# List of top-scoring protein chains for t2k-w0.5 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 1hu4A 288 6.21e-01 1hu4A c.2.1.2 61268 1ap8 213 7.69e-01 1ap8 d.86.1.1 40151 1ae9A 179 1.04e+00 1ae9A d.163.1.1 42153 1louA 101 1.92e+00 1ris d.58.14.1 39323 1koe 172 1.95e+00 1koe d.169.1.5 42448 4xis 387 1.95e+00 4xis c.1.15.3 29421 3xis 387 1.95e+00 4xis c.1.15.3 29423 2xis 387 1.95e+00 4xis c.1.15.3 29427 1cqmA 101 1.95e+00 1ris d.58.14.1 39321 1gw9A 388 1.98e+00 6xia 387 1.98e+00 4xis c.1.15.3 29406 1qjhA 101 2.00e+00 1ris d.58.14.1 39326 1dy1A 188 2.07e+00 1koe d.169.1.5 42450 1eg0C 97 2.30e+00 1ris i.1.1.1 45809 1g1xA 98 2.33e+00 1ris d.58.14.1 39327 1ris 101 2.37e+00 1ris d.58.14.1 39314 1h7zA 194 2.58e+00 1qhvA b.21.1.1 60733 1kz7A 353 2.93e+00 1bccF 109 3.31e+00 1be3F f.2.1.8 43700 1lb1A 353 3.73e+00 1kzgA 353 3.74e+00 1a0dA 440 4.36e+00 1a0cA c.1.15.3 29533 1xymA 386 4.91e+00 4xis c.1.15.3 29415 1xyaA 386 4.93e+00 4xis c.1.15.3 29411 1ib4A 339 5.10e+00 b.80.1.3 62143 1ezm 301 5.82e+00 1hyt d.92.1.2 58980 1qt1A 387 5.89e+00 4xis c.1.15.3 29436 1clkA 387 5.90e+00 4xis c.1.15.3 29438 1jkc 130 6.02e+00 3lzt d.2.1.2 36431 1cxyA 90 6.36e+00 1cyo d.120.1.1 41085 1kt9A 138 6.43e+00 1ktgA 138 6.43e+00 1qcrF 103 6.59e+00 1be3F f.2.1.8 43676 2hea 130 6.69e+00 3lzt d.2.1.2 36433 1be3F 110 6.92e+00 1be3F f.2.1.8 43668 1bnlA 178 7.06e+00 1koe d.169.1.5 42444 2sttA 96 7.20e+00 1awcA a.4.5.21 16163 1f2sI 28 7.39e+00 g.3.2.1 44063 1gnf 46 7.68e+00 1gatA g.39.1.1 45107 1eibA 540 7.86e+00 1ctn b.1.1.5 21874 c.1.8.5 29003 d.26.3.1 38437 1ctn 540 7.89e+00 1ctn b.1.1.5 21876 c.1.8.5 29005 d.26.3.1 38439 1edqA 540 7.98e+00 1ctn b.1.1.5 21873 c.1.8.5 29002 d.26.3.1 38436 1ehnA 540 7.99e+00 1ctn b.1.1.5 21875 c.1.8.5 29004 d.26.3.1 38438 1ffrA 540 8.16e+00 b.1.1.5 59810 c.1.8.5 59811 d.26.3.1 59812 2msbB 115 8.25e+00 1rtm1 d.169.1.1 42356 2msbA 115 8.25e+00 1rtm1 d.169.1.1 42355 1fhoA 119 9.13e+00 1fhoA b.55.1.1 26982 1etc 110 9.51e+00 1awcA a.4.5.21 16162 1xlmA 394 9.54e+00 4xis c.1.15.3 29441 3kmb1 149 9.76e+00 1rtm1 1rtm1 149 1.03e+01 1rtm1 1xlaA 394 1.04e+01 4xis c.1.15.3 29445 4xiaA 393 1.05e+01 4xis c.1.15.3 29439 1buuA 168 1.16e+01 1rtm1 d.169.1.1 42366 h.1.1.1 45388 1ku1A 230 1.16e+01 1a0rG 65 1.16e+01 1tbgE a.137.3.1 19639 1a1s 314 1.18e+01 1othA c.78.1.1 35258 c.78.1.1 35259 1tbgE 68 1.24e+01 1tbgE a.137.3.1 