# List of top-scoring protein chains for t2k-100-30-alpha-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 3gcb 470 4.18e-01 3gcb d.3.1.1 37032 1gcb 454 6.72e-01 3gcb d.3.1.1 37034 1a6r 471 7.94e-01 3gcb d.3.1.1 37033 1paqA 189 8.29e-01 a.118.1.14 94413 1w33A 181 8.61e-01 1f45B 197 9.83e-01 1f45B a.26.1.1 59642 1de4C 640 1.23e+00 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1wn0A 145 1.27e+00 1ciy 590 1.60e+00 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1f4tA 368 1.61e+00 1f4tA a.104.1.1 18973 1gw5B 591 1.86e+00 a.118.1.10 70630 1ecmA 109 2.82e+00 1ecmA a.130.1.1 19492 1h3qA 140 2.83e+00 d.110.4.3 76652 2c12A 439 3.04e+00 1ll2A 333 3.47e+00 c.68.1.14 74005 1ry6A 360 3.74e+00 c.37.1.9 98090 1cx8B 639 3.76e+00 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17783,30764,33852 1cx8A 639 3.93e+00 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17782,30763,33851 2db0A 253 4.34e+00 1jbgA 109 6.62e+00 a.6.1.3 66480 1jfgA 374 7.15e+00 a.128.1.5 66636 1y1xA 191 7.43e+00 1ow4A 129 7.63e+00 a.39.2.1 93628 1zejA 293 7.66e+00 1f24A 402 7.68e+00 1rom a.104.1.1 18953 2a11A 242 7.76e+00 1jfaA 374 8.20e+00 a.128.1.5 66622 1rcwA 231 8.28e+00 a.132.1.4 97299 1cktA 71 8.30e+00 1cktA a.21.1.1 16417 1zb1A 392 8.68e+00 1nx8A 273 8.68e+00 b.82.2.8 86374 1gulA 222 9.17e+00 1pgtA a.45.1.1,c.47.1.5 17675,32969 1cmnA 402 1.04e+01 1rom a.104.1.1 18958 1js8A 394 1.04e+01 a.86.1.1,b.112.1.1 67219,67220 1yyqA 374 1.06e+01 2b67A 204 1.07e+01 1i5nA 146 1.09e+01 1i5nA a.24.10.3 61805 1q8fA 313 1.09e+01 c.70.1.1 96203 2fx0A 201 1.10e+01 1jfbA 404 1.11e+01 a.104.1.1 66624 1e5rA 290 1.12e+01 1e5rA b.82.2.4 59276 2hdhA 293 1.14e+01 2hdhA a.100.1.3,c.2.1.6 18795,30199 2f6hX 419 1.17e+01 1m93B 245 1.21e+01 1dg3A 592 1.24e+01 1dg3A a.114.1.1,c.37.1.8 19078,32153 2aelA 374 1.25e+01 1kiyA 374 1.26e+01 a.128.1.5 72555 1hyp 80 1.28e+01 1hyp a.52.1.1 17806 1kqfC 217 1.31e+01 f.21.1.1 72874 1huxA 270 1.32e+01 1huxA c.55.1.5 61278 1bjwA 382 1.39e+01 1bjwA c.67.1.1 34349 189l 164 1.41e+01 1l92 d.2.1.3 36960 1f5nA 592 1.51e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1b9uA 34 1.54e+01 1b9uA j.35.1.1 46260 1w5fA 353 1.59e+01 1dovA 181 1.61e+01 1dovA a.24.9.1 16627 2astA 159 1.63e+01 1b5pA 385 1.65e+01 c.67.1.1 90403 3thiA 371 1.67e+01 2thiA c.94.1.1 35792 2bptA 861 1.68e+01 1gumA 222 1.68e+01 1pgtA a.45.1.1,c.47.1.5 17683,32977 1t3wA 148 1.77e+01 1c8oA 300 1.79e+01 1c8oA e.1.1.1 42677 1jpzA 473 