# List of top-scoring protein chains for t2k-100-30-str2-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 3.04e-05 a.7.12.1 106025 1xwmA 217 7.27e-04 1wkbA 810 4.06e-02 1vctA 205 1.05e-01 1n81A 186 2.19e-01 a.185.1.1 85388 1jk0A 419 2.39e-01 a.25.1.2 63142 1xqrA 296 2.65e-01 1xqsA 280 3.65e-01 2dc3A 193 4.28e-01 1urvA 190 5.48e-01 1ut0A 190 5.48e-01 a.1.1.2 108012 1z72A 225 5.69e-01 1twfA 1733 7.79e-01 1i50A 1733 8.13e-01 e.29.1.2 61754 1a8h 500 8.38e-01 1a8h a.27.1.1,c.26.1.1 16922,31589 2b05A 246 8.88e-01 1ithA 141 1.17e+00 1ithA a.1.1.2 15623 1tffA 234 1.27e+00 d.3.1.11 106854 2ah6A 208 1.32e+00 2br9A 234 1.44e+00 1aep 161 1.48e+00 1aep a.63.1.1 18139 2c6cA 707 2.09e+00 1us6A 102 3.03e+00 a.2.13.1 107999 2ligA 164 3.19e+00 1vls a.24.2.1 16530 1oq9A 363 3.27e+00 a.25.1.2 87257 1o5hA 214 3.32e+00 a.191.1.1 92497 1wy0A 342 3.39e+00 2awiA 317 3.53e+00 1zgmA 248 3.69e+00 2fnoA 248 3.69e+00 2bk9A 153 3.69e+00 1j1vA 94 3.91e+00 a.4.12.2 83981 1ofcX 304 4.13e+00 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 2fcjA 119 4.15e+00 1kgnA 329 4.43e+00 a.25.1.2 68584 1sgmA 191 4.74e+00 a.4.1.9,a.121.1.1 105537,105538 1ka2A 499 4.94e+00 d.92.1.5 77305 1r2fA 319 5.51e+00 1r2fA a.25.1.2 16800 1ku1A 230 5.54e+00 a.118.3.1 72996 1rfyA 102 5.62e+00 1wcrA 103 5.96e+00 1yozA 116 6.04e+00 1afrA 345 6.77e+00 1afrA a.25.1.2 16805 1ciy 590 7.00e+00 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1ylmA 144 7.26e+00 1iqcA 308 7.46e+00 a.3.1.5,a.3.1.5 66266,66267 1wqgA 185 7.46e+00 1x0vA 354 7.49e+00 2g38A 99 7.58e+00 2db0A 253 7.64e+00 1aijS 301 7.88e+00 6prcM f.26.1.1 43465 1xsm 390 8.13e+00 1xsm a.25.1.2 16804 1np3A 338 8.18e+00 a.100.1.2,c.2.1.6 85946,85947 1aijM 307 8.75e+00 6prcM f.26.1.1 43462 1jq0A 84 9.02e+00 h.3.2.1 71786 1nr6A 473 9.26e+00 a.104.1.1 92085 2fupA 168 9.40e+00 1ouvA 273 9.45e+00 a.118.18.1 93570 1elkA 157 9.64e+00 1dvpA a.118.9.2 19217 1bcfA 158 9.66e+00 1bcfA a.25.1.1 16648 1orjA 130 9.68e+00 a.24.19.1 93456 1g2cL 43 1.05e+01 1g2cL 1dowA 205 1.08e+01 1dovA a.24.9.1 16626 1tqgA 105 1.11e+01 a.24.10.3 107224 1pk5A 248 1.15e+01 a.123.1.1 88139 2dh4A 340 1.19e+01 1z1lA 345 1.23e+01 1i1iP 681 1.23e+01 1i1iP d.92.1.5 40297 1cn4C 166 1.25e+01 1eerA a.26.1.2 16847 2f6hX 419 1.29e+01 2gmyA 153 1.30e+01 1g2cB 43 1.31e+01 1g2cB 1dxrM 323 1.32e+01 6prcM f.26.1.1 43432 1l2iA 261 1.34e+01 a.123.1.1 73503 1rzhM 307 1.35e+01 f.26.1.1 98165 1eumA 165 1.36e+01 1eumA a.25.1.1 59507 1pfvA 551 