# List of top-scoring protein chains for t2k-100-30-stride-ebghtl-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 1yg2A 179 3.50e+00 1debA 54 3.72e+00 1debA h.1.18.1 45660 1jkw 323 4.90e+00 1jkw a.74.1.1,a.74.1.1 18356,18357 1pb6A 212 4.97e+00 a.4.1.9,a.121.1.1 88017,88018 1sesA 421 6.14e+00 1sesA a.2.7.1,d.104.1.1 15710,40710 2aucA 126 6.40e+00 1jeqA 609 6.64e+00 1jeqA a.140.2.1,b.131.1.1,c.62.1.3 64748,90366,90367 127l 164 8.01e+00 d.2.1.3 36745 1f45B 197 9.09e+00 1f45B a.26.1.1 59642 1unlD 208 9.79e+00 109l 164 1.08e+01 1l92 d.2.1.3 36781 1h4lD 147 1.09e+01 a.74.1.1 70873 1tmzA 32 1.11e+01 1tmzA k.1.1.1 46376 1ku1A 230 1.12e+01 a.118.3.1 72996 2aaxA 275 1.16e+01 1oqcA 125 1.19e+01 a.24.15.1 87264 2occF 98 1.20e+01 2occF g.41.5.3 45256 1o6zA 303 1.20e+01 c.2.1.5,d.162.1.1 81107,81108 1v54F 98 1.20e+01 g.41.5.3 100327 2b61A 377 1.30e+01 1ce9A 34 1.31e+01 1ce9C h.1.3.1 45483 1ce9C 34 1.31e+01 1ce9C h.1.3.1 45485 103l 167 1.31e+01 1l92 d.2.1.3 36870 1ffyA 917 1.32e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1qu2A 917 1.32e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16925,26890,31592 1xesA 413 1.36e+01 1nfkA 325 1.39e+01 1a3qA b.1.18.1,b.2.5.3 21929,22444 113l 164 1.44e+01 1l92 d.2.1.3 36678 1kxu 333 1.44e+01 1jkw a.74.1.1,a.74.1.1 18358,18359 1zmtA 254 1.45e+01 1l8dA 112 1.48e+01 h.4.12.1 73687 170l 164 1.55e+01 1l92 d.2.1.3 36968 1p8cA 145 1.55e+01 a.152.1.2 94354 1nh1A 330 1.59e+01 e.45.1.1 91871 120l 164 1.61e+01 1l92 d.2.1.3 36720 125l 164 1.63e+01 1l92 d.2.1.3 36672 1lw9A 164 1.64e+01 d.2.1.3 84727 162l 164 1.66e+01 1l92 d.2.1.3 36749 197l 164 1.66e+01 1l92 d.2.1.3 36911 1l92 164 1.67e+01 1l92 d.2.1.3 36629 1p36A 164 1.67e+01 d.2.1.3 93978 128l 164 1.67e+01 1l92 d.2.1.3 36634 1p65A 73 1.68e+01 d.254.1.1 94156 147l 164 1.69e+01 1l92 d.2.1.3 36864 1vjxA 157 1.69e+01 a.25.1.1 100837 164l 164 1.69e+01 1l92 d.2.1.3 36714 119l 164 1.69e+01 1l92 d.2.1.3 36622 1b6iA 164 1.70e+01 1l92 d.2.1.3 36945 118l 164 1.70e+01 1l92 d.2.1.3 36642 126l 164 1.70e+01 1l92 d.2.1.3 36699 131l 164 1.70e+01 1l92 d.2.1.3 36685 163l 164 1.70e+01 1l92 d.2.1.3 36658 130l 164 1.70e+01 1l92 d.2.1.3 36638 161l 164 1.70e+01 1l92 d.2.1.3 36636 1lshA 1056 