# List of top-scoring protein chains for t2k-100-30-str2 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 1q48A 134 7.67e-02 unknown_sccs -9776 1rvkA 382 1.86e-01 c.1.11.2 -5568 d.54.1.1 -9826 1ec7A 446 3.33e-01 1bqg c.1.11.2 29218 d.54.1.1 38862 1jdfA 447 3.44e-01 c.1.11.2 62897 d.54.1.1 62898 1mdl 359 3.82e-01 2mnr c.1.11.2 29247 d.54.1.1 38891 2mnr 357 7.02e-01 2mnr c.1.11.2 29245 d.54.1.1 38889 1ba1 386 8.08e-01 1ba1 c.55.1.1 33387 c.55.1.1 33388 1bupA 386 8.28e-01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1dkxA 219 8.54e-01 1dkzA unknown_sccs -446 unknown_sccs -3061 1dkzA 219 8.71e-01 1dkzA unknown_sccs -445 unknown_sccs -3060 1kk8B 139 1.06e+00 a.39.1.5 77430 1kay 381 1.23e+00 1ba1 c.55.1.1 33385 c.55.1.1 33386 1bqg 451 1.27e+00 1bqg c.1.11.2 29217 d.54.1.1 38861 1j54A 186 1.34e+00 c.55.3.5 77077 1wdcB 156 1.99e+00 1wdcB a.39.1.5 17302 1a8d 452 2.22e+00 1a8d b.29.1.6 24262 b.42.4.2 25607 1ihrA 76 2.23e+00 1ihrA d.212.1.2 62392 1exqA 154 2.24e+00 1b9dA c.55.3.2 33646 1nu5A 370 2.42e+00 c.1.11.2 -5565 d.54.1.1 -9823 1ekeA 230 2.44e+00 1ekeA c.55.3.1 33572 1diwA 441 2.68e+00 1a8d b.29.1.6 24264 b.42.4.2 25609 1gqyA 475 2.78e+00 c.5.1.1 83305 c.59.1.1 83306 c.72.2.1 83307 1scmB 145 2.79e+00 1wdcB a.39.1.5 17304 1lshB 319 3.26e+00 f.7.1.1 74245 1i6iA 366 3.41e+00 1bg2 c.37.1.9 61844 1fiuA 286 3.70e+00 1fiuA c.52.1.10 33317 1d4xG 126 4.10e+00 1d0nA d.109.1.1 59109 1nm1G 125 4.37e+00 d.109.1.1 80653 1yagG 125 4.39e+00 1d0nA d.109.1.1 40846 1jpdX 324 4.66e+00 c.1.11.2 67014 d.54.1.1 67015 1bl3A 160 4.73e+00 1b9dA c.55.3.2 33655 1s1dA 331 4.91e+00 unknown_sccs -4566 1xgsA 295 4.94e+00 1bn5 a.4.5.25 16216 d.127.1.1 41153 1dmgA 225 4.94e+00 1dmgA c.22.1.1 31036 1b9dA 163 5.10e+00 1b9dA c.55.3.2 33649 1hyvA 166 5.35e+00 1b9dA c.55.3.2 61424 1o6dA 163 5.50e+00 c.116.1.3 -6689 1rlaA 323 5.80e+00 1d3vA c.42.1.1 32561 1b0uA 262 5.91e+00 1b0uA c.37.1.12 32370 1d0hA 469 6.15e+00 1a8d b.29.1.6 24265 b.42.4.2 25610 1iz0A 302 6.23e+00 b.35.1.2 83821 c.2.1.1 83822 1khiA 176 6.28e+00 b.34.5.2 77408 b.40.4.5 77409 1itg 166 6.60e+00 1b9dA c.55.3.2 33661 1a27 289 6.88e+00 1fds c.2.1.2 29839 1p3dA 475 7.24e+00 c.5.1.1 87728 c.59.1.1 87729 c.72.2.1 87730 1o5xA 248 7.48e+00 c.1.1.1 -5157 1g0oA 283 7.59e+00 1ybvA c.2.1.2 60181 1fds 327 7.61e+00 1fds c.2.1.2 29838 1a0cA 438 7.64e+00 1a0cA c.1.15.3 29529 1ma3A 253 7.64e+00 c.31.1.5 78883 1fdt 327 7.91e+00 1fds c.2.1.2 29841 1jtvA 327 7.92e+00 c.2.1.2 84230 1h10A 125 8.28e+00 b.55.1.1 83446 1i5rA 327 8.41e+00 c.2.1.2 83668 1ojrA 274 8.50e+00 c.74.1.1 -8441 1qi6A 475 8.51e+00 1euhA c.82.1.1 35373 1i5sA 367 8.84e+00 1bg2 c.37.1.9 61822 1k1vA 