# 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.soe.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 1g6nA 210 4.50e-23 2cgpA a.4.5.4,b.82.3.2 16100,28139 1hw5A 210 5.19e-23 2cgpA a.4.5.4,b.82.3.2 16098,28137 2cgpA 210 7.93e-23 2cgpA a.4.5.4,b.82.3.2 16102,28141 1i6xA 209 2.07e-22 a.4.5.4,b.82.3.2 83673,83674 2gauA 232 9.58e-17 a.4.5.4,b.82.3.2 134894,134895 2pqqA 149 5.47e-16 2fmyA 220 3.59e-15 2cohA 202 5.65e-14 a.4.5.4,b.82.3.2 130677,130678 2zcwA 202 5.65e-14 2h6bA 250 7.25e-14 2z69A 154 1.02e-13 1vp6A 138 1.10e-12 b.82.3.2 113939 1o5lA 213 1.90e-12 b.82.3.2 92506 1ft9A 222 2.33e-12 1ft9A a.4.5.4,b.82.3.1 16107,28131 1cx4A 305 2.50e-12 b.82.3.2,b.82.3.2 59099,59100 1zybA 232 2.57e-12 a.4.5.4,b.82.3.2 125815,125816 1ne6A 283 5.05e-12 b.82.3.2,b.82.3.2 91831,91832 1rl3A 288 1.37e-11 b.82.3.2,b.82.3.2 104975,104976 1rgs 288 1.66e-11 1rgs 3bpzA 202 2.73e-11 1q3eA 207 5.23e-11 b.82.3.2 95669 2ptmA 198 8.49e-11 1u7eB 154 1.23e-10 2bgcA 238 5.22e-10 a.4.5.4,b.82.3.3 128458,128459 1omiA 248 6.73e-10 b.82.3.3,a.4.5.4 87079,87080 1o7fA 469 2.80e-09 a.4.5.31,b.82.3.2,b.82.3.2 81131,81132,81133 2d93A 134 1.32e-04 1cjgA 62 8.72e-02 1pru a.35.1.5 17112 1yhfA 115 1.31e-01 b.82.1.9 123176 1vj2A 126 1.32e-01 b.82.1.10 100796 1lccA 51 1.37e-01 1pru a.35.1.5 17110 2bjcA 62 1.67e-01 a.35.1.5 128620 3cloA 258 1.87e-01 2j59M 168 2.29e-01 1j58A 385 2.81e-01 b.82.1.2 71531 1trrA 107 2.96e-01 1jhgA a.4.12.1 19017 1jhgA 101 3.11e-01 1jhgA a.4.12.1 19009 3ctaA 230 3.40e-01 1efaA 333 3.64e-01 1tlfA a.35.1.5,c.93.1.1 17106,35691 2fbhA 146 9.17e-01 a.4.5.28 133245 2dbbA 151 9.47e-01 3bj6A 152 1.09e+00 1e79H 146 1.10e+00 1e79H a.2.10.1,b.93.1.1 15721,28438 1dulA 69 1.18e+00 1dulA a.36.1.1 17121 1h8eH 146 1.20e+00 1e79H b.93.1.1 60757 1hq1A 105 1.52e+00 1dulA a.36.1.1 17120 1rp3A 239 1.80e+00 a.4.13.1,a.4.13.2,a.177.1.1 97678,97679,97680 2h09A 155 1.84e+00 2b0lA 102 1.84e+00 a.4.5.66 127641 2bkkA 264 1.88e+00 1rcsA 105 1.90e+00 1jhgA a.4.12.1 19025 3deuA 166 1.95e+00 1m6kA 251 2.20e+00 e.3.1.1 78695 1bw6A 56 2.22e+00 1bw6A a.4.1.7 16052 1yioA 208 2.23e+00 a.4.6.2,c.23.1.1 123326,123327 2d40A 354 2.39e+00 1cauA 181 2.39e+00 1dgwA b.82.1.2 28102 2uuqA 414 2.49e+00 1j7lA 264 2.54e+00 d.144.1.6 62697 3bghA 236 2.61e+00 1dgwA 178 2.62e+00 1dgwA b.82.1.2 28090 1j7iA 264 2.68e+00 1j7iA d.144.1.6 62694 2jn6A 97 2.84e+00 2phlA 397 2.85e+00 1dgwA b.82.1.2,b.82.1.2 28082,28083 2p4oA 306 3.11e+00 1qgpA 77 3.26e+00 1qbjA a.4.5.19 16158 2cavA 445 3.33e+00 1dgwA