# List of top-scoring protein chains for t04-100-30-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 1zq9A 285 3.07e-24 2f4lA 297 1.54e-01 1i4wA 353 2.66e-01 c.66.1.24 66028 1fs1B 141 2.94e-01 1vcbB a.157.1.1,d.42.1.1 19252,38664 1i58A 189 3.61e-01 1b3qA d.122.1.3 61773 2ch4A 320 4.73e-01 1nxuA 333 5.77e-01 c.122.1.1 86389 1s5lA 344 6.14e-01 1dk0A 188 6.41e-01 1b2vA d.35.1.1 38530 1g8kA 825 1.02e+00 1g8jA b.52.2.2,c.81.1.1 26920,35328 1yadA 221 1.04e+00 2azqA 311 1.07e+00 1mvwC 147 1.11e+00 i.15.1.1 79525 1yf3A 259 1.21e+00 2astA 159 1.26e+00 1q0sA 259 1.28e+00 c.66.1.28 95509 1ynuA 473 1.47e+00 1kaeA 434 1.61e+00 c.82.1.2 72247 1oatA 439 1.74e+00 2dkb c.67.1.4 34461 1ofdA 1520 1.97e+00 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 2byjA 439 1.97e+00 2oatA 439 2.16e+00 2dkb c.67.1.4 34452 1eljA 381 2.41e+00 4mbp c.94.1.1 35791 1p1cA 199 2.43e+00 c.66.1.16 87669 1a3aA 148 2.50e+00 1a3aA d.112.1.1 40917 2bylA 439 2.60e+00 1lvaA 258 2.62e+00 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 2furA 209 3.14e+00 1cem 363 3.25e+00 1cem a.102.1.2 18826 1psrA 100 3.26e+00 1psrA a.39.1.2 17180 1vb3A 428 3.33e+00 1fnnA 389 3.33e+00 1fnnA a.4.5.11,c.37.1.20 16129,32426 1jmsA 381 3.64e+00 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1top 162 3.74e+00 1ncx a.39.1.5 17223 1kwfA 363 3.82e+00 a.102.1.2 73078 1zcoA 262 3.82e+00 1m7yA 435 4.00e+00 c.67.1.4 78761 1mbxC 106 4.33e+00 d.45.1.2 78929 1b8gA 429 4.34e+00 1b8gA c.67.1.4 34499 1r6oC 106 4.39e+00 1fiqC 763 4.57e+00 1fiqC d.41.1.1,d.133.1.1 38588,41418 1cnzA 363 4.57e+00 1cnzA c.77.1.1 35061 1x0vA 354 4.61e+00 1ta9A 450 4.98e+00 1tn4 159 5.04e+00 1ncx a.39.1.5 17248 1q8cA 151 5.23e+00 a.79.1.2 96202 1w33A 181 5.51e+00 1xclA 235 5.58e+00 1mijA 152 5.73e+00 a.4.1.1 79150 2ah5A 210 5.74e+00 1j8uA 325 5.94e+00 d.178.1.1 71611 1avsA 90 6.08e+00 1cll a.39.1.5 17226 1x3sA 195 6.72e+00 1a4pA 96 7.21e+00 1b4cA a.39.1.2 17176 1h8dH 260 7.51e+00 5ptp 1tvlA 454 7.75e+00 c.1.16.4 107366 1v97A 1332 7.82e+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 1f20A 435 7.99e+00 b.43.4.1,c.25.1.4 64932,64933 1xpxA 163 8.38e+00 1pyoB 105 8.48e+00 1j6pA 418 8.55e+00 b.92.1.4,c.1.9.9 77089,77090 1wy6A 172 8.57e+00 2fz4A 237 8.91e+00 1ggzA 148 9.01e+00 a.39.1.5 70176 4pah 308 9.27e+00 4pah d.178.1.1 42576 1wbpA 397 9.35e+00 1p57B 255 9.36e+00 b.47.1.2 94126 1vljA 407 9.40e+00 e.22.1.2 108832 1wdkC 390 9.96e+00 c.95.1.1,c.95.1.1 109258,109259 1fo4A 1332 1.03e+01 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 