# 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 1r5qA 102 1.11e-04 unknown_sccs -965 1q6aA 107 6.66e-04 unknown_sccs -960 1v2zA 111 7.20e-03 1flp 142 3.36e-02 1flp a.1.1.2 15011 1moh 142 5.24e-02 1flp a.1.1.2 15012 1b0b 142 7.77e-02 2fal a.1.1.2 15010 1f5xA 208 1.82e-01 1f5xA a.87.1.1 18516 1ufaA 520 2.00e-01 unknown_sccs -421 unknown_sccs -6065 1gvhA 396 2.26e-01 a.1.1.2 70601 b.43.4.2 70602 c.25.1.5 70603 1kktA 511 2.56e-01 a.102.2.1 68687 1dlyA 164 2.84e-01 1dlyA a.1.1.1 14983 1dvpA 220 2.98e-01 1dvpA a.118.9.2 19216 g.50.1.1 45358 1sctB 151 3.53e-01 3sdhA a.1.1.2 15003 1gwiA 411 3.84e-01 a.104.1.1 76364 1k8eA 345 4.27e-01 1o17A 345 4.27e-01 a.46.2.1 80765 c.27.1.1 80766 1iqpA 327 4.42e-01 a.80.1.1 62649 c.37.1.20 62650 1tlqA 189 5.97e-01 1s9pA 227 7.51e-01 1a87 321 8.62e-01 1a87 f.1.1.1 43380 3sdhA 146 8.96e-01 3sdhA a.1.1.2 14984 1sxjE 354 9.22e-01 1sr7A 259 9.89e-01 1b0nB 57 1.20e+00 1b0nB a.34.1.1 17002 1fo3A 460 1.34e+00 1dl2A a.102.2.1 18845 1kmmA 424 1.38e+00 1adjA c.51.1.1 33174 d.104.1.1 40723 1vkeA 133 1.94e+00 1tbmA 326 2.03e+00 1omwA 689 2.03e+00 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1hz4A 373 2.10e+00 a.118.8.2 65960 1hm5A 558 2.12e+00 c.80.1.2 76717 1e5rA 290 2.20e+00 1e5rA b.82.2.4 59276 1jfiB 179 2.25e+00 1jfiB a.22.1.3 62937 1p49A 562 2.47e+00 c.76.1.2 -8432 1a28A 256 2.49e+00 1a28A a.123.1.1 19290 1o0uA 429 2.52e+00 c.118.1.1 80743 1ay7B 89 3.15e+00 1ay7B c.9.1.1 30836 1i27A 73 3.27e+00 1i27A a.4.5.30 61555 1rfmA 344 3.38e+00 c.122.1.1 -8032 1lylA 504 3.93e+00 1lylA b.40.4.1 25261 d.104.1.1 40717 1jmeA 455 4.00e+00 a.104.1.1 66885 1g3jA 532 4.06e+00 3bct a.118.1.1 19114 1qpaA 345 4.17e+00 1arv a.93.1.1 18585 1ltm 320 4.18e+00 1ltm d.2.1.6 36992 1gk4C 84 4.29e+00 h.1.20.1 70205 1qusA 322 4.56e+00 1ltm d.2.1.6 36991 1aj8A 371 4.62e+00 1aj8A a.103.1.1 18900 1brsD 89 4.63e+00 1ay7B c.9.1.1 30825 1j7rA 86 4.80e+00 1j7rA a.39.1.5 62701 1fm2A 169 4.82e+00 1fm2A d.153.1.2 59877 1iomA 377 4.87e+00 a.103.1.1 83698 1kyqA 274 5.14e+00 c.2.1.11 73281 e.37.1.1 73282 1aru 344 5.18e+00 1arv a.93.1.1 18589 1b2sD 90 5.25e+00 1ay7B c.9.1.1 30837 1a3yA 149 5.29e+00 1obpA b.60.1.1 27110 2occE 109 5.29e+00 2occE a.118.11.1 