# List of top-scoring protein chains for t06-100-30-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 3.35e-01 1debA h.1.18.1 45660 1pb6A 212 1.01e+00 a.4.1.9,a.121.1.1 88017,88018 1nh1A 330 1.32e+00 e.45.1.1 91871 1fmhA 33 1.88e+00 1fmhB k.6.1.1 46409 1l8dA 112 2.79e+00 h.4.12.1 73687 1p9iA 31 3.15e+00 h.1.10.1 94390 1o6zA 303 4.46e+00 c.2.1.5,d.162.1.1 81107,81108 1p65A 73 4.83e+00 d.254.1.1 94156 1ns5A 155 5.00e+00 c.116.1.3 80705 1dc1A 323 5.32e+00 1dc1A c.52.1.11 33321 1dofA 403 5.34e+00 1c3cA a.127.1.1 19429 1gotB 340 6.29e+00 1tbgA b.69.4.1 27648 1mtyB 384 6.88e+00 1mtyB a.25.1.2 16740 1fmhB 33 6.95e+00 1fmhB k.6.1.1 46410 1e5pA 151 7.00e+00 1bj7 b.60.1.1 59272 1f5vA 240 7.58e+00 1bkjA d.90.1.1 40255 1hl9A 449 8.32e+00 b.71.1.3,c.1.8.11 90650,90651 1qgtA 149 8.43e+00 1qgtA a.62.1.1 18135 1mwmA 320 8.43e+00 c.55.1.1,c.55.1.1 79580,79581 1qkkA 155 8.51e+00 1dbwA c.23.1.1 31104 1lml 478 8.93e+00 1lml d.92.1.3 40295 1jmtB 28 9.42e+00 1oqcA 125 9.47e+00 a.24.15.1 87264 1h99A 224 9.79e+00 a.142.1.1,a.142.1.1 60814,60815 1k32A 1045 1.04e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1iw0A 215 1.05e+01 a.132.1.1 83720 1msk 331 1.08e+01 1msk d.173.1.1 42495 1scfA 273 1.11e+01 1exzA a.26.1.2 16873 1v54F 98 1.18e+01 g.41.5.3 100327 1syyA 346 1.26e+01 a.25.1.2 106126 1gotG 73 1.30e+01 1tbgE a.137.3.1 19629 2fcwA 109 1.30e+01 1gwiA 411 1.37e+01 a.104.1.1 76364 1l6xB 34 1.37e+01 k.13.1.1 73644 1a6jA 163 1.40e+01 1a6jA d.112.1.1 40915 1f45B 197 1.44e+01 1f45B a.26.1.1 59642 1cq3A 233 1.45e+01 1cq3A b.27.1.1 23923 1ummA 172 1.48e+01 a.3.1.1 107958 1bjaA 95 1.49e+01 1bjaA a.4.5.9 16122 2pvbA 107 1.49e+01 1a75A a.39.1.4 17205 1sh0A 510 1.50e+01 e.8.1.4 98876 1sg0A 230 1.52e+01 2gq1A 332 1.53e+01 1h5oA 42 1.55e+01 g.9.1.2 83484 1jmuB 666 1.55e+01 1bgc 174 1.68e+01 1bgc a.26.1.1 16822 1reqB 637 1.71e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1wdpA 495 1.71e+01 1qkmA 255 1.75e+01 3erdA a.123.1.1 19309 1t6fA 37 1.90e+01 h.1.28.1 106565 1go4E 100 1.91e+01 h.1.22.1 70296 1ehyA 294 1.92e+01 1ehyA c.69.1.11 34693 1obdA 306 1.96e+01 d.143.1.1 86767 1q8bA 105 1.97e+01 d.58.4.6 96201 1t6sA 162 2.00e+01 1yz1A 174 2.03e+01 1uuqA 440 2.04e+01 c.1.8.3 100015 1guuA 52 2.05e+01 a.4.1.3 83332 1jhgA 101 2.06e+01 1jhgA a.4.12.1 19009 1vkeA 133 2.08e+01 a.152.1.2 108650 1m12A 84 2.09e+01 a.64.1.1 84745 2bjfA 329 2.10e+01 1pmi 440 2.10e+01 1pmi b.82.1.3 28114 1h2sA 225 2.16e+01 f.13.1.1 76578 1y0uA 96 2.25e+01 1ihoA 283 2.26e+01 1ihoA c.26.1.4 62390 1q8cA 151 2.30e+01 a.79.1.2 96202 1jdlA 121 2.30e+01 a.3.1.1 66557 1otjA 283 2.35e+01 b.82.2.5 93517 2lisA 136 2.36e+01 1lis a.19.1.1 16405 1t3iA 420 2.36e+01 c.67.1.3 106354 1f1eA 