# 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 1zq9A 285 6.06e-22 1i4wA 353 2.14e-01 c.66.1.24 66028 1i58A 189 2.25e-01 1b3qA d.122.1.3 61773 1fs1B 141 5.16e-01 1vcbB a.157.1.1,d.42.1.1 19252,38664 1nxuA 333 5.33e-01 c.122.1.1 86389 2ch4A 320 6.37e-01 1q0sA 259 6.82e-01 c.66.1.28 95509 2f4lA 297 7.23e-01 1yf3A 259 7.25e-01 1vb3A 428 9.62e-01 1ap4 89 9.64e-01 1ncx a.39.1.5 17253 1o1fC 147 1.20e+00 i.15.1.1 80997 1mvwC 147 1.21e+00 i.15.1.1 79525 1hqvA 191 1.43e+00 1hqvA a.39.1.8 61160 2azqA 311 1.52e+00 1mho 88 1.55e+00 1b4cA a.39.1.2 17171 1s5lA 344 1.61e+00 1ggzA 148 1.74e+00 a.39.1.5 70176 1ak2 233 1.81e+00 1zin c.37.1.1,g.41.2.1 31894,45195 1ta9A 450 1.81e+00 1b3qA 379 1.89e+00 1b3qA a.30.2.1,b.40.7.1,d.122.1.3 16993,25454,41112 2astA 159 1.92e+00 1eljA 381 2.00e+00 4mbp c.94.1.1 35791 1g8kA 825 2.03e+00 1g8jA b.52.2.2,c.81.1.1 26920,35328 1fqvD 149 2.06e+00 1fqvD a.157.1.1,d.42.1.1 19263,38667 1ynuA 473 2.19e+00 1x0vA 354 2.27e+00 1fqvJ 149 2.29e+00 1fqvD a.157.1.1,d.42.1.1 19266,38670 1psrA 100 2.33e+00 1psrA a.39.1.2 17180 1yadA 221 2.54e+00 2be4A 272 2.72e+00 1b4cA 92 2.85e+00 1b4cA a.39.1.2 17169 1zcoA 262 2.94e+00 1top 162 3.21e+00 1ncx a.39.1.5 17223 1dk0A 188 3.26e+00 1b2vA d.35.1.1 38530 1ncx 162 3.80e+00 1ncx a.39.1.5 17222 1cfpA 92 3.91e+00 1b4cA a.39.1.2 17172 1oatA 439 3.96e+00 2dkb c.67.1.4 34461 1avsA 90 4.00e+00 1cll a.39.1.5 17226 2byjA 439 4.06e+00 2oatA 439 4.14e+00 2dkb c.67.1.4 34452 1pyoB 105 4.19e+00 1g8jA 825 4.34e+00 1g8jA b.52.2.2,c.81.1.1 26924,35332 2bjfA 329 4.39e+00 1ofdA 1520 4.51e+00 b.80.4.1,c.1.4.1,d.153.1.1 86935,86936,86937 1a3aA 148 4.58e+00 1a3aA d.112.1.1 40917 1lvaA 258 4.85e+00 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1cll 148 5.13e+00 1cll a.39.1.5 17263 1uwoA 92 5.14e+00 4icb a.39.1.2 17174 1b2vA 188 5.21e+00 1b2vA d.35.1.1 38532 1zac 90 5.34e+00 1ncx a.39.1.5 17236 2bylA 439 5.51e+00 2ax3A 502 5.64e+00 1m7yA 435 6.16e+00 c.67.1.4 78761 1b8gA 429 6.19e+00 1b8gA c.67.1.4 34499 1w7jB 151 6.30e+00 1tn4 159 6.34e+00 1ncx a.39.1.5 17248 1m65A 245 6.48e+00 c.6.3.1 84847 2mysC 149 6.56e+00 1wdcC a.39.1.5 17323 1q8cA 151 6.61e+00 a.79.1.2 96202 1j8uA 325 6.70e+00 d.178.1.1 71611 1a2xA 159 6.73e+00 1ncx a.39.1.5 17251 2ah5A 210 6.81e+00 1p1cA 199 7.23e+00 c.66.1.16 87669 1k9dA 679 7.46e+00 c.1.8.10,d.92.2.2 77292,77293 1ponB 36 7.76e+00 1ponB 1fiqC 763 8.02e+00 1fiqC d.41.1.1,d.133.1.1 38588,41418 