# 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 1xngA 268 2.54e-03 1d2eA 397 1.59e-02 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25701,25741,32136 1cgt 684 5.38e-02 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21815,22484,27722,28709 1gpmA 525 1.39e-01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 2a2pA 129 3.38e-01 1aipE 405 4.54e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1hoe 74 5.24e-01 1hoe b.5.1.1 22833 1exmA 405 6.16e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1dq3A 454 6.21e-01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1w2tA 432 6.62e-01 1aipA 405 6.64e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1zn8A 180 6.82e-01 1ok0A 74 6.91e-01 b.5.1.1 93191 1rzfL 213 6.94e-01 b.1.1.1,b.1.1.2 98152,98153 1rsy 152 7.18e-01 1rsy b.7.1.2 23192 1nezG 128 8.09e-01 b.1.1.1 85592 1eft 405 8.19e-01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 1f6fB 210 8.75e-01 1axiB b.1.2.1,b.1.2.1 22033,22034 1uypA 432 9.43e-01 b.29.1.19,b.67.2.3 100176,100177 1yhfA 115 9.59e-01 1pmzA 86 1.01e+00 a.39.1.10 104195 1s0uA 408 1.09e+00 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 1f7dA 136 1.13e+00 1dun b.85.4.1 28353 1oaqL 120 1.21e+00 b.1.1.1 92708 2bm3A 166 1.21e+00 3ait 74 1.25e+00 1hoe b.5.1.1 22835 1bynA 128 1.30e+00 1rsy b.7.1.2 23193 1kk1A 410 1.33e+00 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1tif 78 1.33e+00 1tif d.15.8.1 37836 1zczA 464 1.45e+00 2b59A 187 1.48e+00 1j83A 180 1.50e+00 b.18.1.12 66430 1a6vL 110 1.56e+00 1mfa b.1.1.1 20256 1bb8 71 1.66e+00 2bb8 d.10.1.1 37478 1adqL 213 1.68e+00 8fabA b.1.1.1,b.1.1.2 20272,21272 1efcA 393 1.72e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25680,25720,32113 1ot1A 686 1.73e+00 b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 87392,87393,87394,87395 1bqhG 129 1.83e+00 1cd8 b.1.1.1 19715 1y7rA 133 1.85e+00 1uldA 150 1.89e+00 b.29.1.3 99545 1b69A 69 2.19e+00 2bb8 d.10.1.1 37479 1m6yA 301 2.22e+00 a.60.13.1,c.66.1.23 78716,78717 1dutA 133 2.31e+00 1dun b.85.4.1 28355 2c78A 405 2.38e+00 1f5aA 513 2.41e+00 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39337,75835,75836 1qmeA 702 2.48e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1ha3A 405 2.53e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1nqeA 594 2.54e+00 f.4.3.3 86027 1q79A 514 2.54e+00 a.160.1.1,d.218.1.3,d.58.16.1 104548,104549,104550 2bb8 71 2.56e+00 2bb8 d.10.1.1 37480 1art 396 2.65e+00 1ajsA