1.38e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1vljA 407 1.39e+01 e.22.1.2 108832 1f4lA 551 1.40e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1xlyA 234 1.45e+01 1fz1C 389 1.45e+01 1mtyB a.25.1.2 16746 1hx1B 114 1.49e+01 1hx1B a.7.7.1 61350 1t33A 224 1.50e+01 a.4.1.9,a.121.1.1 106295,106296 1eyyA 510 1.53e+01 1eyyA c.82.1.1 35389 1vj7A 393 1.56e+01 a.211.1.1,d.218.1.8 100801,100802 1sig 339 1.59e+01 1sig a.177.1.1 19068 1tf5A 844 1.63e+01 a.162.1.1,a.172.1.1,c.37.1.19,c.37.1.19 106834,106835,106836,106837 1gseA 221 1.63e+01 1pgtA a.45.1.1,c.47.1.5 17667,32961 1r9jA 673 1.69e+01 2g3bA 208 1.73e+01 1k6iA 352 1.81e+01 c.2.1.2 68223 1qbkB 890 1.82e+01 1qbkB a.118.1.1 19127 1k6xA 352 1.85e+01 c.2.1.2 68238 1ez0A 510 1.89e+01 1eyyA c.82.1.1 35385 1t5oA 351 1.91e+01 c.124.1.5 106459 1qqeA 292 1.94e+01 1qqeA a.118.8.1 19210 1xgkA 352 1.95e+01 1qsaA 618 2.02e+01 1qsaA a.118.5.1,d.2.1.6 19182,36988 1woyA 500 2.03e+01 1z5hA 780 2.06e+01 2chnA 716 2.13e+01 2fq4A 192 2.20e+01 1jcqA 382 2.20e+01 a.118.6.1 66504 1ld8A 382 2.21e+01 a.118.6.1 73838 2a0b 125 2.27e+01 2a0b a.24.10.1 16630 1o17A 345 2.27e+01 a.46.2.1,c.27.1.1 80765,80766 1k3yA 221 2.29e+01 a.45.1.1,c.47.1.5 77245,77246 1k3lA 221 2.29e+01 a.45.1.1,c.47.1.5 77229,77230 1vls 146 2.29e+01 1vls a.24.2.1 16532 2btdA 210 2.47e+01 1n6bA 473 2.48e+01 a.104.1.1 85359 1lf6A 684 2.55e+01 a.102.1.5,b.30.5.5 77918,77919 1jk0B 345 2.58e+01 a.25.1.2 63143 1a76 326 2.62e+01 1a76 a.60.7.1,c.120.1.2 18091,33361 2g40A 224 2.66e+01 2aexA 346 2.66e+01 1gqeA 365 2.71e+01 e.38.1.1 70351 1r9dA 787 2.75e+01 c.7.1.1 104865 2cj4A 150 2.82e+01 2bxkA 585 2.82e+01 1iyhA 198 2.91e+01 a.45.1.1,c.47.1.5 83790,83791 1m98A 317 2.92e+01 a.175.1.1,d.17.4.6 78866,78867 1gaxA 862 2.94e+01 1gaxA b.51.1.1,c.26.1.1,a.2.7.3,a.27.1.1 26893,31595,75842,75843 1vgmA 378 2.95e+01 1brd 248 2.96e+01 1c3wA f.13.1.1 43404 1i50B 1224 2.96e+01 e.29.1.1 61755 1in6A 334 2.99e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1in4A 334 2.99e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1vg5A 73 3.05e+01 1kpkA 473 3.08e+01 f.20.1.1 68776 1n4kA 381 3.08e+01 a.118.22.1,b.42.6.1 79992,79993 1f44A 324 3.12e+01 a.60.9.1,d.163.1.1 64982,64983 1s4bP 674 3.13e+01 d.92.1.5 105252 1fr0A 125 3.17e+01 2a0b a.24.10.1 59996 1ash 150 3.17e+01 1ash a.1.1.2 15622 1vcsA 102 3.19e+01 1t0qB 330 3.19e+01 a.25.1.2 106221 4crxA 322 3.20e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1s0pA 176 3.21e+01 a.192.1.1 