1y89A 238 1.08e+01 2bjfA 329 1.09e+01 1hlvA 131 1.11e+01 a.4.1.7,a.4.1.7 65854,65855 1wwiA 148 1.13e+01 1g6hA 257 1.18e+01 1gajA c.37.1.12 60318 1p1mA 406 1.19e+01 b.92.1.4,c.1.9.9 87696,87697 2ax3A 502 1.19e+01 1s3aA 102 1.23e+01 1w7jB 151 1.24e+01 1nu5A 370 1.30e+01 c.1.11.2,d.54.1.1 92183,92184 1mho 88 1.30e+01 1b4cA a.39.1.2 17171 2be4A 272 1.33e+01 1riqA 465 1.36e+01 a.203.1.1,d.104.1.1 97516,97517 1mwyA 73 1.45e+01 d.58.17.1 79616 1ou0A 207 1.49e+01 c.23.17.1 93536 1vliA 385 1.53e+01 b.85.1.1,c.1.10.6 108830,108831 1fp1D 372 1.57e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 1cjgA 62 1.63e+01 1pru a.35.1.5 17112 1ni4B 341 1.64e+01 c.36.1.7,c.48.1.2 85729,85730 1c8uA 285 1.64e+01 1c8uA d.38.1.3,d.38.1.3 38547,38548 1cy5A 97 1.65e+01 1cy5A a.77.1.3 18430 1iugA 352 1.73e+01 c.67.1.3 90699 1jalA 363 1.74e+01 c.37.1.8,d.15.10.2 84138,84139 1jy5A 212 1.75e+01 d.124.1.1 71940 1zu4A 320 1.79e+01 1c7nA 399 1.80e+01 1d2fA c.67.1.3 34413 1tib 269 1.93e+01 3tgl c.69.1.17 34738 1j6rA 214 1.93e+01 d.173.1.2 71598 1gt6A 269 1.94e+01 c.69.1.17 76342 1wy1A 172 1.99e+01 1wekA 217 1.99e+01 1dp3A 55 2.00e+01 1dp3A a.55.1.2 59128 1j75A 67 2.01e+01 a.4.5.19 62673 1mgtA 174 2.04e+01 1mgtA a.4.2.1,c.55.7.1 16078,33753 1abv 134 2.06e+01 1abv a.70.1.1 18317 1m65A 245 2.07e+01 c.6.3.1 84847 1pjr 724 2.13e+01 1pjr c.37.1.19,c.37.1.19 32391,32392 1q7eA 428 2.14e+01 c.123.1.1 96035 1mqvA 125 2.18e+01 a.24.3.2 79415 1wmhB 86 2.20e+01 1o50A 157 2.20e+01 d.37.1.1,d.37.1.1 92478,92479 1wrvA 308 2.21e+01 1n9dA 199 2.22e+01 a.26.1.1 85464 2rslA 140 2.22e+01 2rslA c.53.1.1 33345 1rqlA 267 2.23e+01 c.108.1.3 97750 1yfsA 465 2.23e+01 1dmhA 311 2.29e+01 1dmhA b.3.6.1 22633 2gsaA 432 2.31e+01 2gsaA c.67.1.4 34446 1tllA 688 2.32e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1elvA 333 2.36e+01 5ptp b.47.1.2,g.18.1.1 59454,59455 1u04A 771 2.37e+01 b.34.14.1,c.55.3.10 107539,107540 1fp2A 352 2.37e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1vj5A 555 2.38e+01 c.108.1.2,c.69.1.11 100799,100800 1sqiA 393 2.43e+01 d.32.1.3,d.32.1.3 105914,105915 1pt7A 437 2.46e+01 c.123.1.1 95093 1exrA 148 2.47e+01 1cll a.39.1.5 17299 1b3aA 67 2.50e+01 1b3aA d.9.1.1 37410 1zd3A 555 2.55e+01 1iktA 120 2.55e+01 d.106.1.1 66188 2prd 174 2.55e+01 2prd b.40.5.1 25435 1qy6A 274 2.56e+01 b.47.1.1 96574 1o1zA 234 2.56e+01 c.1.18.3 86555 1yovA 537 2.57e+01 1cfzA 162 2.57e+01 1cfzA c.56.1.1 33754 1uhnA 189 2.57e+01 a.39.1.5 99399 2g0qA 173 2.60e+01 1e6cA 173 2.63e+01 1shkA c.37.1.2 