19224 1gk4D 84 5.35e+00 h.1.20.1 70206 1or0A 160 5.41e+00 d.153.1.2 -11415 1jdhA 529 5.43e+00 a.118.1.1 66549 2a0b 125 5.44e+00 2a0b a.24.10.1 16630 1dceA 567 5.50e+00 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 1hr6A 475 5.62e+00 1hr6A d.185.1.1 61164 d.185.1.1 61165 1hsr 344 5.70e+00 1arv a.93.1.1 18592 1n0uA 842 5.70e+00 b.43.3.1 79757 c.37.1.8 79758 d.14.1.1 79759 d.58.11.1 79760 d.58.11.1 79761 1p8cA 145 5.76e+00 unknown_sccs -1927 1arv 344 5.78e+00 1arv a.93.1.1 18590 1s3jA 155 6.18e+00 a.4.5.28 -227 3bct 457 6.19e+00 3bct a.118.1.1 19112 1j8mF 297 6.24e+00 1ng1 a.24.13.1 62742 c.37.1.10 62743 1rw2A 152 6.47e+00 unknown_sccs -1645 1gk4A 84 6.96e+00 h.1.20.1 70203 1kpsB 171 7.25e+00 a.118.12.1 68787 1g73A 162 7.51e+00 1fewA a.7.4.1 16332 1no4A 97 7.56e+00 h.1.24.1 85918 1np3A 338 7.60e+00 a.100.1.2 85946 c.2.1.6 85947 1lycA 343 7.69e+00 a.93.1.1 74344 5csmA 256 7.80e+00 5csmA a.130.1.2 19494 1jqaA 370 7.85e+00 e.22.1.2 67085 1o1yA 239 7.91e+00 c.23.16.1 86554 1qi9A 556 8.36e+00 1qhbA a.111.1.2 19053 1kw4A 89 8.53e+00 a.60.1.2 73077 1ab7 89 8.80e+00 1ay7B c.9.1.1 30835 1j8yF 297 9.24e+00 1ng1 a.24.13.1 62747 c.37.1.10 62748 1dzkA 157 9.30e+00 1obpA b.60.1.1 27096 2mhr 118 9.82e+00 2mhr a.24.4.1 16581 1k5hA 398 9.85e+00 a.69.3.1 68192 c.2.1.3 68193 d.81.1.3 68194 1ukfA 188 9.87e+00 unknown_sccs -8886 1kkhA 317 1.04e+01 d.14.1.5 72645 d.58.26.3 72646 1rh5C 53 1.04e+01 unknown_sccs -12204 1mzgA 146 1.04e+01 d.224.1.1 79696 1d9cA 121 1.06e+01 1d9cA a.26.1.3 16901 1q4mA 221 1.07e+01 unknown_sccs -1910 1bjt 793 1.08e+01 1bjt e.11.1.1 43249 1m7vA 363 1.09e+01 d.174.1.1 78748 1uedA 406 1.09e+01 a.104.1.1 -1459 1a4mA 349 1.09e+01 1a4mA c.1.9.1 29014 1uw4B 248 1.10e+01 unknown_sccs -1560 1gakA 141 1.12e+01 1gakA a.19.1.1 16415 1llp 343 1.14e+01 1arv a.93.1.1 18578 1i7wA 538 1.20e+01 3bct a.118.1.1 61909 1add 349 1.22e+01 1a4mA c.1.9.1 29020 1nogA 177 1.23e+01 a.25.2.2 85923 3tmkA 216 1.36e+01 3tmkA c.37.1.1 31920 1uzxA 169 1.38e+01 d.20.1.2 -9409 2lfb 100 1.42e+01 1lfb a.4.1.1 15990 1spgA 144 1.45e+01 1abwA a.1.1.2 15409 1fkx 349 1.47e+01 1a4mA c.1.9.1 29018 1trlA 62 1.51e+01 1hyt j.78.1.1 18263 1lfb 99 1.51e+01 1lfb a.4.1.1 15989 1mi1A 414 