98300 1gtmA 419 3.21e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1lkoA 191 3.22e+01 a.25.1.1,g.41.5.1 78063,78064 2ashA 381 3.22e+01 1hs6A 611 3.22e+01 1hs6A a.118.1.7,b.98.1.1,d.92.1.13 61233,61234,61235 1wmuB 146 3.29e+01 a.1.1.2 109417 2cb5A 453 3.30e+01 3gcb d.3.1.1 37035 1dk5A 322 3.32e+01 1dk5A a.65.1.1 18192 1dvbA 191 3.32e+01 1ryt a.25.1.1,g.41.5.1 16645,45244 1y8aA 332 3.42e+01 1o9rA 162 3.42e+01 a.25.1.1 86706 1dlc 584 3.43e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23719,27976,43391 1or3A 165 3.44e+01 1nfn a.24.1.1 16522 1ohfA 644 3.46e+01 b.121.4.8 93014 1tn6A 382 3.46e+01 1ryt 190 3.51e+01 1ryt a.25.1.1,g.41.5.1 16646,45245 1wwpA 119 3.52e+01 2a2mA 258 3.53e+01 1vjlA 164 3.54e+01 d.257.1.1 100822 1is1A 185 3.55e+01 d.67.3.1 83704 1b71A 191 3.56e+01 1ryt a.25.1.1,g.41.5.1 16647,45246 1rfzA 168 3.61e+01 a.195.1.1 97411 2ch7A 309 3.62e+01 1gumA 222 3.67e+01 1pgtA a.45.1.1,c.47.1.5 17683,32977 1e2xA 243 3.67e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 2choA 716 3.73e+01 1itwA 741 3.75e+01 c.77.1.2 76793 1av8A 340 3.75e+01 1xikA a.25.1.2 16796 1qkmA 255 3.77e+01 3erdA a.123.1.1 19309 1iygA 133 3.79e+01 a.118.8.1 76947 6prcM 323 3.83e+01 6prcM f.26.1.1 43435 1oqcA 125 3.88e+01 a.24.15.1 87264 1f7cA 231 3.95e+01 1f7cA a.116.1.1 19107 1ee4A 423 3.95e+01 1ee4A a.118.1.1 19128 2gtsA 86 3.96e+01 1gw5A 621 3.97e+01 a.118.1.10 70629 1gmjA 84 3.97e+01 h.4.8.1 65310 1crxA 322 4.00e+01 4crxA a.60.9.1,d.163.1.1 18097,42157 1s2xA 206 4.00e+01 a.47.3.1 105229 1kbuA 349 4.01e+01 a.60.9.1,d.163.1.1 72284,72285 1gm6A 175 4.02e+01 b.60.1.1 70272 1w9cA 321 4.02e+01 1fqiA 147 4.03e+01 1agrE a.91.1.1 18542 1ew3A 159 4.09e+01 1mup b.60.1.1 27114 1mroA 548 4.13e+01 1mroA a.89.1.1,d.58.31.2 18525,39443 2fbqA 235 4.15e+01 1b48A 221 4.17e+01 1pgtA a.45.1.1,c.47.1.5 17703,32997 3crxA 343 4.21e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 1xo0A 324 4.23e+01 1rktA 205 4.27e+01 a.4.1.9,a.121.1.1 97623,97624 1pf4A 582 4.28e+01 c.37.1.12,f.37.1.1 88052,88053 1eemA 241 4.31e+01 1eemA a.45.1.1,c.47.1.5 17717,33011 1uz5A 402 4.35e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1o5kA 306 4.37e+01 c.1.10.1 92504 2a11A 242 4.39e+01 1m3qA 317 4.41e+01 a.96.1.3,d.129.1.2 91184,91185 2bl8A 103 4.43e+01 1ft1A 377 4.43e+01 1ft1A a.118.6.1 19186 2cfuA 658 4.43e+01 1wphA 201 4.44e+01 1l3aA 228 4.46e+01 d.18.1.2 73531 1q0gA 117 4.47e+01 a.24.22.1 104428 1l4aD 87 4.52e+01 h.1.15.1 73562 1paqA 189 