# List of top-scoring protein chains for t2k-100-30-bys-scores 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 1sumB 235 1.92e-04 a.7.12.1 106025 1xwmA 217 6.31e-03 1vctA 205 1.76e-01 2dc3A 193 7.61e-01 1n81A 186 8.96e-01 a.185.1.1 85388 1urvA 190 1.34e+00 1ut0A 190 1.34e+00 a.1.1.2 108012 1tffA 234 1.46e+00 d.3.1.11 106854 1z72A 225 2.00e+00 2fupA 168 2.64e+00 1xqsA 280 2.73e+00 2b05A 246 2.77e+00 1hx1B 114 3.05e+00 1hx1B a.7.7.1 61350 1wwpA 119 3.12e+00 1woyA 500 3.31e+00 1ithA 141 3.46e+00 1ithA a.1.1.2 15623 1afrA 345 3.47e+00 1afrA a.25.1.2 16805 1wkbA 810 3.54e+00 1j1vA 94 3.58e+00 a.4.12.2 83981 1oq9A 363 4.71e+00 a.25.1.2 87257 1brd 248 4.96e+00 1c3wA f.13.1.1 43404 1xqrA 296 4.97e+00 1orjA 130 5.65e+00 a.24.19.1 93456 1a8h 500 6.26e+00 1a8h a.27.1.1,c.26.1.1 16922,31589 1t5oA 351 6.53e+00 c.124.1.5 106459 1ka2A 499 7.84e+00 d.92.1.5 77305 1bk6A 422 8.19e+00 1bk5A a.118.1.1 19133 1wqgA 185 8.47e+00 2ah6A 208 8.73e+00 1orsC 132 8.91e+00 f.14.1.1 87353 1np3A 338 1.04e+01 a.100.1.2,c.2.1.6 85946,85947 1i50A 1733 1.08e+01 e.29.1.2 61754 1dowA 205 1.09e+01 1dovA a.24.9.1 16626 2ligA 164 1.12e+01 1vls a.24.2.1 16530 1jk0A 419 1.13e+01 a.25.1.2 63142 1nc5A 373 1.14e+01 a.102.1.6 85548 1wcrA 103 1.14e+01 1us6A 102 1.15e+01 a.2.13.1 107999 1eerA 166 1.16e+01 1eerA a.26.1.2 16846 2c12A 439 1.22e+01 1jq0A 84 1.22e+01 h.3.2.1 71786 1vljA 407 1.29e+01 e.22.1.2 108832 1gseA 221 1.32e+01 1pgtA a.45.1.1,c.47.1.5 17667,32961 1yozA 116 1.37e+01 2c6cA 707 1.38e+01 2cfuA 658 1.52e+01 2br9A 234 1.57e+01 1lshA 1056 1.63e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1cn4C 166 1.66e+01 1eerA a.26.1.2 16847 1k3lA 221 1.68e+01 a.45.1.1,c.47.1.5 77229,77230 1vcsA 102 1.74e+01 2awiA 317 1.75e+01 1z1lA 345 1.87e+01 1r2fA 319 1.89e+01 1r2fA a.25.1.2 16800 1kq4A 232 1.89e+01 d.207.1.1 68791 2ayuA 417 1.95e+01 1o5kA 306 2.03e+01 c.1.10.1 92504 2f6hX 419 2.03e+01 1k3yA 221 2.05e+01 a.45.1.1,c.47.1.5 77245,77246 1sgmA 191 2.06e+01 a.4.1.9,a.121.1.1 105537,105538 1tqgA 105 2.13e+01 a.24.10.3 107224 1vls 146 2.16e+01 1vls a.24.2.1 16532 1g2cL 43 2.17e+01 1g2cL 1sedA 117 2.21e+01 a.219.1.1 105449 1g2cB 43 2.23e+01 1g2cB 2gmyA 153 2.24e+01 1rpl 251 2.33e+01 1bpyA a.60.12.1,d.218.1.2 75933,75934 1o5hA 214 2.43e+01 a.191.1.1 92497 1r9jA 673 2.46e+01 1ouvA 273 2.49e+01 a.118.18.1 93570 2avpA 70 2.54e+01 1jdpA 441 2.56e+01 c.93.1.1 62906 1fqiA 147 2.67e+01 1agrE a.91.1.1 18542 2chnA 716 2.68e+01 1oqcA 125 2.72e+01 a.24.15.1 87264 1ofcX 304 2.72e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 2fcjA 119 2.75e+01 1rfyA 102 2.75e+01 1ylmA 144 2.75e+01 1is1A 185 2.77e+01 d.67.3.1 83704 1v4eA 299 2.80e+01 a.128.1.1 100296 1zgmA 248 2.87e+01 1twfA 1733 2.88e+01 1o26A 232 2.93e+01 d.207.1.1 86566 1i6zA 135 2.95e+01 a.7.7.1 61861 2ashA 381 2.97e+01 2myo 118 3.01e+01 2myo d.211.1.1 19175 1sig 339 3.11e+01 1sig a.177.1.1 19068 