c.67.1.1 34285 1a6uL 108 2.89e+00 1mfa b.1.1.1 20254 1ariA 396 2.96e+00 1ajsA c.67.1.1 34331 1pamA 686 2.98e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 2gpzA 111 2.98e+00 2a8lA 420 3.08e+00 1cxlA 686 3.16e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21829,22498,27736,28723 1goh 639 3.23e+00 1gof b.1.18.2,b.18.1.1,b.69.1.1 21809,23711,27633 2ait 74 3.40e+00 1hoe b.5.1.1 22837 1ih8A 271 3.51e+00 2nsyA c.26.2.1 62377 1u0tA 307 3.59e+00 e.52.1.1 107567 1nsyA 271 3.62e+00 2nsyA c.26.2.1 31614 2nsyA 271 3.64e+00 2nsyA c.26.2.1 31612 1cd9B 215 3.73e+00 1cto b.1.2.1,b.1.2.1 22041,22042 1sh0A 510 3.88e+00 e.8.1.4 98876 1q2yA 140 3.96e+00 d.108.1.1 95655 1gof 639 4.02e+00 1gof b.1.18.2,b.18.1.1,b.69.1.1 21807,23709,27631 1k3iA 656 4.04e+00 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1d3cA 686 4.22e+00 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21827,22496,27734,28721 1b25A 619 4.37e+00 1b25A a.110.1.1,d.152.1.1 19044,41796 2cokA 113 4.37e+00 1efuA 385 4.45e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25682,25722,32115 1f39A 101 4.48e+00 1umuA b.87.1.1 28386 1kqpA 271 4.57e+00 c.26.2.1 72883 1a65A 504 4.64e+00 1a65A b.6.1.3,b.6.1.3,b.6.1.3 23148,23149,23150 1ifrA 121 4.77e+00 b.1.16.1 71203 1suwA 249 4.89e+00 e.52.1.1 106027 1qisA 396 5.04e+00 1ajsA c.67.1.1 34284 1wh0A 134 5.06e+00 1ahxA 396 5.09e+00 1ajsA c.67.1.1 34293 2bu3A 254 5.18e+00 2b43A 526 5.24e+00 1a6wL 109 5.30e+00 1mfa b.1.1.1 20252 1qtfA 246 5.31e+00 1agjA b.47.1.1 25830 1po5A 476 5.35e+00 a.104.1.1 94963 1kv9A 668 5.37e+00 a.3.1.6,b.70.1.1 73056,73057 1ekgA 127 5.41e+00 1dlxA d.82.2.1 40021 1cqqA 180 5.62e+00 1cqqA b.47.1.4 26422 2ak5A 64 5.90e+00 1ve6A 582 5.90e+00 2a9mL 110 6.01e+00 1zljA 78 6.08e+00 1r26A 125 6.10e+00 c.47.1.1 96847 1jmmA 377 6.18e+00 b.30.6.1 71749 1tzyD 103 6.22e+00 a.22.1.1 107533 1p5hA 428 6.49e+00 c.123.1.1 87802 1aoiB 87 6.60e+00 1aoiB a.22.1.1 16470 1aoiF 87 6.60e+00 1aoiB a.22.1.1 16471 1ru4A 400 6.94e+00 b.80.1.9 97836 1svpA 161 7.03e+00 1svpA b.47.1.3 26384 2fg9A 178 7.34e+00 1b96A 244 7.42e+00 1rvaA c.52.1.2 33268 1uvzA 119 7.45e+00 1vckA 115 7.64e+00 1wcdJ 441 7.66e+00 1lucB 324 7.66e+00 1lucA c.1.16.1 29548 2gjgA 248 7.71e+00 1wy5A 317 7.73e+00 1louA 101 7.78e+00 1ris d.58.14.1 39323 8fabA 212 7.97e+00 8fabA b.1.1.1,b.1.1.2 19772,20882 1aorA 605 8.16e+00 1b25A a.110.1.1,d.152.1.1 19042,41794 1rvaA 244 8.17e+00 1rvaA c.52.1.2 33240 1z0sA 278 8.21e+00 1nkqA 259 