# List of top-scoring protein chains for t2k-100-30-alpha 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 1k3iA 656 7.45e-02 b.1.18.2 68113 b.18.1.1 68114 b.69.1.1 68115 1gof 639 7.78e-02 1gof b.1.18.2 21807 b.18.1.1 23709 b.69.1.1 27631 1goh 639 1.37e-01 1gof b.1.18.2 21809 b.18.1.1 23711 b.69.1.1 27633 1wxrA 1048 1.81e-01 1axkA 394 2.57e-01 1axkA b.29.1.2 24181 b.29.1.11 24315 1cwvA 492 3.14e-01 1cwvA b.1.14.1 22373 b.1.14.1 22374 b.1.14.1 22375 b.1.14.1 22376 d.169.1.3 42442 1phd 414 3.37e-01 1phd a.104.1.1 18913 1dz4A 414 3.40e-01 1phd a.104.1.1 18903 1qmqA 414 3.43e-01 1phd a.104.1.1 18907 5cpp 414 3.73e-01 1phd a.104.1.1 18935 1phb 414 3.79e-01 1phd a.104.1.1 18906 1re9A 414 3.88e-01 1s9aA 257 5.14e-01 b.3.6.1 105379 1kypA 237 5.44e-01 d.22.1.1 73280 2fn0A 437 5.74e-01 1itbB 315 6.62e-01 1itbB b.1.1.4 21720 b.1.1.4 21721 b.1.1.4 21722 1acc 735 6.82e-01 1acc f.11.1.1 43828 1yrcA 414 7.10e-01 1phg 414 7.44e-01 1phd a.104.1.1 18910 1oxdA 227 7.65e-01 d.22.1.1 93687 2nlrA 234 1.01e+00 2nlrA b.29.1.11 24344 1b4vA 504 1.10e+00 1b8sA c.3.1.2 30334 d.16.1.1 37865 1ijhA 504 1.19e+00 c.3.1.2 66161 d.16.1.1 66162 2emo 237 1.26e+00 1ema d.22.1.1 38366 1a0qL 212 1.33e+00 8fabA b.1.1.1 20286 b.1.1.2 21278 1nlr 234 1.33e+00 2nlrA b.29.1.11 24345 1s7kA 182 1.35e+00 2d0oA 610 1.41e+00 1mxtA 504 1.42e+00 c.3.1.2 79671 d.16.1.1 79672 1ema 236 1.43e+00 1ema d.22.1.1 38339 2bsyA 278 1.44e+00 1nt0A 286 1.54e+00 b.23.1.1 86143 b.23.1.1 86144 g.3.11.1 86145 1n4wA 504 1.54e+00 c.3.1.2 91676 d.16.1.1 91677 1b8sA 504 1.92e+00 1b8sA c.3.1.2 30335 d.16.1.1 37866 1ogoX 574 1.93e+00 b.133.1.1 92925 b.80.1.10 92926 2axtO 247 1.97e+00 1n1pA 504 2.05e+00 c.3.1.2 91546 d.16.1.1 91547 1nr0A 611 2.08e+00 b.69.4.1 86078 b.69.4.1 86079 1ju2A 536 2.18e+00 c.3.1.2 77169 d.16.1.1 77170 1m3jA 471 2.19e+00 f.9.1.1 91182 1b9cA 236 2.38e+00 1ema d.22.1.1 38358 1jpc 109 2.52e+00 1b2pA b.78.1.1 27986 1xgyH 219 2.54e+00 1msaA 109 2.92e+00 1b2pA b.78.1.1 27987 1pjpA 226 3.02e+00 5ptp b.47.1.2 26301 1o20A 427 3.03e+00 c.82.1.1 86556 1ig3A 263 3.07e+00 1ig3A b.82.6.1 62358 c.100.1.1 62359 2aamA 309 3.13e+00 1sgzA 389 3.35e+00 b.50.1.2 98872 1s7mA 174 3.41e+00 