# List of top-scoring protein chains for t04-100-30-near-backbone-11-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 1utxA 66 4.00e-06 a.35.1.3 108034 2b5aA 77 1.72e-05 1lmb3 92 3.17e-05 1lmb3 1y7yA 74 3.60e-05 2a6cA 83 5.85e-05 1y9qA 192 9.26e-04 1r69 69 1.35e-03 1r69 a.35.1.2 17028 1adr 76 1.39e-03 1r69 a.35.1.2 17042 1cjgA 62 2.46e-03 1pru a.35.1.5 17112 1dwkA 156 2.70e-03 1dw9A a.35.1.4,d.72.1.1 17075,39606 2bjcA 62 2.74e-03 1hlvA 131 3.90e-03 a.4.1.7,a.4.1.7 65854,65855 1b0nA 111 7.30e-03 1b0nA a.34.1.1,a.35.1.3 17001,17064 1umqA 81 8.51e-03 a.4.1.12 99625 2bnmA 198 9.03e-03 1zzcA 198 1.49e-02 1rzrA 332 1.69e-02 2auwA 170 2.92e-02 2cro 71 3.48e-02 1r69 a.35.1.2 17038 5croA 66 5.99e-02 1orc a.35.1.2 17044 1orc 71 7.03e-02 1orc a.35.1.2 17054 1hw1A 239 2.04e-01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1smtA 122 2.22e-01 1smtA a.4.5.5 16109 1a6i 217 2.61e-01 2tct a.4.1.9,a.121.1.1 16066,19243 1r1tA 122 2.62e-01 a.4.5.5 104769 1jftA 340 3.33e-01 a.35.1.5,c.93.1.1 66652,66653 1qbjA 81 3.43e-01 1qbjA a.4.5.19 16155 1wpkA 146 3.54e-01 1cfr 285 3.57e-01 1cfr c.52.1.7 33312 2cu3A 64 3.81e-01 2fbhA 146 3.84e-01 1u8bA 133 3.86e-01 2tct 207 3.87e-01 2tct a.4.1.9,a.121.1.1 16063,19240 1rzsA 61 4.09e-01 a.35.1.2 105139 1puzA 82 4.86e-01 a.218.1.1 104320 1yseA 141 5.48e-01 1pru 56 5.87e-01 1pru a.35.1.5 17104 1ic8A 194 6.21e-01 a.4.1.1,a.35.1.1 76740,76741 1ngr 85 6.61e-01 1ngr a.77.1.2 18422 1s7oA 113 6.81e-01 a.4.13.3 105354 1fipA 98 7.32e-01 1fipA a.4.1.12 18980 1z67A 135 8.41e-01 1z0xA 220 8.62e-01 1e0eA 55 9.27e-01 1wjcA a.4.10.1 59147 1t56A 216 9.76e-01 a.4.1.9,a.121.1.1 106428,106429 2cg4A 152 1.02e+00 1mixA 206 1.19e+00 a.11.2.1,b.55.1.5 79166,79167 1ku3A 73 1.32e+00 a.4.13.2 73000 1wh8A 111 1.44e+00 1ab4 477 1.76e+00 1ab4 e.11.1.1 43251 1xsvA 113 1.90e+00 1zgwA 139 1.98e+00 1b72B 87 2.00e+00 1akhA a.4.1.1 16001 1af7 274 2.10e+00 1af7 a.58.1.1,c.66.1.8 17928,34203 2ahrA 259 2.14e+00 1j5yA 187 2.17e+00 a.4.5.1,d.94.2.1 71592,71593 1bc5A 269 2.22e+00 1af7 a.58.1.1,c.66.1.8 17929,34204 1etxA 98 2.28e+00 1fipA a.4.1.12 18978 1qb2A 109 2.32e+00 1qb2A a.36.1.1 17125 1g2hA 61 2.48e+00 1g2hA a.4.1.12 60224 1pufB 73 2.51e+00 a.4.1.1 95132 1eg7A 557 2.69e+00 1eg7A c.37.1.10 32241 1wd5A 208 2.70e+00 1p3jA 217 2.78e+00 c.37.1.1,g.41.2.1 94022,94023 1hw5A 210 2.81e+00 2cgpA a.4.5.4,b.82.3.2 16098,28137 1res 43 2.92e+00 1ret a.4.1.2 16023 1nf3A 195 2.99e+00 c.37.1.8 85594 1x2iA 75 2.99e+00 2g7uA 257 3.01e+00 1gqzA 274 3.06e+00 d.21.1.1,d.21.1.1 