154 2.42e+01 a.22.1.2 64927 1wddS 128 2.45e+01 1o4sA 389 2.50e+01 c.67.1.1 86620 1sedA 117 2.55e+01 a.219.1.1 105449 1a93B 34 2.58e+01 1a93B h.1.3.1 45545 1i19A 561 2.59e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1s5lX 50 2.62e+01 1r4gA 53 2.62e+01 a.8.5.1 96996 1euhA 475 2.65e+01 1euhA c.82.1.1 35369 1jgsA 138 2.66e+01 a.4.5.28 66683 1iseA 185 2.70e+01 d.67.3.1 90691 1nd9A 49 2.79e+01 a.6.1.6 85575 1jihA 531 2.82e+01 d.240.1.1,e.8.1.7 90374,90375 1s4nA 348 2.83e+01 c.68.1.16 98501 1n2eA 300 2.84e+01 c.26.1.4 85268 1bouA 139 2.99e+01 1bouA a.88.1.1 18521 1sknP 92 2.99e+01 1sknP a.37.1.1 17127 1qsdA 106 3.01e+01 1qsdA a.7.5.1 16335 1td6A 306 3.10e+01 1a3aA 148 3.14e+01 1a3aA d.112.1.1 40917 1gakA 141 3.15e+01 1gakA a.19.1.1 16415 1bf6A 291 3.18e+01 1pscA c.1.9.3 29065 1otfA 62 3.21e+01 1otfA d.80.1.1 39820 1p80A 753 3.21e+01 c.23.16.3,e.5.1.1 94337,94338 1egwA 77 3.31e+01 1mnmA d.88.1.1 40234 1cxqA 162 3.33e+01 1cxqA c.55.3.2 33621 1ru0A 105 3.33e+01 1qnxA 209 3.41e+01 1qnxA d.111.1.1 40914 1l7vA 326 3.44e+01 f.22.1.1 73672 1hyvA 166 3.44e+01 1b9dA c.55.3.2 61424 1fgkA 310 3.45e+01 1fgkA d.144.1.7 41693 1aj8A 371 3.60e+01 1aj8A a.103.1.1 18900 1pq4A 291 3.62e+01 c.92.2.2 94995 1ixkA 315 3.65e+01 c.66.1.38 90716 1j8bA 112 3.65e+01 d.222.1.1 77101 1lm4A 194 3.66e+01 d.167.1.1 84626 1u0fA 564 3.69e+01 1oe8A 211 3.72e+01 a.45.1.1,c.47.1.5 86905,86906 1r5yA 386 3.74e+01 c.1.20.1 97134 1iomA 377 3.74e+01 a.103.1.1 83698 1pea 385 3.78e+01 1pea c.93.1.1 35662 1dowA 205 3.79e+01 1dovA a.24.9.1 16626 1y8aA 332 3.79e+01 1w6uA 302 3.79e+01 1ubkL 534 3.82e+01 e.18.1.1 88422 1lvoA 302 3.84e+01 b.47.1.4 74284 1r3dA 264 3.87e+01 1dpgA 485 3.90e+01 1dpgA c.2.1.3,d.81.1.5 30074,39989 1qamA 244 3.94e+01 2ercA c.66.1.24 34220 1enfA 212 3.95e+01 3seb b.40.2.2,d.15.6.1 25198,37787 1q79A 514 3.96e+01 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 1nlwA 80 3.99e+01 a.38.1.1 80633 1q1vA 70 3.99e+01 a.159.4.1 104479 1ihjA 98 4.04e+01 1pdr b.36.1.1 62382 1qwgA 251 4.17e+01 c.1.27.1 96473 1t7rA 269 4.18e+01 a.123.1.1 106635 1mhqA 148 4.23e+01 a.118.9.2 84973 1pvgA 418 4.26e+01 d.14.1.3,d.122.1.2 95161,95162 1qf8A 182 4.33e+01 1qf8A g.41.4.1 45212 1g24A 211 4.35e+01 1g24A d.166.1.1 42270 2fgeA 995 4.42e+01 1iqvA 218 4.45e+01 1rss a.75.1.1 62661 1ne7A 289 4.48e+01 c.124.1.1 91833 1q6uA 245 4.49e+01 d.26.1.1 95998 2fji1 399 4.50e+01 1ls9A 91 4.50e+01 a.3.1.1 78177 1qwoA 442 4.58e+01 c.60.1.2 104620 1ye8A 178 4.70e+01 1sx5A 244 4.79e+01 c.52.1.2 99023 1rxqA 178 4.82e+01 a.213.1.1 105118 1t5bA 201 4.83e+01 c.23.5.3 106433 1r4vA 171 4.83e+01 a.197.1.1 97049 1b0nA 111 4.85e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1m0wA 