# 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 1jcqA 382 8.32e-02 a.118.6.1 66504 1ld8A 382 1.88e-01 a.118.6.1 73838 1vk3A 615 2.83e-01 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1d8dA 377 3.39e-01 1ft1A a.118.6.1 19185 3erdA 261 3.60e-01 3erdA a.123.1.1 19293 1l2iA 261 4.07e-01 a.123.1.1 73503 1ft1A 377 4.69e-01 1ft1A a.118.6.1 19186 1jcrA 377 5.95e-01 a.118.6.1 66506 1pq1A 196 6.00e-01 f.1.4.1 -12055 1qbqA 333 7.00e-01 1ft1A a.118.6.1 19187 1a8i 842 7.33e-01 1a8i c.87.1.4 35490 1foeA 377 8.38e-01 1foeA a.87.1.1 18517 b.55.1.1 26969 1gpb 842 9.70e-01 1a8i c.87.1.4 35478 1h5uA 842 1.00e+00 1a8i c.87.1.4 60655 1hg5A 289 1.08e+00 1hg5A unknown_sccs -400 unknown_sccs -1629 1hg2A 289 1.08e+00 1hg5A unknown_sccs -401 unknown_sccs -1630 1hf8A 289 1.15e+00 1hg5A unknown_sccs -399 unknown_sccs -1628 1c8kA 842 1.19e+00 1a8i c.87.1.4 35491 1i7wA 538 1.21e+00 3bct a.118.1.1 61909 1dn1B 267 1.33e+00 1dn1B a.47.2.1 17771 1t7pA 698 1.62e+00 1t7pA c.55.3.5 33712 e.8.1.1 43005 1ua4A 455 1.87e+00 c.72.1.3 -8416 3bct 457 1.95e+00 3bct a.118.1.1 19112 1htjF 210 2.00e+00 1htjF a.91.1.1 61254 1bxlA 181 2.04e+00 1maz f.1.4.1 43396 1dbhA 354 2.21e+00 1awe a.87.1.1 18514 b.55.1.1 26967 1lrzA 426 2.29e+00 a.2.7.4 78167 d.108.1.4 78168 d.108.1.4 78169 1ks8A 433 2.40e+00 a.102.1.2 77519 3ertA 261 2.52e+00 3erdA a.123.1.1 19292 1kgnA 329 2.59e+00 a.25.1.2 68584 1q4mA 221 2.71e+00 unknown_sccs -1910 1cnt1 187 2.89e+00 1cnt3 1n97A 389 3.06e+00 a.104.1.1 80335 1flcB 175 3.09e+00 1flcB h.3.1.1 45716 1jf0A 195 3.46e+00 1ej3A a.39.1.5 62926 1kn1A 160 3.51e+00 a.1.1.3 77455 1af3 196 3.52e+00 1maz f.1.4.1 43397 1m2oA 768 3.55e+00 a.71.2.1 78480 b.2.8.1 78481 c.62.1.2 78482 d.109.2.1 78483 g.41.10.1 78484 1g3jA 532 3.61e+00 3bct a.118.1.1 19114 1ezwA 349 3.62e+00 1ezwA c.1.16.3 29558 1fjgM 126 3.72e+00 1fjfM a.156.1.1 16293 1hg4A 279 3.89e+00 1lbd a.123.1.1 19333 1eg5A 384 4.44e+00 1ecxA c.67.1.3 34429 1ecxA 384 4.48e+00 1ecxA c.67.1.3 34431 1qkmA 255 4.93e+00 3erdA a.123.1.1 19309 1n00A 321 5.25e+00 a.65.1.1 85241 1hiwA 133 5.72e+00 1hiwA a.61.1.1 18122 1el4A 195 5.76e+00 1ej3A a.39.1.5 59453 1rfmA 344 6.13e+00 c.122.1.1 -8032 1dvpA 220 6.47e+00 1dvpA a.118.9.2 19216 g.50.1.1 45358 1cnt2 187 6.78e+00 1cnt3 1allA 160 6.90e+00 1qgwC a.1.1.3 15647 1vsgA 364 7.03e+00 1vsgA h.4.1.1 45782 1bp7A 152 7.12e+00 1bp7A d.95.2.1 40568 1cnt3 187 7.28e+00 1cnt3 1odoA 408 7.30e+00 a.104.1.1 -1463 1mldA 314 7.55e+00 2cmd c.2.1.5 30122 d.162.1.1 42089 1nm8A 616 7.61e+00 c.43.1.3 85872 