83311,83312 2ao9A 155 3.10e+00 1ulyA 192 3.21e+00 1vydA 116 3.25e+00 a.3.1.1 108900 1u3eM 174 3.25e+00 d.4.1.3,d.285.1.1 107640,107641 1j75A 67 3.30e+00 a.4.5.19 62673 1z23A 163 3.32e+00 2fx0A 201 4.12e+00 1i6xA 209 4.32e+00 a.4.5.4,b.82.3.2 83673,83674 1l3sA 580 4.42e+00 c.55.3.5,e.8.1.1 84521,84522 1p4wA 99 4.60e+00 a.4.6.2 87783 2g3bA 208 4.81e+00 1s6lA 212 4.91e+00 2csbA 519 4.92e+00 1u4bA 580 5.12e+00 c.55.3.5,e.8.1.1 107664,107665 1sfxA 109 5.21e+00 a.4.5.50 105505 1o6yA 299 5.23e+00 d.144.1.7 81106 1khcA 147 5.34e+00 b.34.9.2 68608 2a2dA 478 5.76e+00 1bwzA 274 5.81e+00 1bwzA d.21.1.1,d.21.1.1 38337,38338 1nk4A 580 5.81e+00 c.55.3.5,e.8.1.1 91923,91924 1wqaA 455 6.14e+00 1lj9A 144 6.23e+00 a.4.5.28 78035 1xk7A 408 6.43e+00 1fmjA 351 6.89e+00 c.37.1.5 59879 1tn3 137 7.05e+00 1htn d.169.1.1 42423 1umwA 237 7.10e+00 d.223.1.2,d.223.1.2 99631,99632 1j9iA 68 7.16e+00 a.6.1.5 71619 1qzzA 374 7.31e+00 a.4.5.29,c.66.1.12 96719,96720 2awiA 317 7.33e+00 2a2cA 478 7.37e+00 1xwl 580 7.52e+00 1xwl c.55.3.5,e.8.1.1 33708,43001 2ffeA 311 7.61e+00 1qw2A 102 7.69e+00 d.249.1.1 96456 2gkeA 274 8.07e+00 1xa3A 437 8.70e+00 2acjA 66 9.07e+00 2g7gA 213 9.17e+00 2cfxA 144 9.63e+00 1t33A 224 9.67e+00 a.4.1.9,a.121.1.1 106295,106296 1dik 874 9.91e+00 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1pk6C 129 9.98e+00 b.22.1.1 94803 1k78A 149 1.00e+01 a.4.1.5,a.4.1.5 68255,68256 1fxjA 331 1.05e+01 1fwyA b.81.1.4,c.68.1.5 28062,34520 2g9iA 249 1.09e+01 1bia 321 1.10e+01 1bia a.4.5.1,b.34.1.1,d.104.1.2 16083,24447,40787 1wdvA 152 1.15e+01 1dxjA 242 1.18e+01 1cnsA d.2.1.1 36244 1kqpA 271 1.26e+01 c.26.2.1 72883 1xnpA 202 1.28e+01 1vaxA 287 1.29e+01 1xn7A 78 1.29e+01 1neq 74 1.31e+01 1neq a.35.1.2 17063 1m45A 148 1.35e+01 a.39.1.5 78598 1furA 467 1.36e+01 1furA a.127.1.1 19403 1s3jA 155 1.38e+01 a.4.5.28 98437 1q77A 138 1.40e+01 c.26.2.4 96023 1cg2A 393 1.43e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 1q4rA 112 1.47e+01 d.58.4.4 95823 1e3aB 560 1.51e+01 1ajqB 1e0gA 48 1.52e+01 1e01A d.7.1.1 37325 1ih8A 271 1.53e+01 2nsyA c.26.2.1 62377 1kblA 873 1.54e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 2aorA 223 1.59e+01 1y5eA 169 1.60e+01 1jkoC 52 1.64e+01 a.4.1.2 66809 1qusA 322 1.64e+01 1ltm d.2.1.6 36991 2g8yA 385 1.65e+01 1nw1A 429 1.65e+01 d.144.1.8 86286 1jbwA 428 1.66e+01 c.59.1.2,c.72.2.2 62860,62861 1f75A 249 1.67e+01 1f75A c.101.1.1 59662 1w2yA 229 1.69e+01 a.204.1.1 109140 1vddA 228 1.73e+01 e.49.1.1 108519 1xngA 268 1.78e+01 