b.82.1.2,b.82.1.2 28094,28095 1qbjA 81 3.42e+00 1qbjA a.4.5.19 16155 1hlvA 131 3.48e+00 a.4.1.7,a.4.1.7 65854,65855 1l0oC 243 4.06e+00 a.4.13.2 73405 1u8bA 133 4.09e+00 1zpsA 138 4.61e+00 b.168.1.1 125473 1jjgA 102 4.63e+00 b.40.4.5 71696 1mgtA 174 4.81e+00 1mgtA a.4.2.1,c.55.7.1 16078,33753 1xkzA 255 4.87e+00 e.3.1.1 115426 2b9uA 176 5.19e+00 1od5A 492 6.18e+00 b.82.1.2,b.82.1.2 86832,86833 2d5fA 493 6.18e+00 3bpvA 138 6.27e+00 2j7tA 302 6.94e+00 1zgwA 139 7.07e+00 1ku3A 73 7.25e+00 a.4.13.2 73000 2dx0A 138 7.59e+00 1qzzA 374 8.57e+00 a.4.5.29,c.66.1.12 96719,96720 1wpkA 146 8.95e+00 2rn7A 108 9.08e+00 1khxA 227 9.14e+00 b.26.1.1 68631 2o3fA 111 9.38e+00 2ethA 154 9.69e+00 a.4.5.28 132358 1danT 80 9.82e+00 1boy b.1.2.1 21953 1viuA 203 1.00e+01 d.113.1.1 100771 2bnmA 198 1.02e+01 a.35.1.3,b.82.1.10 128835,128836 2ao9A 155 1.04e+01 a.4.1.17 127069 3bkbA 377 1.05e+01 1k3sA 113 1.12e+01 d.198.1.1 68120 2qjvA 270 1.15e+01 1ic8A 194 1.22e+01 a.4.1.1,a.35.1.1 76740,76741 2e9qA 459 1.24e+01 1fs0E 138 1.24e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 2ay1A 394 1.24e+01 1ajsA c.67.1.1 34357 2ea7A 434 1.28e+01 1aqt 138 1.28e+01 1aqt 1in4A 334 1.29e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 2e18A 257 1.31e+01 2cxkA 95 1.35e+01 b.1.18.1 131006 1in6A 334 1.36e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1fxzA 476 1.40e+01 b.82.1.2,b.82.1.2 65059,65060 1sur 215 1.42e+01 1sur 1surA 215 1.42e+01 c.26.2.2 31620 1a04A 215 1.44e+01 1a04A a.4.6.2,c.23.1.1 16234,31089 2dg7A 195 1.47e+01 1upqA 123 1.48e+01 b.55.1.1 113392 1utxA 66 1.49e+01 a.35.1.3 108034 2qgnA 322 1.50e+01 1xd7A 145 1.56e+01 a.4.5.55 109566 1ee8A 266 1.61e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 2bcjB 340 1.62e+01 b.69.4.1 128289 1u2wA 122 1.68e+01 a.4.5.5 119487 2dkfA 431 1.71e+01 1lj9A 144 1.73e+01 a.4.5.28 78035 1d0hA 469 1.74e+01 1a8d b.29.1.6,b.42.4.2 24265,25610 1mt6A 280 1.77e+01 b.76.2.1,b.85.7.1 79446,79447 1hcxA 127 1.78e+01 b.109.1.1 65800 2b8mA 117 1.78e+01 b.82.1.18 128092 1diwA 441 1.79e+01 1a8d b.29.1.6,b.42.4.2 24264,25609 1q1hA 110 1.81e+01 a.4.5.41 95580 1kvkA 395 1.84e+01 d.14.1.5,d.58.26.3 73060,73061 1cnuA 137 1.89e+01 1cof d.109.1.2 40862 1hcrA 52 1.89e+01 1hcrA a.4.1.2 16020 2yvdA 431 1.90e+01 1qrzA 246 1.95e+01 5ptp b.47.1.2 26366 1je8A 82 1.97e+01 a.4.6.2 77108 2gakA 391 2.00e+01 1hw7A 255 2.01e+01 1i7fA d.193.1.1 61297 2dtr 226 2.04e+01 1bi0 3ckdA 312 2.06e+01 2d1hA 109 2.10e+01 a.4.5.50 131125 1a8d 452 2.14e+01 1a8d 1a8dA 