1.52e+01 a.169.1.1 79137 b.55.1.6 79138 1ei1A 391 1.53e+01 1aj6 d.14.1.3 37570 d.122.1.2 41104 1ihp 438 1.55e+01 1ihp c.60.1.2 33993 2dynA 122 1.60e+01 1dynA b.55.1.1 26957 1lehA 364 1.63e+01 1bw9A c.2.1.7 30268 c.58.1.1 33916 1qgrA 876 1.64e+01 1qgrA a.118.1.1 19119 1a8h 500 1.67e+01 1a8h a.27.1.1 16922 c.26.1.1 31589 1csmA 256 1.69e+01 5csmA a.130.1.2 19495 1a0fA 201 1.70e+01 1a0fA a.45.1.1 17737 c.47.1.5 33031 1kvkA 395 1.71e+01 d.14.1.5 73060 d.58.26.3 73061 1ca1 370 1.73e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1i3dA 146 1.75e+01 a.1.1.2 61587 1ffkE 119 1.79e+01 1ffkE d.79.3.1 39812 1or7A 194 1.81e+01 a.4.13.2 87332 a.177.1.1 87333 1r71A 178 1.83e+01 1mroA 548 1.86e+01 1mroA a.89.1.1 18525 d.58.31.2 39443 1dlc 584 1.86e+01 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1iatA 557 1.88e+01 1dqrA c.80.1.2 62123 1fyhA 258 1.88e+01 1d9cA a.26.1.3 16907 a.26.1.3 16908 1ofcX 304 1.90e+01 a.4.1.3 -195 unknown_sccs -199 unknown_sccs -978 2tmkA 216 1.91e+01 3tmkA c.37.1.1 31928 1hbnA 549 1.92e+01 1mroA a.89.1.1 60898 d.58.31.2 60899 1mijA 152 1.93e+01 a.4.1.1 79150 1nnwA 252 1.96e+01 d.159.1.5 80674 1l0oC 243 1.97e+01 a.4.13.2 73405 1sedA 117 1.98e+01 1colA 204 1.98e+01 1a87 f.1.1.1 43378 1dbfA 127 2.01e+01 2chsA d.79.1.2 39761 1jvsA 400 2.01e+01 a.69.3.1 77187 c.2.1.3 77188 d.81.1.3 77189 1nvpB 57 2.13e+01 a.32.1.1 -779 1jq5A 370 2.13e+01 e.22.1.2 67084 1ni4A 365 2.13e+01 c.36.1.7 85728 1huw 166 2.13e+01 1huw a.26.1.1 16831 1lucA 355 2.14e+01 1lucA c.1.16.1 29547 1j2jB 45 2.23e+01 a.7.8.1 84017 1kiyA 374 2.26e+01 a.128.1.5 72555 1v54E 109 2.27e+01 a.118.11.1 -1652 1owcA 427 2.27e+01 1j6rA 214 2.35e+01 d.173.1.2 71598 1anxA 319 2.36e+01 1avc a.65.1.1 18161 1k04A 162 2.37e+01 a.24.14.1 67904 1r1dA 247 2.38e+01 unknown_sccs -8335 1ofdA 1520 2.39e+01 b.80.4.1 86935 c.1.4.1 86936 d.153.1.1 86937 1ntyA 311 2.39e+01 1e1oA 504 2.43e+01 1lylA b.40.4.1 25258 d.104.1.1 40714 1i37A 260 2.50e+01 1a28A a.123.1.1 61583 1f93E 32 2.51e+01 1f93E unknown_sccs 17013 1n2aA 201 2.57e+01 a.45.1.1 -938 c.47.1.5 -7463 1ev7B 317 2.57e+01 1ev7B c.52.1.9 33316 1knvA 293 2.58e+01 c.52.1.7 68707 1iawA 317 2.60e+01 c.52.1.9 62126 1f24A 402 2.66e+01 1rom a.104.1.1 