1rfzA 168 1.80e+01 a.195.1.1 97411 1jggA 60 1.80e+01 2hddA a.4.1.1 62950 1uuhA 159 1.81e+01 d.169.1.4 100008 1na3A 91 1.82e+01 k.38.1.1 85481 6paxA 133 1.86e+01 6paxA a.4.1.5,a.4.1.5 64758,64759 1zk8A 183 1.88e+01 2ap3A 199 1.88e+01 2c3vA 102 1.89e+01 1ez3A 127 1.90e+01 1dn1B a.47.2.1 17768 1jgsA 138 1.91e+01 a.4.5.28 66683 2g8lA 299 1.92e+01 1t1uA 639 1.92e+01 1ztcA 221 1.94e+01 1my6A 199 1.95e+01 a.2.11.1,d.44.1.1 85232,85233 1mgtA 174 1.96e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1aisB 200 1.97e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1pvgA 418 1.98e+01 d.14.1.3,d.122.1.2 95161,95162 1or7A 194 2.04e+01 a.4.13.2,a.177.1.1 87332,87333 1gnyA 153 2.05e+01 b.18.1.11 65404 1zljA 78 2.06e+01 1zrjA 50 2.06e+01 1k4iA 233 2.08e+01 d.115.1.2 72056 2cdnA 201 2.14e+01 1ru3A 732 2.17e+01 e.26.1.3 97835 1wh5A 80 2.18e+01 1gk9B 557 2.20e+01 1efm 393 2.24e+01 1efcA c.37.1.8 64732 1wovA 250 2.24e+01 2cw8A 537 2.24e+01 1afwA 393 2.33e+01 1afwA c.95.1.1,c.95.1.1 35900,35901 2carA 196 2.38e+01 2az4A 429 2.38e+01 1jznA 135 2.41e+01 d.169.1.1 84262 2fm8A 135 2.44e+01 3kvt 115 2.44e+01 1t1dA d.42.1.2 38642 1j34B 123 2.51e+01 d.169.1.1 84049 1wgvA 124 2.55e+01 1x1nA 524 2.57e+01 1o6dA 163 2.62e+01 c.116.1.3 92567 2a5dA 175 2.68e+01 1fgs 428 2.70e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 1rkqA 282 2.75e+01 c.108.1.10 97621 2a61A 145 2.83e+01 1ci4A 89 2.86e+01 1qckA a.60.5.1 17970 1tc3C 51 2.92e+01 1tc3C a.4.1.2 16025 1lci 550 2.95e+01 1lci e.23.1.1 43349 1b4pA 217 2.98e+01 a.45.1.1,c.47.1.5 83158,83159 1zx4A 192 2.98e+01 1r6uA 437 3.02e+01 c.26.1.1 97163 1r9wA 145 3.09e+01 d.89.1.2 97264 1ef1A 294 3.11e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1r71A 178 3.14e+01 a.4.14.1 104823 1kn1A 160 3.15e+01 a.1.1.3 77455 1uj2A 252 3.17e+01 c.37.1.6 99452 1ui0A 205 3.19e+01 c.18.1.2 99411 1zu1A 127 3.22e+01 1us5A 314 3.27e+01 c.94.1.1 99856 1y8aA 332 3.30e+01 2sak 121 3.31e+01 2sak d.15.5.1 37711 1uch 230 3.35e+01 1uch d.3.1.6 37129 1sek 378 3.42e+01 1sek e.1.1.1 42675 3lzt 129 3.48e+01 3lzt d.2.1.2 36245 1oxkB 134 3.49e+01 c.23.1.1 93691 1ufmA 84 3.53e+01 a.4.5.47 107816 1idrA 136 3.54e+01 1dlyA a.1.1.1 62301 1v4eA 299 3.62e+01 a.128.1.1 100296 1fadA 99 3.64e+01 1fadA a.77.1.2 18428 1p0iA 529 3.64e+01 c.69.1.1 93867 1dusA 194 3.68e+01 1dusA c.66.1.4 34182 2cosA 54 3.70e+01 1l2uA 245 3.79e+01 c.1.2.3 73516 2b0lA 102 3.80e+01 1fseA 74 3.83e+01 1fseA a.4.6.2 60000 1v74B 87 3.91e+01 a.24.20.1 100443 1g55A 343 4.11e+01 1g55A c.66.1.26 