4.52e+01 a.118.1.14 94413 1hbnA 549 4.63e+01 1mroA a.89.1.1,d.58.31.2 60898,60899 1rv3A 483 4.66e+01 c.67.1.4 105101 2g5cA 281 4.67e+01 1mtyB 384 4.77e+01 1mtyB a.25.1.2 16740 1dovA 181 4.80e+01 1dovA a.24.9.1 16627 1eq1A 166 4.84e+01 a.63.1.1 64910 1sedA 117 4.84e+01 a.219.1.1 105449 1rj1A 151 4.86e+01 a.29.6.1 97526 1aj8A 371 4.91e+01 1aj8A a.103.1.1 18900 1iqpA 327 4.92e+01 a.80.1.1,c.37.1.20 62649,62650 1mkiA 330 4.93e+01 e.3.1.2 84994 1sflA 238 5.01e+01 2fji1 399 5.02e+01 1jx4A 352 5.03e+01 d.240.1.1,e.8.1.7 90378,90379 1y2mA 716 5.03e+01 1sfcE 96 5.09e+01 1sfcE h.1.15.1 45647 1w68A 390 5.14e+01 a.25.1.2 109216 1m93A 55 5.17e+01 e.1.1.1 91235 1ao6A 585 5.17e+01 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 19354,19355,19356 1sfjA 238 5.20e+01 1h0oA 390 5.21e+01 a.25.1.2 70845 1qcrA 446 5.30e+01 1be3A d.185.1.1,d.185.1.1 59025,59026 1zs4A 83 5.32e+01 1lpe 144 5.33e+01 1nfn a.24.1.1 16524 2cvdA 198 5.36e+01 1jdpA 441 5.40e+01 c.93.1.1 62906 1k28A 584 5.46e+01 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 1n5uA 585 5.60e+01 a.126.1.1,a.126.1.1,a.126.1.1 85339,85340,85341 3lynA 136 5.63e+01 1lis a.19.1.1 16413 1z2cB 383 5.67e+01 1xg7A 250 5.85e+01 1uhnA 189 5.89e+01 a.39.1.5 99399 1zw0A 66 5.90e+01 1pw4A 451 5.96e+01 f.38.1.1 95198 1hw1A 239 6.04e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1k75A 434 6.04e+01 c.82.1.2 68253 1e19A 314 6.08e+01 1b7bA c.73.1.1 34967 1myo 118 6.08e+01 2myo d.211.1.1 19174 1p5zB 263 6.16e+01 c.37.1.1 87815 1pbwA 216 6.17e+01 1pbwA a.116.1.1 19103 1un8A 552 6.18e+01 c.119.1.2,a.208.1.1 103806,99661 1ei1A 391 6.20e+01 1aj6 d.14.1.3,d.122.1.2 37570,41104 1e5rA 290 6.25e+01 1e5rA b.82.2.4 59276 1ge9A 184 6.32e+01 1dd5A d.67.3.1 60463 1mmoB 384 6.34e+01 1mtyB a.25.1.2 16768 1xk4A 93 6.34e+01 1yucA 255 6.37e+01 1dkzA 219 6.46e+01 1dkzA a.8.4.1,b.130.1.1 90345,90346 1z0kB 69 6.52e+01 1wovA 250 6.54e+01 1dik 874 6.60e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1qjbA 245 6.69e+01 1qjaA a.118.7.1 19202 1r2aA 46 6.73e+01 1r2aA a.31.1.1 16995 1b4pA 217 6.76e+01 a.45.1.1,c.47.1.5 83158,83159 1jcrA 377 6.76e+01 a.118.6.1 66506 1gulA 222 6.77e+01 1pgtA a.45.1.1,c.47.1.5 17675,32969 1bbhA 131 6.84e+01 1bbhA a.24.3.2 16546 1d8dA 377 6.87e+01 1ft1A a.118.6.1 19185 1l58 164 6.95e+01 1l92 d.2.1.3 36635 1xfiA 367 7.06e+01 e.50.1.1 109584 1gwcA 230 7.10e+01 a.45.1.1,c.47.1.5 70660,70661 2a2oA 258 7.14e+01 1twfB 1224 7.16e+01 1poiA 317 7.17e+01 1poiA c.124.1.2 