# List of top-scoring protein chains for t2k-100-30-bys 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 1mkmA 249 1.68e-03 a.4.5.33 79242 d.110.2.2 79243 1hqcA 324 1.92e-03 1hqcA a.4.5.11 16127 c.37.1.20 32424 1in4A 334 3.81e-03 1hqcA a.4.5.11 62597 c.37.1.20 62598 1in6A 334 7.37e-03 1hqcA a.4.5.11 62601 c.37.1.20 62602 1jhfA 202 9.92e-02 a.4.5.2 63057 b.87.1.1 63058 1rvkA 382 1.12e-01 c.1.11.2 -5568 d.54.1.1 -9826 1j5yA 187 2.61e-01 a.4.5.1 71592 d.94.2.1 71593 1lea 84 2.61e-01 1lea a.4.5.2 16085 1ad3A 452 2.92e-01 1ad3A c.82.1.1 35335 1fqgA 263 5.69e-01 1btl e.3.1.1 42699 1btl 263 6.11e-01 1btl e.3.1.1 42691 1lshB 319 6.63e-01 f.7.1.1 74245 1vi9A 299 7.45e-01 c.72.1.5 -8393 1okrA 123 8.13e-01 unknown_sccs -235 1q48A 134 8.33e-01 unknown_sccs -9776 1kk8B 139 1.10e+00 a.39.1.5 77430 1ermA 263 1.20e+00 1btl e.3.1.1 42690 1bj7 156 1.27e+00 1bj7 b.60.1.1 27113 1o08A 221 1.37e+00 c.108.1.6 86525 1tml 286 1.42e+00 1tml c.6.1.1 30656 1je8A 82 1.50e+00 a.4.6.2 77108 1i1gA 141 1.90e+00 a.4.5.32 65982 d.58.4.2 65983 1mzbA 136 2.35e+00 unknown_sccs -266 1ryc 294 2.41e+00 1ryc a.93.1.1 18601 1rypC 244 2.82e+00 1rypC d.153.1.4 41934 1a04A 215 3.06e+00 1a04A a.4.6.2 16234 c.23.1.1 31089 1jbgA 109 3.12e+00 a.6.1.3 66480 1r71A 178 3.30e+00 1uylA 236 3.48e+00 2cyp 294 3.54e+00 1ryc a.93.1.1 18600 1hg5A 289 3.69e+00 1hg5A unknown_sccs -400 unknown_sccs -1629 1bqg 451 3.71e+00 1bqg c.1.11.2 29217 d.54.1.1 38861 1hg2A 289 3.72e+00 1hg5A unknown_sccs -401 unknown_sccs -1630 1hf8A 289 3.74e+00 1hg5A unknown_sccs -399 unknown_sccs -1628 1ec7A 446 3.81e+00 1bqg c.1.11.2 29218 d.54.1.1 38862 1fkmA 396 3.97e+00 1fkmA a.69.2.1 18315 a.69.2.1 18316 1m40A 263 4.06e+00 e.3.1.1 74437 1ds4A 292 4.19e+00 1ryc a.93.1.1 59129 1q1hA 110 4.26e+00 unknown_sccs -262 1ccg 291 4.41e+00 1ryc a.93.1.1 18627 1fpxA 352 4.64e+00 1fpxA a.4.5.29 59950 c.66.1.12 59951 1fp2A 352 4.64e+00 1fpxA a.4.5.29 59941 c.66.1.12 59942 1aa7A 158 4.80e+00 1aa7A a.95.1.1 18741 1i4jA 110 4.84e+00 d.55.1.1 76734 1on2A 142 4.84e+00 a.4.5.24 87103 a.76.1.1 87104 1mj5A 302 4.89e+00 c.69.1.8 -8326 1apxA 249 4.91e+00 1ryc a.93.1.1 18669 1yer 228 4.94e+00 1yer d.122.1.1 41101 1moq 368 5.74e+00 1moq c.80.1.1 35302 6paxA 133 6.22e+00 6paxA a.4.1.5 64758 a.4.1.5 64759 1bxeA 113 6.35e+00 1bxeA d.55.1.1 38898 1jdrA 294 6.37e+00 1ryc a.93.1.1 62908 1n9lA 109 6.73e+00 d.110.3.6 85468 1dgrN 79 7.07e+00 1caxB 1b0uA 262 7.23e+00 1b0uA c.37.1.12 32370 1ea3A 164 7.25e+00 1aa7A a.95.1.1 59398 1h2aL 567 7.27e+00 1h2rL e.18.1.1 43299 1jdfA 