1eyyA 510 3.12e+01 1eyyA c.82.1.1 35389 1ez0A 510 3.14e+01 1eyyA c.82.1.1 35385 1na3A 91 3.14e+01 k.38.1.1 85481 1go3F 107 3.16e+01 a.60.8.2 65407 1zejA 293 3.17e+01 2cb5A 453 3.21e+01 3gcb d.3.1.1 37035 2choA 716 3.25e+01 1ash 150 3.28e+01 1ash a.1.1.2 15622 2fpqA 444 3.29e+01 1bk5A 422 3.30e+01 1bk5A a.118.1.1 19130 1nom 248 3.34e+01 1bpyA a.60.12.1,d.218.1.2 75929,75930 1l3aA 228 3.36e+01 d.18.1.2 73531 1zc6A 305 3.37e+01 1z5hA 780 3.39e+01 1wa5B 530 3.49e+01 2fnoA 248 3.52e+01 2b0jA 358 3.57e+01 1nr6A 473 3.63e+01 a.104.1.1 92085 1buyA 166 3.75e+01 1eerA a.26.1.2 16848 1sfcE 96 3.76e+01 1sfcE h.1.15.1 45647 1ciy 590 3.77e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1elkA 157 3.80e+01 1dvpA a.118.9.2 19217 1rcwA 231 3.81e+01 a.132.1.4 97299 1c1gC 284 3.81e+01 1c1gA h.1.5.1 45575 1q06A 135 3.83e+01 a.6.1.3 95493 2dbnA 461 3.85e+01 1kpkA 473 3.85e+01 f.20.1.1 68776 1sfcA 96 3.91e+01 1sfcA h.1.15.1 45643 2gtqA 867 3.93e+01 1myo 118 3.96e+01 2myo d.211.1.1 19174 1pgjA 478 4.02e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 1ee4A 423 4.13e+01 1ee4A a.118.1.1 19128 1ulyA 192 4.19e+01 1s0pA 176 4.24e+01 a.192.1.1 98300 1lf6A 684 4.26e+01 a.102.1.5,b.30.5.5 77918,77919 1y8aA 332 4.34e+01 1k47A 337 4.35e+01 d.14.1.5,d.58.26.4 72040,72041 1jcrA 377 4.36e+01 a.118.6.1 66506 2ethA 154 4.45e+01 1aisB 200 4.48e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1wphA 201 4.54e+01 1k6iA 352 4.58e+01 c.2.1.2 68223 2bs3C 256 4.66e+01 1xgkA 352 4.79e+01 1iqpA 327 4.90e+01 a.80.1.1,c.37.1.20 62649,62650 1gmjA 84 4.91e+01 h.4.8.1 65310 2gtsA 86 4.91e+01 1bpb 248 4.91e+01 1bpyA a.60.12.1,d.218.1.2 75811,75812 2g38A 99 4.95e+01 1l2iA 261 4.97e+01 a.123.1.1 73503 1vg5A 73 4.99e+01 1cojA 212 5.05e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 2dh4A 340 5.11e+01 1n7sA 63 5.18e+01 h.1.15.1 80271 2g40A 224 5.35e+01 2es4D 332 5.45e+01 1k6xA 352 5.52e+01 c.2.1.2 68238 1gw5A 621 5.55e+01 a.118.1.10 70629 1xv5A 401 5.55e+01 1dovA 181 5.61e+01 1dovA a.24.9.1 16627 1jpxA 84 5.73e+01 h.3.2.1 71783 1gtmA 419 5.81e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1z57A 339 5.84e+01 1qjbA 245 5.86e+01 1qjaA a.118.7.1 19202 1h2kA 349 5.92e+01 b.82.2.6 76572 1r9dA 787 5.97e+01 c.7.1.1 104865 1e2xA 243 6.00e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 1ppjA 446 6.06e+01 d.185.1.1,d.185.1.1 104252,104253 1umnA 165 6.06e+01 a.25.1.1 99607 1iseA 185 6.08e+01 d.67.3.1 90691 2cj4A 150 6.13e+01 1s4bP 674 6.15e+01 d.92.1.5 105252 2a5kA 307 6.16e+01 1qfeA 252 6.20e+01 1qfeA c.1.10.1 29167 1l9wA 252 6.21e+01 c.1.10.1 84570 1d8dA 377 6.22e+01 1ft1A a.118.6.1 19185 1gqnA 252 6.28e+01 c.1.10.1 90514 1l4aD 87 6.38e+01 h.1.15.1 73562 1f0yA 302 6.39e+01 2hdhA a.100.1.3,c.2.1.6 18793,30197 1wleA 501 6.41e+01 3crxA 343 6.48e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 1bcfA 158 6.51e+01 1bcfA a.25.1.1 16648 