34153 1x42A 232 7.21e+01 1kaeA 434 7.21e+01 c.82.1.2 72247 1wrdA 103 7.24e+01 1e9rA 437 7.26e+01 c.37.1.11 64827 1z57A 339 7.26e+01 2ayuA 417 7.29e+01 2fbwC 141 7.31e+01 1ha2A 585 7.32e+01 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 60866,60867,60868 1ho8A 480 7.32e+01 1ho8A a.118.1.9 61107 1ift 263 7.34e+01 1mrj d.165.1.1 42211 1gw5B 591 7.35e+01 a.118.1.10 70630 1h6pA 203 7.36e+01 a.146.1.1 60690 1nznA 126 7.36e+01 a.118.8.1 92382 2azeB 106 7.37e+01 1jmxA 494 7.37e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66901,66902,66903,66904,66905 2a0iA 330 7.42e+01 5ukdA 194 7.55e+01 1zin c.37.1.1 31851 1p4xA 250 7.58e+01 a.4.5.28,a.4.5.28 87784,87785 1hz4A 373 7.61e+01 a.118.8.2 65960 1t6jA 714 7.66e+01 1e7aA 585 7.67e+01 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 19360,19361,19362 1cuk 203 7.67e+01 1hjp a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 1ppjA 446 7.68e+01 d.185.1.1,d.185.1.1 104252,104253 1pv6A 417 7.70e+01 f.38.1.2 95151 1ialA 453 7.70e+01 1bk5A a.118.1.1 19116 1p0zA 131 7.84e+01 d.110.6.1 93882 2viuB 175 7.85e+01 1hgeB h.3.1.1 45676 3hmgB 175 7.85e+01 1hgeB h.3.1.1 45704 1dd5A 185 7.88e+01 1dd5A d.67.3.1 39564 1c20A 128 7.92e+01 1c20A a.4.3.1 16079 1aisB 200 7.95e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1bj5 585 7.95e+01 1bj5 a.126.1.1,a.126.1.1,a.126.1.1 19369,19370,19371 1bvp1 349 8.02e+01 1bvp1 2h88C 140 8.03e+01 1l0lA 446 8.07e+01 d.185.1.1,d.185.1.1 84482,84483 1ir6A 424 8.08e+01 c.107.1.2 71342 1v66A 65 8.10e+01 1qdbA 473 8.15e+01 1qdbA a.138.1.3 19688 1txqB 86 8.15e+01 1w2yA 229 8.15e+01 a.204.1.1 109140 1hgeB 175 8.15e+01 1hgeB h.3.1.1 45680 1po5A 476 8.16e+01 a.104.1.1 94963 1xouA 192 8.17e+01 1clc 639 8.19e+01 1clc a.102.1.2,b.1.18.2 18835,21872 170l 164 8.24e+01 1l92 d.2.1.3 36968 1bd3A 243 8.25e+01 1bd3A c.61.1.1 34098 1d3uB 201 8.27e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1ab8A 220 8.29e+01 1azsA d.58.29.1 39414 1go3F 107 8.29e+01 a.60.8.2 65407 1qbqA 333 8.33e+01 1ft1A a.118.6.1 19187 1us7B 265 8.33e+01 a.205.1.1 99858 1kqqA 139 8.38e+01 a.4.3.1 72885 1y1nA 291 8.46e+01 1bz4A 144 8.46e+01 1nfn a.24.1.1 16521 1biqA 375 8.51e+01 1xikA a.25.1.2 16786 1u9lA 70 8.55e+01 a.60.4.2 107751 1ajqA 209 8.57e+01 1ajqA d.153.1.2 41840 1r71A 178 8.58e+01 a.4.14.1 104823 1y10A 407 8.71e+01 1qgtA 149 8.77e+01 1qgtA a.62.1.1 18135 1xpcA 248 8.79e+01 1jsxA 207 8.83e+01 c.66.1.20 71846 1ym3A 215 8.85e+01 1o9iA 266 8.88e+01 a.25.1.3 92671