# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl-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 1zq9A 285 6.98e-26 2ax3A 502 7.09e-01 1lvaA 258 1.33e+00 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1i58A 189 1.48e+00 1b3qA d.122.1.3 61773 2astA 159 1.93e+00 2gfnA 209 1.97e+00 1yf3A 259 2.97e+00 1p35A 299 3.09e+00 1p35A b.28.1.1 23925 1j8uA 325 3.52e+00 d.178.1.1 71611 1hlvA 131 3.58e+00 a.4.1.7,a.4.1.7 65854,65855 1fs1B 141 3.61e+00 1vcbB a.157.1.1,d.42.1.1 19252,38664 1vb3A 428 3.70e+00 2ch4A 320 3.70e+00 1q0sA 259 3.91e+00 c.66.1.28 95509 1pah 308 4.02e+00 4pah d.178.1.1 42578 4pah 308 4.19e+00 4pah d.178.1.1 42576 1dmwA 307 4.25e+00 4pah d.178.1.1 42580 2g7gA 213 4.35e+00 1x0vA 354 4.79e+00 2bjfA 329 4.91e+00 2f4lA 297 5.10e+00 1zrn 232 5.34e+00 1qq5A c.108.1.1 43323 1jud 232 5.40e+00 1qq5A c.108.1.1 43325 2azqA 311 5.81e+00 1mlwA 301 6.31e+00 d.178.1.1 79289 1it2A 146 6.40e+00 a.1.1.2 66365 1i4wA 353 6.41e+00 c.66.1.24 66028 1g8jA 825 6.48e+00 1g8jA b.52.2.2,c.81.1.1 26924,35332 1mvwC 147 6.57e+00 i.15.1.1 79525 1o1fC 147 6.57e+00 i.15.1.1 80997 2f4mA 295 6.61e+00 1jmsA 381 6.91e+00 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1dk0A 188 7.09e+00 1b2vA d.35.1.1 38530 1b2vA 188 7.22e+00 1b2vA d.35.1.1 38532 1m65A 245 7.25e+00 c.6.3.1 84847 1s69A 124 7.42e+00 a.1.1.1 105305 1v97A 1332 7.97e+00 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 108436,108437,108438,108439,108440,108441 2bvpA 276 8.09e+00 1fo4A 1332 8.35e+00 a.56.1.1,d.15.4.2,d.41.1.1,d.87.2.1,d.133.1.1,d.145.1.3 17910,37695,38586,40227,41416,41758 2ygsA 92 8.51e+00 1cy5A a.77.1.3 18431 1nxuA 333 8.67e+00 c.122.1.1 86389 1yadA 221 8.84e+00 1b3jA 274 9.72e+00 1agdA b.1.1.2,d.19.1.1 20855,38319 1kjvA 284 9.93e+00 b.1.1.2,d.19.1.1 77421,77422 1cy5A 97 1.00e+01 1cy5A a.77.1.3 18430 1cqxA 403 1.02e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1a3aC 148 1.09e+01 1a3aA d.112.1.1 40919 1q16C 225 1.16e+01 f.21.3.1 95549 1zu4A 320 1.21e+01 1wy1A 172 1.29e+01 1ryc 294 1.34e+01 1ryc a.93.1.1 18601 1dp3A 55 1.37e+01 1dp3A a.55.1.2 59128 1ds4A 292 1.38e+01 1ryc a.93.1.1 59129 1p57B 255 1.44e+01 b.47.1.2 94126 1qyrA 252 1.45e+01 c.66.1.24 104657 1ccg 291 1.47e+01 1ryc a.93.1.1 18627 2cyp 294 1.63e+01 1ryc a.93.1.1 18600 1hqvA 191 1.63e+01 1hqvA a.39.1.8 61160 1a2f 291 1.65e+01 1ryc a.93.1.1 18619 1ap4 89 1.67e+01 1ncx a.39.1.5 17253 1y5iC 225 1.67e+01 1umdA 367 1.67e+01 c.36.1.11 99599 1a2g 291 1.70e+01 1ryc a.93.1.1 18620 1fqvJ 149 1.73e+01 1fqvD a.157.1.1,d.42.1.1 19266,38670 1dseA 292 1.73e+01 1ryc a.93.1.1 59130 2prd 174 1.73e+01 2prd b.40.5.1 25435 1zcoA 262 1.75e+01 1fp1D 372 