# 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 2bitX 165 3.40e-32 1dywA 173 4.30e-32 2cpl b.62.1.1 27505 1ihgA 370 4.36e-32 2cpl a.118.8.1,b.62.1.1 62380,62381 2rmcA 182 5.44e-32 2cpl b.62.1.1 27491 1awsA 164 6.07e-32 2cpl b.62.1.1 27431 1cwoA 165 7.81e-32 2cpl b.62.1.1 27445 2cpl 165 7.88e-32 2cpl b.62.1.1 27420 1awqA 164 8.84e-32 2cpl b.62.1.1 27461 1qoiA 177 9.09e-32 2cpl b.62.1.1 27490 1a58 177 1.16e-31 2cpl b.62.1.1 27495 1yndA 165 1.70e-31 1zcxA 178 2.44e-31 1xo7A 166 2.44e-31 2cfeA 162 5.36e-31 1vdnA 162 1.18e-30 1h0pA 182 3.15e-30 b.62.1.1 76450 1zkcA 197 1.75e-29 2a2nA 176 1.90e-29 1xwnA 174 3.07e-29 2fu0A 160 2.85e-28 2b71A 196 7.31e-28 1j2aA 166 6.10e-25 b.62.1.1 90779 1v9tA 166 1.40e-24 b.62.1.1 108451 1lopA 164 6.79e-24 2cpl b.62.1.1 27510 1clh 166 2.77e-23 2cpl b.62.1.1 27512 1zoxA 113 1.27e+00 1lq9A 112 1.39e+00 d.58.4.3 78129 1qupA 222 1.46e+00 1qupA b.1.8.1,d.58.17.1 22301,39352 1uunA 184 2.28e+00 f.6.1.2 100012 1oa4A 222 2.31e+00 b.29.1.11 86731 1pbyA 489 3.07e+00 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 1yo8A 634 3.14e+00 2bm3A 166 3.34e+00 1jjuA 489 3.63e+00 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66774,66775,66776,66777,66778 2gk3A 256 4.39e+00 2b59A 187 4.75e+00 2b8mA 117 5.07e+00 1vj0A 380 5.43e+00 b.35.1.2,c.2.1.1 100786,100787 1fnhA 271 5.96e+00 1fnhA b.1.2.1,b.1.2.1,b.1.2.1 21976,21977,21978 1sq2N 113 6.56e+00 b.1.1.1 105881 1ay1H 213 6.88e+00 1igtB b.1.1.1,b.1.1.2 20243,21255 1kv9A 668 7.11e+00 a.3.1.6,b.70.1.1 73056,73057 3stdA 165 7.31e+00 3stdA d.17.4.1 38073 2std 172 7.92e+00 3stdA d.17.4.1 38085 1zx8A 136 8.13e+00 1vr0A 247 8.55e+00 1b77A 228 8.64e+00 1b77A d.131.1.2,d.131.1.2 41362,41363 1k2fA 190 9.53e+00 b.8.1.2 68054 1ciy 590 1.01e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1fvuB 125 1.05e+01 1ixxB d.169.1.1 42346 2bdvA 231 1.12e+01 1mdbA 539 1.19e+01 e.23.1.1 79008 1idpA 172 1.27e+01 d.17.4.1 83685 1dc1A 323 1.28e+01 1dc1A c.52.1.11 33321 1qmpA 130 1.35e+01 1dz3A c.23.1.1 31106 1cr5A 189 1.36e+01 1cr5A b.52.2.3,d.31.1.1 26931,38465 2bw2A 140 1.40e+01 1dz3A 130 1.51e+01 1dz3A c.23.1.1 31105 1ul7A 102 1.60e+01 d.129.6.1 99540 1fh0A 221 1.69e+01 1cs8A d.3.1.1 59832 1do6A 124 1.70e+01 1do6A b.1.13.1 22361 1xn5A 146 1.71e+01 1tl2A 236 1.76e+01 1tl2A b.67.1.1 27541 2gf9A 189 1.79e+01 1xfsA 178 1.91e+01 d.129.3.5 109589 2gefA 217 1.97e+01 1np1A 184 2.01e+01 1np1A b.60.1.1 27155 1wloA 136 2.06e+01 1o04A 500 2.08e+01 c.82.1.1 86508 1b88A 114 2.25e+01 1tcrA b.1.1.1 20608 1qlpA 394 2.25e+01 1ovaA e.1.1.1 42628 1k4nA 192 2.39e+01 d.32.1.5 72059 1khvA 516 2.44e+01 e.8.1.4 68627 1std 172 2.45e+01 3stdA d.17.4.1 38089 1mxiA 160 2.47e+01 c.116.1.1 79646 1barA 140 2.52e+01 1bfg b.42.1.1 25504 1z4xA 532 2.60e+01 1q5fA 156 2.62e+01 d.24.1.1 104536 1gsoA 431 2.64e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1qr0A 