b.144.1.1 98649 1m3iA 471 3.44e+00 f.9.1.1 91178 1e4fT 419 3.45e+00 1e4fT c.55.1.1 33453 c.55.1.1 33454 1w2tA 432 3.56e+00 1jv2A 957 3.57e+00 b.1.15.1 67334 b.1.15.1 67335 b.1.15.1 67336 b.69.8.1 67337 1fknA 391 3.74e+00 1fknA b.50.1.2 26879 1h6rA 236 3.87e+00 d.22.1.1 65683 2bsdA 264 3.92e+00 2bbkH 355 4.11e+00 2bbkH b.69.2.1 27634 1nhcA 336 4.15e+00 b.80.1.3 91879 1qcxA 359 4.57e+00 1qcxA b.80.1.2 28028 1ju3A 583 4.61e+00 b.18.1.13 67300 c.69.1.21 67301 1dmaA 214 4.67e+00 1aerA d.166.1.1 42251 1z4xA 532 4.68e+00 1klt 226 4.88e+00 5ptp b.47.1.2 26300 1czfA 362 5.05e+00 1czfA b.80.1.3 28031 1yal 218 5.15e+00 1cs8A d.3.1.1 37025 1yp2A 451 5.17e+00 1z4vA 532 5.18e+00 1e3uA 246 5.49e+00 1fofA e.3.1.1 42755 1nnlA 225 5.84e+00 c.108.1.4 85906 1uypA 432 5.99e+00 b.29.1.19 100176 b.67.2.3 100177 1aoqA 567 6.13e+00 1qksA a.3.1.2 15934 b.70.2.1 27692 1aerA 205 6.15e+00 1aerA d.166.1.1 42249 1k4fA 248 6.21e+00 e.3.1.1 68138 1gv9A 260 6.50e+00 b.29.1.13 70596 1knvA 293 6.53e+00 c.52.1.7 68707 1xg8A 111 6.71e+00 1fxzA 476 6.83e+00 b.82.1.2 65059 b.82.1.2 65060 1a3gA 308 7.06e+00 1daaA e.17.1.1 43286 1fofA 246 7.20e+00 1fofA e.3.1.1 42763 1k55A 246 7.27e+00 e.3.1.1 68156 2bibA 547 7.66e+00 1gl4A 285 7.75e+00 d.22.1.2 65286 g.3.11.5 65287 1jv2B 692 7.76e+00 b.1.15.1 67338 c.62.1.1 67339 d.200.1.1 67340 g.3.11.6 67341 g.3.11.6 67342 1x1iA 752 7.84e+00 1bihA 395 8.18e+00 1bihA b.1.1.4 21752 b.1.1.4 21753 b.1.1.4 21754 b.1.1.4 21755 2bm5A 186 8.41e+00 1jb7A 495 8.44e+00 1otcA b.40.4.3 62836 b.40.4.3 62837 b.40.4.3 62838 1f5jA 199 8.50e+00 1axkA b.29.1.11 24342 1t2bA 397 8.61e+00 1qksA 567 8.67e+00 1qksA a.3.1.2 15951 b.70.2.1 27710 1jmmA 377 8.69e+00 b.30.6.1 71749 1j0mA 752 9.05e+00 a.102.3.2 83910 b.24.1.1 83911 b.30.5.2 83912 1nn6A 228 9.06e+00 b.47.1.2 85893 1pvc2 271 9.08e+00 1aym2 1uacH 114 9.22e+00 b.1.1.1 99132 1clc 639 9.29e+00 1clc a.102.1.2 18835 b.1.18.2 21872 1pd21 199 9.29e+00 1pd21 1xhcA 367 9.38e+00 1xipA 388 9.66e+00 1onwA 390 9.66e+00 b.92.1.7 87172 c.1.9.13 87173 1otcA 495 9.75e+00 1otcA b.40.4.3 25307 b.40.4.3 25308 b.40.4.3 25309 1a0jA 223 9.77e+00 5ptp b.47.1.2 26002 1pfo 500 9.80e+00 1pfo f.9.1.1 43826 1vorW 173 9.94e+00 