1.88e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1vgmA 378 1.90e+01 1a3aA 148 1.91e+01 1a3aA d.112.1.1 40917 1k9dA 679 1.95e+01 c.1.8.10,d.92.2.2 77292,77293 1fqvD 149 1.98e+01 1fqvD a.157.1.1,d.42.1.1 19263,38667 1ac4 294 2.01e+01 1ryc a.93.1.1 18657 1rwtA 232 2.08e+01 f.43.1.1 97992 1u60A 310 2.11e+01 e.3.1.2 107692 1s5lA 344 2.22e+01 1j6pA 418 2.26e+01 b.92.1.4,c.1.9.9 77089,77090 1mgtA 174 2.29e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1l8nA 679 2.29e+01 c.1.8.10,d.92.2.2 84564,84565 1p1mA 406 2.32e+01 b.92.1.4,c.1.9.9 87696,87697 2ercA 244 2.33e+01 2ercA c.66.1.24 34224 1cem 363 2.40e+01 1cem a.102.1.2 18826 1g8kA 825 2.47e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1vllA 334 2.50e+01 c.2.1.13 108834 1abv 134 2.56e+01 1abv a.70.1.1 18317 1xx1A 285 2.59e+01 1ek8A 185 2.61e+01 1ek8A d.67.3.1 59444 1kcw 1046 2.62e+01 1kcw b.6.1.3,b.6.1.3,b.6.1.3,b.6.1.3,b.6.1.3,b.6.1.3 23151,23152,23153,23154,23155,23156 1zs4A 83 2.65e+01 1irxA 523 2.66e+01 a.97.1.2,c.26.1.1 71378,71379 1e8xA 961 2.70e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1ncx 162 2.73e+01 1ncx a.39.1.5 17222 1top 162 2.75e+01 1ncx a.39.1.5 17223 1qamA 244 2.75e+01 2ercA c.66.1.24 34220 1y89A 238 2.79e+01 2btoA 473 2.79e+01 1cwwA 102 2.80e+01 1cy5A a.77.1.3 18434 2abk 211 2.86e+01 2abk a.96.1.1 18743 1mkrA 294 2.87e+01 a.93.1.1 84997 1j6rA 214 2.89e+01 d.173.1.2 71598 1fyvA 161 2.95e+01 1fyvA c.23.2.1 31127 1pyoB 105 3.05e+01 2eutA 294 3.06e+01 1xl7A 612 3.08e+01 1zk8A 183 3.09e+01 2ah5A 210 3.15e+01 1ofdA 1520 3.17e+01 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1xclA 235 3.29e+01 1v4aA 440 3.32e+01 a.24.16.4,d.218.1.9 108350,108351 1urjA 1136 3.32e+01 1glaG 501 3.33e+01 1glcG c.55.1.4,c.55.1.4 33507,33508 1h8dH 260 3.35e+01 5ptp 1aorA 605 3.40e+01 1b25A a.110.1.1,d.152.1.1 19042,41794 1fiqC 763 3.41e+01 1fiqC d.41.1.1,d.133.1.1 38588,41418 1vljA 407 3.41e+01 e.22.1.2 108832 1ra6A 461 3.42e+01 e.8.1.4 104879 1kfuS 184 3.43e+01 a.39.1.8 68574 1z53A 294 3.50e+01 1kb9I 55 3.50e+01 f.23.14.1 77324 1zbyA 294 3.52e+01 2aplA 157 3.53e+01 1oaoC 729 3.53e+01 e.26.1.3 86746 1cfpA 92 3.54e+01 1b4cA a.39.1.2 17172 1a1mA 278 3.60e+01 1agdA b.1.1.2,d.19.1.1 20753,38266 1ezvI 55 3.60e+01 1be3J f.23.14.1 59553 1omoA 322 3.65e+01 c.2.1.13 104017 1peqA 714 3.66e+01 a.98.1.1,c.7.1.2 104131,104132 2f05A 105 3.66e+01 1cnzA 363 3.73e+01 1cnzA c.77.1.1 35061 1dkfA 233 3.77e+01 3erdA a.123.1.1 19280 1jdrA 294 3.81e+01 1ryc a.93.1.1 62908 1gr0A 367 3.86e+01 c.2.1.3,d.81.1.3 70379,70380 1lj9A 144 3.90e+01 a.4.5.28 78035 1onqA 283 3.90e+01 b.1.1.2,d.19.1.1 93365,93366 1kwfA 363 3.92e+01 a.102.1.2 73078 1g73A 162 3.94e+01 1fewA a.7.4.1 16332 