491 4.88e+01 c.30.1.4,d.142.1.6 78363,78364 1iu4A 331 4.90e+01 d.3.1.8 71430 1azsA 220 4.94e+01 1azsA d.58.29.1 39416 1d2mA 665 4.94e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1epuA 591 4.96e+01 1dn1A e.25.1.1 43358 1h21A 247 4.97e+01 a.138.1.3 76510 1nthA 458 4.97e+01 c.1.25.1 80730 1gjjA 168 5.00e+01 a.140.1.1,a.140.1.1 83291,83292 1mw5A 187 5.05e+01 d.259.1.1 91477 1tbfA 347 5.05e+01 a.211.1.2 106743 1j5wA 298 5.06e+01 d.104.1.1 71589 1nogA 177 5.08e+01 a.25.2.2 85923 1pwxA 254 5.11e+01 c.2.1.2 95262 1ov9A 50 5.15e+01 a.155.1.1 93591 1ajsA 412 5.16e+01 1ajsA c.67.1.1 34276 1kgdA 180 5.21e+01 c.37.1.1 68582 1ad1A 266 5.21e+01 1aj2 c.1.21.1 29668 1mc2A 122 5.22e+01 a.133.1.2 74622 1c7gA 456 5.22e+01 c.67.1.2 90415 1q3eA 207 5.24e+01 b.82.3.2 95669 1sflA 238 5.24e+01 2gnxA 365 5.24e+01 1am9A 82 5.32e+01 1am9A a.38.1.1 17140 1lshA 1056 5.34e+01 a.118.4.1,f.7.1.1,f.7.1.1 74242,74243,74244 1rijA 25 5.38e+01 k.32.1.1 104951 1ik9A 213 5.39e+01 b.59.1.1,h.1.11.1 66176,66177 1pvaA 110 5.40e+01 1a75A a.39.1.4 17207 1k87A 669 5.40e+01 a.176.1.1,c.1.23.2 77286,77287 1llmC 88 5.51e+01 g.37.1.1,g.37.1.1 91059,91060 1onrA 316 5.54e+01 1onrA c.1.10.1 29169 1a5t 334 5.59e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1ri9A 102 5.67e+01 b.34.2.1 97506 1gq6A 313 5.73e+01 c.42.1.1 70341 1ckeA 227 5.78e+01 1ckeA c.37.1.1 31846 1ffyA 917 5.79e+01 1qu2A a.27.1.1,b.51.1.1,c.26.1.1 16926,26891,31593 1bcpB 199 5.79e+01 1bcpB b.40.2.1,d.169.1.2 25120,42429 1wmaA 276 5.80e+01 1pu6A 218 5.82e+01 a.96.1.5 95123 1sauA 115 5.85e+01 1r2zA 274 5.87e+01 a.156.1.2,b.113.1.1,g.39.1.8 96892,96893,96894 1junA 44 5.89e+01 1junA h.1.3.1 45540 1jae 471 5.94e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1a8rA 221 6.01e+01 1a8rA d.96.1.1 40587 1o3uA 135 6.05e+01 a.24.16.3 86615 2ilk 160 6.08e+01 2ilk a.26.1.3 16885 1exqA 154 6.11e+01 1b9dA c.55.3.2 33646 1w4xA 542 6.18e+01 c.3.1.5,c.3.1.5 109171,109172 1b9hA 388 6.20e+01 1b9hA c.67.1.4 34488 1m4iA 181 6.20e+01 d.108.1.1 74457 1kv5A 250 6.21e+01 c.1.1.1 73052 1hc7A 477 6.22e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1pjhA 280 6.25e+01 c.14.1.3 94761 1a62 130 6.27e+01 1a62 a.140.3.1,b.40.4.5 64708,64709 1nd4A 264 6.28e+01 d.144.1.6 91815 1al3 324 6.32e+01 1al3 c.94.1.1 35835 1t3uA 104 6.34e+01 d.244.1.1 99120 1qhtA 775 6.39e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1y0bA 197 6.39e+01 1fiuA 286 6.39e+01 1fiuA c.52.1.10 33317 1hruA 188 6.40e+01 1hruA d.115.1.1 40926 1ofwA 296 6.55e+01 a.138.1.1 92850 1o6aA 96 6.61e+01 b.139.1.1 92562 1k92A 455 6.66e+01 c.26.2.1,d.210.1.1 68325,68326 1g79A 218 6.67e+01 1ci0A b.45.1.1 25752 1nfp 228 6.69e+01 1nfp c.1.16.2 29555 