8.48e+00 d.177.1.1 103862 1b97A 244 8.76e+00 1rvaA c.52.1.2 33252 1hq3D 103 8.82e+00 1aoiB a.22.1.1 16464 1wdcB 156 8.90e+00 1wdcB a.39.1.5 17302 2fhxA 246 8.97e+00 1lv7A 257 9.31e+00 c.37.1.20 78232 1odkA 235 9.39e+00 c.56.2.1 86863 1spa 396 9.41e+00 1ajsA c.67.1.1 34291 1b94A 244 9.63e+00 1rvaA c.52.1.2 33250 1kx5B 102 9.64e+00 a.22.1.1 77594 1wqsA 173 9.72e+00 1wruA 379 9.73e+00 1obdA 306 9.81e+00 d.143.1.1 86767 1j9bA 141 9.85e+00 c.47.1.12 66459 2g6fX 59 1.02e+01 1hlvA 131 1.03e+01 a.4.1.7,a.4.1.7 65854,65855 1asg 396 1.05e+01 1ajsA c.67.1.1 34335 1yu0A 381 1.06e+01 1x8hA 228 1.06e+01 1zeqX 84 1.07e+01 1ars 396 1.07e+01 1ajsA c.67.1.1 34287 1jj2E 177 1.08e+01 1ffk1 d.141.1.1,d.141.1.1 63089,63090 1s72E 178 1.12e+01 d.141.1.1,d.141.1.1 105323,105324 1avyA 74 1.15e+01 1avyB h.1.17.1 45656 1ofdA 1520 1.17e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1bymA 97 1.19e+01 1bi0 b.34.1.2 24458 1v70A 105 1.20e+01 1vk3A 615 1.21e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 2bl0C 142 1.23e+01 1fs0E 138 1.24e+01 1aqt a.2.10.1,b.93.1.1 59997,59998 1w4vA 119 1.24e+01 1w85I 49 1.25e+01 1wlyA 333 1.25e+01 1bjmA 216 1.25e+01 8fabA b.1.1.1,b.1.1.2 20524,21460 1g3kA 174 1.26e+01 1nedA d.153.1.4 41989 1csbB 205 1.26e+01 1theB 1wzoA 246 1.26e+01 1sy6A 204 1.27e+01 b.1.1.4,b.1.1.4 106111,106112 1zvhA 134 1.28e+01 2fs2A 151 1.28e+01 1j7xA 302 1.30e+01 c.14.1.2 66425 1qyaA 307 1.34e+01 d.21.1.2,d.21.1.2 104653,104654 1ptmA 329 1.34e+01 c.77.1.3 95104 1ut7A 171 1.36e+01 b.143.1.1 99906 1y8tA 324 1.39e+01 1theB 260 1.39e+01 1theB d.3.1.1 37057 1ebdC 41 1.47e+01 1ebdC a.9.1.1 16355 1hm2A 700 1.49e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 61083,61084,61085 1ebfA 358 1.53e+01 1ebuA c.2.1.3,d.81.1.2 30033,39948 1x0vA 354 1.53e+01 1llwA 1520 1.56e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1v8hA 107 1.56e+01 1vk6A 269 1.59e+01 d.113.1.4,d.113.1.4 100851,100852 2as0A 396 1.59e+01 1aa0 113 1.59e+01 1aa0 h.1.17.1 45659 1avyB 74 1.61e+01 1avyB h.1.17.1 45657 1mylA 53 1.63e+01 1bazA a.43.1.1 17427 1v6tA 255 1.66e+01 1eonA 245 1.66e+01 1rvaA c.52.1.2 33238 1kb0A 677 1.66e+01 a.3.1.6,b.70.1.1 68378,68379 1vjgA 218 1.66e+01 c.23.10.6 100810 1vsd 152 1.66e+01 1cxqA c.55.3.2 33625 1emsA 440 1.69e+01 1emsA d.13.1.1,d.160.1.1 37520,42086 1kk8B 139 1.70e+01 a.39.1.5 77430 1qtnA 164 1.70e+01 1pauA c.17.1.1 30999 1qxmA 300 1.71e+01 b.42.2.1,b.42.2.1 96533,96534 2a8jA 420 1.71e+01 1vqoE 178 1.72e+01 