# List of top-scoring protein chains for t2k-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 1d2zA 108 3.55e-02 1d2zA a.77.1.1 18437 1b4vA 504 1.57e-01 1b8sA c.3.1.2 30334 d.16.1.1 37865 1ijhA 504 1.59e-01 c.3.1.2 66161 d.16.1.1 66162 1b8sA 504 1.91e-01 1b8sA c.3.1.2 30335 d.16.1.1 37866 1fnuA 221 3.42e-01 3seb b.40.2.2 25212 d.15.6.1 37801 3cox 507 3.61e-01 1b8sA c.3.1.2 30332 d.16.1.1 37863 1mntA 76 1.11e+00 1bazA a.43.1.1 17453 4xiaA 393 1.26e+00 4xis c.1.15.3 29439 1g2nA 264 1.28e+00 1lbd a.123.1.1 60227 1ggwA 140 1.35e+00 1ggwA a.39.1.5 60490 1a2yB 116 1.64e+00 1gc1H b.1.1.1 19927 3seb 238 1.81e+00 3seb b.40.2.2 25184 d.15.6.1 37773 1d5mC 239 1.88e+00 3seb b.40.2.2 25185 d.15.6.1 37774 1aj8A 371 2.15e+00 1aj8A a.103.1.1 18900 1gtqA 140 2.16e+00 1b66A d.96.1.2 40661 1g73C 121 2.21e+00 1g3fA g.52.1.1 45375 1g7jB 116 2.27e+00 1f3rB b.1.1.1 19933 1pls 113 2.43e+00 1pls b.55.1.1 26965 1agjA 242 2.53e+00 1agjA b.47.1.1 25827 1fohA 664 2.65e+00 1fohA c.3.1.2 30381 c.47.1.10 33078 d.16.1.2 37900 1gq8A 319 2.68e+00 1vfaB 116 2.97e+00 1gc1H b.1.1.1 19929 1ayoA 130 3.14e+00 1ayoA b.2.4.1 22431 1b66A 140 3.29e+00 1b66A d.96.1.2 40657 1i7pA 274 3.43e+00 b.43.4.2 66048 c.25.1.1 66049 1qqfA 277 3.63e+00 1c3d a.102.4.4 18875 1eu8A 409 4.34e+00 1eu8A c.94.1.1 59502 1l5jA 865 4.45e+00 1eiwA 111 4.59e+00 1eiwA c.23.3.1 31130 1fdlH 218 4.74e+00 1igtB b.1.1.1 19961 b.1.1.2 21021 1f28A 297 5.17e+00 1bkpA d.117.1.1 59608 1prxA 224 5.21e+00 1prxA c.47.1.10 33076 1qlwA 328 5.76e+00 1qlwA c.69.1.15 34722 1ebmA 317 6.09e+00 1ebmA a.96.1.3 18751 d.129.1.2 41300 1reqB 637 6.30e+00 1reqB c.1.19.1 29621 c.23.6.1 31248 1reqD 637 6.44e+00 1reqB c.1.19.1 29623 c.23.6.1 31250 1ko9A 345 6.55e+00 a.96.1.3 68717 d.129.1.2 68718 3ldh 330 7.35e+00 3ldh i.12.1.1 46015 1e6oH 219 7.36e+00 1igtB b.1.1.1 20495 b.1.1.2 21453 1id1A 153 7.39e+00 1id1A c.2.1.9 62286 1fnd 314 7.41e+00 1fnc b.43.4.2 25626 c.25.1.1 31516 1jj2M 186 7.93e+00 1ffkK c.55.4.1 63098 1pmy 123 8.02e+00 1bqk b.6.1.1 22888 1fnc 314 8.16e+00 1fnc b.43.4.2 25627 c.25.1.1 31517 1f89A 291 8.23e+00 d.160.1.1 64988 1ndh 272 8.34e+00 1ndh b.43.4.2 25662 c.25.1.1 31552 1ffkK 186 8.49e+00 1ffkK c.55.4.1 33731 1mlcB 218 9.39e+00 1igtB b.1.1.1 20053 b.1.1.2 21095 1ayx 492 9.91e+00 1ayx a.102.1.1 18825 1a6wH 120 9.97e+00 1mfa b.1.1.1 20253 1qgtA 149 1.05e+01 1qgtA a.62.1.1 18135 1xbrA 184 1.08e+01 1xbrA b.2.5.1 22458 1irqA 71 1.15e+01 a.43.1.2 66297 1jhgA 101 1.18e+01 1jhgA a.107.1.1 19009 1a3lH 218 1.19e+01 1mfa b.1.1.1 20241 b.1.1.2 21253 1jj2R 84 1.31e+01 1ffkP d.12.1.1 63103 1trrA 107 1.37e+01 1jhgA a.107.1.1 19017 1glm 470 1.39e+01 1ayx a.102.1.1 18821 1kpgA 287 1.40e+01 c.66.1.18 68735 1qg0A 308 1.42e+01 1fnc b.43.4.2 25639 c.25.1.1 31529 1iibA 106 1.45e+01 1iibA c.44.2.1 32648 1jy3N 53 1.46e+01 h.1.8.1 67446 1b0nB 57 1.48e+01 1b0nB a.34.1.1 17002 1ezvD 245 1.49e+01 1be3D a.3.1.3 59546 f.2.1.8 59547 1k26A 156 1.49e+01 2wrpR 107 1.50e+01 1jhgA a.107.1.1 19010 1pytA 94 1.57e+01 1pytA d.58.3.1 39064 1byqA 228 1.63e+01 1yer d.122.1.1 41100 1gp1A 198 1.63e+01 1gp1A c.47.1.10 33059 1g3fA 117 1.67e+01 1g3fA g.52.1.1 45378 1acf 125 1.68e+01 