59296 1paqA 189 2.65e+01 a.118.1.14 94413 1dcs 311 2.67e+01 1dcs b.82.2.1 28124 1d2zB 153 2.68e+01 1d2zB a.77.1.2 18439 1h3lA 87 2.70e+01 a.177.1.1 76639 1s2wA 295 2.71e+01 c.1.12.7 98407 1womA 271 2.73e+01 1v74B 87 2.76e+01 a.24.20.1 100443 1e8aA 91 2.76e+01 1b4cA a.39.1.2 17188 1e79D 482 2.81e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 18272,26437,32317 2fexA 188 2.84e+01 1xqoA 256 2.87e+01 2cwyA 94 2.89e+01 1m45A 148 2.91e+01 a.39.1.5 78598 1xiuA 230 2.95e+01 2f3yA 148 3.03e+01 1cf9A 753 3.03e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 1f44A 324 3.04e+01 a.60.9.1,d.163.1.1 64982,64983 1g2nA 264 3.15e+01 1lbd a.123.1.1 60227 1kq3A 376 3.16e+01 e.22.1.2 68790 1afwA 393 3.19e+01 1afwA c.95.1.1,c.95.1.1 35900,35901 1g4yR 148 3.19e+01 1cll a.39.1.5 60252 2basA 431 3.21e+01 1y82A 157 3.22e+01 1swvA 267 3.23e+01 1hr6B 443 3.24e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 2cw6A 298 3.27e+01 1hufA 140 3.30e+01 1hufA d.195.1.1 61272 1yarA 233 3.34e+01 1ton 235 3.35e+01 5ptp b.47.1.2 26307 1lj9A 144 3.37e+01 a.4.5.28 78035 1qqeA 292 3.39e+01 1qqeA a.118.8.1 19210 2a2cA 478 3.52e+01 1wouA 123 3.57e+01 c.47.1.16 109471 1y37A 304 3.58e+01 1sffA 426 3.58e+01 c.67.1.4 105482 1zrn 232 3.64e+01 1qq5A c.108.1.1 43323 1rw6A 210 3.65e+01 a.47.4.1 105113 2a2dA 478 3.66e+01 1ecmA 109 3.66e+01 1ecmA a.130.1.1 19492 2fswA 107 3.67e+01 2f62A 161 3.69e+01 1p80A 753 3.74e+01 c.23.16.3,e.5.1.1 94337,94338 2f2tA 161 3.74e+01 2d2mB 142 3.79e+01 1kb9I 55 3.80e+01 f.23.14.1 77324 1ngnA 155 3.81e+01 a.96.1.2 85697 1mlwA 301 3.82e+01 d.178.1.1 79289 3seb 238 3.82e+01 3seb b.40.2.2,d.15.6.1 25184,37773 2ahyA 110 3.87e+01 1sgwA 214 3.88e+01 c.37.1.12 105541 1h8eD 482 3.89e+01 1skyE a.69.1.1,b.49.1.1,c.37.1.11 60747,60748,60749 1sglA 209 3.91e+01 d.124.1.1 105536 1k94A 165 3.93e+01 a.39.1.8 68333 1xvjA 109 3.95e+01 1zmdA 474 3.96e+01 1rwyA 109 3.98e+01 a.39.1.4 98002 1j1hA 144 3.99e+01 b.111.1.1 77056 2fh5A 185 4.07e+01 1yrrA 382 4.08e+01 1lwjA 441 4.11e+01 b.71.1.1,c.1.8.1 74303,74304 1k6wA 426 4.13e+01 b.92.1.2,c.1.9.5 68236,68237 2bjcA 62 4.13e+01 1a79A 171 4.17e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1n8vA 112 4.18e+01 a.118.21.1 85457 1vi0A 206 4.19e+01 a.4.1.9,a.121.1.1 100720,100721 1wy5A 317 4.21e+01 2g7gA 213 4.22e+01 1v02A 565 4.24e+01 c.1.8.4 108194 1y1pA 342 4.26e+01 1kqzA 273 4.30e+01 c.1.8.5 68844 2a0jA 149 4.30e+01 1o6dA 163 4.31e+01 c.116.1.3 92567 1xo0A 324 4.33e+01 1alvA 173 4.34e+01 1alvA a.39.1.8 17370 1ju2A 536 4.35e+01 