# 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 1debA 54 1.84e+00 1debA h.1.18.1 45660 1nh1A 330 1.90e+00 e.45.1.1 91871 1sesA 421 2.80e+00 1sesA a.2.7.1,d.104.1.1 15710,40710 1jkw 323 3.31e+00 1jkw a.74.1.1,a.74.1.1 18356,18357 1yg2A 179 3.51e+00 1o6zA 303 6.54e+00 c.2.1.5,d.162.1.1 81107,81108 1konA 249 6.63e+00 e.39.1.1 72823 1kxu 333 7.11e+00 1jkw a.74.1.1,a.74.1.1 18358,18359 1vjxA 157 7.97e+00 a.25.1.1 100837 1pb6A 212 8.23e+00 a.4.1.9,a.121.1.1 88017,88018 1ce9C 34 9.03e+00 1ce9C h.1.3.1 45485 1ce9A 34 9.68e+00 1ce9C h.1.3.1 45483 1jeqA 609 9.69e+00 1jeqA a.140.2.1,b.131.1.1,c.62.1.3 64748,90366,90367 1fmhA 33 9.94e+00 1fmhB k.6.1.1 46409 1tmzA 32 1.14e+01 1tmzA k.1.1.1 46376 1mwmA 320 1.38e+01 c.55.1.1,c.55.1.1 79580,79581 1l8dA 112 1.39e+01 h.4.12.1 73687 2cw9A 194 1.39e+01 2aucA 126 1.49e+01 2az4A 429 1.51e+01 1lshA 1056 1.52e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1p9iA 31 1.61e+01 h.1.10.1 94390 2occF 98 1.67e+01 2occF g.41.5.3 45256 1ny6A 267 1.75e+01 c.37.1.20 92321 1fmhB 33 1.87e+01 1fmhB k.6.1.1 46410 1f5vA 240 1.87e+01 1bkjA d.90.1.1 40255 1xvxA 312 1.88e+01 1cq3A 233 1.90e+01 1cq3A b.27.1.1 23923 2a3qA 170 1.95e+01 2eulA 156 1.96e+01 2ztaA 34 1.98e+01 2ztaA h.1.3.1 45474 1mtyB 384 1.99e+01 1mtyB a.25.1.2 16740 1xesA 413 2.00e+01 1p65A 73 2.06e+01 d.254.1.1 94156 1wmiB 67 2.15e+01 1dc1A 323 2.25e+01 1dc1A c.52.1.11 33321 1oqcA 125 2.28e+01 a.24.15.1 87264 1h99A 224 2.29e+01 a.142.1.1,a.142.1.1 60814,60815 1q1gA 276 2.32e+01 c.56.2.1 95574 1fz1C 389 2.34e+01 1mtyB a.25.1.2 16746 1cg7A 93 2.38e+01 1cktA a.21.1.1 16428 1syyA 346 2.38e+01 a.25.1.2 106126 1msk 331 2.43e+01 1msk d.173.1.1 42495 1lk3A 160 2.46e+01 a.26.1.3 73950 1k7yA 577 2.54e+01 a.46.1.1,c.23.6.1,d.173.1.1 68272,68273,68274 1gotG 73 2.55e+01 1tbgE a.137.3.1 19629 2fvhA 120 2.56e+01 1f45B 197 2.60e+01 1f45B a.26.1.1 59642 1dovA 181 2.67e+01 1dovA a.24.9.1 16627 1iw0A 215 2.71e+01 a.132.1.1 83720 2cb5A 453 2.72e+01 3gcb d.3.1.1 37035 1h4lD 147 2.72e+01 a.74.1.1 70873 1wzdA 215 2.75e+01 1v54F 98 2.76e+01 g.41.5.3 100327 2gq1A 332 2.91e+01 1dofA 403 2.91e+01 1c3cA a.127.1.1 19429 1wn0A 145 2.92e+01 1ns5A 155 2.92e+01 c.116.1.3 80705 127l 164 2.96e+01 d.2.1.3 36745 1nfkA 325 2.96e+01 1a3qA b.1.18.1,b.2.5.3 21929,22444 1a0rG 65 3.02e+01 1tbgE a.137.3.1 19639 1e7tA 59 3.05e+01 2g09A 297 3.05e+01 