41 8.91e+00 a.37.1.1 71999 1d0nA 729 9.16e+00 1d0nA d.109.1.1 40834 d.109.1.1 40835 d.109.1.1 40836 d.109.1.1 40837 d.109.1.1 40838 d.109.1.1 40839 1fsz 372 9.17e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1d3vA 323 9.29e+00 1d3vA c.42.1.1 32559 1o08A 221 9.38e+00 c.108.1.6 86525 1huxA 270 9.77e+00 1huxA c.55.1.5 61278 1r71A 178 9.79e+00 1zpdA 568 9.87e+00 1zpdA c.31.1.3 31741 c.36.1.5 31785 c.36.1.9 31786 1qmhA 347 9.87e+00 1qmhA c.47.2.1 33082 d.68.2.1 39568 1uwvA 433 9.97e+00 unknown_sccs -3950 unknown_sccs -8107 1bj7 156 1.01e+01 1bj7 b.60.1.1 27113 1ceo 343 1.02e+01 1ceo c.1.8.3 28808 1jeyB 565 1.06e+01 1jeqB unknown_sccs -4431 unknown_sccs -7995 1gt7A 274 1.07e+01 c.74.1.1 70398 8dfr 189 1.08e+01 1aoeA c.71.1.1 34895 1ad3A 452 1.10e+01 1ad3A c.82.1.1 35335 1bpr 191 1.11e+01 1dkzA unknown_sccs 43319 1vjpA 394 1.14e+01 c.2.1.3 -5897 d.81.1.3 -10480 1lgyA 269 1.16e+01 3tgl c.69.1.17 34758 1ybvA 283 1.17e+01 1ybvA c.2.1.2 29948 1dljA 402 1.17e+01 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1a8vA 121 1.21e+01 1a62 a.140.3.1 64712 b.40.4.5 64713 1m1nB 522 1.22e+01 c.92.2.3 78418 1auiA 521 1.26e+01 1auiA d.159.1.3 42085 2minB 522 1.27e+01 1qguB c.92.2.3 35610 1khdA 345 1.27e+01 a.46.2.1 77400 c.27.1.1 77401 1m8uA 173 1.28e+01 b.11.1.1 -3027 b.11.1.1 -3028 1az9 457 1.31e+01 1az9 c.55.2.1 33547 d.127.1.1 41164 1jeqB 565 1.31e+01 1jeqB unknown_sccs -4432 unknown_sccs -7996 1byqA 228 1.32e+01 1yer d.122.1.1 41100 3minB 522 1.35e+01 1qguB c.92.2.3 35606 1fgs 428 1.37e+01 1fgs c.59.1.2 33959 c.72.2.2 34962 1om1A 332 1.37e+01 d.144.1.7 -11318 1ptmA 329 1.40e+01 unknown_sccs -8456 1mwmA 320 1.41e+01 c.55.1.1 79580 c.55.1.1 79581 1cec 343 1.42e+01 1ceo c.1.8.3 28809 1iqsA 88 1.42e+01 d.214.1.1 71278 1g8yA 279 1.42e+01 1g8yA c.37.1.11 32302 1lyxA 248 1.48e+01 c.1.1.1 78304 1dliA 402 1.49e+01 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1j93A 353 1.50e+01 c.1.22.1 66454 1i39A 225 1.50e+01 1ekeA c.55.3.1 61585 1g5aA 628 1.54e+01 b.71.1.1 65152 c.1.8.1 65153 1nlfA 279 1.56e+01 c.37.1.11 85850 1gw0A 559 1.63e+01 b.6.1.3 70623 b.6.1.3 70624 b.6.1.3 70625 1jpmA 366 1.65e+01 c.1.11.2 67031 d.54.1.1 67032 1lp4A 332 1.67e+01 d.144.1.7 74170 1jx4A 352 1.67e+01 unknown_sccs -10188 unknown_sccs -11898 2phlA 397 1.71e+01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1yer 228 1.73e+01 1yer d.122.1.1 41101 1k8kA 418 1.73e+01 c.55.1.1 68305 c.55.1.1 68306 1vybA 238 1.73e+01 1frvB 536 1.75e+01 1h2rL e.18.1.1 43296 1hdiA 413 1.76e+01 16pk c.86.1.1 60964 1j7xA 302 1.78e+01 c.14.1.2 66425 1napA 70 1.78e+01 1tvxA d.9.1.1 37445 1h8mA 140 1.79e+01 1h8mA d.110.4.1 60782 1qg7A 67 