1.71e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 196l 164 1.71e+01 1l92 d.2.1.3 36927 195l 164 1.72e+01 1l92 d.2.1.3 36841 145l 164 1.74e+01 1l92 d.2.1.3 36860 1h99A 224 1.74e+01 a.142.1.1,a.142.1.1 60814,60815 165l 164 1.75e+01 1l92 d.2.1.3 36680 158l 164 1.75e+01 1l92 d.2.1.3 36747 156l 164 1.75e+01 1l92 d.2.1.3 36709 143l 164 1.75e+01 1l92 d.2.1.3 36857 166l 164 1.76e+01 1l92 d.2.1.3 36681 198l 164 1.76e+01 1l92 d.2.1.3 36785 167lA 164 1.76e+01 1l92 d.2.1.3 36937 140l 164 1.77e+01 1l92 d.2.1.3 36891 199l 164 1.77e+01 1l92 d.2.1.3 36855 1fmhA 33 1.78e+01 1fmhB k.6.1.1 46409 138l 164 1.78e+01 1l92 d.2.1.3 36679 160l 164 1.80e+01 1l92 d.2.1.3 36748 141l 164 1.80e+01 1l92 d.2.1.3 36863 155l 164 1.81e+01 1l92 d.2.1.3 36762 157l 164 1.81e+01 1l92 d.2.1.3 36717 111l 164 1.82e+01 1l92 d.2.1.3 36661 1p4wA 99 1.84e+01 a.4.6.2 87783 107l 164 1.89e+01 1l92 d.2.1.3 36690 1dofA 403 1.90e+01 1c3cA a.127.1.1 19429 112l 164 1.92e+01 1l92 d.2.1.3 36677 137lA 164 1.94e+01 1l92 d.2.1.3 36791 114l 164 1.96e+01 1l92 d.2.1.3 36663 110l 164 1.97e+01 1l92 d.2.1.3 36684 1h68A 239 1.97e+01 f.13.1.1 60664 2fggA 101 2.02e+01 1h2sA 225 2.09e+01 f.13.1.1 76578 2a6cA 83 2.10e+01 1zw0A 66 2.12e+01 1ehyA 294 2.12e+01 1ehyA c.69.1.11 34693 169lA 164 2.14e+01 1l92 d.2.1.3 36963 175lA 164 2.15e+01 1l92 d.2.1.3 36924 5tmpA 213 2.16e+01 5tmpA c.37.1.1 31931 1l58 164 2.18e+01 1l92 d.2.1.3 36635 1pwxA 254 2.19e+01 c.2.1.2 95262 139l 164 2.20e+01 1l92 d.2.1.3 36643 115l 164 2.21e+01 1l92 d.2.1.3 36700 1cq3A 233 2.22e+01 1cq3A b.27.1.1 23923 108l 164 2.27e+01 1l92 d.2.1.3 36669 189l 164 2.27e+01 1l92 d.2.1.3 36960 159l 164 2.28e+01 1l92 d.2.1.3 36682 177l 164 2.29e+01 1l92 d.2.1.3 36958 4tmkA 213 2.30e+01 5tmpA c.37.1.1 31930 122l 164 2.30e+01 1l92 d.2.1.3 36667 146l 164 2.35e+01 1l92 d.2.1.3 36763 123l 164 2.37e+01 1l92 d.2.1.3 36697 142l 164 2.38e+01 1l92 d.2.1.3 36874 1q1vA 70 2.40e+01 a.159.4.1 104479 152l 164 2.43e+01 1l92 d.2.1.3 36904 1q1gA 276 2.44e+01 c.56.2.1 95574 171l 164 2.45e+01 1l92 d.2.1.3 36962 102l 165 2.46e+01 1l92 d.2.1.3 36724 3lynA 136 2.49e+01 1lis a.19.1.1 16413 144l 164 2.50e+01 1l92 d.2.1.3 36893 1ithA 141 2.56e+01 1ithA a.1.1.2 15623 1vkeA 133 2.57e+01 a.152.1.2 108650 180lA 164 2.59e+01 1l92 d.2.1.3 36867 