1fnf 368 9.96e+00 1fnf b.1.2.1 21972 b.1.2.1 21973 b.1.2.1 21974 b.1.2.1 21975 1ruxA 951 9.98e+00 1dhx 1g6sA 427 1.01e+01 1eps d.68.2.2 39584 1jxpA 186 1.02e+01 1jxpA b.47.1.3 26402 1jmxB 349 1.02e+01 b.69.2.2 66906 1tffA 234 1.03e+01 d.3.1.11 106854 3kvt 115 1.03e+01 1t1dA d.42.1.2 38642 1v5vA 401 1.04e+01 1itvA 195 1.08e+01 b.66.1.1 76791 2aujD 309 1.10e+01 1ve6A 582 1.11e+01 2pil 159 1.12e+01 2pil d.24.1.1 38376 1pfxC 235 1.17e+01 5ptp b.47.1.2 26353 1gnyA 153 1.18e+01 b.18.1.11 65404 1cgt 684 1.20e+01 1cxlA b.1.18.2 21815 b.3.1.1 22484 b.71.1.1 27722 c.1.8.1 28709 1h54A 754 1.21e+01 a.102.1.4 60634 b.30.5.3 60635 1ik6A 369 1.21e+01 c.36.1.7 66174 c.48.1.2 66175 1rzfH 235 1.21e+01 b.1.1.1 98150 b.1.1.2 98151 1t5rA 284 1.22e+01 f.6.1.1 106465 1axsB 221 1.23e+01 1mfa b.1.1.1 20201 b.1.1.2 21217 2bspA 420 1.25e+01 1pcl b.80.1.1 28023 1ttuA 477 1.27e+01 b.1.18.1 107305 b.2.5.8 107306 b.42.7.1 107307 1pz7A 204 1.28e+01 b.29.1.4 95405 2blcA 238 1.28e+01 1wdaA 670 1.29e+01 b.2.9.1 109243 b.6.1.6 109244 d.126.1.5 109245 1eps 427 1.30e+01 1eps d.68.2.2 39586 1dkuA 317 1.31e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1mn4A 282 1.31e+01 b.2.5.7 79313 1f3eA 386 1.34e+01 1pud c.1.20.1 29661 1x31C 206 1.35e+01 1z9fA 153 1.37e+01 1hg8A 349 1.37e+01 b.80.1.3 65830 2madH 373 1.38e+01 2bbkH b.69.2.1 27639 1djnA 729 1.38e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 1y4wA 518 1.40e+01 1qa7B 217 1.40e+01 1havA b.47.1.4 26426 1a0sP 413 1.41e+01 1a0tP f.4.3.2 43797 3rp2A 224 1.49e+01 1a7s b.47.1.2 26298 1rxwA 336 1.49e+01 a.60.7.1 98059 c.120.1.2 98060 1ztxH 219 1.51e+01 1tme1 274 1.52e+01 2mev1 1lp3A 519 1.52e+01 b.121.5.2 74169 2f6kA 307 1.54e+01 1qbiA 454 1.54e+01 1c9uA b.68.2.1 27619 16pk 415 1.55e+01 16pk c.86.1.1 35454 1rlmA 271 1.57e+01 1rwhA 757 1.58e+01 a.102.3.2 97984 b.24.1.1 97985 b.30.5.2 97986 1h4uA 265 1.58e+01 1h4uA d.22.1.2 60622 g.3.11.5 60623 2b8lA 405 1.59e+01 1q47A 495 1.60e+01 b.69.12.1 104532 1kb0A 677 1.61e+01 a.3.1.6 68378 b.70.1.1 68379 1djqA 729 1.61e+01 2tmdA c.1.4.1 28614 c.3.1.1 30315 c.4.1.1 30600 2bjrA 368 1.62e+01 1oe9A 795 1.65e+01 b.34.3.1 92792 c.37.1.9 92793 1w50A 411 1.65e+01 b.50.1.2 