1v97A 1332 8.32e+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 1m46A 148 8.41e+00 a.39.1.5 78599 1sz2A 332 8.41e+00 1f20A 435 8.50e+00 b.43.4.1,c.25.1.4 64932,64933 1a3aC 148 8.53e+00 1a3aA d.112.1.1 40919 1fnnA 389 8.83e+00 1fnnA a.4.5.11,c.37.1.20 16129,32426 3cln 148 8.88e+00 1cll a.39.1.5 17286 1vljA 407 9.07e+00 e.22.1.2 108832 1m45A 148 9.08e+00 a.39.1.5 78598 1jmsA 381 9.12e+00 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1r6oC 106 9.16e+00 1cem 363 9.20e+00 1cem a.102.1.2 18826 1l8nA 679 9.52e+00 c.1.8.10,d.92.2.2 84564,84565 1a4pA 96 9.52e+00 1b4cA a.39.1.2 17176 1vliA 385 9.68e+00 b.85.1.1,c.1.10.6 108830,108831 1mbxC 106 9.68e+00 d.45.1.2 78929 1q18A 332 9.68e+00 c.55.1.7,c.55.1.7 104470,104471 1crxA 322 1.02e+01 4crxA a.60.9.1,d.163.1.1 18097,42157 1b3jA 274 1.06e+01 1agdA b.1.1.2,d.19.1.1 20855,38319 1dmwA 307 1.06e+01 4pah d.178.1.1 42580 1kwfA 363 1.09e+01 a.102.1.2 73078 1llwA 1520 1.11e+01 b.80.4.1,c.1.4.1,d.153.1.1 74017,74018,74019 4pah 308 1.18e+01 4pah d.178.1.1 42576 1fo4A 1332 1.20e+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 1wdkC 390 1.21e+01 c.95.1.1,c.95.1.1 109258,109259 1khhA 198 1.27e+01 c.66.1.16 68615 1f44A 324 1.28e+01 a.60.9.1,d.163.1.1 64982,64983 1h8dH 260 1.35e+01 5ptp 1zu4A 320 1.36e+01 4crxA 322 1.36e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1fp2A 352 1.39e+01 1fpxA a.4.5.29,c.66.1.12 59941,59942 1pah 308 1.41e+01 4pah d.178.1.1 42578 1fcbA 511 1.42e+01 1gox c.1.4.1,d.120.1.1 28620,41087 1gal 583 1.46e+01 1gpeA c.3.1.2,d.16.1.1 30386,37950 1xo0A 324 1.46e+01 2g7gA 213 1.49e+01 1n9dA 199 1.50e+01 a.26.1.1 85464 2anxA 146 1.50e+01 1it2A 146 1.52e+01 a.1.1.2 66365 1aj4 161 1.58e+01 1ncx a.39.1.5 17244 1hlvA 131 1.58e+01 a.4.1.7,a.4.1.7 65854,65855 1kbuA 349 1.59e+01 a.60.9.1,d.163.1.1 72284,72285 1kjvA 284 1.60e+01 b.1.1.2,d.19.1.1 77421,77422 1cf3A 583 1.62e+01 1gpeA c.3.1.2,d.16.1.1 30385,37949 1xclA 235 1.65e+01 1e8aA 91 1.69e+01 1b4cA a.39.1.2 17188 1d2zB 153 1.75e+01 1d2zB a.77.1.2 18439 1k1xA 659 1.76e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 2fexA 188 1.78e+01 1lwjA 441 1.79e+01 b.71.1.1,c.1.8.1 74303,74304 1t3cA 421 1.79e+01 d.92.1.7 106343 1h3lA 87 1.79e+01 a.177.1.1 76639 1fyvA 161 1.80e+01 1fyvA c.23.2.1 31127 1fp1D 372 1.81e+01 1fpqA a.4.5.29,c.66.1.12 59939,59940 2basA 431 1.81e+01 3seb 238 1.90e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1dkfA 