452 2.14e+01 b.29.1.6,b.42.4.2 24262,25607 1mdc 133 2.15e+01 1hmt 2e52A 300 2.16e+01 1de4C 640 2.17e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1fx7A 230 2.19e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 60088,60089,60090 1c3hA 137 2.21e+01 b.22.1.1 90405 1mdcA 131 2.26e+01 b.60.1.2 27198 1iz6A 138 2.28e+01 b.34.5.2,b.40.4.5 76976,76977 2i7pA 362 2.35e+01 1gvmA 136 2.40e+01 b.109.1.1 70612 1h3iA 293 2.41e+01 b.76.2.1,b.85.7.1 76635,76636 1gotB 340 2.49e+01 1tbgA b.69.4.1 27648 2qf2A 624 2.54e+01 1qs2A 401 2.56e+01 1qs1A d.166.1.1,d.166.1.1 42268,42269 1h8vA 218 2.61e+01 2nlrA b.29.1.11 60795 1xahA 354 2.62e+01 2pw4A 188 2.66e+01 3bruA 222 2.69e+01 2fqpA 97 2.72e+01 1hs7A 97 2.78e+01 1hs7A a.47.2.1 61236 2f4iA 197 2.78e+01 b.40.11.1 132923 3dczA 207 2.82e+01 1ukkA 142 2.84e+01 d.227.1.1 99491 3bqxA 150 2.86e+01 1e2xA 243 2.88e+01 1e2xA a.4.5.6,a.78.1.1 16113,18443 2v95A 371 2.88e+01 2pexA 153 2.91e+01 2h0bA 184 2.93e+01 3bddA 142 2.96e+01 1ez3A 127 2.97e+01 1dn1B a.47.2.1 17768 2a0jA 149 2.99e+01 1r69 69 2.99e+01 1r69 1r69A 69 2.99e+01 a.35.1.2 17028 1r1uA 106 3.03e+01 a.4.5.5 104771 2om6A 235 3.04e+01 1boy 219 3.05e+01 1boy 1khbA 625 3.06e+01 c.91.1.1,c.109.1.1 68606,68607 1a0rB 340 3.07e+01 1tbgA b.69.4.1 27658 2pfwA 116 3.08e+01 2jrnA 163 3.11e+01 2hq2A 354 3.12e+01 e.62.1.1 136656 1m4iA 181 3.16e+01 d.108.1.1 74457 2qenA 350 3.18e+01 1b1bA 140 3.19e+01 1bi0 a.4.5.24,a.76.1.1 16215,18421 1pmi 440 3.20e+01 1pmi 1pmiA 440 3.20e+01 b.82.1.3 28114 2o38A 120 3.20e+01 2g7uA 257 3.22e+01 1iazA 179 3.25e+01 1iazA b.97.1.1 62131 2ictA 94 3.25e+01 1r8mE 203 3.26e+01 a.118.3.1 97242 1v30A 124 3.29e+01 d.269.1.1 113496 2coiA 386 3.30e+01 1khiA 176 3.35e+01 b.34.5.2,b.40.4.5 77408,77409 1br0A 120 3.37e+01 a.47.2.1 17772 1ue1A 164 3.42e+01 b.40.4.3 99243 2p8gA 162 3.45e+01 1rqbA 539 3.46e+01 a.5.7.2,c.1.10.5 105057,105058 1tbgA 340 3.46e+01 1tbgA b.69.4.1 27649 1pbv 195 3.47e+01 1pbv 1pbvA 195 3.47e+01 a.118.3.1 19179 2ofyA 86 3.49e+01 2dtrA 226 3.53e+01 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 2hft 218 3.54e+01 1boy 2hftA 218 3.54e+01 b.1.2.1,b.1.2.1 21951,21952 1ulyA 192 3.57e+01 a.4.5.58 113297 1i1gA 141 3.60e+01 a.4.5.32,d.58.4.2 65982,65983 1t16A 427 3.62e+01 f.4.3.4 106242 1jkoC 52 3.68e+01 a.4.1.2 66809 1oa2A 218 3.70e+01 b.29.1.11 86721 2cu1A 103 3.70e+01 d.15.2.2 130802 3pmgA 561 3.70e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 2rckA 225 3.72e+01 2infA 359 3.77e+01 2b5tI 432 3.80e+01 e.1.1.1 