853 1iso 416 2.15e+01 1iso c.77.1.1 35065 1jigA 146 2.18e+01 1dn1B 267 2.20e+01 1dn1B a.47.2.1 17771 3mdeA 385 2.20e+01 3mdeA a.29.3.1 16594 e.6.1.1 42855 1qpaA 345 2.26e+01 1arv a.93.1.1 18585 2mysB 166 2.31e+01 1wdcB a.39.1.5 17308 1f1eA 154 2.34e+01 a.22.1.2 64927 1hlvA 131 2.57e+01 a.4.1.7 65854 a.4.1.7 65855 1ezvI 55 2.57e+01 1be3J f.2.1.8 59553 1ajsA 412 2.59e+01 1ajsA c.67.1.1 34276 2cmd 312 2.60e+01 2cmd c.2.1.5 30135 d.162.1.1 42102 1ef4A 55 2.64e+01 1ef4A a.4.11.1 16272 1rro 108 2.66e+01 1a75A a.39.1.4 17195 1jpdX 324 2.68e+01 c.1.11.2 67014 d.54.1.1 67015 1hh7A 114 2.70e+01 1ycc a.3.1.1 15896 1i8oA 114 2.72e+01 1ycc a.3.1.1 61979 1fgjA 546 2.73e+01 1fgjA a.138.1.3 19679 1fwxA 595 2.74e+01 b.6.1.4 60069 b.69.3.1 60070 1hyp 80 2.84e+01 1hyp a.52.1.1 17806 2bmhA 455 2.94e+01 1bu7A a.104.1.1 18941 1gp8A 40 2.96e+01 2gp8A j.58.1.1 46342 1b93A 152 2.98e+01 1b93A c.24.1.2 31507 1avaA 403 3.00e+01 1jdc b.71.1.1 27797 c.1.8.1 28784 1qdbA 473 3.00e+01 1qdbA a.138.1.3 19688 2pth 193 3.02e+01 2pth c.56.3.1 33793 1jlvA 209 3.04e+01 1a75A 108 3.04e+01 1a75A a.39.1.4 17216 2xis 387 3.05e+01 4xis c.1.15.3 29427 2shpA 525 3.06e+01 2shpA c.45.1.2 32683 d.93.1.1 40533 d.93.1.1 40534 1crn 46 3.06e+01 1cbn g.13.1.1 44622 1khcA 147 3.13e+01 b.34.9.2 68608 1ap6A 198 3.13e+01 1avmA a.2.11.1 15746 d.44.1.1 38705 1c4oA 664 3.15e+01 1d2mA c.37.1.13 32415 c.37.1.13 32416 1jqjC 343 3.17e+01 a.80.1.1 67097 c.37.1.13 67098 1hhsA 664 3.20e+01 1hi0P e.8.1.6 61045 1cawB 184 3.23e+01 1caxB b.82.1.2 28113 1hi0P 664 3.27e+01 1hi0P e.8.1.6 61051 1qbjA 81 3.28e+01 1qbjA a.4.5.19 16155 1fehA 574 3.31e+01 1fehA c.96.1.1 36015 d.15.4.2 37690 d.58.1.5 38998 1pbgA 468 3.31e+01 1e70M c.1.8.4 28946 1c3oC 1073 3.32e+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 1hta 69 3.34e+01 1a7w a.22.1.2 16476 1hyvA 166 3.37e+01 1b9dA c.55.3.2 61424 1k8kC 372 3.38e+01 b.69.4.1 68308 1bouA 139 3.39e+01 1bouA a.88.1.1 18521 8rucA 475 3.46e+01 1burA c.1.14.1 29339 d.58.9.1 39245 1i50J 70 3.47e+01 a.4.11.1 61764 2pviA 157 3.52e+01 3pviA c.52.1.6 33302 1g4yR 148 3.54e+01 1cll a.39.1.5 60252 1dik 874 3.56e+01 1dik c.1.12.2 29304 c.8.1.1 30702 d.142.1.5 41572 2pvbA 107 3.57e+01 1a75A a.39.1.4 17205 1rkd 309 3.58e+01 1rkd c.72.1.1 34928 1ck9A 104 3.59e+01 1ck9A d.79.3.1 39806 1b93B 152 3.73e+01 1b93A c.24.1.2 31508 1kkcA 221 3.75e+01 a.2.11.1 68660 d.44.1.1 68661 1f0yA 302 3.86e+01 2hdhA a.100.1.3 18793 c.2.1.6 30197 1fpoA 171 3.87e+01 1fpoA a.2.3.1 15693 a.23.1.1 16487 1toh 343 3.90e+01 4pah d.178.1.1 42573 1jjrA 151 3.90e+01 a.140.2.1 66772 1mn1 357 3.92e+01 1arv a.93.1.1 18667 1eqnA 321 3.92e+01 1dd9A e.13.1.1 43256 1e3pA 757 3.96e+01 1e3hA a.4.9.1 16258 b.40.4.5 25328 d.14.1.4 37574 d.14.1.4 37575 d.52.3.1 38811 d.101.1.1 40697 d.101.1.1 40698