1t6sA 162 3.06e+01 1pal 108 3.07e+01 1a75A a.39.1.4 17209 1fnuA 221 3.12e+01 3seb b.40.2.2,d.15.6.1 25212,37801 2pvbA 107 3.14e+01 1a75A a.39.1.4 17205 1gotB 340 3.18e+01 1tbgA b.69.4.1 27648 1oqyA 368 3.22e+01 a.5.2.1,a.5.2.1,a.189.1.1,d.15.1.1 93439,93440,93441,93442 2bduA 297 3.24e+01 1wt4A 73 3.26e+01 1ybxA 143 3.28e+01 1kddA 36 3.29e+01 h.1.3.1 68472 2bl0B 145 3.32e+01 1zw0A 66 3.33e+01 1dowA 205 3.33e+01 1dovA a.24.9.1 16626 2a6cA 83 3.36e+01 1yhnB 65 3.39e+01 1b9xB 68 3.44e+01 1tbgE a.137.3.1 19638 2fpqA 444 3.55e+01 1dx4A 586 3.61e+01 2bce c.69.1.1 34622 1ziiA 34 3.63e+01 2ztaA h.1.3.1 45479 3lynA 136 3.67e+01 1lis a.19.1.1 16413 2vsgA 358 3.71e+01 2vsgA h.4.1.1 45780 109l 164 3.73e+01 1l92 d.2.1.3 36781 2a1dD 329 3.79e+01 1yviA 149 3.79e+01 1h68A 239 3.80e+01 f.13.1.1 60664 1p80A 753 3.85e+01 c.23.16.3,e.5.1.1 94337,94338 1lml 478 3.89e+01 1lml d.92.1.3 40295 1cf9A 753 3.90e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 1ku1A 230 3.92e+01 a.118.3.1 72996 1tp4A 97 4.03e+01 a.189.1.1 107183 1e5pA 151 4.05e+01 1bj7 b.60.1.1 59272 1xkqA 280 4.06e+01 1scfA 273 4.09e+01 1exzA a.26.1.2 16873 1h2sA 225 4.10e+01 f.13.1.1 76578 1reqB 637 4.13e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1q1vA 70 4.15e+01 a.159.4.1 104479 1qamA 244 4.18e+01 2ercA c.66.1.24 34220 1f82A 424 4.18e+01 1f82A d.92.1.7 40307 1kd9A 36 4.19e+01 h.1.3.1 68466 1trrA 107 4.27e+01 1jhgA a.4.12.1 19017 1iq3A 110 4.28e+01 1iq3A a.39.1.6 62640 1f83A 425 4.35e+01 1f82A d.92.1.7 40306 2a0jA 149 4.35e+01 1ihqA 38 4.35e+01 k.31.1.1 66144 2fcwA 109 4.36e+01 1tbgA 340 4.40e+01 1tbgA b.69.4.1 27649 1xxbA 78 4.43e+01 1xxaA d.74.2.1 39706 1tbgE 68 4.45e+01 1tbgE a.137.3.1 19630 1gwiA 411 4.51e+01 a.104.1.1 76364 1jhgA 101 4.58e+01 1jhgA a.4.12.1 19009 1dipA 78 4.61e+01 1dipA h.1.12.1 45632 2b61A 377 4.64e+01 131l 164 4.64e+01 1l92 d.2.1.3 36685 166l 164 4.65e+01 1l92 d.2.1.3 36681 113l 164 4.69e+01 1l92 d.2.1.3 36678 1wddS 128 4.72e+01 1b6iA 164 4.72e+01 1l92 d.2.1.3 36945 2adoA 196 4.73e+01 1ykhB 132 4.74e+01 1a6jA 163 4.78e+01 1a6jA d.112.1.1 40915 1ehyA 294 4.82e+01 1ehyA c.69.1.11 34693 7reqB 637 4.82e+01 1reqB c.1.19.1,c.23.6.1 29617,31244 2wrpR 107 4.85e+01 1jhgA a.4.12.1 19010 1lj2A 110 4.87e+01 h.1.13.2 73926 2ercA 244 4.88e+01 2ercA c.66.1.24 34224 103l 167 4.94e+01 1l92 d.2.1.3 36870 2etxA 209 4.96e+01 1xxcA 