233 1.90e+01 3erdA a.123.1.1 19280 1swvA 267 1.91e+01 3crxA 343 1.93e+01 4crxA a.60.9.1,d.163.1.1 18101,42161 1kaeA 434 1.94e+01 c.82.1.2 72247 2fz4A 237 1.98e+01 1xl7A 612 1.99e+01 1se4 239 2.02e+01 3seb b.40.2.2,d.15.6.1 25187,37776 1ri5A 298 2.08e+01 c.66.1.34 97502 1d5mC 239 2.09e+01 3seb b.40.2.2,d.15.6.1 25185,37774 2bvpA 276 2.10e+01 1ecmA 109 2.10e+01 1ecmA a.130.1.1 19492 1kq3A 376 2.10e+01 e.22.1.2 68790 1w33A 181 2.10e+01 1dp3A 55 2.11e+01 1dp3A a.55.1.2 59128 1wy6A 172 2.11e+01 1mlwA 301 2.15e+01 d.178.1.1 79289 1fzpB 123 2.22e+01 1fznD a.4.5.28 19008 1g6hA 257 2.24e+01 1gajA c.37.1.12 60318 2a74A 643 2.26e+01 1eq2A 310 2.26e+01 1eq2A c.2.1.2 29814 1ccg 291 2.31e+01 1ryc a.93.1.1 18627 1g4yR 148 2.32e+01 1cll a.39.1.5 60252 1u04A 771 2.32e+01 b.34.14.1,c.55.3.10 107539,107540 1j6rA 214 2.32e+01 d.173.1.2 71598 1fpxA 352 2.34e+01 1fpxA a.4.5.29,c.66.1.12 59950,59951 1uhnA 189 2.38e+01 a.39.1.5 99399 1v02A 565 2.39e+01 c.1.8.4 108194 1kfuS 184 2.39e+01 a.39.1.8 68574 1cxqA 162 2.41e+01 1cxqA c.55.3.2 33621 1k75A 434 2.43e+01 c.82.1.2 68253 1ds4A 292 2.44e+01 1ryc a.93.1.1 59129 2f3yA 148 2.48e+01 1ryc 294 2.51e+01 1ryc a.93.1.1 18601 1pk5A 248 2.52e+01 a.123.1.1 88139 1rqlA 267 2.58e+01 c.108.1.3 97750 1qhhC 115 2.61e+01 1pjr 1pjr 724 2.65e+01 1pjr c.37.1.19,c.37.1.19 32391,32392 2eutA 294 2.66e+01 1dseA 292 2.67e+01 1ryc a.93.1.1 59130 1p57B 255 2.69e+01 b.47.1.2 94126 1irxA 523 2.69e+01 a.97.1.2,c.26.1.1 71378,71379 1a2f 291 2.70e+01 1ryc a.93.1.1 18619 1jdrA 294 2.72e+01 1ryc a.93.1.1 62908 2ahyA 110 2.75e+01 2btoA 473 2.75e+01 2f62A 161 2.75e+01 1pt7A 437 2.79e+01 c.123.1.1 95093 1mkrA 294 2.80e+01 a.93.1.1 84997 1g2nA 264 2.80e+01 1lbd a.123.1.1 60227 1j6pA 418 2.80e+01 b.92.1.4,c.1.9.9 77089,77090 2f2tA 161 2.81e+01 1eg5A 384 2.84e+01 1ecxA c.67.1.3 34429 2d2mB 142 2.96e+01 1ac4 294 2.98e+01 1ryc a.93.1.1 18657 1sd4A 126 2.99e+01 a.4.5.39 105428 2pgd 482 2.99e+01 2pgd a.100.1.1,c.2.1.6 18778,30190 1aa8A 347 2.99e+01 1an9A 1p1mA 406 3.00e+01 b.92.1.4,c.1.9.9 87696,87697 1a2g 291 3.03e+01 1ryc a.93.1.1 18620 2f4qA 346 3.04e+01 1xiuA 230 3.06e+01 1tvlA 454 3.06e+01 c.1.16.4 107366 1cy5A 97 3.07e+01 1cy5A a.77.1.3 18430 1lj9A 144 3.07e+01 a.4.5.28 78035 1b3aA 67 3.08e+01 1b3aA d.9.1.1 37410 1q7eA 428 3.08e+01 c.123.1.1 96035 1ghtA 105 3.08e+01 2rslA c.53.1.1 60526 1j1hA 144 3.15e+01 b.111.1.1 77056 1j55A 95 3.15e+01 a.39.1.2 77078 2rslA 140 