447 7.57e+00 c.1.11.2 62897 d.54.1.1 62898 2mnr 357 7.59e+00 2mnr c.1.11.2 29245 d.54.1.1 38889 1fsz 372 7.77e+00 1fsz c.32.1.1 31750 d.79.2.1 39802 1a6dA 545 7.80e+00 1a6dA a.129.1.2 19488 c.8.5.2 30819 d.56.1.2 38936 1qhaA 917 7.88e+00 1qhaA c.55.1.3 33467 c.55.1.3 33468 c.55.1.3 33469 c.55.1.3 33470 1nb8A 353 8.15e+00 d.3.1.9 80385 1lvhA 221 8.20e+00 c.108.1.6 74282 1k1vA 41 8.69e+00 a.37.1.1 71999 1wdcB 156 9.01e+00 1wdcB a.39.1.5 17302 1gr5A 547 9.33e+00 i.16.1.1 65478 1nt4A 391 9.35e+00 c.60.1.2 -7942 1h8pA 109 9.36e+00 g.14.1.2 70916 g.14.1.2 70917 1mdl 359 9.40e+00 2mnr c.1.11.2 29247 d.54.1.1 38891 1k8kA 418 9.53e+00 c.55.1.1 68305 c.55.1.1 68306 1aj8A 371 9.72e+00 1aj8A a.103.1.1 18900 1byqA 228 9.89e+00 1yer d.122.1.1 41100 1kit 757 1.01e+01 1kit b.29.1.8 24272 b.29.1.8 24273 b.68.1.1 27616 1iz7A 295 1.02e+01 c.69.1.8 76982 1p0kA 349 1.05e+01 c.1.4.1 87648 1cv2A 296 1.06e+01 1bn6A c.69.1.8 34680 1i6iA 366 1.08e+01 1bg2 c.37.1.9 61844 1yagG 125 1.08e+01 1d0nA d.109.1.1 40846 1ukz 203 1.10e+01 1zin c.37.1.1 31840 1bx4A 345 1.13e+01 1bx4A c.72.1.1 34935 1nlfA 279 1.14e+01 c.37.1.11 85850 1e3oC 160 1.19e+01 1au7A a.4.1.1 59197 a.35.1.1 59198 1pq4A 291 1.22e+01 c.92.2.2 -8633 1vypX 364 1.22e+01 1vyrA 364 1.25e+01 1efiD 103 1.27e+01 3chbD b.40.2.1 24870 1yrnB 83 1.27e+01 1akhB a.4.1.1 15986 2cavA 445 1.30e+01 1dgwA b.82.1.2 28094 b.82.1.2 28095 1oafA 261 1.30e+01 a.93.1.1 86734 1g8yA 279 1.32e+01 1g8yA c.37.1.11 32302 1q08A 99 1.33e+01 a.6.1.3 -381 1dgwX 79 1.36e+01 1caxB b.82.1.2 28091 1e2xA 243 1.36e+01 1e2xA a.4.5.6 16113 a.78.1.1 18443 1ltsD 103 1.41e+01 3chbD b.40.2.1 24900 1b0zA 445 1.42e+01 2pgi c.80.1.2 35309 2pgi 445 1.42e+01 2pgi c.80.1.2 35308 1crl 534 1.43e+01 1thg c.69.1.17 34765 1hfeL 421 1.43e+01 1fehA c.96.1.1 36018 d.58.1.5 39001 1hw1A 239 1.43e+01 1e2xA a.4.5.6 16111 a.78.1.1 18441 1bjaA 95 1.45e+01 1bjaA a.4.5.9 16122 1jq5A 370 1.45e+01 e.22.1.2 67084 1hkbA 917 1.47e+01 1qhaA c.55.1.3 33479 c.55.1.3 33480 c.55.1.3 33481 c.55.1.3 33482 1xat 212 1.49e+01 2xat b.81.1.3 28059 1pmt 203 1.50e+01 1a0fA a.45.1.1 17740 c.47.1.5 33034 1eyvA 156 1.54e+01 1eyvA a.79.1.1 18446 1k78A 149 1.54e+01 a.4.1.5 68255 a.4.1.5 68256 1m2aA 110 1.54e+01 c.47.1.11 78472 1m2bA 110 1.59e+01 c.47.1.11 78474 1h0pA 182 1.64e+01 b.62.1.1 76450 1akhB 83 1.67e+01 1akhB a.4.1.1 15985 1quqA 129 1.69e+01 1quqA b.40.4.3 25303 1ecmA 109 1.70e+01 1ecmA a.130.1.1 19492 1l7vA 326 1.70e+01 f.22.1.1 73672 1g2oA 268 1.70e+01 1b8oA c.56.2.1 60228 1czaN 917 1.74e+01 1qhaA c.55.1.3 