78 4.97e+01 1xxaA d.74.2.1 39712 1jmuB 666 4.98e+01 1bl3A 160 5.03e+01 1b9dA c.55.3.2 33655 1lw9A 164 5.08e+01 d.2.1.3 84727 162l 164 5.11e+01 1l92 d.2.1.3 36749 1k32A 1045 5.11e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1exzA 141 5.12e+01 1exzA a.26.1.2 16877 1dipB 78 5.14e+01 1dipB h.1.12.1 45633 1envA 123 5.18e+01 1envA h.3.2.1 45726 1k28A 584 5.18e+01 b.40.8.1,b.108.1.2,d.2.1.3 68049,68050,68051 170l 164 5.20e+01 1l92 d.2.1.3 36968 125l 164 5.21e+01 1l92 d.2.1.3 36672 1x4tA 92 5.28e+01 1jmtB 28 5.30e+01 1eqcA 394 5.34e+01 1cz1A c.1.8.3 28811 1ithA 141 5.38e+01 1ithA a.1.1.2 15623 1cz1A 394 5.39e+01 1cz1A c.1.8.3 28839 2mysB 166 5.43e+01 1wdcB a.39.1.5 17308 1vkeA 133 5.43e+01 a.152.1.2 108650 118l 164 5.43e+01 1l92 d.2.1.3 36642 1r4gA 53 5.47e+01 a.8.5.1 96996 1om2A 95 5.50e+01 1om2A a.23.4.1 16520 1qkkA 155 5.53e+01 1dbwA c.23.1.1 31104 120l 164 5.56e+01 1l92 d.2.1.3 36720 180lA 164 5.56e+01 1l92 d.2.1.3 36867 1q8bA 105 5.57e+01 d.58.4.6 96201 1a3aA 148 5.60e+01 1a3aA d.112.1.1 40917 128l 164 5.75e+01 1l92 d.2.1.3 36634 1pwxA 254 5.76e+01 c.2.1.2 95262 102l 165 5.77e+01 1l92 d.2.1.3 36724 159l 164 5.79e+01 1l92 d.2.1.3 36682 1cxqA 162 5.79e+01 1cxqA c.55.3.2 33621 1otjA 283 5.83e+01 b.82.2.5 93517 1mhyB 395 5.84e+01 1mtyB a.25.1.2 16781 160l 164 5.86e+01 1l92 d.2.1.3 36748 5tmpA 213 5.88e+01 5tmpA c.37.1.1 31931 1bgeB 175 5.95e+01 1bgc a.26.1.1 16824 172l 164 5.95e+01 1l92 d.2.1.3 36905 1l92 164 5.96e+01 1l92 d.2.1.3 36629 1p8cA 145 5.98e+01 a.152.1.2 94354 1t6fA 37 6.02e+01 h.1.28.1 106565 171l 164 6.02e+01 1l92 d.2.1.3 36962 175lA 164 6.07e+01 1l92 d.2.1.3 36924 130l 164 6.07e+01 1l92 d.2.1.3 36638 1s4nA 348 6.10e+01 c.68.1.16 98501 2f4mB 61 6.11e+01 110l 164 6.20e+01 1l92 d.2.1.3 36684 1ubkL 534 6.20e+01 e.18.1.1 88422 1is1A 185 6.22e+01 d.67.3.1 83704 1b1zA 219 6.23e+01 3seb b.40.2.2,d.15.6.1 25216,37805 1pveA 72 6.25e+01 a.189.1.1 104322 1o4sA 389 6.26e+01 c.67.1.1 86620 112l 164 6.26e+01 1l92 d.2.1.3 36677 1wuiL 534 6.28e+01 111l 164 6.28e+01 1l92 d.2.1.3 36661 123l 164 6.29e+01 1l92 d.2.1.3 36697 1h2rL 534 6.30e+01 1h2rL e.18.1.1 43298 197l 164 6.31e+01 1l92 d.2.1.3 36911 1bjaA 95 6.32e+01 1bjaA a.4.5.9 16122 1yz1A 174 6.34e+01 144l 164 6.34e+01 1l92 d.2.1.3 36893 1unlD 208 6.38e+01 164l 164 6.38e+01 1l92 d.2.1.3 36714 1nzeA 149 6.39e+01 a.24.18.1 92374 122l 164 