127905 2r1jL 68 3.81e+01 1h09A 338 3.84e+01 b.109.1.1,c.1.8.8 83420,83421 1rwiA 270 3.86e+01 b.68.9.1 97987 1adrA 76 3.88e+01 a.35.1.2 17042 2ggtA 164 3.90e+01 c.47.1.10 135156 2a61A 145 3.91e+01 a.4.5.28 126187 2a6cA 83 3.91e+01 a.35.1.13 126236 1hw1A 239 3.97e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 3bnwA 181 3.97e+01 1o8vA 134 3.97e+01 b.60.1.2 86680 2ch9A 131 3.98e+01 1ftrA 296 4.00e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1qadA 111 4.01e+01 1qadA d.93.1.1 40498 1r8sE 203 4.02e+01 a.118.3.1 97248 2ejxA 139 4.08e+01 1i7fA 292 4.13e+01 1i7fA d.193.1.1 61888 2f01A 127 4.18e+01 b.61.1.1 132647 2uwqA 86 4.20e+01 1eyqA 222 4.20e+01 1eypA d.36.1.1 38534 1z6jT 211 4.22e+01 b.1.2.1,b.1.2.1 124527,124528 1gkrA 458 4.22e+01 b.92.1.3,c.1.9.6 70251,70252 1fseA 74 4.27e+01 1fseA a.4.6.2 60000 3cjnA 162 4.31e+01 3bk2A 562 4.34e+01 2e5eA 101 4.36e+01 1g55A 343 4.41e+01 1g55A c.66.1.26 34247 4matA 278 4.47e+01 1c24A d.127.1.1 41150 2fupA 168 4.49e+01 a.47.5.1 134184 2qikA 285 4.54e+01 2cro 71 4.57e+01 1r69 2croA 71 4.57e+01 a.35.1.2 17038 1umqA 81 4.63e+01 a.4.1.12 99625 2nruA 307 4.66e+01 2hu5A 582 4.72e+01 b.69.7.2,c.69.1.33 136763,136764 1jkmA 358 4.73e+01 1jkmA c.69.1.2 34633 2pia 321 4.75e+01 2pia 2piaA 321 4.75e+01 b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 2uxqA 402 4.83e+01 1h30A 422 4.87e+01 b.29.1.4,b.29.1.4 76604,76605 1dgfA 497 4.87e+01 1cf9A e.5.1.1 42782 2oibA 301 4.89e+01 1h8gA 95 4.92e+01 b.109.1.1 65735 3c7bB 366 4.93e+01 1dghB 498 4.95e+01 1cf9A e.5.1.1 42791 1c24A 263 4.95e+01 1c24A d.127.1.1 41148 1xnzA 264 4.95e+01 d.127.1.1 115673 2b5aA 77 4.96e+01 a.35.1.3 127882 1dn1B 267 5.01e+01 1dn1B a.47.2.1 17771 2dtvA 397 5.03e+01 1lliA 92 5.03e+01 1lmb3 a.35.1.2 17025 1kpgA 287 5.04e+01 c.66.1.18 68735 1smtA 122 5.08e+01 1smtA a.4.5.5 16109 2qkoA 215 5.15e+01 1t4wA 196 5.18e+01 b.2.5.2 106427 1h9oA 112 5.20e+01 1qadA d.93.1.1 60837 1w3fA 315 5.21e+01 1lwdA 413 5.23e+01 c.77.1.1 78265 1sfxA 109 5.27e+01 a.4.5.50 105505 2aacA 177 5.30e+01 2arcA b.82.4.1 28150 2z1yA 397 5.34e+01 1du6A 64 5.35e+01 1akhA a.4.1.1 16002 2ev0A 142 5.42e+01 a.4.5.24,a.76.1.1 132413,132414 1vpbA 451 5.44e+01 d.283.1.1 113950 1wljA 189 5.46e+01 c.55.3.5 114734 1u5dA 108 5.47e+01 b.55.1.1 119536 1qfoA 119 5.53e+01 1qfoA b.1.1.1 19708 1lm5A 214 5.58e+01 d.211.2.1 74029 1k78A 149 5.61e+01 a.4.1.5,a.4.1.5 68255,68256 1hi9A 274 5.64e+01 1hi9A c.99.1.1 61063 1kyzA 365 5.66e+01 a.4.5.29,c.66.1.12 73312,73313 1luqA 127 5.69e+01 b.61.1.1 