1qwoA 442 2.63e+01 c.60.1.2 104620 1cg7A 93 2.63e+01 1cktA a.21.1.1 16428 1mwmA 320 2.64e+01 c.55.1.1,c.55.1.1 79580,79581 1fmhB 33 2.65e+01 1fmhB k.6.1.1 46410 1f5vA 240 2.65e+01 1bkjA d.90.1.1 40255 1wmiB 67 2.66e+01 1pmi 440 2.76e+01 1pmi b.82.1.3 28114 1sedA 117 2.84e+01 a.219.1.1 105449 2ztaA 34 2.85e+01 2ztaA h.1.3.1 45474 176lA 164 2.93e+01 1l92 d.2.1.3 36942 172l 164 2.93e+01 1l92 d.2.1.3 36905 1xlyA 234 2.94e+01 1hniB 427 2.98e+01 1rthA e.8.1.2 43045 1akn 579 3.03e+01 2bce c.69.1.1 34626 2fvhA 120 3.04e+01 1swyA 164 3.12e+01 1sx7A 164 3.12e+01 1m12A 84 3.13e+01 a.64.1.1 84745 1jgjA 217 3.14e+01 1c3wA f.13.1.1 62952 129l 164 3.14e+01 1l92 d.2.1.3 36660 173l 164 3.20e+01 1l92 d.2.1.3 36728 149l 164 3.23e+01 1l92 d.2.1.3 36959 2eulA 156 3.23e+01 1m4iA 181 3.24e+01 d.108.1.1 74457 1p9iA 31 3.32e+01 h.1.10.1 94390 1a8q 274 3.32e+01 1brt c.69.1.12 34702 1qamA 244 3.34e+01 2ercA c.66.1.24 34220 1k28A 584 3.36e+01 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 1eetA 557 3.44e+01 1rthA c.55.3.1,e.8.1.2 33608,43078 1a0rG 65 3.50e+01 1tbgE a.137.3.1 19639 2a3qA 170 3.50e+01 104lA 166 3.55e+01 1l92 d.2.1.3 36969 1cf9A 753 3.56e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 1lis 136 3.59e+01 1lis a.19.1.1 16406 2lisA 136 3.59e+01 1lis a.19.1.1 16405 192l 164 3.62e+01 1l92 d.2.1.3 36815 1gwiA 411 3.74e+01 a.104.1.1 76364 1yhnB 65 3.78e+01 1b9xB 68 3.82e+01 1tbgE a.137.3.1 19638 1z2iA 358 3.84e+01 1ykhB 132 3.85e+01 1wn0A 145 3.88e+01 1mc2A 122 3.91e+01 a.133.1.2 74622 1jfkA 134 3.97e+01 a.39.1.5 66639 2a0jA 149 4.03e+01 1r0wA 286 4.07e+01 c.37.1.12 96754 1ziiA 34 4.15e+01 2ztaA h.1.3.1 45479 1ns5A 155 4.16e+01 c.116.1.3 80705 1q5dA 419 4.16e+01 a.104.1.1 95891 2ts1 419 4.16e+01 2ts1 c.26.1.1 31564 1foeA 377 4.32e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 151l 164 4.32e+01 1l92 d.2.1.3 36944 1lox 662 4.35e+01 1lox a.119.1.2,b.12.1.1 19238,23638 1p80A 753 4.36e+01 c.23.16.3,e.5.1.1 94337,94338 1ad4A 266 4.37e+01 1aj2 c.1.21.1 29670 1jthD 77 4.41e+01 h.1.15.1 67273 1e7tA 59 4.60e+01 2az4A 429 4.61e+01 2ercA 244 4.62e+01 2ercA c.66.1.24 34224 2pvbA 107 4.73e+01 1a75A a.39.1.4 17205 1lk3A 160 4.74e+01 a.26.1.3 73950 1ihqA 38 4.79e+01 k.31.1.1 66144 1ad1A 