1.80e+01 a.104.1.1 67069 2u2fA 85 1.81e+01 2u2fA d.58.7.1 39167 1htjF 210 1.81e+01 1htjF a.91.1.1 61254 1keyA 235 1.84e+01 a.118.16.1 72389 1b33B 161 1.91e+01 1qgwC a.1.1.3 15650 1eny 268 1.93e+01 1eny c.2.1.2 29910 155l 164 2.00e+01 1l92 d.2.1.3 36762 1fs7A 485 2.00e+01 1qdbA a.138.1.3 19691 1etpA 190 2.03e+01 1etpA a.3.1.4,a.3.1.4 15962,15963 1yrbA 262 2.08e+01 2br9A 234 2.12e+01 1kn1B 161 2.13e+01 a.1.1.3 77456 1ash 150 2.15e+01 1ash a.1.1.2 15622 1qdbA 473 2.22e+01 1qdbA a.138.1.3 19688 1f0cA 305 2.27e+01 1c8oA e.1.1.1 42676 1dkiA 371 2.30e+01 1dkiA d.3.1.1 37090 1o5kA 306 2.30e+01 c.1.10.1 92504 145l 164 2.32e+01 1l92 d.2.1.3 36860 1aueA 100 2.39e+01 1nsgB a.24.7.1 16615 1kpsB 171 2.40e+01 a.118.12.1 68787 1jnyA 435 2.41e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2aq8A 269 2.42e+01 2grrB 170 2.47e+01 1g60A 260 2.49e+01 c.66.1.11 70151 1dowA 205 2.53e+01 1dovA a.24.9.1 16626 158l 164 2.60e+01 1l92 d.2.1.3 36747 1g5gB 481 2.62e+01 f.12.1.1,h.3.2.1 65157,65158 2fbnA 198 2.64e+01 123l 164 2.66e+01 1l92 d.2.1.3 36697 1ybdA 239 2.74e+01 1hx1B 114 2.74e+01 1hx1B a.7.7.1 61350 1lqtA 456 2.75e+01 c.3.1.1,c.4.1.1 74198,74199 1uc2A 481 2.76e+01 d.261.1.1 99161 1eia 207 2.80e+01 1eia a.28.3.1,a.73.1.1 16951,18331 1m32A 366 2.80e+01 c.67.1.3 78508 2b1eA 564 2.83e+01 170l 164 2.85e+01 1l92 d.2.1.3 36968 166l 164 2.91e+01 1l92 d.2.1.3 36681 1myt 146 2.93e+01 1a6m a.1.1.2 15207 109l 164 2.95e+01 1l92 d.2.1.3 36781 165l 164 2.98e+01 1l92 d.2.1.3 36680 2c6cA 707 2.98e+01 144l 164 2.99e+01 1l92 d.2.1.3 36893 1heuA 374 3.00e+01 2ohxA b.35.1.2,c.2.1.1 60979,60980 156l 164 3.03e+01 1l92 d.2.1.3 36709 110l 164 3.03e+01 1l92 d.2.1.3 36684 118l 164 3.04e+01 1l92 d.2.1.3 36642 1f60A 458 3.04e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1sdiA 213 3.15e+01 a.198.1.1 105437 1g4uS 383 3.15e+01 1g4uS a.24.11.1,c.45.1.2 16643,32691 1g5gA 481 3.17e+01 f.12.1.1,h.3.2.1 65155,65156 2ahqA 76 3.18e+01 1dq3A 454 3.20e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1f44A 324 3.21e+01 a.60.9.1,d.163.1.1 64982,64983 2cw9A 194 3.24e+01 1au1A 166 3.26e+01 1ifa a.26.1.3 16889 1zid 268 3.26e+01 1eny c.2.1.2 29911 1ewqA 765 3.29e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 111l 164 3.31e+01 1l92 d.2.1.3 36661 1ll0A 339 3.31e+01 c.68.1.14 73995 1l58 164 3.33e+01 1l92 d.2.1.3 36635 2gdqA 382 3.34e+01 107l 164 3.36e+01 1l92 d.2.1.3 36690 113l 164 3.36e+01 1l92 d.2.1.3 36678 1yxcA 292 3.40e+01 1jmeA 