c.43.1.3 85873 1nrfA 262 7.95e+00 e.3.1.1 -11780 1alq 266 8.08e+00 1btl e.3.1.1 42707 1qv1A 195 8.22e+00 a.39.1.5 -830 1c3jA 351 8.43e+00 1c3jA c.87.1.1 35459 1s9pA 227 8.50e+00 1nznA 126 9.47e+00 a.118.8.1 -1616 1li5A 461 9.57e+00 a.27.1.1 73912 c.26.1.1 73913 1gmjA 84 9.58e+00 h.4.8.1 65310 1f3aA 222 1.01e+01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1jdhA 529 1.02e+01 a.118.1.1 66549 1jixA 351 1.02e+01 1c3jA c.87.1.1 63081 1jf2A 195 1.05e+01 1ej3A a.39.1.5 62930 1rh5A 436 1.06e+01 unknown_sccs -12298 1mgn 154 1.08e+01 1a6m a.1.1.2 15097 1a6m 151 1.08e+01 1a6m a.1.1.2 15018 1g9zA 152 1.09e+01 1bp7A d.95.2.1 60408 1b4uA 139 1.11e+01 1bouA a.88.1.1 18523 1j27A 102 1.14e+01 unknown_sccs -10116 1j7xA 302 1.17e+01 c.14.1.2 66425 1id3B 102 1.18e+01 a.22.1.1 66113 1bzpA 153 1.19e+01 1a6m a.1.1.2 15020 1e3aA 260 1.20e+01 1ajqA d.153.1.2 41838 1mmoG 162 1.21e+01 1mtyG a.23.3.1 16512 1bouA 139 1.24e+01 1bouA a.88.1.1 18521 1jg7A 351 1.24e+01 1c3jA c.87.1.1 62945 1mtyG 162 1.28e+01 1mtyG a.23.3.1 16498 1l6nA 289 1.30e+01 a.61.1.1 73624 a.73.1.1 73625 1gm7A 209 1.31e+01 d.153.1.2 65302 1maz 221 1.34e+01 1maz f.1.4.1 43393 2bgu 351 1.38e+01 1c3jA c.87.1.1 35460 1v92A 46 1.46e+01 a.5.2.3 -357 1umvX 122 1.47e+01 a.133.1.2 -1994 1gk9A 260 1.47e+01 d.153.1.2 65246 2spo 154 1.54e+01 1a6m a.1.1.2 15053 7aatA 401 1.55e+01 1ajsA c.67.1.1 34250 1mbd 153 1.58e+01 1a6m a.1.1.2 15033 1aisA 182 1.59e+01 1ytbA d.129.1.1 41288 d.129.1.1 41289 1rqjA 299 1.61e+01 a.128.1.1 -1774 1pnkA 209 1.62e+01 1ajqA d.153.1.2 41839 1ihgA 370 1.67e+01 2cpl a.118.8.1 62380 b.62.1.1 62381 1on2A 142 1.69e+01 a.4.5.24 87103 a.76.1.1 87104 1rztA 331 1.71e+01 a.60.6.1 -1023 a.60.12.1 -1030 d.218.1.2 -9807 1ajqA 209 1.73e+01 1ajqA d.153.1.2 41840 1ndbA 596 1.75e+01 c.43.1.3 80411 c.43.1.3 80412 1k3yA 221 1.78e+01 a.45.1.1 77245 c.47.1.5 77246 1iatA 557 1.79e+01 1dqrA c.80.1.2 62123 1hzpA 335 1.80e+01 1hn9A c.95.1.1 61455 c.95.1.1 61456 1vj7A 393 1.81e+01 unknown_sccs -1265 unknown_sccs -9814 1top 162 1.82e+01 1ncx a.39.1.5 17223 1ho8A 480 1.84e+01 1ho8A a.118.1.9 61107 1gseA 221 1.90e+01 1pgtA a.45.1.1 17667 c.47.1.5 32961 1ai7A 209 1.95e+01 1ajqA d.153.1.2 41845 1n46A 258 1.96e+01 a.123.1.1 85315 1c1kA 217 1.98e+01 1c1kA a.120.1.1 19239 1csc 433 1.99e+01 1csh a.103.1.1 18886 1ncx 162 1.99e+01 1ncx a.39.1.5 17222 1ez3A 127 2.11e+01 1dn1B a.47.2.1 17768 1h97A 147 2.23e+01 1h97A a.1.1.2 60812 1qgtA 149 2.23e+01 1qgtA a.62.1.1 18135 1fd9A 213 2.23e+01 1fd9A d.26.1.1 59771 1csh 435 2.28e+01 1csh