6.42e+01 1l92 d.2.1.3 36667 1kd8A 36 6.44e+01 h.1.3.1 68460 1dgcA 62 6.46e+01 2dgcA h.1.3.1 45506 146l 164 6.47e+01 1l92 d.2.1.3 36763 199l 164 6.51e+01 1l92 d.2.1.3 36855 2bzsA 236 6.51e+01 2bjfA 329 6.53e+01 198l 164 6.53e+01 1l92 d.2.1.3 36785 1sedA 117 6.57e+01 a.219.1.1 105449 138l 164 6.60e+01 1l92 d.2.1.3 36679 1pvgA 418 6.63e+01 d.14.1.3,d.122.1.2 95161,95162 104lA 166 6.63e+01 1l92 d.2.1.3 36969 1ewcA 214 6.63e+01 3seb b.40.2.2,d.15.6.1 25199,37788 1guuA 52 6.63e+01 a.4.1.3 83332 147l 164 6.65e+01 1l92 d.2.1.3 36864 1sh0A 510 6.71e+01 e.8.1.4 98876 1ummA 172 6.73e+01 a.3.1.1 107958 2f6hX 419 6.75e+01 107l 164 6.78e+01 1l92 d.2.1.3 36690 156l 164 6.80e+01 1l92 d.2.1.3 36709 2c8sA 172 6.81e+01 161l 164 6.82e+01 1l92 d.2.1.3 36636 1r0wA 286 6.82e+01 c.37.1.12 96754 119l 164 6.82e+01 1l92 d.2.1.3 36622 169lA 164 6.85e+01 1l92 d.2.1.3 36963 177l 164 6.87e+01 1l92 d.2.1.3 36958 126l 164 6.88e+01 1l92 d.2.1.3 36699 2b1fA 34 6.89e+01 158l 164 6.89e+01 1l92 d.2.1.3 36747 143l 164 6.91e+01 1l92 d.2.1.3 36857 2ftuA 118 6.93e+01 141l 164 6.93e+01 1l92 d.2.1.3 36863 1vsd 152 6.94e+01 1cxqA c.55.3.2 33625 1l58 164 6.95e+01 1l92 d.2.1.3 36635 1t6jA 714 6.95e+01 1a0rB 340 6.97e+01 1tbgA b.69.4.1 27658 196l 164 6.99e+01 1l92 d.2.1.3 36927 142l 164 6.99e+01 1l92 d.2.1.3 36874 2aaxA 275 7.02e+01 176lA 164 7.02e+01 1l92 d.2.1.3 36942 152l 164 7.03e+01 1l92 d.2.1.3 36904 195l 164 7.04e+01 1l92 d.2.1.3 36841 1zdc 35 7.05e+01 1fc2C k.13.1.1 46434 140l 164 7.07e+01 1l92 d.2.1.3 36891 163l 164 7.09e+01 1l92 d.2.1.3 36658 165l 164 7.09e+01 1l92 d.2.1.3 36680 1sg0A 230 7.10e+01 1zmeC 70 7.10e+01 1zmeC g.38.1.1,h.1.3.1 45081,45514 1b9dA 163 7.13e+01 1b9dA c.55.3.2 33649 2ts1 419 7.14e+01 2ts1 c.26.1.1 31564 173l 164 7.15e+01 1l92 d.2.1.3 36728 1l5zA 155 7.15e+01 c.23.1.1 77722 1zx1A 231 7.15e+01 1xkyA 301 7.16e+01 1wgzA 510 7.16e+01 155l 164 7.17e+01 1l92 d.2.1.3 36762 1p4wA 99 7.17e+01 a.4.6.2 87783 1hkkA 364 7.18e+01 c.1.8.5,d.26.3.1 90634,90635 1xxaA 78 7.19e+01 1xxaA d.74.2.1 39700 1l6xB 34 7.20e+01 k.13.1.1 73644 157l 164 7.20e+01 1l92 d.2.1.3 36717 1lg2A 365 7.21e+01 c.1.8.5,d.26.3.1 77950,77951 1reqD 637 7.28e+01 1reqB c.1.19.1,c.23.6.1 29623,31250 1b4uA 139 7.29e+01 1bouA a.88.1.1 18523 1q8cA 151 7.30e+01 a.79.1.2 96202 129l 164 7.35e+01 1l92 d.2.1.3 36660 1bouA 139 7.35e+01 1bouA a.88.1.1 18521 1sknP 