c.3.1.2,d.16.1.1 77169,77170 1wstA 417 4.36e+01 1np8A 159 4.37e+01 a.39.1.8 92022 1d8dA 377 4.39e+01 1ft1A a.118.6.1 19185 2ba2A 85 4.41e+01 4crxA 322 4.45e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1yi8A 351 4.46e+01 1ra0A 430 4.54e+01 1qyrA 252 4.55e+01 c.66.1.24 104657 1sczA 233 4.62e+01 c.43.1.1 98802 1e94F 449 4.63e+01 1do0A c.37.1.20 32443 1r5lA 262 4.66e+01 a.5.3.1,c.13.1.1 97099,97100 1ujmA 342 4.70e+01 1rlmA 271 4.71e+01 1olrA 224 4.73e+01 b.29.1.11 93330 2a0kA 161 4.76e+01 1mo7A 213 4.81e+01 d.220.1.1 85028 1ydyA 356 4.81e+01 2fm9A 215 4.84e+01 1aa8A 347 4.88e+01 1an9A 1t4hA 290 4.89e+01 d.144.1.7 106420 1it2A 146 4.89e+01 a.1.1.2 66365 1rxwA 336 5.00e+01 a.60.7.1,c.120.1.2 98059,98060 1r5rA 119 5.02e+01 a.39.2.1 97104 1gxmA 332 5.07e+01 a.102.5.1 76371 1xuuA 349 5.11e+01 1p35A 299 5.12e+01 1p35A b.28.1.1 23925 1a7s 221 5.14e+01 1a7s b.47.1.2 26284 1wmaA 276 5.21e+01 1i7dA 659 5.22e+01 1d6mA e.10.1.1 61886 1lokA 291 5.26e+01 c.56.5.4 78122 1ciy 590 5.28e+01 1ciy b.18.1.3,b.77.2.1,f.1.3.1 23720,27977,43392 1vl5A 260 5.28e+01 c.66.1.41 108720 1kjvA 284 5.31e+01 b.1.1.2,d.19.1.1 77421,77422 1np3A 338 5.50e+01 a.100.1.2,c.2.1.6 85946,85947 2anpA 291 5.51e+01 1t8qA 336 5.56e+01 c.1.18.3 106669 1q5dA 419 5.57e+01 a.104.1.1 95891 2a74A 643 5.59e+01 1sh7A 284 5.60e+01 2sak 121 5.62e+01 2sak d.15.5.1 37711 1rlmB 271 5.65e+01 2b33A 140 5.66e+01 1amp 291 5.67e+01 1amp c.56.5.4 33837 1wrdA 103 5.70e+01 1ddgA 374 5.71e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1om1A 332 5.74e+01 d.144.1.7 93347 1cpt 412 5.83e+01 1cpt a.104.1.1 18968 1v96A 149 5.84e+01 1rtqA 299 5.85e+01 c.56.5.4 97819 1ru3A 732 5.91e+01 e.26.1.3 97835 1scuA 288 5.99e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1h0hB 214 6.06e+01 d.58.1.5 76437 1ydwA 362 6.07e+01 1wr8A 231 6.08e+01 1ohvA 472 6.14e+01 c.67.1.4 93031 1eg7A 557 6.14e+01 1eg7A c.37.1.10 32241 1c02A 166 6.24e+01 1qspA a.24.10.2 16633 2b9lA 394 6.28e+01 1t0fA 276 6.36e+01 1m2rA 327 6.44e+01 d.144.1.7 84760 1q5qA 259 6.44e+01 d.153.1.4 95904 1xl7A 612 6.48e+01 1pp0A 199 6.49e+01 d.103.1.1 104211 1glcG 501 6.53e+01 1glcG c.55.1.4,c.55.1.4 33519,33520 2d0oB 125 6.55e+01 1wf3A 301 6.56e+01 1gz6A 319 6.58e+01 c.2.1.2 76410 1rkqA 282 6.64e+01 c.108.1.10 97621 1qxyA 252 6.66e+01 d.127.1.1 96565 1ih8A 271 6.67e+01 2nsyA c.26.2.1 62377 2bvpA 276 6.67e+01 2etgA 296 6.73e+01 1nh1A 330 6.74e+01 e.45.1.1 91871 2bce 581 6.78e+01 2bce c.69.1.1 34625 1yarH 217 6.79e+01 1zoqC 47 6.80e+01 2aaoA 166 6.83e+01 1gln 