33463 c.55.1.3 33464 c.55.1.3 33465 c.55.1.3 33466 2xat 212 1.78e+01 2xat b.81.1.3 28058 1vjzA 341 1.78e+01 c.1.8.3 -5318 1dqsA 393 1.79e+01 1dqsA e.22.1.1 43347 1jx4A 352 1.80e+01 unknown_sccs -10188 unknown_sccs -11898 1allA 160 1.81e+01 1qgwC a.1.1.3 15647 1eywA 331 1.82e+01 1pscA c.1.9.3 29057 1hkcA 917 1.85e+01 1qhaA c.55.1.3 33475 c.55.1.3 33476 c.55.1.3 33477 c.55.1.3 33478 1g40A 244 1.86e+01 1e5gA g.18.1.1 44823 g.18.1.1 44824 g.18.1.1 44825 g.18.1.1 44826 1fipA 98 1.86e+01 1fipA unknown_sccs 18980 1ds6B 180 1.89e+01 1rhoA b.1.18.8 21898 1c7qA 445 1.90e+01 2pgi c.80.1.2 35307 1ki1B 352 1.92e+01 a.87.1.1 72497 b.55.1.1 72498 1i0dA 332 1.93e+01 1pscA c.1.9.3 61487 1qnxA 209 1.93e+01 1qnxA d.111.1.1 40914 1r1dA 247 1.95e+01 unknown_sccs -8335 1rypB 250 1.96e+01 1rypB d.153.1.4 41933 1dgmA 363 1.97e+01 1bx4A c.72.1.1 34936 1ua4A 455 1.97e+01 c.72.1.3 -8416 1o7eA 276 1.99e+01 e.3.1.1 -11766 1s1dA 331 2.00e+01 unknown_sccs -4566 1d0nA 729 2.01e+01 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 1iupA 282 2.04e+01 c.69.1.10 76815 1cleA 534 2.06e+01 1thg c.69.1.17 34771 1iatA 557 2.06e+01 1dqrA c.80.1.2 62123 1ubkL 534 2.07e+01 e.18.1.1 88422 1oz9A 150 2.09e+01 unknown_sccs -10588 1h2rL 534 2.09e+01 1h2rL e.18.1.1 43298 1n40A 396 2.09e+01 a.104.1.1 79977 1lgr 468 2.10e+01 1lgr d.15.9.1 37837 d.128.1.1 41167 1eeoA 321 2.10e+01 1pty c.45.1.2 32655 1k61A 60 2.11e+01 a.4.1.1 77270 1o20A 427 2.12e+01 c.82.1.1 86556 1hm5A 558 2.12e+01 c.80.1.2 76717 1bob 320 2.12e+01 1bob d.108.1.1 40816 1tvxA 75 2.15e+01 1tvxA d.9.1.1 37441 1gt1A 159 2.16e+01 b.60.1.1 -4436 1pscA 365 2.18e+01 1pscA c.1.9.3 29058 1gc5A 467 2.19e+01 1gc5A c.72.1.3 60429 1f52A 468 2.23e+01 1lgr d.15.9.1 37839 d.128.1.1 41169 1vmoA 163 2.23e+01 1vmoA b.77.1.1 27974 1jfgA 374 2.26e+01 a.128.1.5 66636 1q06A 135 2.29e+01 a.6.1.3 -375 1n9bA 265 2.31e+01 e.3.1.1 85463 1mnmC 87 2.32e+01 1akhB a.4.1.1 15983 2phlA 397 2.32e+01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1hn2A 159 2.33e+01 b.60.1.1 65890 1us6A 102 2.34e+01 1do6A 124 2.34e+01 1do6A b.1.13.1 22361 1top 162 2.38e+01 1ncx a.39.1.5 17223 1pta 318 2.40e+01 1pscA c.1.9.3 29064 1pty 321 2.43e+01 1pty c.45.1.2 32656 1gw0A 559 2.43e+01 b.6.1.3 70623 b.6.1.3 70624 b.6.1.3 70625 2lgsA 468 2.47e+01 1lgr d.15.9.1 37838 d.128.1.1 41168 1ihrA 76 2.47e+01 1ihrA d.212.1.2 62392 1djrD 103 2.48e+01 3chbD b.40.2.1 24865 1c9kA 180 2.49e+01 1c9kB c.37.1.11 32363 1hzyA 332 2.52e+01 1pscA c.1.9.3 61468 1d4xG 126 2.53e+01 1d0nA d.109.1.1 59109 1h61A 364 