34247 1vkiA 181 4.12e+01 d.116.1.1 108664 1y10A 407 4.13e+01 1mucA 373 4.16e+01 1mucA c.1.11.2,d.54.1.1 29236,38880 1cex 214 4.19e+01 1cex c.69.1.30 31285 1lsuA 147 4.25e+01 c.2.1.9 74250 1fjlA 81 4.31e+01 2hddA a.4.1.1 16017 1akhA 61 4.32e+01 1akhA a.4.1.1 15980 1sy7A 715 4.37e+01 1fo8A 343 4.38e+01 1foaA c.68.1.10 59927 1b9mA 265 4.40e+01 1b9mA a.4.5.8,b.40.6.2,b.40.6.2 16118,58938,58939 1dat 174 4.43e+01 2fha a.25.1.1 16677 1zud2 66 4.43e+01 1rz4A 226 4.68e+01 a.4.5.53,a.118.1.18 105131,105132 1ffa 214 4.71e+01 1cex c.69.1.30 31289 1esc 306 4.93e+01 1esc c.23.10.1 31334 1yub 245 4.96e+01 2ercA c.66.1.24 34219 1dbxA 158 4.97e+01 1dbuA d.116.1.1 40928 1qqsA 174 4.97e+01 1nglA b.60.1.1 27143 1j0aA 325 5.10e+01 c.79.1.1 83871 1jksA 294 5.10e+01 d.144.1.7 71710 1vdyA 140 5.11e+01 2cxxA 190 5.13e+01 1dzkA 157 5.17e+01 1obpA b.60.1.1 27096 1gd0A 122 5.19e+01 1dptA d.80.1.3 39834 1vljA 407 5.23e+01 e.22.1.2 108832 1x2mA 64 5.24e+01 1bec 238 5.26e+01 1bec b.1.1.1,b.1.1.2 20627,21561 1zs4A 83 5.26e+01 1mdc 133 5.28e+01 1hmt b.60.1.2 27198 1w3iA 293 5.30e+01 c.1.10.1 109152 1qyrA 252 5.35e+01 c.66.1.24 104657 1xqoA 256 5.42e+01 1gdvA 85 5.43e+01 1ctj a.3.1.1 60458 1z7yA 322 5.45e+01 1ecfA 504 5.45e+01 1ecfB c.61.1.1,d.153.1.1 34053,41820 1f2tB 148 5.47e+01 1f2tB 2culA 232 5.48e+01 2g5dA 422 5.48e+01 1uw4A 91 5.55e+01 d.58.7.4 100071 1cf2O 337 5.64e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 2a1fA 247 5.67e+01 1gvnB 287 5.70e+01 c.37.1.21 76354 1kyqA 274 5.70e+01 c.2.1.11,e.37.1.1 73281,73282 1z7wA 322 5.72e+01 1kl9A 182 5.74e+01 b.40.4.5 72681 1tqnA 486 5.74e+01 a.104.1.1 107238 1hq1A 105 5.77e+01 1dulA a.36.1.1 17120 1lvaA 258 5.82e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1vi9A 299 5.82e+01 c.72.1.5 100750 1mkmA 249 5.82e+01 a.4.5.33,d.110.2.2 79242,79243 1nfp 228 5.83e+01 1nfp c.1.16.2 29555 1vhxA 150 5.86e+01 c.55.3.8 100712 1p1mA 406 5.88e+01 b.92.1.4,c.1.9.9 87696,87697 6gsvA 217 5.88e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1vkmA 297 5.93e+01 c.138.1.1 108670 1ei6A 406 5.93e+01 c.76.1.4 90443 1hcrA 52 6.07e+01 1hcrA a.4.1.2 16020 1l6oA 95 6.08e+01 b.36.1.1 84534 1eu1A 780 6.09e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1jpaA 312 6.14e+01 d.144.1.7 67011 1uocA 289 6.20e+01 c.55.3.9 99686 1l0lA 446 6.21e+01 d.185.1.1,d.185.1.1 84482,84483 2gw6A 123 6.34e+01 1y6uA 70 6.34e+01 1fsgA 233 6.34e+01 1qk3A c.61.1.1 34029 1qd1A 325 6.39e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1vk0A 206 6.51e+01 