1.80e+01 1a15A d.9.1.1 37449 1uylA 236 1.81e+01 1ltqA 301 1.83e+01 c.108.1.9 78208 c.37.1.1 78209 1icpA 376 1.84e+01 1oyc c.1.4.1 62270 1a16 440 1.86e+01 1az9 c.55.2.1 33548 d.127.1.1 41165 1lpuA 332 1.87e+01 d.144.1.7 74177 2itg 163 1.88e+01 1b9dA c.55.3.2 33669 1r6wA 322 1.89e+01 c.1.11.2 -5563 d.54.1.1 -9821 1sbxA 106 1.90e+01 1uzbA 516 1.90e+01 c.82.1.1 -8552 2rmcA 182 1.94e+01 2cpl b.62.1.1 27491 1nbwA 607 1.95e+01 c.8.6.1 80393 c.55.1.6 80394 c.55.1.6 80395 1e0tA 470 1.96e+01 1a49A b.58.1.1 27064 c.1.12.1 29292 c.49.1.1 33146 1hf8A 289 1.96e+01 1hg5A unknown_sccs -399 unknown_sccs -1628 1rypE 242 1.98e+01 1rypE d.153.1.4 41936 1kczA 413 2.00e+01 c.1.11.2 68451 d.54.1.1 68452 1j6uA 469 2.04e+01 c.5.1.1 77094 c.59.1.1 77095 c.72.2.1 77096 1a15A 67 2.04e+01 1a15A d.9.1.1 37451 3chbD 104 2.04e+01 3chbD b.40.2.1 24970 1euhA 475 2.04e+01 1euhA c.82.1.1 35369 1lfwA 470 2.05e+01 c.56.5.4 77942 d.58.19.1 77943 1a62 130 2.07e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1hg5A 289 2.10e+01 1hg5A unknown_sccs -400 unknown_sccs -1629 1cqwA 295 2.10e+01 1b6g c.69.1.8 34679 1bn7A 294 2.11e+01 1bn6A c.69.1.8 34677 1a58 177 2.13e+01 2cpl b.62.1.1 27495 4xiaA 393 2.14e+01 4xis c.1.15.3 29439 1elpA 173 2.16e+01 1amm b.11.1.1 23596 b.11.1.1 23597 1gr0A 367 2.18e+01 c.2.1.3 70379 d.81.1.3 70380 1pjqA 457 2.21e+01 c.2.1.11 -5904 c.90.1.1 -8611 e.37.1.1 -12004 1e3oC 160 2.22e+01 1au7A a.4.1.1 59197 a.35.1.1 59198 1qysA 106 2.22e+01 unknown_sccs -13432 2bbvC 363 2.23e+01 2bbvA b.121.4.4 23325 1bea 127 2.24e+01 1bea a.52.1.2 17826 1ry9A 145 2.25e+01 d.198.1.1 -9020 2vil 126 2.26e+01 2vil d.109.1.1 40830 3pgk 416 2.26e+01 16pk c.86.1.1 35451 1tvxA 75 2.26e+01 1tvxA d.9.1.1 37441 1fhvA 323 2.27e+01 1fhuA c.1.11.2 29235 d.54.1.1 38879 1ixmA 192 2.29e+01 1ixmA d.123.1.1 41114 3il8 72 2.30e+01 1tvxA d.9.1.1 37356 1djrD 103 2.30e+01 3chbD b.40.2.1 24865 1r5jA 337 2.31e+01 unknown_sccs -8471 1prtF 98 2.34e+01 1prtF b.40.2.1 25140 1bfa 134 2.34e+01 1bea a.52.1.2 17827 1ltsD 103 2.34e+01 3chbD b.40.2.1 24900 2vik 126 2.37e+01 2vil d.109.1.1 40829 1a3yA 149 2.37e+01 1obpA b.60.1.1 27110 1n13B 113 2.37e+01 1vi9A 299 2.38e+01 c.72.1.5 -8393 1efiD 103 2.41e+01 3chbD b.40.2.1 24870 2hsdA 253 2.42e+01 1e6wA c.2.1.2 29866 1bn6A 294 2.44e+01 1bn6A c.69.1.8 34678 1gw9A 388 2.44e+01 c.1.15.3 70658 1hyeA 313 2.45e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1php 394 2.48e+01 16pk c.86.1.1 35452 1l6rA 227 2.49e+01 c.108.1.10 77768 1ixmB 192 2.49e+01 1ixmA d.123.1.1 41115 1dzkA 157 2.54e+01 1obpA b.60.1.1 27096 2aaa 484 2.55e+01 7taa b.71.1.1 27777 c.1.8.1 28764 1slvA 142 2.58e+01 1sluA b.16.1.1 23688 1ubkL 