# 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.soe.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 2itbA 206 1.55e-01 1h6gA 256 7.26e-01 1h6gA a.24.9.1,a.24.9.1 60669,60670 1pfvA 551 1.34e+00 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 1f4lA 551 1.37e+00 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 1qqtA 551 1.38e+00 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 16923,31590,45175 3bqoA 211 1.54e+00 1mxrA 375 1.57e+00 a.25.1.2 85197 1ymtA 246 1.75e+00 1krqA 167 2.67e+00 a.25.1.1 68855 1av8A 340 3.09e+00 1xikA a.25.1.2 16796 2f6hX 419 3.24e+00 1t7rA 269 3.38e+00 a.123.1.1 106635 1xikA 375 3.43e+00 1xikA a.25.1.2 16784 1ribA 375 3.59e+00 1xikA a.25.1.2 16788 1vkeA 133 3.97e+00 a.152.1.2 108650 3caxA 369 4.05e+00 2ax9A 256 4.12e+00 a.123.1.1 127481 2ax8A 256 4.19e+00 1biqA 375 4.37e+00 1xikA a.25.1.2 16786 2ax6A 256 4.93e+00 a.123.1.1 127479 1txdA 385 5.38e+00 a.87.1.1,b.55.1.1 107422,107423 2vpzC 253 5.54e+00 3c6gA 479 6.51e+00 2h7oA 303 6.59e+00 1n97A 389 6.69e+00 a.104.1.1 80335 1csh 435 6.97e+00 1csh 1cshA 435 6.97e+00 a.103.1.1 18880 1rp3A 239 7.44e+00 a.4.13.1,a.4.13.2,a.177.1.1 97678,97679,97680 1jfgA 374 7.59e+00 a.128.1.5 66636 2aelA 374 7.84e+00 1h6oA 204 7.95e+00 a.146.1.1 60689 1ps1A 337 8.38e+00 1ps1A a.128.1.4 19450 1jsdB 176 8.91e+00 h.3.1.1 63259 2uxwA 607 9.06e+00 1tqyA 424 9.59e+00 c.95.1.1,c.95.1.1 107245,107246 1wwmA 190 1.03e+01 a.132.1.3 121363 2pg0A 385 1.07e+01 1kiyA 374 1.10e+01 a.128.1.5 72555 1yyqA 374 1.11e+01 1jpnA 296 1.12e+01 a.24.13.1,c.37.1.10 67039,67040 2oewA 380 1.12e+01 1twfB 1224 1.14e+01 e.29.1.1 112726 3c3rA 380 1.21e+01 1h68A 239 1.21e+01 f.13.1.1 118486 1ls1A 295 1.23e+01 a.24.13.1,c.37.1.10 78170,78171 1epwA 1290 1.24e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1ng1 294 1.28e+01 1ng1 1oj7A 408 1.34e+01 e.22.1.2 103971 1qusA 322 1.36e+01 1ltm d.2.1.6 36991 1iw0A 215 1.40e+01 a.132.1.1 83720 1r03A 182 1.45e+01 a.25.1.1 104675 1z21A 112 1.47e+01 a.243.1.2 124367 1jgjA 217 1.52e+01 1c3wA f.13.1.1 62952 1ltm 320 1.52e+01 1ltm 1yucA 255 1.52e+01 1wzdA 215 1.54e+01 a.132.1.1 121493 1cfr 285 1.58e+01 1cfr 1cfrA 285 1.58e+01 c.52.1.7 33312 1x4tA 92 1.60e+01 a.2.15.1 121698 2oltA 227 1.62e+01 2fm9A 215 1.73e+01 a.257.1.1 133770 1h2sA 225 1.80e+01 f.13.1.1 76578 3bdzA 397 1.80e+01 2ps5A 374 1.81e+01 1h21A 247 1.82e+01 a.138.1.3 76510 3biqA 467 1.90e+01 1p7tA 731 1.99e+01 c.1.13.1 94319 2nwlA 422 2.00e+01 2oexA 351 2.01e+01 1t2bA 397 2.02e+01 1uedA 406 2.09e+01 a.104.1.1 99256 1p8cA 145 2.13e+01 a.152.1.2 94354 1sayA 361 2.14e+01 1sayA c.2.1.4,c.23.12.2 30102,31362 1wwiA 148 2.17e+01 a.22.1.4 121362 1au1A 166 2.24e+01 1ifa a.26.1.3 16889 1pjcA 361 2.24e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1qbqA 333 2.28e+01 1ft1A a.118.6.1 19187 1onxA 390 2.31e+01 