# 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 1irw 108 3.33e-01 1ycc a.3.1.1 15855 5cytR 104 4.37e-01 1ycc a.3.1.1 15878 1d2zA 108 5.53e-01 1d2zA a.77.1.1 18437 1ycc 108 5.74e-01 1ycc a.3.1.1 15834 1ezvD 245 6.58e-01 1be3D a.3.1.3 59546 f.2.1.8 59547 1fnuA 221 6.76e-01 3seb b.40.2.2 25212 d.15.6.1 37801 1ccr 112 7.15e-01 1ycc a.3.1.1 15877 1ytc 112 7.72e-01 1ycc a.3.1.1 15835 1g73C 121 1.70e+00 1g3fA g.52.1.1 45375 1byqA 228 1.73e+00 1yer d.122.1.1 41100 1qnrA 344 1.82e+00 1qnoA c.1.8.3 28834 1b65A 375 1.98e+00 1b65A d.154.1.1 42020 1yer 228 2.01e+00 1yer d.122.1.1 41101 1qnoA 344 2.37e+00 1qnoA c.1.8.3 28838 1qo7A 394 2.40e+00 1qo7A c.69.1.11 34697 1ckiA 317 2.40e+00 1csn d.144.1.1 41660 1aj8A 371 2.67e+00 1aj8A a.103.1.1 18900 1i7pA 274 2.70e+00 b.43.4.2 66048 c.25.1.1 66049 1mntA 76 3.47e+00 1bazA a.43.1.1 17453 3seb 238 3.86e+00 3seb b.40.2.2 25184 d.15.6.1 37773 1d5mC 239 4.00e+00 3seb b.40.2.2 25185 d.15.6.1 37774 1ggwA 140 4.09e+00 1ggwA a.39.1.5 60490 1ndh 272 5.41e+00 1ndh b.43.4.2 25662 c.25.1.1 31552 1ijhA 504 6.00e+00 c.3.1.2 66161 d.16.1.1 66162 1b4vA 504 6.11e+00 1b8sA c.3.1.2 30334 d.16.1.1 37865 1qlwA 328 6.67e+00 1qlwA c.69.1.15 34722 1fohA 664 6.96e+00 1fohA c.3.1.2 30381 c.47.1.10 33078 d.16.1.2 37900 1b8sA 504 7.62e+00 1b8sA c.3.1.2 30335 d.16.1.1 37866 1g2nA 264 7.77e+00 1lbd a.123.1.1 60227 1c2rA 116 8.71e+00 1ycc a.3.1.1 15887 1ton 235 8.74e+00 5ptp b.47.1.2 26307 1a2yB 116 9.34e+00 1gc1H b.1.1.1 19927 1h4wA 224 9.65e+00 b.47.1.2 65622 1f28A 297 9.69e+00 1bkpA d.117.1.1 59608 3cox 507 9.83e+00 1b8sA c.3.1.2 30332 d.16.1.1 37863 1prxA 224 9.90e+00 1prxA c.47.1.10 33076 1qqfA 277 1.00e+01 1c3d a.102.4.4 18875 1am7A 158 1.03e+01 1am7A d.2.1.4 36981 1pls 113 1.03e+01 1pls b.55.1.1 26965 1bbl 51 1.07e+01 1bbl a.9.1.1 16356 1fnd 314 1.15e+01 1fnc b.43.4.2 25626 c.25.1.1 31516 1g7jB 116 1.20e+01 1f3rB b.1.1.1 19933 1rypH 205 1.24e+01 d.153.1.4 41876 1co6A 107 1.28e+01 1ycc a.3.1.1 15894 1ebmA 317 1.29e+01 1ebmA a.96.1.3 18751 d.129.1.2 41300 1gtqA 140 1.34e+01 1b66A d.96.1.2 40661 1fnc 314 1.36e+01 1fnc b.43.4.2 25627 c.25.1.1 31517 1ayoA 130 1.37e+01 1ayoA b.2.4.1 22431 1eu8A 409 1.42e+01 1eu8A c.94.1.1 59502 1ko9A 345 1.42e+01 a.96.1.3 68717 d.129.1.2 68718 1b0nB 57 1.54e+01 1b0nB a.34.1.1 17002 1mkaA 171 1.60e+01 1mkaA d.38.1.2 38543 1vfaB 116 1.64e+01 1gc1H b.1.1.1 19929 1cezA 883 1.69e+01 1cezA e.8.1.3 43110 1qg0A 308 1.70e+01 1fnc b.43.4.2 25639 c.25.1.1 31529 1b24A 188 1.71e+01 1b24A d.95.2.1 40573 d.95.2.1 40574 5ptp 223 1.71e+01 5ptp