# 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 1r5qA 102 8.99e-05 unknown_sccs -965 1v2zA 111 1.20e-03 1q6aA 107 1.46e-03 unknown_sccs -960 1a87 321 2.41e-02 1a87 f.1.1.1 43380 1dvpA 220 1.00e-01 1dvpA a.118.9.2 19216 g.50.1.1 45358 1gvhA 396 1.26e-01 a.1.1.2 70601 b.43.4.2 70602 c.25.1.5 70603 1sxjE 354 1.34e-01 1jfiB 179 1.64e-01 1jfiB a.22.1.3 62937 1hz4A 373 2.06e-01 a.118.8.2 65960 1flp 142 2.17e-01 1flp a.1.1.2 15011 1moh 142 2.17e-01 1flp a.1.1.2 15012 1dlyA 164 2.24e-01 1dlyA a.1.1.1 14983 1gntA 553 2.55e-01 e.26.1.1 70290 1e2uA 553 2.56e-01 1e1dA e.26.1.1 43362 1b0b 142 2.90e-01 2fal a.1.1.2 15010 1p8cA 145 3.76e-01 unknown_sccs -1927 1kktA 511 4.39e-01 a.102.2.1 68687 1s9pA 227 4.40e-01 1p49A 562 4.97e-01 c.76.1.2 -8432 1vkeA 133 5.34e-01 1aj8A 371 6.44e-01 1aj8A a.103.1.1 18900 1tlqA 189 7.56e-01 1f5xA 208 9.63e-01 1f5xA a.87.1.1 18516 1sctB 151 1.07e+00 3sdhA a.1.1.2 15003 1e1dA 553 1.10e+00 1e1dA e.26.1.1 43363 1iqpA 327 1.21e+00 a.80.1.1 62649 c.37.1.20 62650 1gwiA 411 1.23e+00 a.104.1.1 76364 1k8eA 345 1.40e+00 1o17A 345 1.40e+00 a.46.2.1 80765 c.27.1.1 80766 1sr7A 259 1.47e+00 1iomA 377 1.49e+00 a.103.1.1 83698 1ufaA 520 1.73e+00 unknown_sccs -421 unknown_sccs -6065 1b4pA 217 1.95e+00 a.45.1.1 83158 c.47.1.5 83159 1on0A 158 1.95e+00 d.108.1.1 87095 1a28A 256 2.06e+00 1a28A a.123.1.1 19290 1fnnA 389 2.11e+00 1fnnA a.4.5.11 16129 c.37.1.20 32426 1k5hA 398 2.25e+00 a.69.3.1 68192 c.2.1.3 68193 d.81.1.3 68194 1knvA 293 2.34e+00 c.52.1.7 68707 6gsvA 217 2.44e+00 1b8xA a.45.1.1 17633 c.47.1.5 32925 1ufhA 180 2.54e+00 d.108.1.1 88485 1uzxA 169 2.58e+00 d.20.1.2 -9409 1fo3A 460 2.68e+00 1dl2A a.102.2.1 18845 1e5rA 290 2.73e+00 1e5rA b.82.2.4 59276 1s3jA 155 2.84e+00 a.4.5.28 -227 1ltm 320 2.89e+00 1ltm d.2.1.6 36992 1qusA 322 2.91e+00 1ltm d.2.1.6 36991 1g73A 162 2.91e+00 1fewA a.7.4.1 16332 1omwA 689 3.12e+00 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1kmmA 424 3.13e+00 1adjA c.51.1.1 33174 d.104.1.1 40723 1hsr 344 3.38e+00 1arv a.93.1.1 18592 1kpsB 171 3.43e+00 a.118.12.1 68787 1iznA 286 3.51e+00 e.43.1.1 83847 1rfzA 168 3.52e+00 unknown_sccs -1206 1aru 344 3.55e+00 1arv a.93.1.1 18589 1arv 344 3.57e+00 1arv a.93.1.1 18590 1keaA 221 3.72e+00 a.96.1.2 68491 1b0nB 57 3.74e+00 1b0nB a.34.1.1 17002 1o0uA 429 3.85e+00 c.118.1.1 80743 1gk4C 84 3.96e+00 h.1.20.1 70205 3sdhA 146 3.96e+00 3sdhA a.1.1.2 14984 1j2jB 45 4.28e+00 a.7.8.1 84017 1iatA 557 4.29e+00 1dqrA c.80.1.2 62123 1keiA 316 4.30e+00 d.92.1.2 77349 1qwlA 505 4.30e+00 e.5.1.1 -11823 1cqxA 403 4.73e+00 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1m6kA 251 4.75e+00 e.3.1.1 78695 1dl2A 511 4.90e+00 1dl2A