1h3lA 87 3.98e+01 a.177.1.1 76639 1ztdA 133 4.00e+01 1w7jB 151 4.11e+01 1ichA 112 4.14e+01 a.77.1.2 71182 1bu6O 501 4.14e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 1ru3A 732 4.17e+01 e.26.1.3 97835 1gaxA 862 4.20e+01 1gaxA b.51.1.1,c.26.1.1,a.2.7.3,a.27.1.1 26893,31595,75842,75843 1t4hA 290 4.23e+01 d.144.1.7 106420 1lufA 343 4.25e+01 d.144.1.7 78223 2ba2A 85 4.29e+01 1glcG 501 4.30e+01 1glcG c.55.1.4,c.55.1.4 33519,33520 1iseA 185 4.31e+01 d.67.3.1 90691 1o22A 170 4.35e+01 d.238.1.1 86557 2a5vA 213 4.36e+01 1lkxA 697 4.45e+01 c.37.1.9 73981 1elvA 333 4.49e+01 5ptp b.47.1.2,g.18.1.1 59454,59455 1ee4A 423 4.51e+01 1ee4A a.118.1.1 19128 1k5nA 276 4.59e+01 b.1.1.2,d.19.1.1 77266,77267 2jdxA 385 4.60e+01 1jdw d.126.1.2 41139 1kvkA 395 4.62e+01 d.14.1.5,d.58.26.3 73060,73061 1fcbA 511 4.67e+01 1gox c.1.4.1,d.120.1.1 28620,41087 2fjbA 643 4.69e+01 1wdkC 390 4.70e+01 c.95.1.1,c.95.1.1 109258,109259 1tedA 393 4.72e+01 c.95.1.2 106807 1gajA 257 4.86e+01 1gajA c.37.1.12 60416 3crxA 343 4.87e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 2fh5A 185 4.88e+01 1zcxA 178 4.94e+01 1dywA 173 4.94e+01 2cpl b.62.1.1 27505 1ggzA 148 4.99e+01 a.39.1.5 70176 2awpA 198 5.05e+01 1fcyA 236 5.10e+01 2lbd a.123.1.1 19282 1wrvA 308 5.19e+01 1p4kA 295 5.28e+01 d.153.1.5 87772 1lccA 51 5.29e+01 1pru a.35.1.5 17110 3lck 271 5.34e+01 1fmk d.144.1.7 41686 1jalA 363 5.48e+01 c.37.1.8,d.15.10.2 84138,84139 1q5dA 419 5.51e+01 a.104.1.1 95891 1llwA 1520 5.52e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 1a1oA 276 5.54e+01 1agdA b.1.1.2,d.19.1.1 20751,38265 1pulA 125 5.58e+01 1a5v 162 5.59e+01 1cxqA c.55.3.2 33629 1mjgM 729 5.60e+01 e.26.1.3 79204 1lmzA 187 5.60e+01 a.96.1.4 74037 9gafA 295 5.61e+01 1apyA d.153.1.5 42008 1ynuA 473 5.62e+01 1ir3A 306 5.63e+01 1fmk d.144.1.7 41702 2evaA 307 5.72e+01 1afwA 393 5.85e+01 1afwA c.95.1.1,c.95.1.1 35900,35901 1txuA 273 5.86e+01 a.222.1.1 107439 1h54A 754 5.91e+01 a.102.1.4,b.30.5.3 60634,60635 1ahtH 259 5.95e+01 5ptp 1o0yA 260 5.97e+01 c.1.10.1 80756 1qpcA 279 5.99e+01 1fgkA d.144.1.7 41685 1guxB 152 6.03e+01 1guxB a.74.1.3 18389 1gcvB 136 6.04e+01 1cg5B a.1.1.2 15589 1go3F 107 6.08e+01 a.60.8.2 65407 1c0aA 585 6.10e+01 1c0aA b.40.4.1,d.74.4.1,d.104.1.1 25246,39731,40767 1fewA 184 6.10e+01 1fewA a.7.4.1 16334 1m46A 148 6.14e+01 a.39.1.5 78599 1zt1A 277 6.18e+01 1kbuA 349 6.20e+01 a.60.9.1,d.163.1.1 72284,72285 1fzoA 274 6.22e+01 1agdA b.1.1.2,d.19.1.1 60155,60156 1xqoA 256 6.27e+01 1dg3A 592 6.29e+01 1dg3A a.114.1.1,c.37.1.8 19078,32153 2cruA 118 6.30e+01 1g6hA 257 6.30e+01 1gajA c.37.1.12 60318 1g2nA 264 6.30e+01 1lbd a.123.1.1 60227 1l8wA 348 6.31e+01 a.154.1.1 