3nul d.110.1.1 40882 1a1x 108 1.69e+01 1a1x b.63.1.1 27514 1dliA 402 1.70e+01 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1dljA 402 1.71e+01 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1yer 228 1.75e+01 1yer d.122.1.1 41101 1ncs 47 1.77e+01 1ncs g.37.1.1 45040 1ct9A 553 1.82e+01 1ct9A c.26.2.1 31616 d.153.1.1 41834 1gai 472 1.85e+01 1ayx a.102.1.1 18819 1jy2N 53 1.88e+01 h.1.8.1 67440 1xo1A 291 1.92e+01 1exnA a.60.7.1 18086 c.53.1.2 33356 1m4vA 204 1.96e+01 1gsmA 210 1.99e+01 b.1.1.4 65535 b.1.1.4 65536 1kwhA 492 2.01e+01 c.94.1.1 68876 1bqk 124 2.04e+01 1bqk b.6.1.1 22889 1jljA 189 2.05e+01 c.57.1.1 63169 1a49A 530 2.07e+01 1a49A b.58.1.1 27026 c.1.12.1 29255 c.49.1.1 33109 1ihcA 188 2.14e+01 1di6A c.57.1.1 62379 1c2rA 116 2.17e+01 1ycc a.3.1.1 15887 1exnB 290 2.18e+01 1exnA a.60.7.1 18089 c.53.1.2 33359 1g291 372 2.37e+01 1g291 1c5cH 215 2.37e+01 1igtB b.1.1.1 20475 b.1.1.2 21439 1lghB 45 2.43e+01 1lghB f.3.1.1 43734 1phm 310 2.43e+01 1phm b.13.1.2 59015 b.13.1.2 59016 1qamA 244 2.44e+01 2ercA c.66.1.9 34220 2ahjB 212 2.52e+01 2ahjB b.34.4.4 24599 1yprA 125 2.56e+01 3nul d.110.1.1 40888 1jcqA 382 2.59e+01 a.118.6.1 66504 1jqlB 140 2.61e+01 c.37.1.13 63234 1ddlA 188 2.66e+01 1auyA b.10.1.2 23317 1uox 296 2.67e+01 1uox d.96.1.4 40673 d.96.1.4 40674 1ffkY 49 2.68e+01 1ffkY a.137.1.1 19624 1mml 265 2.71e+01 1mml e.8.1.2 43015 1mtyB 384 2.80e+01 1mtyB a.25.1.2 16740 1qbqA 333 2.81e+01 1ft1A a.118.6.1 19187 1is2A 661 2.82e+01 1eyvA 156 2.84e+01 1eyvA a.79.1.1 18446 1jrkA 156 2.84e+01 487dL 133 2.86e+01 1mmsA i.1.1.2 45839 1ld8A 382 2.90e+01 1g6uA 48 2.90e+01 1g6uA k.9.1.1 46425 1azwA 313 2.98e+01 1qtrA c.69.1.7 34658 1nseA 444 3.00e+01 1nseA d.174.1.1 42534 1put 106 3.00e+01 1ayfA d.15.4.1 37680 1kp9B 287 3.08e+01 c.66.1.18 68734 1jx2B 315 3.10e+01 c.37.1.8 67404 1mmsA 140 3.10e+01 1mmsA a.4.7.1 16247 d.47.1.1 38766 1fshA 105 3.14e+01 1fshA a.4.5.31 60006 1iw2A 182 3.17e+01 1vih 71 3.22e+01 1vih d.51.1.1 38807 1ahjB 212 3.24e+01 2ahjB b.34.4.4 24601 1diiC 80 3.29e+01 1diiC a.3.1.1 15925 1jmxB 349 3.29e+01 b.69.2.2 66906 1dmzA 158 3.31e+01 1qu5A b.26.1.2 23921 2leu 37 3.33e+01 2leu j.3.1.1 46068 1exnA 290 3.35e+01 1exnA a.60.7.1 18088 c.53.1.2 33358 1vcaA 202 3.41e+01 1vcaA b.1.1.3 21649 b.1.1.4 21685 1tetH 210 3.42e+01 1igtB b.1.1.1 19903 b.1.1.2 20997 1h2rS 267 3.43e+01 2frvA e.19.1.1 43310 1iba 101 3.43e+01 1iba d.95.1.1 40567 1ihjA 98 3.47e+01 1pdr b.36.1.1 62382 1c5yB 253 3.47e+01 5ptp 1hylA 230 3.49e+01 5ptp b.47.1.2 26076 1mmoB 384 3.57e+01 1mtyB a.25.1.2 16768 1d2nA 272 3.62e+01 1d2nA c.37.1.13 32428 1vpfA 102 3.66e+01 1vpfA g.17.1.1 44767 1qmvA 197 3.67e+01 1qq2A c.47.1.10 33066 1nkr 201 3.68e+01 1nkr b.1.1.4 21799 b.1.1.4 21800 1gj7B 253 3.70e+01 1g0xA 197 3.71e+01 1nkr b.1.1.4 21805 b.1.1.4 21806 1nsf 273 3.73e+01 1d2nA c.37.1.13 32429 1vqb 87 3.73e+01 1gvp b.40.4.7 25370 1lf7A 182 3.74e+01 1bag 425 3.80e+01 1bag b.71.1.1 27720 c.1.8.1 28707 1lbd 282 3.82e+01 1lbd a.123.1.1 19279 2rmcA 182 3.83e+01 2cpl b.62.1.1 27491 1d8dA 377 3.85e+01 1ft1A a.118.6.1 19185 1dywA 173 3.91e+01 2cpl b.62.1.1 27505 1ffkP 84 3.91e+01 1ffkP d.12.1.1 37493