a.103.1.1 18880 1gmjD 84 2.31e+01 h.4.8.1 65313 1evsA 187 2.34e+01 1evsA a.26.1.1 16845 1e29A 135 2.35e+01 1e29A a.3.1.1 59161 1l1jA 239 2.37e+01 b.47.1.1 84516 1orsC 132 2.39e+01 f.14.1.1 87353 1fcbA 511 2.39e+01 1gox c.1.4.1 28620 d.120.1.1 41087 1ezfA 340 2.39e+01 1ezfA a.128.1.2 19440 1amz 435 2.40e+01 1csh a.103.1.1 18884 1tbmA 326 2.56e+01 1oc2A 348 2.57e+01 c.2.1.2 -5753 1nkpA 88 2.69e+01 a.38.1.1 80573 1iv8A 720 2.69e+01 b.71.1.1 76842 c.1.8.1 76843 1q8iA 783 2.70e+01 c.55.3.5 -7635 e.8.1.1 -11885 1s5lB 510 2.70e+01 1e70M 501 2.75e+01 1e70M c.1.8.4 28926 1cuk 203 2.78e+01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1k3lA 221 2.78e+01 a.45.1.1 77229 c.47.1.5 77230 1qmqA 414 2.79e+01 1phd a.104.1.1 18907 1mu5A 471 2.85e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1gmjC 84 2.87e+01 h.4.8.1 65312 1pgtA 210 2.88e+01 1pgtA a.45.1.1 17515 c.47.1.5 32809 1brwA 433 2.92e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1e4mM 501 2.95e+01 1e70M c.1.8.4 59226 1d9cA 121 2.97e+01 1d9cA a.26.1.3 16901 1qsdA 106 2.99e+01 1qsdA a.7.5.1 16335 1i7gA 287 3.02e+01 a.123.1.1 71121 1kepA 348 3.04e+01 c.2.1.2 68536 6cts 433 3.06e+01 1csh a.103.1.1 18891 1auwA 468 3.08e+01 1auwA a.127.1.1 19416 1e6qM 501 3.09e+01 1e70M c.1.8.4 28920 1hjp 203 3.11e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1r5zA 323 3.13e+01 unknown_sccs -12289 1clqA 903 3.13e+01 1clqA c.55.3.5 33717 e.8.1.1 43006 1m4rA 151 3.21e+01 a.26.1.3 84799 1nyhA 166 3.23e+01 h.1.23.1 86403 1rp4A 389 3.26e+01 1be3C 379 3.29e+01 1be3C f.32.1.1 75805 f.21.1.2 75806 1q44A 326 3.33e+01 c.37.1.5 -7037 1kbjA 412 3.33e+01 c.1.4.1 72280 1mumA 295 3.34e+01 c.1.12.7 85108 1ic2A 81 3.40e+01 h.1.5.1 62247 1ihoA 283 3.40e+01 1ihoA c.26.1.4 62390 1miwA 404 3.42e+01 a.173.1.1 79162 d.218.1.4 79163 1ik9A 213 3.45e+01 b.59.1.1 66176 h.1.11.1 66177 1in6A 334 3.45e+01 1hqcA a.4.5.11 62601 c.37.1.20 62602 1iwhB 146 3.49e+01 a.1.1.2 76883 1e8aA 91 3.49e+01 1b4cA a.39.1.2 17188 1dk5A 322 3.69e+01 1dk5A a.65.1.1 18192 1j5vA 351 3.78e+01 c.72.1.1 71585 1f16A 192 3.79e+01 1f16A f.1.4.1 43400 2bidA 197 3.79e+01 2bidA f.1.4.1 43398 1ltdA 506 3.82e+01 1gox c.1.4.1 28618 d.120.1.1 41086 1iwgA 1053 3.84e+01 d.58.44.1 76874 d.58.44.1 76875 d.58.44.1 76876 d.58.44.1 76877 d.225.1.1 76878 d.225.1.1 76879 f.35.1.1 76880 f.35.1.1 76881 1gw5A 621 3.88e+01 a.118.1.10 70629 1odfA 290 3.94e+01 c.37.1.6 -7045 1iygA 133 3.97e+01 a.118.8.1 76947 1r9lA 309 3.99e+01 c.94.1.1 -8700 1lox 662 3.99e+01 1lox a.119.1.2 19238 b.12.1.1 23638