228 2.66e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1qcsA 211 2.68e+01 1qcsA b.52.2.3,d.31.1.1 26927,38461 1zvnA 99 2.78e+01 2sil 381 2.85e+01 3sil b.68.1.1 27543 2aexA 346 2.86e+01 1y791 680 2.88e+01 1ghqB 134 3.03e+01 1ghqB g.18.1.1,g.18.1.1 60522,60523 1ntyA 311 3.07e+01 a.87.1.1,b.55.1.1 103873,103874 1hxmD 242 3.15e+01 b.1.1.1,b.1.1.2 61373,61374 1t5rA 284 3.24e+01 f.6.1.1 106465 1a8y 367 3.24e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1bf8 205 3.28e+01 1qpxA b.1.11.1,b.7.2.1 22332,23214 3sil 379 3.35e+01 3sil b.68.1.1 27542 1p63A 144 3.41e+01 b.42.1.1 94153 1fjgE 162 3.45e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1s2oA 244 3.45e+01 1bvh 157 3.47e+01 1dg9A c.44.1.1 32640 1u5kA 244 3.58e+01 1z4vA 532 3.60e+01 2b4wA 315 3.65e+01 1jqzA 146 3.66e+01 b.42.1.1 67109 1djnA 729 3.67e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28612,30313,30598 1svmA 377 3.74e+01 1zk5A 176 3.74e+01 1o94A 729 3.74e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1w44A 331 3.75e+01 1befA 181 3.78e+01 1befA b.47.1.3 26419 1v5sA 126 3.79e+01 d.129.6.1 108384 1vr8A 142 3.79e+01 1j5eE 161 3.87e+01 d.14.1.1,d.50.1.2 71547,71548 1m8uA 173 3.94e+01 b.11.1.1,b.11.1.1 91233,91234 1bev1 281 3.94e+01 1aym1 1ly2A 130 3.94e+01 g.18.1.1,g.18.1.1 74335,74336 1djqA 729 3.99e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28614,30315,30600 1gggA 226 4.06e+01 1lst c.94.1.1 35817 1agjA 242 4.08e+01 1agjA b.47.1.1 25827 1bu6O 501 4.19e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1wdnA 226 4.22e+01 1lst c.94.1.1 35816 1rg8A 146 4.26e+01 1il8A 72 4.34e+01 1tvxA d.9.1.1 37365 1s8nA 205 4.37e+01 c.23.1.1 105374 1fa0B 537 4.56e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39336,75839,75840 1nbfA 353 4.58e+01 d.3.1.9 80387 1gowA 489 4.59e+01 1qvbA c.1.8.4 28981 1klnA 605 4.63e+01 1xwl c.55.3.5,e.8.1.1 33693,42986 1eesA 178 4.67e+01 1eesA c.37.1.8 32073 1iw2A 182 4.68e+01 b.60.1.1 71468 1lf7A 182 4.71e+01 b.60.1.1 73878 1w96A 554 4.73e+01 1yoxA 250 4.84e+01 1a45 173 4.84e+01 1amm b.11.1.1,b.11.1.1 23602,23603 2bh9A 489 4.86e+01 1c0eA 157 4.89e+01 1dg9A c.44.1.1 32638 1gggB 226 4.95e+01 1lst c.94.1.1 35818 1asyA 490 5.02e+01 1b8aA b.40.4.1,d.104.1.1 25242,40763 2pii 112 5.11e+01 2pii d.58.5.1 39071 2ai4A 119 5.17e+01 1wc9A 169 5.29e+01 1x9uA 116 5.31e+01 1wv3A 238 5.33e+01 1wggA 96 5.35e+01 1em2A 229 5.36e+01 1em2A d.129.3.2 41321 2c43A 323 5.38e+01 1b9vA 390 5.40e+01 2qwc b.68.1.1 27603 1d5rA 324 5.46e+01 1d5rA b.7.1.1,c.45.1.1 23181,32697 1prq 125 5.55e+01 3nul d.110.1.1 40883 1zjcA 418 5.57e+01 1ux6A 350 5.59e+01 b.29.1.16,g.75.1.1 100145,100146 2g6yA 217 5.61e+01 1xipA 388 5.63e+01 1ok8A 394 5.63e+01 b.1.18.4,f.10.1.1 93236,93237 1w1kA 560 5.63e+01 d.58.32.1,d.145.1.1 109059,109060 1afcA 140 5.66e+01 1bfg b.42.1.1 