1nlqA 108 1.77e+01 b.121.3.1 85853 1tuaA 191 1.81e+01 d.51.1.1,d.51.1.1 107321,107322 1kapP 479 1.83e+01 1sat b.80.7.1,d.92.1.6 28012,40298 1avyC 74 1.84e+01 1avyB h.1.17.1 45658 2f9lA 199 1.90e+01 1zvyA 136 1.90e+01 1psuA 140 1.90e+01 d.38.1.5 88285 1j1bA 420 1.92e+01 d.144.1.7 90758 1idsA 207 1.92e+01 1avmA a.2.11.1,d.44.1.1 15722,38730 1a48 306 1.92e+01 1a48 d.143.1.1 41590 1hxmA 229 1.92e+01 1hxmA b.1.1.1,b.1.1.2 61367,61368 1pvyA 227 1.93e+01 d.115.1.2 95195 2azwA 148 1.94e+01 1mvfA 135 1.94e+01 b.1.1.1 85141 1k07A 263 1.94e+01 d.157.1.1 77218 1sx5A 244 1.97e+01 c.52.1.2 99023 1yb3A 175 1.97e+01 1cxqA 162 1.98e+01 1cxqA c.55.3.2 33621 1qdlB 195 1.99e+01 1qdlB c.23.16.1 31437 1a5v 162 1.99e+01 1cxqA c.55.3.2 33629 1l1eA 287 2.04e+01 c.66.1.18 73454 1f89A 291 2.06e+01 d.160.1.1 64988 1ml9A 302 2.08e+01 b.85.7.1 79282 1hup 141 2.09e+01 1rtm1 d.169.1.1,h.1.1.1 42354,45422 1te5A 257 2.09e+01 d.153.1.1 106795 1pguA 615 2.12e+01 b.69.4.1,b.69.4.1 88069,88070 1asu 162 2.12e+01 1cxqA c.55.3.2 33626 1aqt 138 2.14e+01 1aqt a.2.10.1,b.93.1.1 15718,28435 1j8mF 297 2.15e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1eo9A 209 2.16e+01 3pchA b.3.6.1 22731 1snnA 227 2.17e+01 d.115.1.2 105821 1mdiA 105 2.20e+01 1erv c.47.1.1 32755 1i8nA 126 2.21e+01 1i8nA g.10.1.2 61976 1m4vA 204 2.22e+01 b.40.2.2,d.15.6.1 74459,74460 1v1hA 103 2.24e+01 b.83.1.1,h.1.17.1 108243,108244 1arhA 396 2.24e+01 1ajsA c.67.1.1 34321 1jm1A 204 2.25e+01 b.33.1.1 71745 1ox3A 109 2.27e+01 h.1.17.1 93668 1xi1A 575 2.32e+01 1suh 146 2.32e+01 1edhA b.1.6.1 22206 1theA 260 2.32e+01 1theB d.3.1.1 37056 1vr8A 142 2.33e+01 1cjsA 219 2.35e+01 1cjsA e.24.1.1 43354 1rz4A 226 2.36e+01 a.4.5.53,a.118.1.18 105131,105132 1edhA 226 2.37e+01 1edhA b.1.6.1,b.1.6.1 22198,22199 1s3cA 141 2.40e+01 1xzoA 174 2.42e+01 1mvwB 145 2.47e+01 i.15.1.1 79524 1j8yF 297 2.55e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1id3B 102 2.58e+01 a.22.1.1 66113 1id0A 152 2.60e+01 d.122.1.3 66111 1fe0A 68 2.61e+01 1cc8A d.58.17.1 39345 2d13A 227 2.63e+01 1ub3A 220 2.64e+01 c.1.10.1 88395 1cp2A 269 2.64e+01 1cp2A c.37.1.10 32269 1plc 99 2.65e+01 1plc b.6.1.1 22846 1scmB 145 2.65e+01 1wdcB a.39.1.5 17304 1hfuA 503 2.66e+01 b.6.1.3,b.6.1.3,b.6.1.3 65827,65828,65829 1nkiA 135 2.67e+01 d.32.1.2 91941 1oivA 191 2.68e+01 c.37.1.8 93076 2pdd 43 2.69e+01 1ebdC a.9.1.1 16358 1bssA 244 2.69e+01 1rvaA c.52.1.2 33256 1yu2A 381 2.70e+01 1ugpB 226 2.70e+01 b.34.4.4 107832 1mhnA 