a.102.2.1 18844 1kyqA 274 4.93e+00 c.2.1.11 73281 e.37.1.1 73282 1j7lA 264 5.03e+00 d.144.1.6 62697 1lycA 343 5.07e+00 a.93.1.1 74344 1axn 323 5.21e+00 1avc a.65.1.1 18149 1kx5A 135 5.27e+00 a.22.1.1 77593 2tmnE 316 5.29e+00 1hyt d.92.1.2 59055 1kkhA 317 5.31e+00 d.14.1.5 72645 d.58.26.3 72646 1hyt 316 5.33e+00 1hyt d.92.1.2 59005 8tlnE 316 5.33e+00 1hyt d.92.1.2 59075 6tmnE 316 5.33e+00 1hyt d.92.1.2 59071 1hm5A 558 5.49e+00 c.80.1.2 76717 1giqA 413 5.67e+00 d.166.1.1 76224 d.166.1.1 76225 1gk4D 84 6.32e+00 h.1.20.1 70206 1mroA 548 6.47e+00 1mroA a.89.1.1 18525 d.58.31.2 39443 1ornA 226 6.47e+00 a.96.1.1 87342 1hr6A 475 6.61e+00 1hr6A d.185.1.1 61164 d.185.1.1 61165 1odoA 408 6.77e+00 a.104.1.1 -1463 1hbnA 549 6.91e+00 1mroA a.89.1.1 60898 d.58.31.2 60899 1f07A 321 6.99e+00 1ezwA c.1.16.3 59560 1hvd 319 7.20e+00 1avc a.65.1.1 18154 1hq3C 136 7.41e+00 1aoiA a.22.1.1 16454 1m33A 258 7.45e+00 c.69.1.26 78514 1csc 433 7.74e+00 1csh a.103.1.1 18886 1i27A 73 8.03e+00 1i27A a.4.5.30 61555 2mhr 118 8.10e+00 2mhr a.24.4.1 16581 1j7iA 264 8.12e+00 1j7iA d.144.1.6 62694 1aoiA 116 8.27e+00 1aoiA a.22.1.1 16462 1d1dA 262 8.40e+00 1d1dA a.28.3.1 16958 a.73.1.1 18335 1r71A 178 8.44e+00 1jplA 171 8.66e+00 a.118.9.2 67027 1rfmA 344 8.75e+00 c.122.1.1 -8032 1gk4A 84 8.76e+00 h.1.20.1 70203 1hu4A 288 8.77e+00 1hu4A 1n5dA 288 8.77e+00 c.2.1.2 80030 1a8b 318 8.84e+00 1avc a.65.1.1 18171 1anxA 319 8.96e+00 1avc a.65.1.1 18161 1srqA 341 9.10e+00 1uurA 473 9.13e+00 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1mzgA 146 9.54e+00 d.224.1.1 79696 1colA 204 9.70e+00 1a87 f.1.1.1 43378 1mi1A 414 9.83e+00 a.169.1.1 79137 b.55.1.6 79138 6cts 433 1.02e+01 1csh a.103.1.1 18891 1em9A 154 1.03e+01 1d1dA a.73.1.1 18333 1hlb 158 1.05e+01 1hlb a.1.1.2 15625 1oq9A 363 1.05e+01 a.25.1.2 87257 1j8mF 297 1.06e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1j8yF 297 1.06e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1epwA 1290 1.10e+01 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1jvsA 400 1.12e+01 a.69.3.1 77187 c.2.1.3 77188 d.81.1.3 77189 1h97A 147 1.14e+01 1h97A a.1.1.2 60812 1ukfA 188 1.16e+01 unknown_sccs -8886 1fd9A 213 1.18e+01 1fd9A d.26.1.1 59771 2mysB 166 1.19e+01 1wdcB a.39.1.5 17308 1tbmA 326 1.23e+01 1ofcX 304 1.23e+01 a.4.1.3 -195 unknown_sccs -199 unknown_sccs -978 1ursA 402 1.26e+01 c.94.1.1 -8651 1afrA 345 1.27e+01 1afrA a.25.1.2 16805 1hq3D 103 1.28e+01 1aoiB a.22.1.1 16464 1yfm 488 1.29e+01 1furA a.127.1.1 19413 1aoiF 87 1.29e+01 1aoiB a.22.1.1 16471 1kx5B 102 1.30e+01 a.22.1.1 77594 1o1yA 239 1.30e+01 c.23.16.1 86554 1aoiB 87 1.30e+01 1aoiB a.22.1.1 16470 1jwgA 147 1.30e+01 a.118.9.2 