455 3.43e+01 a.104.1.1 66885 2a6nA 292 3.46e+01 160l 164 3.52e+01 1l92 d.2.1.3 36748 1z5hA 780 3.52e+01 1sfjA 238 3.53e+01 1yw3A 208 3.54e+01 2cdqA 510 3.57e+01 1sctB 151 3.59e+01 3sdhA a.1.1.2 15003 256bA 106 3.61e+01 256bA a.24.3.1 16539 172l 164 3.61e+01 1l92 d.2.1.3 36905 1r1hA 696 3.65e+01 d.92.1.4 104756 1hw1A 239 3.69e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 130l 164 3.70e+01 1l92 d.2.1.3 36638 1gkpA 458 3.71e+01 b.92.1.3,c.1.9.6 70231,70232 131l 164 3.72e+01 1l92 d.2.1.3 36685 1l92 164 3.74e+01 1l92 d.2.1.3 36629 143l 164 3.75e+01 1l92 d.2.1.3 36857 114l 164 3.75e+01 1l92 d.2.1.3 36663 146l 164 3.76e+01 1l92 d.2.1.3 36763 2azqA 311 3.80e+01 138l 164 3.80e+01 1l92 d.2.1.3 36679 1b6iA 164 3.80e+01 1l92 d.2.1.3 36945 108l 164 3.83e+01 1l92 d.2.1.3 36669 1gk4D 84 3.83e+01 h.1.20.1 70206 1rom 403 3.85e+01 1rom a.104.1.1 18963 1ug3A 339 3.91e+01 1uw4B 248 3.91e+01 a.118.1.14 100072 1qz4A 213 3.93e+01 a.198.1.1 96613 1k7yA 577 3.94e+01 a.46.1.1,c.23.6.1,d.173.1.1 68272,68273,68274 2thiA 379 3.99e+01 2thiA c.94.1.1 35794 176lA 164 4.01e+01 1l92 d.2.1.3 36942 112l 164 4.03e+01 1l92 d.2.1.3 36677 137lA 164 4.04e+01 1l92 d.2.1.3 36791 1rvgA 305 4.05e+01 c.1.10.2 97920 142l 164 4.05e+01 1l92 d.2.1.3 36874 173l 164 4.07e+01 1l92 d.2.1.3 36728 1rqjA 299 4.08e+01 a.128.1.1 97744 2beqA 38 4.09e+01 1wdgA 94 4.10e+01 h.3.3.1 109248 177l 164 4.12e+01 1l92 d.2.1.3 36958 1e7lA 157 4.15e+01 1en7A a.140.4.1,d.4.1.5 64728,64729 1yoyA 175 4.17e+01 120l 164 4.20e+01 1l92 d.2.1.3 36720 1x52A 124 4.26e+01 2absA 383 4.29e+01 147l 164 4.37e+01 1l92 d.2.1.3 36864 1b3uA 588 4.39e+01 1b3uA a.118.1.2 19135 1dgmA 363 4.39e+01 1bx4A c.72.1.1 34936 119l 164 4.39e+01 1l92 d.2.1.3 36622 1m70A 190 4.39e+01 a.3.1.4,a.3.1.4 91200,91201 1dmtA 696 4.40e+01 1dmtA d.92.1.4 40296 1liiA 363 4.40e+01 c.72.1.1 73921 152l 164 4.41e+01 1l92 d.2.1.3 36904 126l 164 4.41e+01 1l92 d.2.1.3 36699 1xx6A 191 4.42e+01 1vh6A 145 4.44e+01 a.24.19.1 100644 191l 164 4.45e+01 1l92 d.2.1.3 36826 129l 164 4.46e+01 1l92 d.2.1.3 36660 174lA 164 4.56e+01 1l92 d.2.1.3 36956 1lw9A 164 4.59e+01 d.2.1.3 84727 159l 164 4.59e+01 1l92 d.2.1.3 36682 102l 165 4.63e+01 1l92 d.2.1.3 36724 1mp1A 111 4.64e+01 a.188.1.1 91382 164l 164 4.67e+01 1l92 d.2.1.3 36714 2bzpA 226 4.67e+01 1gk4A 84 4.69e+01 h.1.20.1 70203 1nhyA 219 4.69e+01 a.45.1.1,c.47.1.5 80520,80521 1rw6A 210 4.73e+01 a.47.4.1 105113 115l 164 4.73e+01 1l92 d.2.1.3 36700 1dhpA 292 4.76e+01 