2.54e+01 1oyc c.1.4.1 60657 1obpA 159 2.60e+01 1obpA b.60.1.1 27092 3chbD 104 2.65e+01 3chbD b.40.2.1 24970 1mkiA 330 2.66e+01 e.3.1.2 84994 1np1A 184 2.66e+01 1np1A b.60.1.1 27155 1dgrV 79 2.69e+01 1caxB b.82.1.2 28099 1e85A 127 2.72e+01 1bbhA a.24.3.2 16549 1nm1G 125 2.75e+01 d.109.1.1 80653 1llfA 534 2.78e+01 c.69.1.17 78094 1kl9A 182 2.80e+01 b.40.4.5 72681 1h8mA 140 2.80e+01 1h8mA d.110.4.1 60782 1qe5A 266 2.81e+01 1b8oA c.56.2.1 33784 1i5sA 367 2.83e+01 1bg2 c.37.1.9 61822 1ncx 162 2.84e+01 1ncx a.39.1.5 17222 1fh9A 312 2.86e+01 1taxA c.1.8.3 28913 2kinA 238 2.88e+01 1bg2 c.37.1.9 32190 1iz6A 138 2.96e+01 b.34.5.2 76976 b.40.4.5 76977 1k2xB 143 2.97e+01 1ud9A 245 2.98e+01 1jfaA 374 3.05e+01 a.128.1.5 66622 1hq1A 105 3.07e+01 1dulA a.36.1.1 17120 1gln 468 3.07e+01 1gln a.97.1.1 18752 c.26.1.1 31588 1j27A 102 3.08e+01 unknown_sccs -10116 1l2lA 457 3.11e+01 c.72.1.3 77656 1c6vX 81 3.18e+01 1ihvA b.34.7.1 24641 1mxrA 375 3.22e+01 a.25.1.2 85197 1m2dA 110 3.30e+01 c.47.1.11 78476 1a62 130 3.31e+01 1a62 a.140.3.1 64708 b.40.4.5 64709 1h2sA 225 3.32e+01 f.13.1.1 76578 1bia 321 3.33e+01 1bia a.4.5.1 16083 b.34.1.1 24447 d.104.1.2 40787 1dgkN 917 3.34e+01 1qhaA c.55.1.3 33487 c.55.1.3 33488 c.55.1.3 33489 c.55.1.3 33490 1bib 321 3.38e+01 1bia a.4.5.1 16084 b.34.1.1 24448 d.104.1.2 40788 1kay 381 3.39e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1riqA 465 3.40e+01 unknown_sccs -1295 d.104.1.1 -10769 1iygA 133 3.45e+01 a.118.8.1 76947 1rw2A 152 3.49e+01 unknown_sccs -1645 1dqrA 557 3.53e+01 1dqrA c.80.1.2 35305 1a73A 163 3.54e+01 1a73A d.4.1.3 37145 1vgwA 231 3.57e+01 c.68.1.13 -8237 1cpcA 162 3.57e+01 1cpcA a.1.1.3 15643 1exqA 154 3.57e+01 1b9dA c.55.3.2 33646 1uesA 191 3.59e+01 1s5lU 134 3.63e+01 1e2uA 553 3.72e+01 1e1dA e.26.1.1 43362 1fseA 74 3.73e+01 1fseA a.4.6.2 60000 1ba1 386 3.73e+01 1ba1 c.55.1.1 33387 c.55.1.1 33388 2ahjC 206 3.75e+01 2ahjA d.149.1.1 41773 1pysB 785 3.79e+01 1pysB a.6.1.1 16299 a.6.1.1 16300 b.40.4.4 25311 d.58.13.1 39310 d.104.1.1 40779 d.138.1.1 41455 1j09A 468 3.81e+01 a.97.1.1 77025 c.26.1.1 77026 1qnnA 191 3.82e+01 1avmA a.2.11.1 15792 d.44.1.1 38755 1e1dA 553 3.83e+01 1e1dA e.26.1.1 43363 2ahjA 206 3.83e+01 2ahjA d.149.1.1 41772 1l9gA 192 3.84e+01 c.18.1.2 84568 1pa1A 310 3.87e+01 c.45.1.2 -7332 1kq3A 376 3.89e+01 e.22.1.2 68790 1a8d 452 3.91e+01 1a8d b.29.1.6 24262 b.42.4.2 25607 1caxB 184 3.93e+01 1caxB b.82.1.2 28105 1qb5D 99 3.95e+01 b.40.2.1 88357 1deeG 54 3.97e+01 1fc2C a.8.1.1 16343 1p9oA 313 3.99e+01 unknown_sccs -8423