91128 2fvkA 559 5.76e+01 b.92.1.3,c.1.9.6 134204,134205 3biqA 467 5.76e+01 2z0aA 79 5.79e+01 1awe 130 5.89e+01 1awe 2nyxA 168 5.90e+01 1axiB 236 5.93e+01 1axiB b.1.2.1,b.1.2.1 21997,21998 2i8gA 151 5.96e+01 1dfx 125 6.00e+01 1dfx 1pdr 99 6.08e+01 1pdr 2zg5A 397 6.10e+01 1xuvA 178 6.14e+01 d.129.3.5 116069 1s3jA 155 6.14e+01 a.4.5.28 98437 1nf3C 128 6.24e+01 b.36.1.1 85596 2g5fA 450 6.25e+01 d.161.1.1 134654 2genA 197 6.35e+01 a.4.1.9,a.121.1.1 135062,135063 1zyoA 191 6.36e+01 1b8iB 63 6.41e+01 1akhA a.4.1.1 16011 1i39A 225 6.45e+01 1ekeA c.55.3.1 61585 1f5tA 121 6.46e+01 1bi0 a.4.5.24,a.76.1.1 16203,18409 2np5A 203 6.46e+01 a.4.1.9,a.121.1.1 138424,138425 5csmA 256 6.48e+01 5csmA a.130.1.2 19494 2cg4A 152 6.55e+01 a.4.5.32,d.58.4.2 130417,130418 2nxvA 249 6.55e+01 2z15A 130 6.55e+01 1lnwA 147 6.57e+01 a.4.5.28 78104 1be9A 119 6.61e+01 1pdr b.36.1.1 24774 2opkA 112 6.71e+01 1j3mA 129 6.74e+01 d.129.7.1 103836 2bf6A 449 6.85e+01 1v5tA 90 6.86e+01 d.15.1.1 108385 1rzsA 61 6.90e+01 a.35.1.2 105139 1vyoA 128 7.04e+01 1m3iA 471 7.14e+01 f.9.1.1 91178 1qs1A 462 7.16e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1hd2A 161 7.16e+01 c.47.1.10 60962 1fxkC 133 7.27e+01 1fxkC a.2.5.1 15702 1c0wA 225 7.27e+01 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16211,18417,24455 1fipA 98 7.29e+01 1fipA a.4.1.12 18980 2d0oA 610 7.32e+01 c.8.6.1,c.55.1.6,c.55.1.6 131075,131076,131077 1zylA 328 7.32e+01 1orvA 728 7.36e+01 b.70.3.1,c.69.1.24 87354,87355 1kd6A 179 7.41e+01 b.97.1.1 68459 3cewA 125 7.43e+01 1j5yA 187 7.44e+01 a.4.5.1,d.94.2.1 71592,71593 2qtwB 546 7.44e+01 1bi0 226 7.45e+01 1bi0 1ddjA 247 7.49e+01 5ptp b.47.1.2 26362 2gpiA 91 7.51e+01 2q12A 265 7.54e+01 3bb6A 127 7.54e+01 1kxu 333 7.55e+01 1jkw 1kxuA 333 7.55e+01 a.74.1.1,a.74.1.1 18358,18359 2qtqA 213 7.57e+01 1cuk 203 7.59e+01 1hjp 1cukA 203 7.59e+01 a.5.1.1,a.60.2.1,b.40.4.2 16273,17946,25265 2hnlA 225 7.60e+01 1d2eA 397 7.65e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 2f4qA 346 7.66e+01 1nkqA 259 7.66e+01 d.177.1.1 103862 1poiB 260 7.68e+01 1poiB c.124.1.3 34155 2arcA 164 7.69e+01 2arcA b.82.4.1 28148 3ba3A 145 7.69e+01 1ij8A 128 7.70e+01 b.61.1.1 62480 2p9rA 102 7.79e+01 1nqnA 122 7.79e+01 b.61.1.1 86042 1b72B 87 7.80e+01 1akhA a.4.1.1 16001 1tfe 145 7.85e+01 1tfe 1tfeA 145 7.85e+01 d.43.1.1 38680 3bs3A 76 7.89e+01 2ddhA 661 7.91e+01 a.29.3.2,a.29.3.2,e.6.1.2 131394,131395,131396 2i9dA 217 7.92e+01 1pufB 73 7.93e+01 a.4.1.1 95132 1pp7U 131 7.95e+01 a.4.5.44 94973