c.55.3.5 100839 1yg6A 193 6.51e+01 1ip9A 85 6.55e+01 1ip9A d.15.2.2 62638 1x71A 178 6.58e+01 1uhaA 82 6.61e+01 g.3.1.1,g.3.1.1 99395,99396 1e5kA 201 6.65e+01 1fr9A c.68.1.8 34578 1bj7 156 6.65e+01 1bj7 b.60.1.1 27113 1dgwY 93 6.68e+01 1caxB 1i8oA 114 6.76e+01 1ycc a.3.1.1 61979 1howA 373 6.81e+01 1hcl d.144.1.7 41679 2f0aA 98 6.84e+01 1omiA 248 6.85e+01 b.82.3.3,a.4.5.4 87079,87080 1dlwA 116 6.88e+01 1dlyA a.1.1.1 14982 2fzsA 193 6.89e+01 2b0tA 738 6.89e+01 1e4mM 501 6.91e+01 1e70M c.1.8.4 59226 2a5lA 200 6.92e+01 2fa8A 105 6.99e+01 1vi0A 206 6.99e+01 a.4.1.9,a.121.1.1 100720,100721 1rqjA 299 7.02e+01 a.128.1.1 97744 1ryt 190 7.04e+01 1ryt a.25.1.1,g.41.5.1 16646,45245 1huxA 270 7.07e+01 1huxA c.55.1.5 61278 1pht 85 7.09e+01 1ckaA b.34.2.1 24483 2gauA 232 7.14e+01 1j6pA 418 7.18e+01 b.92.1.4,c.1.9.9 77089,77090 2afdA 88 7.20e+01 1b71A 191 7.23e+01 1ryt a.25.1.1,g.41.5.1 16647,45246 1x89A 178 7.25e+01 2aq4A 434 7.27e+01 1w36D 608 7.27e+01 1zndA 174 7.30e+01 1xmkA 79 7.35e+01 1wy0A 342 7.36e+01 1in0A 163 7.42e+01 d.58.49.1,d.58.49.1 83694,83695 1je8A 82 7.43e+01 a.4.6.2 77108 1qy1A 174 7.46e+01 b.60.1.1 96568 1td2A 287 7.53e+01 c.72.1.5 106765 1e2uA 553 7.59e+01 1e1dA e.26.1.1 43362 1vqvA 306 7.61e+01 1t8hA 277 7.61e+01 d.194.1.2 106664 2fcr 173 7.69e+01 1rcf c.23.5.1 31151 1t3lA 337 7.74e+01 b.34.2.1,c.37.1.1 106358,106359 1ct5A 256 7.79e+01 1ct5A c.1.6.2 28663 1va0A 239 7.84e+01 1q8yA 373 7.85e+01 d.144.1.7 96234 1lkoA 191 7.93e+01 a.25.1.1,g.41.5.1 78063,78064 1jv4A 162 7.98e+01 b.60.1.1 67343 1fyeA 229 7.98e+01 1fyeA c.23.16.4 31477 1neeA 138 8.00e+01 d.241.1.1,g.59.1.1 91841,91842 2agcA 162 8.00e+01 1s1iG 119 8.01e+01 i.1.1.1 105181 1m1sA 116 8.07e+01 b.1.11.2 84747 1jhgA 101 8.07e+01 1jhgA a.4.12.1 19009 1fe0A 68 8.07e+01 1cc8A d.58.17.1 39345 1eo1A 124 8.10e+01 1eo1A c.55.5.1 33739 1xd3A 230 8.20e+01 1nsj 205 8.25e+01 1nsj c.1.2.4 28560 1zv1A 65 8.28e+01 2gfnA 209 8.34e+01 1mnaA 298 8.47e+01 c.69.1.22 79322 1lb2B 84 8.53e+01 a.60.3.1 77871 1wxiA 275 8.54e+01 2rspA 124 8.57e+01 2rspB b.50.1.1 26771 1g8kA 825 8.72e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1gntA 553 8.74e+01 e.26.1.1 70290 2ccyA 128 8.77e+01 2ccyA a.24.3.2 16544 1ihgA 370 8.78e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 2g03A 194 8.81e+01 1nofA 383 8.81e+01 b.71.1.2,c.1.8.3 92020,92021 1ixcA 294 8.85e+01 a.4.5.37,c.94.1.1 83764,83765 1qlmA 316 8.87e+01 1qlmA d.147.1.1 41765 2an9A 207 8.97e+01 1yzfA 195 8.97e+01 1s7mA 174 8.98e+01 b.144.1.1 98649