59 2.74e+01 b.34.9.1 84964 1gmyA 261 2.76e+01 d.3.1.1 76236 1vkyA 347 2.76e+01 e.53.1.1 108696 2fp7B 172 2.78e+01 1xer 103 2.88e+01 1xer d.58.1.3 38990 1l9fA 389 2.89e+01 c.3.1.2,d.16.1.3 73716,73717 1wmzA 140 2.92e+01 d.169.1.1 109422 1vr0A 247 2.95e+01 1eblB 317 2.95e+01 1hn9A c.95.1.2,c.95.1.2 35975,35976 1eny 268 2.97e+01 1eny c.2.1.2 29910 2a7yA 83 3.00e+01 1brlB 324 3.01e+01 1lucA c.1.16.1 29554 1caxB 184 3.01e+01 1caxB b.82.1.2 28105 1jj2S 119 3.04e+01 1ffkQ b.34.5.1 63104 1uwvA 433 3.05e+01 b.40.4.12,c.66.1.40 100128,100129 1s72T 120 3.05e+01 b.34.5.1 105339 2pcy 99 3.06e+01 1plc b.6.1.1 22849 2rhe 114 3.10e+01 8fabA b.1.1.1 20523 1cq3A 233 3.11e+01 1cq3A b.27.1.1 23923 1ni5A 433 3.16e+01 c.26.2.5,d.229.1.1 80533,80534 1yu4A 381 3.16e+01 2rveA 244 3.16e+01 1rvaA c.52.1.2 33283 1el5A 389 3.16e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1hlcA 129 3.18e+01 1c1lA b.29.1.3 24208 1oixA 191 3.18e+01 1i6uA 130 3.19e+01 d.140.1.1 61850 1xcbA 211 3.21e+01 a.4.5.38,c.2.1.12 109552,109553 1e19A 314 3.21e+01 1b7bA c.73.1.1 34967 1czfA 362 3.22e+01 1czfA b.80.1.3 28031 1lba 146 3.28e+01 1lba d.118.1.1 41062 1hn9A 317 3.30e+01 1hn9A c.95.1.2,c.95.1.2 35977,35978 1wu7A 434 3.36e+01 1hnjA 317 3.37e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1yukA 103 3.40e+01 1kv7A 488 3.41e+01 b.6.1.3,b.6.1.3,b.6.1.3 68873,68874,68875 1cojA 212 3.43e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1squA 155 3.45e+01 d.252.1.1 98971 1dqeA 137 3.49e+01 1dqeA a.39.2.1 17388 1tu7A 208 3.57e+01 1cb8A 678 3.57e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1rcwA 231 3.60e+01 a.132.1.4 97299 2asi 360 3.61e+01 2rmpA b.50.1.2 26824 1h8eD 482 3.62e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1eblA 317 3.64e+01 1hn9A c.95.1.2,c.95.1.2 35973,35974 1oxxK 353 3.67e+01 b.40.6.3,c.37.1.12 93715,93716 1k9uA 78 3.75e+01 a.39.1.10 84348 1ru8A 232 3.82e+01 c.26.2.1 97849 1yezA 68 3.84e+01 1hic 51 3.84e+01 4htcI g.3.15.2 44371 1ezvA 430 3.84e+01 1be3A d.185.1.1,d.185.1.1 59541,59542 1pne 140 3.85e+01 1pne d.110.1.1 40866 1ws0A 156 3.86e+01 1j7lA 264 3.87e+01 d.144.1.6 62697 1avbA 226 3.89e+01 1led b.29.1.1 24158 1ireB 228 3.89e+01 b.34.4.4 76770 3pcgA 200 3.94e+01 3pchA b.3.6.1 22647 1a78A 134 3.95e+01 1c1lA b.29.1.3 24212 1ebuA 358 3.96e+01 1ebuA c.2.1.3,d.81.1.2 30035,39950 1fmtB 314 3.96e+01 1fmtA b.46.1.1,c.65.1.1 25759,34175 1yu1A 381 3.96e+01 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