19630 1b9xB 68 1.25e+01 1tbgE a.137.3.1 19638 1gotG 73 1.34e+01 1tbgE a.137.3.1 19629 1mctI 28 1.45e+01 g.3.2.1 44062 1fbtA 190 1.47e+01 1bif c.60.1.4 34004 1kx0A 149 1.49e+01 1fujA 221 1.53e+01 1a7s b.47.1.2 26349 1dmzA 158 1.53e+01 1qu5A b.26.1.2 23921 1kwzA 149 1.54e+01 1cd1A 315 1.65e+01 1cd1A b.1.1.2 21579 d.19.1.1 38155 1tipA 191 1.67e+01 1bif c.60.1.4 34006 1e3tA 203 1.73e+01 1d4oA c.31.1.4 31749 1qhxA 178 1.73e+01 1qhsA c.37.1.3 31936 1qhsA 178 1.73e+01 1qhsA c.37.1.3 31938 1qu5A 182 1.73e+01 1qu5A b.26.1.2 23922 1qhnA 178 1.76e+01 1qhsA c.37.1.3 31937 1b0tA 106 1.92e+01 1a6l d.58.1.2 38965 1gmiA 136 1.97e+01 b.7.1.1 65309 1qd6C 240 2.00e+01 1qd5A 1qd5A 275 2.20e+01 1qd5A f.4.2.1 43748 1khcA 147 2.20e+01 b.34.9.2 68608 1fw3A 275 2.21e+01 1qd5A f.4.2.1 60054 1im0A 275 2.25e+01 f.4.2.1 66210 1havB 217 2.27e+01 1havA b.47.1.4 26424 1havA 217 2.27e+01 1havA b.47.1.4 26423 1ayyA 151 2.29e+01 1apyA d.153.1.5 42016 1qa7A 215 2.42e+01 1havA b.47.1.4 26425 1inuA 130 2.45e+01 3lzt d.2.1.2 36485 1qa7B 219 2.46e+01 1havA b.47.1.4 26426 3crd 100 2.47e+01 3crd a.77.1.1 18429 1fihA 154 2.50e+01 1rtm1 d.169.1.1 42396 h.1.1.1 45404 1dxiA 388 2.55e+01 4xis c.1.15.3 29407 1ede 310 2.59e+01 1b6g c.69.1.8 34662 1be0 310 2.59e+01 1b6g c.69.1.8 34663 1b6g 310 2.62e+01 1b6g c.69.1.8 34661 1av1A 201 2.63e+01 1av1A h.5.1.1 45796 1bcj1 154 2.72e+01 1rtm1 1afb1 154 2.75e+01 1rtm1 1bch1 154 2.76e+01 1rtm1 1e31B 142 2.84e+01 1f3hA g.52.1.1 45380 1ijdB 42 2.87e+01 f.3.1.1 66156 1gxrA 337 2.91e+01 1vid 221 3.04e+01 1vid c.66.1.1 34178 1gfuA 130 3.05e+01 3lzt d.2.1.2 36532 1jj2H 167 3.07e+01 1ffkF d.41.4.1 63093 1di5A 129 3.07e+01 3lzt d.2.1.2 36565 1lm3B 106 3.23e+01 1qq3A 106 3.27e+01 256bA a.24.3.1 16541 1sur 215 3.27e+01 1sur c.26.2.2 31620 256bA 106 3.29e+01 256bA a.24.3.1 16539 1g8kA 825 3.32e+01 1g8jA b.52.2.2 26920 c.81.1.1 35328 1igoA 205 3.34e+01 1g8jA 825 3.39e+01 1g8jA b.52.2.2 26924 c.81.1.1 35332 1f3hA 142 3.49e+01 1f3hA g.52.1.1 45381 1hnr 47 3.58e+01 1hnr a.55.1.1 17896 1gc0A 398 3.67e+01 1ekbB 235 3.68e+01 5ptp b.47.1.2 26282 1bwmA 249 3.74e+01 1bec b.1.1.1 20620 b.1.1.1 20643 1vpc 45 3.76e+01 1vpc j.11.1.1 46138 1danH 254 3.87e+01 5ptp b.47.1.2 26292 1jbuH 254 3.87e+01 5ptp b.47.1.2 62856 1jjfA 268 3.87e+01 c.69.1.2 66765 1yal 218 3.91e+01 1cs8A d.3.1.1 37025 1jt2A 268 3.93e+01 1gfvA 130 4.00e+01 3lzt d.2.1.2 36512