1dhpA c.1.10.1 29097 195l 164 4.78e+01 1l92 d.2.1.3 36841 103l 167 4.78e+01 1l92 d.2.1.3 36870 1wy1A 172 4.80e+01 1qgrA 876 4.84e+01 1qgrA a.118.1.1 19119 1zs3A 182 4.84e+01 1pv9A 348 4.84e+01 c.55.2.1,d.127.1.1 95157,95158 1p36A 164 4.89e+01 d.2.1.3 93978 1jalA 363 4.90e+01 c.37.1.8,d.15.10.2 84138,84139 1r0vA 305 4.90e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1e2xA 243 4.90e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 2a6lA 292 4.97e+01 163l 164 5.03e+01 1l92 d.2.1.3 36658 1en7A 157 5.08e+01 1en7A a.140.4.1,d.4.1.5 64733,64734 149l 164 5.11e+01 1l92 d.2.1.3 36959 1asx 159 5.15e+01 1a6dA c.8.5.2 30821 180lA 164 5.17e+01 1l92 d.2.1.3 36867 2eiaB 206 5.20e+01 1eia a.28.3.1,a.73.1.1 16950,18330 125l 164 5.23e+01 1l92 d.2.1.3 36672 128l 164 5.23e+01 1l92 d.2.1.3 36634 1emy 153 5.27e+01 1a6m a.1.1.2 15204 1v7bA 185 5.34e+01 198l 164 5.35e+01 1l92 d.2.1.3 36785 1sflA 238 5.35e+01 5eat 548 5.36e+01 5eat a.102.4.1,a.128.1.3 18853,19445 1yviA 149 5.36e+01 162l 164 5.36e+01 1l92 d.2.1.3 36749 1j1jA 240 5.43e+01 a.118.16.1 90762 1vkeA 133 5.46e+01 a.152.1.2 108650 1hqvA 191 5.49e+01 1hqvA a.39.1.8 61160 2gnoA 305 5.58e+01 167lA 164 5.58e+01 1l92 d.2.1.3 36937 197l 164 5.58e+01 1l92 d.2.1.3 36911 1jysA 242 5.59e+01 c.56.2.1 77216 141l 164 5.64e+01 1l92 d.2.1.3 36863 1aab 83 5.65e+01 1cktA a.21.1.1 16420 1r8eA 278 5.67e+01 a.6.1.3,d.60.1.1 104843,104844 192l 164 5.71e+01 1l92 d.2.1.3 36815 1e2uA 553 5.71e+01 1e1dA e.26.1.1 43362 1wcrA 103 5.75e+01 2ex0A 399 5.75e+01 1vf6C 72 5.82e+01 a.194.1.1 100602 3crxA 343 5.82e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 1u00A 227 5.85e+01 1wz7A 111 5.86e+01 190l 164 5.86e+01 1l92 d.2.1.3 36892 1uok 558 5.91e+01 1uok b.71.1.1,c.1.8.1 27801,28788 1w2wA 211 5.92e+01 c.124.1.5 109130 2masA 314 5.93e+01 2masA c.70.1.1 34810 1xo0A 324 5.93e+01 196l 164 5.93e+01 1l92 d.2.1.3 36927 1ee2A 373 5.99e+01 2ohxA b.35.1.2,c.2.1.1 24663,29679 1u9lA 70 5.99e+01 a.60.4.2 107751 1n46A 258 6.06e+01 a.123.1.1 85315 199l 164 6.12e+01 1l92 d.2.1.3 36855 140l 164 6.15e+01 1l92 d.2.1.3 36891 2bmaA 470 6.16e+01 175lA 164 6.17e+01 1l92 d.2.1.3 36924 1ej2A 181 6.19e+01 1f9aA c.26.1.3 59414 1ywmA 200 6.19e+01 1dxeA 256 6.27e+01 1dxeA c.1.12.5 29310 1n8kA 374 6.35e+01 b.35.1.2,c.2.1.1 80298,80299 1wy2A 351 6.35e+01 1aq3A 129 6.38e+01 1msc d.85.1.1 40079 2ms2A 129 6.39e+01 1msc d.85.1.1 40049 151l 164 6.39e+01 1l92 d.2.1.3 36944 1ofcX 304 