534 2.61e+01 e.18.1.1 88422 1axdA 209 2.63e+01 1gnwA a.45.1.1 17730 c.47.1.5 33024 1r2rA 248 2.69e+01 c.1.1.1 -5147 2mysB 166 2.69e+01 1wdcB a.39.1.5 17308 1h2rL 534 2.73e+01 1h2rL e.18.1.1 43298 1xis 387 2.75e+01 4xis c.1.15.3 29422 4xis 387 2.75e+01 4xis c.1.15.3 29421 1jnrB 150 2.75e+01 d.58.1.5 66969 1mnzA 388 2.76e+01 c.1.15.3 79328 1udsA 255 2.77e+01 d.14.1.4 -9055 d.101.1.1 -10745 1hdcA 253 2.78e+01 1e6wA c.2.1.2 29862 1bcpF 99 2.79e+01 1prtF b.40.2.1 25142 1n83A 270 2.81e+01 a.123.1.1 80276 1agrE 205 2.81e+01 1agrE a.91.1.1 18538 3xis 387 2.81e+01 4xis c.1.15.3 29423 1seiA 130 2.82e+01 1seiA d.140.1.1 41463 1gm5A 780 2.83e+01 unknown_sccs 65298 b.40.4.9 65299 c.37.1.19 65300 c.37.1.19 65301 1o7zA 77 2.83e+01 d.9.1.1 86660 1pfjA 108 2.84e+01 1kmvA 186 2.84e+01 c.71.1.1 72757 1k8cA 322 2.85e+01 c.1.7.1 72172 1m2rA 327 2.91e+01 d.144.1.7 84760 1mi3A 322 2.91e+01 c.1.7.1 -5257 1tph1 247 2.91e+01 1amk 1ji2A 585 2.95e+01 b.1.18.2 71672 b.71.1.1 71673 c.1.8.1 71674 2dpg 485 2.97e+01 1dpgA c.2.1.3 30076 d.81.1.5 39991 1hg2A 289 3.01e+01 1hg5A unknown_sccs -401 unknown_sccs -1630 1f5mA 180 3.01e+01 1f5mB d.110.2.1 40895 1sluA 142 3.05e+01 1sluA b.16.1.1 23685 1dk4A 252 3.07e+01 1dk4A e.7.1.1 42970 1lwyA 324 3.09e+01 a.96.1.3 78285 d.129.1.2 78286 1f5mB 180 3.10e+01 1f5mB d.110.2.1 40896 2bbvA 363 3.13e+01 2bbvA b.121.4.4 23323 1nnhA 294 3.14e+01 d.104.1.1 -10772 1nq7A 244 3.16e+01 a.123.1.1 -1682 1mpxA 615 3.19e+01 b.18.1.13 85041 c.69.1.21 85042 1v6sA 390 3.22e+01 c.86.1.1 -8567 1nox 205 3.24e+01 1nox d.90.1.1 40242 1mw9X 592 3.27e+01 e.10.1.1 -11986 1crxA 322 3.32e+01 4crxA a.60.9.1 18097 d.163.1.1 42157 1q1hA 110 3.33e+01 unknown_sccs -262 1jbwA 428 3.34e+01 c.59.1.2 62860 c.72.2.2 62861 1mwvA 714 3.38e+01 a.93.1.3 85161 a.93.1.3 85162 1div 149 3.39e+01 1div d.99.1.1 40692 d.100.1.1 40693 1h0pA 182 3.39e+01 b.62.1.1 76450 1fhuA 320 3.42e+01 1fhuA c.1.11.2 29234 d.54.1.1 38878 1mucA 373 3.43e+01 1mucA c.1.11.2 29236 d.54.1.1 38880 1llfA 534 3.47e+01 c.69.1.17 78094 1gg4A 452 3.49e+01 1gg4A c.98.1.1 58985 c.59.1.1 33957 c.72.2.1 58986 1q0bA 367 3.52e+01 c.37.1.9 -7105 1h2aL 567 3.57e+01 1h2rL e.18.1.1 43299 4crxA 322 3.57e+01 4crxA a.60.9.1 18095 d.163.1.1 42155 1erv 105 3.61e+01 1erv c.47.1.1 32743 1jr7A 311 3.71e+01 b.82.2.3 63255 1gz8A 299 3.74e+01 d.144.1.7 83405 2xat 212 3.76e+01 2xat b.81.1.3 28058 1eztA 166 3.77e+01 1agrE a.91.1.1 18541 1us6A 102 3.84e+01 1m3qA 317 3.87e+01 a.96.1.3 -1288 d.129.1.2 -11006 1o89A 345 3.91e+01 b.35.1.2 -3703 c.2.1.1 -5727 2tmdA 729 3.95e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1hqcA 324 3.96e+01 1hqcA a.4.5.11 16127 c.37.1.20 32424