73704 1uj8A 77 6.31e+01 4crxA 322 6.31e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1jdw 423 6.34e+01 1jdw d.126.1.2 41129 1kyqA 274 6.36e+01 c.2.1.11,e.37.1.1 73281,73282 1g6oA 330 6.43e+01 1g6oA c.37.1.11 32430 1asu 162 6.48e+01 1cxqA c.55.3.2 33626 1fehA 574 6.50e+01 1fehA c.96.1.1,d.15.4.2,d.58.1.5 36015,37690,38998 1theB 260 6.53e+01 1theB d.3.1.1 37057 1gks 78 6.62e+01 1cc5 a.3.1.1 15909 1z5vA 474 6.63e+01 1c5lH 259 6.79e+01 5ptp 1s3aA 102 6.80e+01 1m7yA 435 6.80e+01 c.67.1.4 78761 1vsd 152 6.80e+01 1cxqA c.55.3.2 33625 1nekD 115 6.80e+01 f.21.2.2 80432 1sd4A 126 6.82e+01 a.4.5.39 105428 2cdcA 366 6.89e+01 1b3qA 379 6.92e+01 1b3qA a.30.2.1,b.40.7.1,d.122.1.3 16993,25454,41112 1ddgA 374 6.97e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1wa5B 530 7.00e+01 1bk6A 422 7.01e+01 1bk5A a.118.1.1 19133 1f5nA 592 7.03e+01 1dg3A a.114.1.1,c.37.1.8 19077,32152 1mkiA 330 7.04e+01 e.3.1.2 84994 1tvlA 454 7.06e+01 c.1.16.4 107366 1cxqA 162 7.06e+01 1cxqA c.55.3.2 33621 1wbpA 397 7.07e+01 1yarA 233 7.09e+01 2av1A 275 7.12e+01 1xiuA 230 7.17e+01 1xfjA 261 7.28e+01 d.194.1.2 109585 1b8gA 429 7.48e+01 1b8gA c.67.1.4 34499 2b9lA 394 7.49e+01 1ioj 57 7.50e+01 1ioj j.39.1.1 46293 1ydmA 187 7.50e+01 1aj4 161 7.56e+01 1ncx a.39.1.5 17244 1f20A 435 7.61e+01 b.43.4.1,c.25.1.4 64932,64933 1hwxA 501 7.70e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 2b25A 336 7.71e+01 1fzpB 123 7.87e+01 1fznD a.4.5.28 19008 1oatA 439 7.93e+01 2dkb c.67.1.4 34461 4lbd 267 7.93e+01 2lbd a.123.1.1 19289 1yqfA 203 7.93e+01 1khhA 198 7.93e+01 c.66.1.16 68615 1f44A 324 7.94e+01 a.60.9.1,d.163.1.1 64982,64983 1ihgA 370 7.99e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1lqtA 456 8.00e+01 c.3.1.1,c.4.1.1 74198,74199 1tffA 234 8.00e+01 d.3.1.11 106854 1ym3A 215 8.02e+01 2lbd 267 8.09e+01 2lbd a.123.1.1 19287 1yzyA 413 8.12e+01 2aj2A 208 8.16e+01 1oe0A 230 8.24e+01 c.37.1.1 92788 1xvjA 109 8.25e+01 2bjcA 62 8.26e+01 1g1eB 89 8.29e+01 1g1eB a.59.1.1 17931 1hqcA 324 8.34e+01 1hqcA a.4.5.11,c.37.1.20 16127,32424 1sh7A 284 8.36e+01 1nrfA 262 8.37e+01 e.3.1.1 92086 6gsvA 217 8.43e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1hwyA 501 8.48e+01 1hwyA c.2.1.7,c.58.1.1 30262,33910 1xw5A 217 8.52e+01 1zt7A 276 8.57e+01 1bpoA 494 8.64e+01 1bpoA a.118.1.4,b.69.6.1 19143,27670 1bjt 793 8.70e+01 1bjt e.11.1.1 43249 1b4cA 92 8.74e+01 1b4cA a.39.1.2 17169 2byjA 439 8.81e+01 1qbqA 333 8.90e+01 1ft1A a.118.6.1 19187 1riiA 265 8.91e+01 1mvcA 240 8.96e+01 a.123.1.1 79499 1qrzA 246 8.98e+01 5ptp b.47.1.2 26366 1lxa 262 8.98e+01 1lxa b.81.1.1 28052 1tib 269 8.99e+01 3tgl c.69.1.17 34738 8kme2 259 8.99e+01 1ucyE 1yucA 255 9.00e+01