3.21e+01 2rslA c.53.1.1 33345 2fxaA 207 3.22e+01 2ew2A 316 3.23e+01 2ygsA 92 3.24e+01 1cy5A a.77.1.3 18431 1gajA 257 3.25e+01 1gajA c.37.1.12 60416 1ltdA 506 3.25e+01 1gox c.1.4.1,d.120.1.1 28618,41086 1qxyA 252 3.27e+01 d.127.1.1 96565 1s3aA 102 3.27e+01 2d0oB 125 3.27e+01 1mfqC 129 3.27e+01 a.36.1.1 79046 1womA 271 3.29e+01 1paqA 189 3.33e+01 a.118.1.14 94413 1wy5A 317 3.40e+01 1jenB 67 3.44e+01 1jenB d.156.1.1 42029 1rlmA 271 3.44e+01 1eqtA 68 3.48e+01 1b3aA d.9.1.1 37412 1jcrA 377 3.48e+01 a.118.6.1 66506 2furA 209 3.50e+01 2a19B 284 3.56e+01 2a0kA 161 3.58e+01 1oq9A 363 3.63e+01 a.25.1.2 87257 1a6dB 543 3.63e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19489,30820,38937 1zbyA 294 3.66e+01 1z53A 294 3.67e+01 1ju2A 536 3.77e+01 c.3.1.2,d.16.1.1 77169,77170 1go3F 107 3.77e+01 a.60.8.2 65407 1wekA 217 3.79e+01 1ohuA 175 3.83e+01 f.1.4.1 93029 1sqiA 393 3.84e+01 d.32.1.3,d.32.1.3 105914,105915 1rlmB 271 3.88e+01 1q7zA 566 3.88e+01 c.1.21.2,c.1.26.1 96090,96091 1wvfA 520 3.92e+01 1scuA 288 3.94e+01 2scuA c.2.1.8,c.23.4.1 30307,31135 1cnzA 363 3.94e+01 1cnzA c.77.1.1 35061 2cyp 294 3.99e+01 1ryc a.93.1.1 18600 1qcwA 410 4.02e+01 1gox c.1.4.1 28622 1yucA 255 4.08e+01 1sffA 426 4.10e+01 c.67.1.4 105482 1jalA 363 4.15e+01 c.37.1.8,d.15.10.2 84138,84139 2ba2A 85 4.18e+01 2bce 581 4.18e+01 2bce c.69.1.1 34625 1sg6A 393 4.18e+01 e.22.1.1 105522 1nekD 115 4.23e+01 f.21.2.2 80432 1nsyA 271 4.24e+01 2nsyA c.26.2.1 31614 2b61A 377 4.27e+01 1aj5A 173 4.27e+01 1alvA a.39.1.8 17367 1a79A 171 4.29e+01 1a79A c.52.2.1,d.75.1.1 33340,39739 1kb9I 55 4.31e+01 f.23.14.1 77324 1yrrA 382 4.35e+01 1qamA 244 4.37e+01 2ercA c.66.1.24 34220 1c8uA 285 4.37e+01 1c8uA d.38.1.3,d.38.1.3 38547,38548 1yeyA 444 4.39e+01 1ahtH 259 4.39e+01 5ptp 1rw6A 210 4.40e+01 a.47.4.1 105113 1ahr 146 4.43e+01 1cll a.39.1.5 17287 1olrA 224 4.44e+01 b.29.1.11 93330 1e94F 449 4.47e+01 1do0A c.37.1.20 32443 1mvcA 240 4.49e+01 a.123.1.1 79499 1ki9A 192 4.51e+01 c.37.1.1 84404 1hufA 140 4.55e+01 1hufA d.195.1.1 61272 1b8rA 108 4.57e+01 1a75A a.39.1.4 17201 1dcs 311 4.58e+01 1dcs b.82.2.1 28124 2scuA 288 4.59e+01 2scuA c.2.1.8,c.23.4.1 30303,31131 1k8hA 133 4.66e+01 b.111.1.1 72176 1x3sA 195 4.71e+01 1aa2 108 4.73e+01 1bkrA a.40.1.1 17395 1vgmA 378 4.83e+01 1y1xA 191 4.83e+01 1lokA 291 4.83e+01 c.56.5.4 78122 1ak8 76 4.84e+01 1cll a.39.1.5 17281 1qbqA 333 4.90e+01 1ft1A a.118.6.1 19187 1osa 148 