6.43e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 1lrv 244 6.44e+01 1lrv a.118.1.5 19146 1gntA 553 6.49e+01 e.26.1.1 70290 2a35A 215 6.55e+01 1ass 159 6.55e+01 1a6dA c.8.5.2 30818 168lA 164 6.66e+01 1l92 d.2.1.3 36975 122l 164 6.70e+01 1l92 d.2.1.3 36667 1t94A 459 6.75e+01 d.240.1.1,e.8.1.7 106701,106702 157l 164 6.79e+01 1l92 d.2.1.3 36717 2ohxA 374 6.84e+01 2ohxA b.35.1.2,c.2.1.1 24669,29685 171l 164 6.86e+01 1l92 d.2.1.3 36962 1crxA 322 6.89e+01 4crxA a.60.9.1,d.163.1.1 18097,42157 169lA 164 7.01e+01 1l92 d.2.1.3 36963 4crxA 322 7.04e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1a71A 374 7.13e+01 2ohxA b.35.1.2,c.2.1.1 24673,29689 1v4eA 299 7.15e+01 a.128.1.1 100296 161l 164 7.17e+01 1l92 d.2.1.3 36636 2d2mB 142 7.17e+01 1ois 223 7.21e+01 1a36A e.15.1.1 43267 1w9gA 104 7.25e+01 1vsgA 364 7.28e+01 1vsgA h.4.1.1 45782 1a3aC 148 7.28e+01 1a3aA d.112.1.1 40919 1vg5A 73 7.32e+01 1hetA 374 7.34e+01 2ohxA b.35.1.2,c.2.1.1 60975,60976 1e94F 449 7.35e+01 1do0A c.37.1.20 32443 1ea1A 455 7.48e+01 1ea1A a.104.1.1 18970 1syyA 346 7.51e+01 a.25.1.2 106126 1gk4C 84 7.51e+01 h.1.20.1 70205 1y74A 57 7.53e+01 1pwhA 327 7.58e+01 c.79.1.1 95224 1wleA 501 7.62e+01 1hybA 181 7.64e+01 1f9aA c.26.1.3 61399 2fnaA 357 7.66e+01 139l 164 7.66e+01 1l92 d.2.1.3 36643 1l8rA 101 7.72e+01 a.6.1.4 73700 1zx0A 236 7.72e+01 1vlmA 219 7.76e+01 c.66.1.41 108836 2gyqA 175 7.78e+01 1vk4A 298 7.83e+01 c.72.1.1 100850 1kbuA 349 7.89e+01 a.60.9.1,d.163.1.1 72284,72285 1zeeA 403 7.92e+01 1h65A 270 7.94e+01 c.37.1.8 65640 1lla 628 7.98e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1ialA 453 8.00e+01 1bk5A a.118.1.1 19116 1ifa 158 8.10e+01 1ifa a.26.1.3 16892 1ll1 590 8.18e+01 1lla a.85.1.1,a.86.1.1,b.1.18.3 18488,18499,21864 1zk8A 183 8.21e+01 1tk1A 260 8.23e+01 d.248.1.1 107066 1xl3C 92 8.27e+01 1dp4A 435 8.41e+01 1dp4A c.93.1.1 35710 1axeA 374 8.45e+01 2ohxA b.35.1.2,c.2.1.1 24681,29697 1w9cA 321 8.47e+01 1wkqA 164 8.48e+01 c.97.1.2 109393 1f0yA 302 8.51e+01 2hdhA a.100.1.3,c.2.1.6 18793,30197 1qoyA 318 8.58e+01 1qoyA h.4.4.1 45788 1a3aA 148 8.59e+01 1a3aA d.112.1.1 40917 1h6gA 256 8.59e+01 1h6gA a.24.9.1,a.24.9.1 60669,60670 1s35A 214 8.61e+01 a.7.1.1,a.7.1.1 98420,98421 1im8A 244 8.62e+01 c.66.1.14 66212 1jf8A 131 8.76e+01 c.44.1.1 66621 2ap3A 199 8.81e+01 2bmhA 455 8.83e+01 1bu7A a.104.1.1 18941 1oglA 283 8.84e+01 a.204.1.1 92922 1axgA 374 8.92e+01 2ohxA b.35.1.2,c.2.1.1 24691,29707 1s5lX 50 8.96e+01 1x46A 150 8.96e+01