92 7.38e+01 1sknP a.37.1.1 17127 1slqA 278 7.44e+01 f.47.1.1 105719 1p36A 164 7.46e+01 d.2.1.3 93978 1epuA 591 7.47e+01 1dn1A e.25.1.1 43358 1egwA 77 7.47e+01 1mnmA d.88.1.1 40234 145l 164 7.47e+01 1l92 d.2.1.3 36860 1euhA 475 7.49e+01 1euhA c.82.1.1 35369 4tmkA 213 7.50e+01 5tmpA c.37.1.1 31930 1qkmA 255 7.56e+01 3erdA a.123.1.1 19309 167lA 164 7.63e+01 1l92 d.2.1.3 36937 139l 164 7.65e+01 1l92 d.2.1.3 36643 2au5A 139 7.68e+01 2bcjB 340 7.68e+01 2dgcA 63 7.69e+01 2dgcA h.1.3.1 45497 149l 164 7.70e+01 1l92 d.2.1.3 36959 1cjtA 217 7.74e+01 1azsA d.58.29.1 39419 1enfA 212 7.81e+01 3seb b.40.2.2,d.15.6.1 25198,37787 1b0nA 111 7.81e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1a93B 34 7.83e+01 1a93B h.1.3.1 45545 1ht9A 76 7.84e+01 4icb a.39.1.1 61252 2fk8A 318 7.85e+01 1otfA 62 7.86e+01 1otfA d.80.1.1 39820 1v9dA 340 7.90e+01 a.207.1.1 100535 1qghA 156 7.91e+01 1qghA a.25.1.1 16728 1jfkA 134 7.92e+01 a.39.1.5 66639 1a5v 162 7.94e+01 1cxqA c.55.3.2 33629 2fbqA 235 7.95e+01 2au3A 407 7.96e+01 1t3iA 420 7.98e+01 c.67.1.3 106354 1rxqA 178 7.98e+01 a.213.1.1 105118 1txjA 171 8.00e+01 b.88.1.2 107424 2fji1 399 8.03e+01 1ekjA 221 8.03e+01 1ekjB c.53.2.1 33364 1ihjA 98 8.04e+01 1pdr b.36.1.1 62382 1lis 136 8.07e+01 1lis a.19.1.1 16406 2lisA 136 8.07e+01 1lis a.19.1.1 16405 114l 164 8.07e+01 1l92 d.2.1.3 36663 1ekjB 221 8.09e+01 1ekjB c.53.2.1 33365 1yt3A 375 8.09e+01 1td6A 306 8.15e+01 168lA 164 8.15e+01 1l92 d.2.1.3 36975 1jj2U 70 8.22e+01 1ffkS a.2.2.1 63106 1s72V 71 8.22e+01 a.2.2.1 105341 1ydiA 263 8.30e+01 151l 164 8.30e+01 1l92 d.2.1.3 36944 2b43A 526 8.32e+01 1jgjA 217 8.38e+01 1c3wA f.13.1.1 62952 1gakA 141 8.50e+01 1gakA a.19.1.1 16415 1wmaA 276 8.53e+01 1q6cA 495 8.53e+01 c.1.8.1 95970 2cybA 323 8.57e+01 1hyvA 166 8.59e+01 1b9dA c.55.3.2 61424 1go4E 100 8.59e+01 h.1.22.1 70296 1hl9A 449 8.62e+01 b.71.1.3,c.1.8.11 90650,90651 1bw0A 416 8.65e+01 1bw0A c.67.1.1 34385 1zvzA 279 8.65e+01 1ci6B 63 8.68e+01 1ci6B h.1.3.1 45549 1mopA 300 8.77e+01 c.26.1.4 85035 2sas 185 8.79e+01 2sas a.39.1.5 17258 1qsdA 106 8.84e+01 1qsdA a.7.5.1 16335 1ihoA 283 8.85e+01 1ihoA c.26.1.4 62390 1xl7A 612 8.86e+01 1xlyA 234 8.87e+01 115l 164 8.90e+01 1l92 d.2.1.3 36700 108l 164 8.91e+01 1l92 d.2.1.3 36669 1ru0A 105 8.93e+01 1lqwA 183 8.96e+01 d.167.1.1 74210 1foeA 377 8.99e+01 1foeA a.87.1.1,b.55.1.1 18517,26969