1n35A 1267 6.70e+01 e.8.1.4 79935 1ccwB 483 6.73e+01 1cb7B c.1.19.2 29646 1srqA 341 6.75e+01 e.55.1.1 105967 1q6hA 224 6.75e+01 d.26.1.1 95975 1o6dA 163 6.80e+01 c.116.1.3 92567 1o5kA 306 6.82e+01 c.1.10.1 92504 1r0dA 206 6.83e+01 a.216.1.1 104715 1j1iA 296 6.84e+01 c.69.1.10 83977 1xs0A 136 6.92e+01 1kdgA 546 7.03e+01 c.3.1.2,d.16.1.1 77337,77338 1ej6D 418 7.04e+01 i.7.1.1 45970 1r6dA 337 7.08e+01 c.2.1.2 97148 1bc5A 269 7.13e+01 1af7 a.58.1.1,c.66.1.8 17929,34204 1t0fA 276 7.15e+01 1ejxA 100 7.17e+01 d.8.1.1 83182 1ovnA 248 7.17e+01 a.71.1.1,c.47.1.7 93602,93603 1kkhA 317 7.21e+01 d.14.1.5,d.58.26.3 72645,72646 1sv6A 269 7.21e+01 d.177.1.1 106043 1d3bB 91 7.26e+01 1d3bB b.38.1.1 24804 1gd8A 118 7.27e+01 d.188.1.1 60445 1f1mA 164 7.30e+01 1ggqA a.24.12.1 59598 1sgmA 191 7.33e+01 a.4.1.9,a.121.1.1 105537,105538 1qo0D 196 7.39e+01 1qo0D c.23.1.3 31125 1sbyA 254 7.42e+01 4ubpA 101 7.43e+01 1ubpA d.8.1.1 37352 1kl9A 182 7.44e+01 b.40.4.5 72681 1vpbA 451 7.45e+01 1bebA 162 7.61e+01 1bebA b.60.1.1 27115 1mswD 883 7.63e+01 e.8.1.3 79427 1h4rA 314 7.68e+01 a.11.2.1,b.55.1.5,d.15.1.4 65616,65617,65618 1yocA 147 7.68e+01 1tn3 137 7.68e+01 1htn d.169.1.1 42423 1or7A 194 7.71e+01 a.4.13.2,a.177.1.1 87332,87333 1rylA 167 7.71e+01 d.276.1.1 105124 3bamA 213 7.78e+01 1bam c.52.1.3 33288 1g55A 343 7.85e+01 1g55A c.66.1.26 34247 1t0yA 122 7.85e+01 d.15.1.1 99066 1oheA 348 7.85e+01 c.45.1.1,c.45.1.1 87013,87014 1pq1A 196 7.88e+01 f.1.4.1 94986 1t7lA 766 7.91e+01 1e8yA 966 7.92e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1goiA 499 7.94e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1m40A 263 7.95e+01 e.3.1.1 74437 1q9bA 43 8.01e+01 g.3.1.1 96257 1uq5A 263 8.02e+01 d.165.1.1 99778 2gqrA 237 8.03e+01 1i8oA 114 8.05e+01 1ycc a.3.1.1 61979 1no4A 97 8.09e+01 h.1.24.1 85918 1i5pA 633 8.10e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 1t0tV 248 8.17e+01 d.58.4.10 106229 1sgwA 214 8.32e+01 c.37.1.12 105541 1e3dB 542 8.33e+01 1h2rL e.18.1.1 59189 1oe4A 247 8.36e+01 c.18.1.3 86895 1m22A 503 8.37e+01 c.117.1.1 78464 1knqA 175 8.52e+01 c.37.1.17 72786 1sgoA 139 8.56e+01 d.82.3.1 98857 1tr0A 108 8.56e+01 d.58.4.4 107261 1s7iA 124 8.58e+01 d.58.4.9 105353 3nul 130 8.60e+01 3nul d.110.1.1 40891 1iybA 208 8.63e+01 d.124.1.1 90720 1fseA 74 8.71e+01 1fseA a.4.6.2 60000 1it2A 146 8.76e+01 a.1.1.2 66365 1brwA 433 8.83e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1m0uA 249 8.84e+01 a.45.1.1,c.47.1.5 78359,78360 1h7cA 108 8.89e+01 a.7.5.1 70914 1h9dB 134 8.90e+01 2jhbA b.54.1.1 60822 1r6fA 310 8.92e+01 e.46.1.1 97149 1rr7A 129 8.94e+01 a.4.1.14 105075 1nnhA 294 8.96e+01 d.104.1.1 92005 1qtnA 164 8.99e+01 1pauA c.17.1.1 30999