109173 12e8H 221 1.66e+01 1igtB b.1.1.1 20269 b.1.1.2 21269 1a0tP 413 1.66e+01 1a0tP f.4.3.2 43794 1oa4A 222 1.70e+01 b.29.1.11 86731 1ujkA 147 1.72e+01 a.118.9.2 99457 1k4gA 386 1.73e+01 c.1.20.1 72054 1a1rA 198 1.75e+01 1jxpA b.47.1.3 26406 1ay2 159 1.77e+01 2pil d.24.1.1 38377 1iirA 415 1.77e+01 1iirA c.87.1.5 62453 2a46A 238 1.78e+01 1p30A 952 1.81e+01 b.121.2.2 93964 b.121.2.2 93965 1yocA 147 1.85e+01 1w7jA 795 1.88e+01 1jmaA 290 1.89e+01 b.1.1.1 63177 1dj0A 264 1.90e+01 1dj0A d.265.1.1 90337 1kjkA 64 1.92e+01 d.10.1.4 72613 2c26A 260 1.93e+01 1rhi1 288 1.94e+01 1pov1 1afoA 40 1.96e+01 1afoA j.35.1.1 46257 1rypB 250 1.98e+01 1rypB d.153.1.4 41933 1htyA 1015 1.99e+01 a.8.3.1 83064 b.30.5.6 83065 c.6.2.1 83066 1j2zA 270 1.99e+01 b.81.1.1 90805 1kqaA 203 2.01e+01 b.81.1.3 72868 1krrA 203 2.01e+01 b.81.1.3 72899 1h3gA 601 2.02e+01 b.1.18.2 90594 b.71.1.1 90595 c.1.8.1 90596 2fxqA 264 2.02e+01 1rloA 271 2.03e+01 1mz5A 638 2.03e+01 b.29.1.15 79679 b.68.1.1 79680 1xnkA 196 2.04e+01 1h1aA 191 2.10e+01 b.29.1.11 83450 1yymG 313 2.11e+01 1mexL 213 2.12e+01 b.1.1.1 91259 b.1.1.2 91260 1em2A 229 2.12e+01 1em2A d.129.3.2 41321 1rlmB 271 2.12e+01 1ibsA 317 2.13e+01 c.61.1.2 66107 c.61.1.2 66108 1xhkA 187 2.13e+01 1ee6A 197 2.14e+01 1ee6A b.80.1.1 28024 1sr4B 261 2.14e+01 d.151.1.1 105949 1scs 237 2.15e+01 1nls b.29.1.1 23930 2bw8A 227 2.15e+01 1lay 256 2.16e+01 1lay b.57.1.1 27014 1n1tA 641 2.19e+01 b.29.1.15 79821 b.68.1.1 79822 1j1xH 114 2.19e+01 b.1.1.1 77063 1d5bB 221 2.20e+01 8fabA b.1.1.1 20205 b.1.1.2 21221 1h0bA 256 2.21e+01 b.29.1.11 83422 1pvuA 154 2.23e+01 3pviA c.52.1.6 33306 1o94A 729 2.25e+01 c.1.4.1 81200 c.3.1.1 81201 c.4.1.1 81202 1jwgA 147 2.26e+01 a.118.9.2 71911 1uf2C 421 2.31e+01 a.115.1.3 99291 b.19.1.1 99292 1go3E 187 2.31e+01 b.40.4.5 83054 d.230.1.1 83055 1o12A 376 2.33e+01 b.92.1.5 80758 c.1.9.10 80759 2ffsA 157 2.34e+01 1wcqA 601 2.36e+01 1q4gA 553 2.36e+01 a.93.1.2 95789 g.3.11.1 95790 1zpdA 568 2.38e+01 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1dkrA 317 2.40e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1hzxA 349 2.40e+01 1f88A f.13.1.2 61466 1y7bA 542 2.40e+01 1lkvX 232 2.40e+01 a.118.14.1 