18953 1j7lA 264 2.73e+01 d.144.1.6 62697 1ks9A 291 2.73e+01 a.100.1.7 68857 c.2.1.6 68858 1a27 289 2.74e+01 1fds c.2.1.2 29839 1rypJ 204 2.77e+01 d.153.1.4 41878 1go3F 107 2.80e+01 a.60.8.2 65407 1rjdA 334 2.81e+01 unknown_sccs -8079 1qmgA 524 2.88e+01 1qmgA a.100.1.2 18785 c.2.1.6 30182 1pmnA 364 2.90e+01 d.144.1.7 -11297 1ecmA 109 2.91e+01 1ecmA a.130.1.1 19492 1e2uA 553 2.91e+01 1e1dA e.26.1.1 43362 1g0uI 205 2.94e+01 d.153.1.4 41891 1llwA 1520 2.98e+01 b.80.4.1 74017 c.1.4.1 74018 d.153.1.1 74019 1i4tB 224 2.99e+01 h.4.7.1 61730 1kl1A 419 3.10e+01 c.67.1.4 72663 1qwlA 505 3.13e+01 e.5.1.1 -11823 1kkjA 419 3.13e+01 c.67.1.4 72647 1ku3A 73 3.16e+01 a.4.13.2 73000 1gjjA 168 3.16e+01 a.140.1.1 83291 a.140.1.1 83292 1cf3A 583 3.18e+01 1gpeA c.3.1.2 30385 d.16.1.1 37949 1qagA 226 3.23e+01 1qagA a.40.1.1 17400 a.40.1.1 17401 1gcuA 295 3.23e+01 1gcuA c.2.1.3 30063 d.81.1.4 39978 1jr3A 373 3.25e+01 a.80.1.1 63245 c.37.1.20 63246 1g2nA 264 3.26e+01 1lbd a.123.1.1 60227 1hcuA 503 3.27e+01 a.102.2.1 65796 1e4iA 447 3.30e+01 1e70M c.1.8.4 59225 1hw6A 278 3.31e+01 1frb c.1.7.1 61296 1a80 277 3.32e+01 1frb c.1.7.1 28700 1aoiB 87 3.34e+01 1aoiB a.22.1.1 16470 1qlaC 256 3.35e+01 1qlaC f.21.2.1 43722 1ufhA 180 3.36e+01 d.108.1.1 88485 1jfbA 404 3.38e+01 a.104.1.1 66624 1m3wA 32 3.39e+01 k.8.1.1 78575 1f07A 321 3.40e+01 1ezwA c.1.16.3 59560 1ov2A 99 3.42e+01 a.13.1.1 -457 1gntA 553 3.47e+01 e.26.1.1 70290 1jfgA 374 3.56e+01 a.128.1.5 66636 1dkgA 197 3.57e+01 1dkgA b.73.1.1 27812 h.1.9.1 45626 1yveJ 524 3.58e+01 1qmgA a.100.1.2 18790 c.2.1.6 30187 1tr1A 447 3.59e+01 1e70M c.1.8.4 28957 1qs1A 462 3.61e+01 1qs1A d.166.1.1 42260 d.166.1.1 42261 1kv9A 668 3.63e+01 a.3.1.6 73056 b.70.1.1 73057 1kx5B 102 3.65e+01 a.22.1.1 77594 1jfaA 374 3.68e+01 a.128.1.5 66622 1j77A 209 3.70e+01 1j77A a.132.1.2 62674 1kx5A 135 3.71e+01 a.22.1.1 77593 1tgoA 773 3.72e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1itkA 731 3.74e+01 a.93.1.3 71417 a.93.1.3 71418 1aoiF 87 3.82e+01 1aoiB a.22.1.1 16471 1r3nA 462 3.85e+01 c.56.5.4 -7872 d.58.19.1 -10096 1yveI 524 3.93e+01 1qmgA a.100.1.2 18789 c.2.1.6 30186 1hq3D 103 3.96e+01 1aoiB a.22.1.1 16464 1nw1A 429 3.96e+01 d.144.1.8 86286