2azeB 106 6.53e+01 1eumA 165 6.56e+01 1eumA a.25.1.1 59507 1p9sA 300 6.57e+01 b.47.1.4 87999 1vj7A 393 6.59e+01 a.211.1.1,d.218.1.8 100801,100802 1x0vA 354 6.60e+01 1z8uA 102 6.60e+01 1yceA 89 6.63e+01 1ddnA 226 6.65e+01 1bi0 a.4.5.24,a.76.1.1 16207,18413 1y37A 304 6.66e+01 1g2rA 100 6.68e+01 1g2rA d.192.1.1 60231 1tn6A 382 6.70e+01 1ecl 597 6.73e+01 1ecl e.10.1.1 43238 2fbqA 235 6.78e+01 1o17A 345 6.85e+01 a.46.2.1,c.27.1.1 80765,80766 2fji1 399 6.87e+01 2ahrA 259 6.91e+01 4crxA 322 6.96e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1zv1A 65 6.98e+01 1sd4A 126 7.05e+01 a.4.5.39 105428 1a4rA 191 7.11e+01 1ctqA c.37.1.8 32063 1ft1A 377 7.12e+01 1ft1A a.118.6.1 19186 1qdbA 473 7.13e+01 1qdbA a.138.1.3 19688 1jadA 251 7.13e+01 h.4.10.1 66461 1hw1A 239 7.15e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1yg2A 179 7.27e+01 1eguA 731 7.31e+01 1eguA a.102.3.2,b.24.1.1,b.30.5.2 18850,23899,24423 1mroA 548 7.31e+01 1mroA a.89.1.1,d.58.31.2 18525,39443 1tv9A 335 7.36e+01 1tfe 145 7.38e+01 1tfe d.43.1.1 38680 1be3A 446 7.43e+01 1be3A d.185.1.1,d.185.1.1 58950,58951 1m93A 55 7.45e+01 e.1.1.1 91235 1gqeA 365 7.49e+01 e.38.1.1 70351 2e2aA 105 7.57e+01 a.7.2.1 88499 1b48A 221 7.59e+01 1pgtA a.45.1.1,c.47.1.5 17703,32997 1q0gA 117 7.61e+01 a.24.22.1 104428 1a8i 842 7.65e+01 1a8i c.87.1.4 35490 1l0lA 446 7.67e+01 d.185.1.1,d.185.1.1 84482,84483 1ei1A 391 7.76e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1hbnA 549 7.82e+01 1mroA a.89.1.1,d.58.31.2 60898,60899 1qbqA 333 7.89e+01 1ft1A a.118.6.1 19187 1bbhA 131 7.89e+01 1bbhA a.24.3.2 16546 1eduA 149 7.93e+01 1eduA a.118.9.1 19215 1hs6A 611 7.94e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1an0A 190 8.00e+01 1ctqA c.37.1.8 32066 1yrbA 262 8.03e+01 1a17 166 8.06e+01 1a17 a.118.8.1 19206 2a0iA 330 8.09e+01 1crxA 322 8.09e+01 4crxA a.60.9.1,d.163.1.1 18097,42157 2blnA 305 8.22e+01 1z96A 40 8.24e+01 2btdA 210 8.26e+01 1f7cA 231 8.28e+01 1f7cA a.116.1.1 19107 1abbA 828 8.29e+01 1a8i c.87.1.4 35536 1eyhA 144 8.32e+01 1eduA a.118.9.1 19214 1ek8A 185 8.34e+01 1ek8A d.67.3.1 59444 1rj1A 151 8.35e+01 a.29.6.1 97526 1eo0A 77 8.35e+01 1eo0A a.48.3.1 17790 2amdA 311 8.35e+01 1uf2A 1019 8.40e+01 e.28.1.2 99289 1cpt 412 8.44e+01 1cpt a.104.1.1 18968 1c8kA 842 8.47e+01 1a8i c.87.1.4 35491 1q2wA 308 8.48e+01 b.47.1.4 88355 1ku1A 230 8.50e+01 a.118.3.1 72996 1x6mA 196 8.50e+01 2g5cA 281 8.52e+01 1kq3A 376 8.57e+01 e.22.1.2 68790 1qlaC 256 8.65e+01 1qlaC f.21.2.1 43722 1pbwA 216 8.70e+01 1pbwA a.116.1.1 19103 1wzdA 215 8.73e+01 1pw4A 451 8.77e+01 f.38.1.1 95198 2ch7A 309 8.79e+01 1h6oA 204 8.81e+01 a.146.1.1 60689 1kbuA 349 8.90e+01 a.60.9.1,d.163.1.1 72284,72285 1dd5A 185 8.94e+01 1dd5A d.67.3.1 39564 1r5qA 102 8.95e+01 a.186.1.1 97103 1pz1A 333 8.97e+01 c.1.7.1 95390 1yqgA 263 8.99e+01 1bf6A 291 9.00e+01 1pscA c.1.9.3 29065 1uhnA 189 9.00e+01 a.39.1.5 99399