b.47.1.2 25831 1hj9A 226 1.85e+01 b.47.1.2 65845 1g3fA 117 1.89e+01 1g3fA g.52.1.1 45378 1ayx 492 1.94e+01 1ayx a.102.1.1 18825 1pjcA 361 1.96e+01 1sayA c.2.1.4 30101 c.23.12.2 31361 1fdlH 218 1.97e+01 1igtB b.1.1.1 19961 b.1.1.2 21021 1pjbA 361 1.99e+01 1sayA c.2.1.4 30103 c.23.12.2 31363 4xiaA 393 1.99e+01 4xis c.1.15.3 29439 1eiwA 111 2.06e+01 1eiwA c.23.3.1 31130 1sayA 361 2.12e+01 1sayA c.2.1.4 30102 c.23.12.2 31362 1a3lH 218 2.12e+01 1mfa b.1.1.1 20241 b.1.1.2 21253 1b66A 140 2.13e+01 1b66A d.96.1.2 40657 1dlfH 124 2.44e+01 1igtB b.1.1.1 20383 1f7zA 233 2.45e+01 5ptp b.47.1.2 59681 1bueA 265 2.46e+01 1btl e.3.1.1 42727 1agjA 242 2.48e+01 1agjA b.47.1.1 25827 1l5jA 865 2.50e+01 1e8tA 454 2.54e+01 1e8tA b.68.1.1 59387 1ej5A 107 2.60e+01 1ej5A a.68.1.1 18268 1f89A 291 2.66e+01 d.160.1.1 64988 1gq8A 319 2.68e+01 1ffkZ 92 2.69e+01 1ffkZ g.41.8.3 45317 1mlcB 218 2.69e+01 1igtB b.1.1.1 20053 b.1.1.2 21095 1ia9A 280 2.77e+01 1ia9A d.144.1.5 62113 1hc7A 477 2.78e+01 1hc7A c.51.1.1 60938 d.104.1.1 60939 g.56.1.1 60940 1fxkC 133 2.78e+01 1fxkC a.2.5.1 15702 1jj22 92 2.80e+01 1ffkZ 1kpgA 287 2.81e+01 c.66.1.18 68735 1e8uA 454 2.86e+01 1e8tA b.68.1.1 59389 1qlnA 883 2.91e+01 1cezA e.8.1.3 43111 1gj7B 253 2.95e+01 1irqA 71 3.07e+01 a.43.1.2 66297 1id1A 153 3.07e+01 1id1A c.2.1.9 62286 1rtfB 252 3.10e+01 5ptp 1bt4A 362 3.11e+01 1bjnA c.67.1.4 34468 1que 303 3.12e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1reqD 637 3.18e+01 1reqB c.1.19.1 29623 c.23.6.1 31250 1qbqA 333 3.23e+01 1ft1A a.118.6.1 19187 1nsf 273 3.23e+01 1d2nA c.37.1.13 32429 1c5yB 253 3.23e+01 5ptp 1ayfA 105 3.24e+01 1ayfA d.15.4.1 37684 1xbrA 184 3.24e+01 1xbrA b.2.5.1 22458 1reqB 637 3.25e+01 1reqB c.1.19.1 29621 c.23.6.1 31248 2bbkL 125 3.29e+01 2bbkL g.21.1.1 44882 1ayfB 105 3.38e+01 1ayfA d.15.4.1 37685 1d2nA 272 3.42e+01 1d2nA c.37.1.13 32428 1qgtA 149 3.45e+01 1qgtA a.62.1.1 18135 1i86A 389 3.46e+01 c.95.1.2 66068 c.95.1.2 66069 1dliA 402 3.49e+01 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1ql3A 99 3.53e+01 1ycc a.3.1.1 15822 1acf 125 3.55e+01 3nul d.110.1.1 40882 1pytA 94 3.63e+01 1pytA d.58.3.1 39064 1dljA 402 3.68e+01 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1mml 265 3.68e+01 1mml e.8.1.2 43015 155c 135 3.73e+01 1ycc a.3.1.1 15900 1bal 51 3.82e+01 1bbl a.9.1.1 16357 1ft9A 222 3.87e+01 1ft9A a.4.5.4 16107 b.82.3.1 28131 1pmy 123 3.91e+01 1bqk b.6.1.1 22888 1hh7A 114 3.91e+01 1ycc a.3.1.1 15896 1kkcA 221 3.94e+01 a.2.11.1 68660 d.44.1.1 68661 1h2aS 317 3.98e+01 2frvA e.19.1.1 43311