266 4.80e+01 1aj2 c.1.21.1 29668 1n2eA 300 4.80e+01 c.26.1.4 85268 1mopA 300 4.81e+01 c.26.1.4 85035 1hmvB 440 4.92e+01 1rthA e.8.1.2 43047 168lA 164 4.99e+01 1l92 d.2.1.3 36975 1bw0A 416 5.01e+01 1bw0A c.67.1.1 34385 2etxA 209 5.02e+01 1lj2A 110 5.03e+01 h.1.13.2 73926 1fz1C 389 5.06e+01 1mtyB a.25.1.2 16746 1gotB 340 5.07e+01 1tbgA b.69.4.1 27648 2bcjB 340 5.09e+01 1lqwA 183 5.09e+01 d.167.1.1 74210 2adoA 196 5.12e+01 1lmhA 184 5.13e+01 d.167.1.1 74036 1utuA 108 5.16e+01 1lm4A 194 5.16e+01 d.167.1.1 84626 1vasA 137 5.18e+01 2end a.18.1.1 16404 2cw9A 194 5.25e+01 1egwA 77 5.29e+01 1mnmA d.88.1.1 40234 2fxaA 207 5.32e+01 1h8aC 128 5.32e+01 a.4.1.3,a.4.1.3 65731,65732 1ihp 438 5.37e+01 1ihp c.60.1.2 33993 1hniA 558 5.42e+01 1rthA c.55.3.1,e.8.1.2 33586,43044 1g2cI 52 5.47e+01 1g2cI h.3.2.1 45771 2fpqA 444 5.47e+01 1a8s 273 5.50e+01 1brt c.69.1.12 34710 1v9nA 360 5.50e+01 1ar1B 298 5.52e+01 2occB b.6.1.2,f.17.2.1 23037,43619 2a1dD 329 5.53e+01 2cb5A 453 5.54e+01 3gcb d.3.1.1 37035 1aqlA 532 5.63e+01 2bce c.69.1.1 34627 1aj8A 371 5.72e+01 1aj8A a.103.1.1 18900 1n6eA 1071 5.75e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 80149,80150,80151,80152 1ofwA 296 5.76e+01 a.138.1.1 92850 1k32A 1045 5.77e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1dlwA 116 5.80e+01 1dlyA a.1.1.1 14982 2achA 360 5.88e+01 1c8oA e.1.1.1 42626 1cxpC 466 5.88e+01 1mhlC 1d2vC 466 5.90e+01 1mhlC 1mhlC 466 5.93e+01 1mhlC 1h6oA 204 5.98e+01 a.146.1.1 60689 1y0uA 96 6.04e+01 1e5pA 151 6.14e+01 1bj7 b.60.1.1 59272 1pal 108 6.18e+01 1a75A a.39.1.4 17209 1zt2B 212 6.19e+01 1dowA 205 6.22e+01 1dovA a.24.9.1 16626 1td6A 306 6.26e+01 1konA 249 6.28e+01 e.39.1.1 72823 1a4pA 96 6.38e+01 1b4cA a.39.1.2 17176 1f1eA 154 6.38e+01 a.22.1.2 64927 1w4xA 542 6.46e+01 c.3.1.5,c.3.1.5 109171,109172 1byb 495 6.51e+01 1byb c.1.8.1 28790 1xkyA 301 6.54e+01 174lA 164 6.55e+01 1l92 d.2.1.3 36956 1q6cA 495 6.59e+01 c.1.8.1 95970 1v3hA 495 6.62e+01 c.1.8.1 108303 1bf6A 291 6.63e+01 1pscA c.1.9.3 29065 1o3uA 135 6.64e+01 a.24.16.3 86615 2basA 431 6.65e+01 1hl8A 449 6.66e+01 b.71.1.3,c.1.8.11 90646,90647 2givA 295 6.67e+01 1wdpA 495 6.74e+01 1x4tA 92 6.74e+01 1envA 123 6.75e+01 1envA h.3.2.1 45726 1imvA 398 6.80e+01 e.1.1.1 