73980 1sw6A 327 2.40e+01 1sw6A d.211.1.1 19176 2c1iA 431 2.43e+01 1l9hA 349 2.44e+01 f.13.1.2 73720 1pw4A 451 2.46e+01 f.38.1.1 95198 1xbsA 149 2.46e+01 1v8yA 170 2.46e+01 1i1kA 309 2.47e+01 1daaA e.17.1.1 61533 1bt7 186 2.49e+01 1jxpA b.47.1.3 26418 1prn 289 2.49e+01 3prn f.4.3.1 43762 1iweA 457 2.50e+01 c.37.1.10 71486 2bl9A 238 2.51e+01 3prn 289 2.54e+01 3prn f.4.3.1 43761 2azeC 46 2.54e+01 1dowA 205 2.56e+01 1dovA a.24.9.1 16626 1vm6A 228 2.57e+01 c.2.1.3 108876 d.81.1.3 108877 1do6A 124 2.58e+01 1do6A b.1.13.1 22361 1ztxL 212 2.58e+01 1nxjA 183 2.59e+01 c.8.7.1 86382 1cf1A 404 2.60e+01 1cf1A b.1.18.11 21907 b.1.18.11 21908 2cxkA 95 2.60e+01 2pviA 157 2.61e+01 3pviA c.52.1.6 33302 1lcyA 325 2.62e+01 b.36.1.4 73834 b.47.1.1 73835 1z02A 446 2.62e+01 2bnh 457 2.64e+01 1a4yA c.10.1.1 30850 1mvpA 124 2.64e+01 2rspB b.50.1.1 26775 1ikpA 613 2.67e+01 b.29.1.7 66182 d.166.1.1 66183 f.1.5.1 66184 1a0nB 69 2.69e+01 1bbzA b.34.2.1 24469 1aerB 195 2.71e+01 1aerA d.166.1.1 42250 1h1iD 350 2.71e+01 b.82.1.5 76472 1wpoB 256 2.74e+01 1lay b.57.1.1 27013 1hwwA 1015 2.75e+01 a.8.3.1 83067 b.30.5.6 83068 c.6.2.1 83069 1cknA 330 2.79e+01 1ckmA b.40.4.6 25360 d.142.2.3 41587 2tmdA 729 2.80e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1cpn 208 2.83e+01 1axkA b.29.1.2 24175 1b3oA 514 2.83e+01 1ak5 c.1.5.1 28640 1fkoB 440 2.83e+01 1rthA e.8.1.2 43095 2c4xA 260 2.86e+01 2ashA 381 2.86e+01 1suuA 312 2.87e+01 b.68.10.1 99006 1mnnA 340 2.87e+01 b.2.5.7 79324 1c7sA 858 2.90e+01 1qba b.1.18.2 21812 b.2.2.3 22408 c.1.8.6 29011 d.92.2.1 40410 1xjcA 169 2.95e+01 3pviA 157 2.98e+01 3pviA c.52.1.6 33300 1srqA 341 3.01e+01 e.55.1.1 105967 1na6A 404 3.02e+01 b.142.1.1 91748 c.52.1.22 91749 1umdB 324 3.03e+01 c.36.1.7 99600 c.48.1.2 99601 1yfsA 465 3.03e+01 1avbA 226 3.03e+01 1led b.29.1.1 24158 35c8H 217 3.03e+01 8fabA b.1.1.1 20297 b.1.1.2 21289 1ohfA 644 3.03e+01 b.121.4.8 93014 1zclA 180 3.08e+01 1ajkA 214 3.13e+01 1axkA b.29.1.2 24176 2awaA 390 3.15e+01 1ic7H 114 3.15e+01 1f3rB b.1.1.1 62258 1p2zA 968 3.18e+01 b.121.2.2 93962 b.121.2.2 93963 1jmuB 666 3.18e+01 1aomA 567 3.21e+01 1qksA b.70.2.1 27694 1m1nB 522 3.25e+01 c.92.2.3 78418 1i7oA 429 