4.90e+01 1cll a.39.1.5 17300 1nu5A 370 4.90e+01 c.1.11.2,d.54.1.1 92183,92184 1mzbA 136 4.91e+01 a.4.5.42 91497 1zmdA 474 4.93e+01 1cf9A 753 4.93e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 1tllA 688 5.00e+01 b.43.4.1,c.23.5.2,c.25.1.4 107128,107129,107130 1gt6A 269 5.01e+01 c.69.1.17 76342 1gln 468 5.05e+01 1gln a.97.1.1,c.26.1.1 18752,31588 1ru3A 732 5.09e+01 e.26.1.3 97835 1sb8A 352 5.15e+01 c.2.1.2 105410 1amp 291 5.15e+01 1amp c.56.5.4 33837 1gr0A 367 5.18e+01 c.2.1.3,d.81.1.3 70379,70380 2fh5A 185 5.18e+01 1a6o 332 5.20e+01 1a6o 2gsaA 432 5.20e+01 2gsaA c.67.1.4 34446 2nsyA 271 5.22e+01 2nsyA c.26.2.1 31612 1ni4B 341 5.25e+01 c.36.1.7,c.48.1.2 85729,85730 1yruB 74 5.25e+01 2ghjA 118 5.26e+01 1p35A 299 5.32e+01 1p35A b.28.1.1 23925 1g5yA 238 5.36e+01 1lbd a.123.1.1 60294 1db1A 259 5.36e+01 1db1A a.123.1.1 19329 1vl5A 260 5.41e+01 c.66.1.41 108720 1j75A 67 5.41e+01 a.4.5.19 62673 1tib 269 5.41e+01 3tgl c.69.1.17 34738 1ft1A 377 5.43e+01 1ft1A a.118.6.1 19186 1pbwA 216 5.45e+01 1pbwA a.116.1.1 19103 1rxwA 336 5.54e+01 a.60.7.1,c.120.1.2 98059,98060 1w19A 160 5.54e+01 1wbpA 397 5.57e+01 1jcjA 260 5.61e+01 c.1.10.1 66499 1iseA 185 5.62e+01 d.67.3.1 90691 1khbA 625 5.67e+01 c.91.1.1,c.109.1.1 68606,68607 1glcG 501 5.67e+01 1glcG c.55.1.4,c.55.1.4 33519,33520 1zd3A 555 5.68e+01 1elvA 333 5.72e+01 5ptp b.47.1.2,g.18.1.1 59454,59455 1na6A 404 5.74e+01 b.142.1.1,c.52.1.22 91748,91749 1mioB 458 5.74e+01 1qguB c.92.2.3 35602 1rwtA 232 5.75e+01 f.43.1.1 97992 1xx1A 285 5.78e+01 1y89A 238 5.78e+01 1jb0F 164 5.82e+01 1jb0F f.23.16.1 62825 1wmaA 276 5.83e+01 1wrvA 308 5.84e+01 1np8A 159 5.86e+01 a.39.1.8 92022 1o6dA 163 5.86e+01 c.116.1.3 92567 5pal 109 5.87e+01 1a75A a.39.1.4 17215 1xb4A 202 5.89e+01 1p80A 753 5.89e+01 c.23.16.3,e.5.1.1 94337,94338 1z77A 200 5.90e+01 1sczA 233 5.98e+01 c.43.1.1 98802 1oaoC 729 5.98e+01 e.26.1.3 86746 1x42A 232 5.98e+01 1np3A 338 6.00e+01 a.100.1.2,c.2.1.6 85946,85947 1fcyA 236 6.02e+01 2lbd a.123.1.1 19282 1ngnA 155 6.04e+01 a.96.1.2 85697 1zq1C 633 6.05e+01 1wjxA 122 6.07e+01 1vj5A 555 6.07e+01 c.108.1.2,c.69.1.11 100799,100800 1cii 602 6.08e+01 1cii f.1.1.1,h.4.3.1 43381,45787 1yemA 179 6.08e+01 1j09A 468 6.08e+01 a.97.1.1,c.26.1.1 77025,77026 1o63A 219 6.12e+01 c.94.1.1 92540 1or7C 90 6.12e+01 a.180.1.1 87336 1qb2A 109 6.12e+01 1qb2A a.36.1.1 17125 1otjA 283 6.13e+01 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