62591 1gotG 73 6.84e+01 1tbgE a.137.3.1 19629 2bykB 128 6.86e+01 1mtyB 384 6.88e+01 1mtyB a.25.1.2 16740 1zmbA 290 6.90e+01 1f0cA 305 6.92e+01 1c8oA e.1.1.1 42676 2gf4A 100 6.93e+01 1f4qA 165 6.96e+01 1alvA a.39.1.8 17360 191l 164 7.03e+01 1l92 d.2.1.3 36826 2mtaC 147 7.05e+01 2mtaC a.3.1.1 15908 1eq1A 166 7.07e+01 a.63.1.1 64910 2aplA 157 7.09e+01 1sg6A 393 7.16e+01 e.22.1.1 105522 1jb0L 154 7.21e+01 1jb0L f.31.1.1 62829 1e3dB 542 7.27e+01 1h2rL e.18.1.1 59189 1kddA 36 7.29e+01 h.1.3.1 68472 1tbgA 340 7.29e+01 1tbgA b.69.4.1 27649 2gq1A 332 7.32e+01 1h5wA 309 7.39e+01 e.27.1.1 65635 1m93A 55 7.40e+01 e.1.1.1 91235 1osa 148 7.41e+01 1cll a.39.1.5 17300 1xeqA 103 7.48e+01 1xmiA 291 7.54e+01 2ajfA 597 7.54e+01 1hdj 77 7.57e+01 1bqz a.2.3.1 15696 1hleA 345 7.58e+01 1ovaA e.1.1.1 42618 1gehA 444 7.60e+01 c.1.14.1,d.58.9.1 65181,65182 2f4wA 187 7.60e+01 1pvgA 418 7.61e+01 d.14.1.3,d.122.1.2 95161,95162 1dipB 78 7.62e+01 1dipB h.1.12.1 45633 2hmiA 558 7.76e+01 1rthA c.55.3.1,e.8.1.2 33604,43106 2ftuA 118 7.80e+01 1kdxA 81 7.84e+01 1kdxA a.12.1.1 16375 2dvh 79 8.02e+01 1c53 a.3.1.1 15803 1ireA 204 8.04e+01 d.149.1.1 76769 2a84A 300 8.09e+01 1bl3A 160 8.13e+01 1b9dA c.55.3.2 33655 1tn4 159 8.14e+01 1ncx a.39.1.5 17248 1t01A 255 8.22e+01 a.24.9.1,a.24.9.1 106188,106189 1uz3A 102 8.30e+01 2vsgA 358 8.32e+01 2vsgA h.4.1.1 45780 1hddC 61 8.34e+01 2hddA a.4.1.1 15978 1ummA 172 8.38e+01 a.3.1.1 107958 2c8sA 172 8.38e+01 1pea 385 8.40e+01 1pea c.93.1.1 35662 1rkeA 262 8.41e+01 a.24.9.1,a.24.9.1 97608,97609 1ihoA 283 8.44e+01 1ihoA c.26.1.4 62390 1ugpA 203 8.45e+01 d.149.1.1 107831 2fbqA 235 8.51e+01 2b1fA 34 8.53e+01 1lml 478 8.55e+01 1lml d.92.1.3 40295 1kqqA 139 8.56e+01 a.4.3.1 72885 1c20A 128 8.58e+01 1c20A a.4.3.1 16079 1b9dA 163 8.62e+01 1b9dA c.55.3.2 33649 1a75A 108 8.65e+01 1a75A a.39.1.4 17216 1i9zA 347 8.70e+01 1i9yA d.151.1.2 62102 1c8oA 300 8.76e+01 1c8oA e.1.1.1 42677 1jj7A 260 8.76e+01 c.37.1.12 63114 2a07F 93 8.78e+01 1w6uA 302 8.79e+01 1tikA 213 8.82e+01 c.23.5.3 107003 1n4qB 377 8.86e+01 a.102.4.3 91636 1hyvA 166 8.87e+01 1b9dA c.55.3.2 61424 1dipA 78 8.88e+01 1dipA h.1.12.1 45632 1mtpA 323 8.89e+01 e.1.1.1 85107 2b8wA 328 8.90e+01 1bg8A 89 8.97e+01 1bg8A a.57.1.1 17925