b.92.1.7,c.1.9.13 87176,87177 3ck6A 252 2.39e+01 1qb2A 109 2.41e+01 1qb2A a.36.1.1 17125 1ybqB 390 2.44e+01 2lbd 267 2.48e+01 2lbd 1fcyA 236 2.51e+01 2lbd a.123.1.1 19282 2ifuA 307 2.55e+01 1zu4A 320 2.60e+01 3d9nA 145 2.63e+01 2j67A 178 2.65e+01 1glqA 209 2.66e+01 1pgtA a.45.1.1,c.47.1.5 17588,32882 1h99A 224 2.66e+01 a.142.1.1,a.142.1.1 60814,60815 1bvp1 349 2.73e+01 1bvp1 1bjt 793 2.78e+01 1bjt 1bjtA 793 2.78e+01 e.11.1.1 43249 2aaxA 275 2.83e+01 1hz4A 373 2.83e+01 a.118.8.2 65960 2bptA 861 2.85e+01 a.118.1.1 128951 1k0fA 277 2.89e+01 c.92.2.2 71974 1wyuB 474 2.95e+01 c.67.1.7 121453 1toaA 313 2.96e+01 1toaA c.92.2.2 35598 1rtwA 220 3.03e+01 a.132.1.3 97823 2r40D 266 3.03e+01 1i5pA 633 3.07e+01 1i5pA b.18.1.3,b.77.2.1,f.1.3.1 61817,61818,61819 2px6A 316 3.09e+01 1za0A 275 3.10e+01 a.25.1.2 124774 2o9gA 234 3.16e+01 1sw6A 327 3.18e+01 1sw6A d.211.1.1 19176 2c2jA 211 3.20e+01 1k04A 162 3.21e+01 a.24.14.1 67904 1sedA 117 3.25e+01 a.219.1.1 105449 1pb6A 212 3.28e+01 a.4.1.9,a.121.1.1 88017,88018 2gb7A 305 3.30e+01 2q9fA 456 3.33e+01 2a6tA 271 3.35e+01 a.242.1.1,d.113.1.7 126309,126310 2c0wA 50 3.38e+01 1maz 221 3.48e+01 1maz 1tn6A 382 3.49e+01 a.118.6.1 112527 2or0A 414 3.51e+01 2arkA 188 3.52e+01 c.23.5.8 127202 2yzrA 330 3.52e+01 2nnwA 376 3.53e+01 2zfoD 155 3.68e+01 1fkmA 396 3.70e+01 1fkmA a.69.2.1,a.69.2.1 18315,18316 2awiA 317 3.71e+01 a.35.1.11,a.118.8.4 127435,127436 1u19A 349 3.72e+01 f.13.1.2 112953 1cqxA 403 3.77e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 1v54A 514 3.86e+01 f.24.1.1 100321 1afrA 345 3.87e+01 1afrA a.25.1.2 16805 2avkA 136 3.89e+01 2bdwA 362 3.91e+01 2hr3A 147 3.91e+01 a.4.5.28 136678 1onwA 390 4.01e+01 b.92.1.7,c.1.9.13 87172,87173 3b96A 587 4.03e+01 2occA 514 4.07e+01 2occA f.24.1.1 43518 2qf9A 179 4.11e+01 1v4aA 440 4.22e+01 a.24.16.4,d.218.1.9 108350,108351 1qkrA 188 4.23e+01 1qkrA a.24.9.1 16628 2dbhA 102 4.25e+01 1pgtA 210 4.26e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 2h6fA 382 4.27e+01 a.118.6.1 136185 1pbe 394 4.29e+01 1pbe 1pbeA 394 4.29e+01 c.3.1.2,d.16.1.2 30338,37869 1aqwA 209 4.30e+01 1pgtA a.45.1.1,c.47.1.5 17517,32811 2hi4A 495 4.30e+01 1ovlA 271 4.33e+01 a.123.1.1 87455 1giqA 413 4.34e+01 d.166.1.1,d.166.1.1 76224,76225 2np5A 203 4.34e+01 a.4.1.9,a.121.1.1 138424,138425 3c1jA 424 4.35e+01 2bb6A 414 4.36e+01 1qgtA 149 4.42e+01 1qgtA a.62.1.1 18135 1k0iA 394 4.46e+01 c.3.1.2,d.16.1.2 67942,67943 1mfqC 129 4.47e+01 a.36.1.1 79046 1mhlC 466 4.49e+01 1mhlC 1a8rA 221 4.51e+01 1a8rA d.96.1.1 40587 1kmkA 406 4.53e+01 c.67.1.3 68696 1cj3A 392 4.55e+01 1pbe c.3.1.2,d.16.1.2 30347,37878 2a2rA 210 4.57e+01 a.45.1.1,c.47.1.5 126058,126059 1gakA 141 4.64e+01 1gakA a.19.1.1 16415 3bhcA 249 4.65e+01 1omwA 689 4.67e+01 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 2i5uA 83 4.71e+01 1jf9A 408 