468 6.85e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1wmbA 260 6.87e+01 1cxqA 162 6.87e+01 1cxqA c.55.3.2 33621 1ng6A 148 6.90e+01 a.182.1.1 85670 1j09A 468 7.00e+01 a.97.1.1,c.26.1.1 77025,77026 1fnoA 417 7.00e+01 d.58.19.1,c.56.5.4 70145,75841 1x31D 99 7.02e+01 1fcyA 236 7.04e+01 2lbd a.123.1.1 19282 2anxA 146 7.06e+01 1x7dA 350 7.09e+01 1nr3A 122 7.14e+01 d.236.1.1 86092 1nz0A 118 7.17e+01 d.14.1.2 86433 1z8gA 372 7.19e+01 2hvm 273 7.20e+01 1cnv c.1.8.5 28985 1d2fA 390 7.21e+01 1d2fA c.67.1.3 34411 1o54A 277 7.24e+01 c.66.1.13 92482 1t3cA 421 7.24e+01 d.92.1.7 106343 1guxB 152 7.26e+01 1guxB a.74.1.3 18389 2b61A 377 7.27e+01 1onqA 283 7.30e+01 b.1.1.2,d.19.1.1 93365,93366 2beiA 170 7.32e+01 1pvmA 184 7.33e+01 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 2fdoA 94 7.38e+01 1fexA 59 7.41e+01 a.4.1.3 59803 1hr6A 475 7.52e+01 1hr6A d.185.1.1,d.185.1.1 61164,61165 1f1zA 273 7.54e+01 1f1zA a.4.5.27,c.52.1.16 16081,33334 1zx0A 236 7.54e+01 1fseA 74 7.58e+01 1fseA a.4.6.2 60000 1mvcA 240 7.61e+01 a.123.1.1 79499 1wh8A 111 7.62e+01 1q0vA 81 7.64e+01 j.105.1.1 95514 1x42A 232 7.66e+01 1g8fA 511 7.67e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1oa4A 222 7.72e+01 b.29.1.11 86731 1vzqH 250 7.73e+01 1xd7A 145 7.76e+01 a.4.5.55 109566 1jenB 67 7.78e+01 1jenB d.156.1.1 42029 2a9uA 144 7.79e+01 1yemA 179 7.86e+01 1zk8A 183 7.87e+01 1wdcC 156 7.87e+01 1wdcC a.39.1.5 17317 1kqpA 271 7.94e+01 c.26.2.1 72883 1dj7A 117 7.95e+01 1dj7A g.36.1.1 44997 1z1zA 131 7.98e+01 2ethA 154 8.02e+01 1wz7A 111 8.04e+01 2f4qA 346 8.20e+01 1p4kA 295 8.20e+01 d.153.1.5 87772 1ks9A 291 8.28e+01 a.100.1.7,c.2.1.6 68857,68858 2fi0A 81 8.29e+01 1qy1A 174 8.30e+01 b.60.1.1 96568 1oaoC 729 8.35e+01 e.26.1.3 86746 1owcA 427 8.36e+01 a.103.1.1 104039 1xx1A 285 8.44e+01 1bu6O 501 8.46e+01 1glcG c.55.1.4,c.55.1.4 33499,33500 2cw9A 194 8.46e+01 2dorA 311 8.53e+01 2dorA c.1.4.1 28593 1dugA 234 8.60e+01 1b8xA a.45.1.1,c.47.1.5 17718,33012 1dorA 311 8.63e+01 2dorA c.1.4.1 28595 1zndA 174 8.63e+01 1wd6A 123 8.65e+01 1xfcA 384 8.66e+01 1otjA 283 8.66e+01 b.82.2.5 93517 1na6A 404 8.68e+01 b.142.1.1,c.52.1.22 91748,91749 1v6tA 255 8.73e+01 2fi9A 128 8.73e+01 1eq2A 310 8.76e+01 1eq2A c.2.1.2 29814 1go3F 107 8.83e+01 a.60.8.2 65407 1qcwA 410 8.84e+01 1gox c.1.4.1 28622 1cjxA 357 8.87e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1u60A 310 8.87e+01 e.3.1.2 107692 1sf9A 128 8.87e+01 b.34.15.1 98831 2b7eA 59 8.99e+01 1yzxA 226 9.00e+01 1rypC 244 9.00e+01 1rypC d.153.1.4 41934