3.25e+01 1i7oA d.177.1.1 61893 d.177.1.1 61894 1a3rH 218 3.28e+01 1igtB b.1.1.1 19781 b.1.1.2 20891 2bkdN 134 3.28e+01 1hxkA 1015 3.28e+01 a.8.3.1 83070 b.30.5.6 83071 c.6.2.1 83072 1b12A 248 3.29e+01 1b12A b.87.1.2 28388 1mkmA 249 3.30e+01 a.4.5.33 79242 d.110.2.2 79243 1iyhA 198 3.30e+01 a.45.1.1 83790 c.47.1.5 83791 1s3rA 535 3.31e+01 1nls 237 3.31e+01 1nls b.29.1.1 23928 2a74A 643 3.31e+01 1mtyD 512 3.38e+01 1mhyD a.25.1.2 16742 1an7A 136 3.40e+01 1seiA d.140.1.1 41465 2btzA 394 3.40e+01 1i8dA 213 3.41e+01 b.43.4.3 61953 b.43.4.3 61954 1h1iC 350 3.41e+01 b.82.1.5 76471 1sfp 114 3.41e+01 1sfp b.23.1.1 23895 1by5A 714 3.42e+01 1by5A f.4.3.3 43800 1kzhA 555 3.43e+01 c.89.1.1 73361 1mmoD 512 3.43e+01 1mhyD a.25.1.2 16770 1dovA 181 3.44e+01 1dovA a.24.9.1 16627 1o75A 415 3.44e+01 b.1.20.1 81117 b.1.20.1 81118 b.120.1.1 81119 1fi8A 228 3.44e+01 5ptp b.47.1.2 26374 1dqiA 124 3.46e+01 1do6A b.1.13.1 22357 1ltoA 245 3.47e+01 b.47.1.2 84707 1shfA 59 3.48e+01 1bbzA b.34.2.1 24462 1dxjA 242 3.48e+01 1cnsA d.2.1.1 36244 1bh3 289 3.50e+01 3prn f.4.3.1 43766 1ecmA 109 3.51e+01 1ecmA a.130.1.1 19492 1xdyA 298 3.53e+01 1yq2A 1024 3.55e+01 1k8tA 510 3.57e+01 e.41.1.1 68316 1xfxA 777 3.58e+01 2apoA 357 3.59e+01 1f82A 424 3.63e+01 1f82A d.92.1.7 40307 1pud 386 3.67e+01 1pud c.1.20.1 29658 1eemA 241 3.68e+01 1eemA a.45.1.1 17717 c.47.1.5 33011 1ev2E 220 3.69e+01 1cvsC b.1.1.4 21738 b.1.1.4 21739 1qvbA 481 3.69e+01 1qvbA c.1.8.4 28983 1rwrA 301 3.69e+01 b.80.1.11 97990 1xfdA 723 3.71e+01 1oq1A 223 3.73e+01 b.29.1.17 93408 1pxgA 382 3.78e+01 c.1.20.1 95287 1gv3A 248 3.79e+01 a.2.11.1 70585 d.44.1.1 70586 2be6D 37 3.80e+01 1x24A 180 3.82e+01 1ile 821 3.83e+01 1ile a.27.1.1 16924 b.51.1.1 26889 c.26.1.1 31591 2mprA 421 3.84e+01 2mprA f.4.3.2 43788 1h4rA 314 3.89e+01 a.11.2.1 65616 b.55.1.5 65617 d.15.1.4 65618 1azgB 67 3.92e+01 1bbzA b.34.2.1 24471 1kmtA 141 3.95e+01 b.1.18.8 77442 1ahtH 259 3.96e+01 5ptp 1gttA 429 3.96e+01 d.177.1.1 70529 d.177.1.1 70530 1ckmA 330 3.98e+01 1ckmA b.40.4.6 25358 d.142.2.3 41585 1oaoC 729 3.99e+01 e.26.1.3 86746 1ve9A 347 3.99e+01 c.4.1.2 100571 d.16.1.3 100572 1dqqA 214 3.99e+01 8fabA b.1.1.1 20420 b.1.1.2 21390