4.76e+01 1c0nA c.67.1.3 62931 1lbkA 208 4.78e+01 a.45.1.1,c.47.1.5 73809,73810 1c8bA 371 4.81e+01 1c8bA c.56.1.2 59082 2quqA 562 4.90e+01 1x3zB 72 4.93e+01 a.189.1.1 121674 1vkmA 297 4.98e+01 c.138.1.1 108670 2h1nA 567 5.01e+01 1brwA 433 5.07e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 2dvmA 439 5.10e+01 1d8hA 311 5.15e+01 1d8iA d.63.1.1 39544 1unlD 208 5.15e+01 a.74.1.1 113326 1iybA 208 5.19e+01 d.124.1.1 90720 1fchA 368 5.20e+01 1fchA a.118.8.1 19212 1souA 194 5.28e+01 c.124.1.6 105858 1d8cA 723 5.28e+01 1d8cA c.1.13.1 29325 1a6dA 545 5.29e+01 1a6dA a.129.1.2,c.8.5.2,d.56.1.2 19488,30819,38936 2i0mA 216 5.30e+01 2veqA 565 5.30e+01 2qsfX 171 5.35e+01 2e9xA 149 5.37e+01 1a93A 34 5.41e+01 1a93A h.1.3.1 45543 1qu7A 227 5.49e+01 1qu7A h.4.5.1 45789 1ykjA 394 5.53e+01 1gkzA 388 5.59e+01 a.29.5.1,d.122.1.4 65268,65269 2a19B 284 5.67e+01 2ddhA 661 5.75e+01 a.29.3.2,a.29.3.2,e.6.1.2 131394,131395,131396 1kqfC 217 5.78e+01 f.21.1.1 72874 1ash 150 5.79e+01 1ash 1ashA 150 5.79e+01 a.1.1.2 15622 2dy1A 665 5.79e+01 1a75A 108 5.82e+01 1a75A a.39.1.4 17216 1vf1A 229 5.86e+01 1eqfA 280 6.00e+01 1eqfA a.29.2.1,a.29.2.1 16972,16973 1yoyA 175 6.08e+01 a.211.1.1 123795 1v2aA 210 6.14e+01 a.45.1.1,c.47.1.5 100263,100264 2gm6A 208 6.17e+01 1a9cA 221 6.25e+01 1a8rA d.96.1.1 40602 17gsA 210 6.32e+01 1pgtA a.45.1.1,c.47.1.5 17524,32818 2ot3A 274 6.33e+01 a.222.1.1 139311 2h79A 269 6.48e+01 1ji0A 240 6.53e+01 c.37.1.12 71665 3bg2A 444 6.56e+01 1jm0A 50 6.59e+01 k.8.1.1 66870 1qjaA 245 6.61e+01 1qjaA a.118.7.1 19204 1y76A 62 6.66e+01 a.194.1.1 122683 1ar1A 558 6.67e+01 2occA f.24.1.1 43618 1msk 331 6.68e+01 1msk 1mskA 331 6.68e+01 d.173.1.1 42495 1zejA 293 6.70e+01 1cwyA 500 6.75e+01 1cwyA c.1.8.1 28789 1eswA 500 6.81e+01 1cwyA c.1.8.1 59500 2pbeA 294 6.81e+01 1tm0A 350 6.81e+01 d.21.1.3 107147 3c02A 258 6.83e+01 2b5dX 528 6.85e+01 a.8.3.3,c.6.2.4 127886,127887 2hr2A 159 6.91e+01 1otkA 249 6.94e+01 a.25.1.2 93521 1bbhA 131 6.98e+01 1bbhA a.24.3.2 16546 1keyA 235 7.05e+01 a.118.16.1 72389 1b25A 619 7.12e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 2pq8A 278 7.14e+01 2givA 295 7.18e+01 d.108.1.1 135253 2qkmB 266 7.33e+01 1r0dA 206 7.43e+01 a.216.1.1 104715 3crjA 199 7.44e+01 1e70M 501 7.63e+01 1e70M c.1.8.4 28926 1zs4A 83 7.63e+01 a.35.1.9 125585 2paqA 201 7.66e+01 a.211.1.1 139643 1e4mM 501 7.74e+01 1e70M c.1.8.4 59226 2azjA 289 7.78e+01 1qhaA 917 7.79e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33467,33468,33469,33470 2ph5A 480 7.81e+01 1ytzT 107 7.87e+01 h.1.25.1 124024 1a28A 256 7.87e+01 1a28A a.123.1.1 19290 1ft1A 377 7.87e+01 1ft1A a.118.6.1 19186 1nr6A 473 7.88e+01 a.104.1.1 92085 1p7gA 222 7.90e+01 a.2.11.1,d.44.1.1 94223,94224 1vqrA 297 7.94e+01 a.211.1.3 114015 2j2fA 363 7.97e+01 1izoA 417 7.97e+01 a.104.1.1 83851 2grmA 317 7.99e+01