25506 2c5uA 375 5.68e+01 1mpgA 282 5.88e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 1e8gA 560 5.97e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1eeoA 321 5.99e+01 1pty c.45.1.2 32655 1iz1A 294 6.00e+01 a.4.5.37,c.94.1.1 83823,83824 1amm 174 6.05e+01 1amm b.11.1.1,b.11.1.1 23587,23588 1vaoA 560 6.07e+01 1qltA d.58.32.1,d.145.1.1 39461,41724 4gcr 174 6.17e+01 1amm b.11.1.1,b.11.1.1 23589,23590 1z7mA 344 6.19e+01 1kbvA 327 6.27e+01 b.6.1.3,b.6.1.3 68395,68396 1pvtA 238 6.29e+01 c.74.1.1 95189 2tmdA 729 6.30e+01 2tmdA c.1.4.1,c.3.1.1,c.4.1.1 28616,30317,30602 2agcA 162 6.39e+01 2atpB 115 6.42e+01 1jer 138 6.42e+01 2cbp b.6.1.1 23022 1kmoA 774 6.46e+01 f.4.3.3 72753 1elpA 173 6.49e+01 1amm b.11.1.1,b.11.1.1 23596,23597 1xppA 115 6.68e+01 1ag8A 499 6.79e+01 1bpwA c.82.1.1 35341 1l4iA 206 6.82e+01 b.1.11.1,b.7.2.1 73564,73565 1zirA 173 6.90e+01 1po0A 751 6.97e+01 f.4.3.3 94960 1uumA 372 6.98e+01 c.1.4.1 100010 1j3kA 280 7.02e+01 c.71.1.1 84070 1jmxA 494 7.18e+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 1adwA 123 7.19e+01 1bqk b.6.1.1 22893 1sffA 426 7.20e+01 c.67.1.4 105482 1m16A 146 7.21e+01 b.42.1.1 91164 1vfjA 116 7.25e+01 1olmA 403 7.34e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1i5hW 50 7.38e+01 1i5hW b.72.1.1 61785 1a8p 258 7.40e+01 1fdr b.43.4.2,c.25.1.1 25654,31544 1ymmE 249 7.41e+01 2bhmA 164 7.53e+01 1h4xA 117 7.59e+01 1auz c.13.2.1 60626 1o26A 232 7.64e+01 d.207.1.1 86566 1fjrA 195 7.66e+01 1fjrA b.102.1.1 59855 1gpl 432 7.67e+01 1gpl b.12.1.2,c.69.1.19 23645,34793 1a7fB 29 7.70e+01 g.1.1.1 43943 1q1oA 98 7.78e+01 d.15.2.2 95596 1bqcA 302 7.84e+01 1bqcA c.1.8.3 28831 1phr 157 7.84e+01 1dg9A c.44.1.1 32635 1r9wA 145 7.89e+01 d.89.1.2 97264 1nb8A 353 7.92e+01 d.3.1.9 80385 1qltA 560 7.92e+01 1qltA d.58.32.1,d.145.1.1 39457,41720 1cjbA 231 7.95e+01 1qk3A c.61.1.1 34079 1o9wA 177 8.05e+01 b.2.3.5 86713 2ar9A 278 8.07e+01 1rlhA 173 8.09e+01 d.256.1.1 97646 1zxfA 155 8.12e+01 1dim 381 8.24e+01 3sil b.68.1.1 27544 2b0aA 186 8.25e+01 1wriA 93 8.25e+01 1bv8A 138 8.27e+01 1ayoA b.2.4.1 22430 1wnlA 235 8.32e+01 1r0wA 286 8.48e+01 c.37.1.12 96754 2kfnA 605 8.58e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1a4rA 191 8.60e+01 1ctqA c.37.1.8 32063 1jt7A 146 8.61e+01 b.42.1.1 67255 1zxcA 263 8.66e+01 1b2iA 83 8.66e+01 5hpgA g.14.1.1 44640 1pswA 348 8.72e+01 c.87.1.7 88287 1kq4A 232 8.73e+01 d.207.1.1 68791 1o6uA 403 8.80e+01 a.5.3.1,b.132.1.1,c.13.1.1 92589,92590,92591 1u0sY 118 8.85e+01 c.23.1.1 107566 1rlmA 271 8.85e+01 1ve4A 206 8.87e+01 1us5A 314 8.88e+01 c.94.1.1 99856 1jb2A 127 8.88e+01 d.17.4.2 71624 1krhA 338 8.90e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1bkcI 256 8.90e+01 1bkcA d.92.1.10 40334 1a5dA 173 8.92e+01 1amm b.11.1.1,b.11.1.1 23614,23615 2fjlA 150 8.92e+01 1tmy 120 8.93e+01 1dbwA c.23.1.1 31083