71911 1ujkA 147 1.30e+01 a.118.9.2 -1623 1qlaC 256 1.30e+01 1qlaC f.21.2.1 43722 1dbhA 354 1.31e+01 1awe a.87.1.1 18514 b.55.1.1 26967 1m7vA 363 1.31e+01 d.174.1.1 78748 1fewA 184 1.31e+01 1fewA a.7.4.1 16334 1csh 435 1.32e+01 1csh a.103.1.1 18880 1np3A 338 1.33e+01 a.100.1.2 85946 c.2.1.6 85947 1amz 435 1.34e+01 1csh a.103.1.1 18884 3bct 457 1.35e+01 3bct a.118.1.1 19112 1dceA 567 1.36e+01 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 1fyhA 258 1.36e+01 1d9cA a.26.1.3 16907 a.26.1.3 16908 1dqrA 557 1.38e+01 1dqrA c.80.1.2 35305 1a8a 318 1.41e+01 1avc a.65.1.1 18169 1trlA 62 1.42e+01 1hyt j.78.1.1 18263 2ran 316 1.42e+01 1avc a.65.1.1 18170 1g2nA 264 1.44e+01 1lbd a.123.1.1 60227 1fm2A 169 1.46e+01 1fm2A d.153.1.2 59877 1or0A 160 1.47e+01 d.153.1.2 -11415 1qwoA 442 1.49e+01 1qpaA 345 1.52e+01 1arv a.93.1.1 18585 1s35A 214 1.58e+01 a.7.1.1 -391 a.7.1.1 -392 1fkx 349 1.59e+01 1a4mA c.1.9.1 29018 1am3 70 1.59e+01 2cyp 294 1.60e+01 1ryc a.93.1.1 18600 1mijA 152 1.60e+01 a.4.1.1 79150 1n3kA 130 1.61e+01 a.77.1.4 79965 1avc 673 1.62e+01 1avc a.65.1.1 18178 a.65.1.1 18179 1hta 69 1.63e+01 1a7w a.22.1.2 16476 1iawA 317 1.64e+01 c.52.1.9 62126 1f5sA 211 1.65e+01 1f5sA c.108.1.4 59656 1j97A 211 1.65e+01 1f5sA c.108.1.4 62753 1l7mA 211 1.66e+01 c.108.1.4 73664 1vkmA 297 1.68e+01 1pmnA 364 1.68e+01 d.144.1.7 -11297 1ev7B 317 1.68e+01 1ev7B c.52.1.9 33316 1uddA 226 1.69e+01 1a8o 70 1.71e+01 1a8o a.28.3.1 16953 1khdA 345 1.71e+01 a.46.2.1 77400 c.27.1.1 77401 1jq5A 370 1.72e+01 e.22.1.2 67084 1jqaA 370 1.72e+01 e.22.1.2 67085 1r9dA 787 1.72e+01 1qv1A 195 1.73e+01 a.39.1.5 -830 1lwdA 413 1.76e+01 c.77.1.1 78265 1fqvD 149 1.80e+01 1fqvD a.157.1.1 19263 d.42.1.1 38667 1fqvJ 149 1.81e+01 1fqvD a.157.1.1 19266 d.42.1.1 38670 1dd8A 406 1.81e+01 1dd8A c.95.1.1 35932 c.95.1.1 35933 1oeqA 418 1.82e+01 1ek4A 418 1.82e+01 1dd8A c.95.1.1 59436 c.95.1.1 59437 1no4A 97 1.85e+01 h.1.24.1 85918 2occE 109 1.87e+01 2occE a.118.11.1 19224 1kl1A 419 1.88e+01 c.67.1.4 72663 1dd5A 185 1.88e+01 1dd5A d.67.3.1 39564 1rh5C 53 1.89e+01 unknown_sccs -12204 1iuqA 367 1.92e+01 c.112.1.1 -8440 1i7wA 538 1.93e+01 3bct a.118.1.1 61909 1q6hA 224 1.97e+01 d.26.1.1 -9487 1uedA 406 1.99e+01 a.104.1.1 -1459 1ei1A 391 2.00e+01 1aj6 d.14.1.3 37570 d.122.1.2 41104 1ltdA 506 2.02e+01 1gox c.1.4.1 28618 d.120.1.1 41086 1rw2A 152 2.03e+01 unknown_sccs -1645 1a4mA 349 2.05e+01 1a4mA c.1.9.1 29014 1add 349 2.05e+01 1a4mA c.1.9.1 29020 1jr3A 373 2.06e+01 a.80.1.1 63245 c.37.1.20 63246 1dc1A 323 2.07e+01 1dc1A c.52.1.11 33321 1qc7A 101 2.07e+01 1qc7A a.118.14.1 18456 1q4mA 221 2.12e+01 unknown_sccs -1910 1jmeA 455 2.16e+01 a.104.1.1 66885 1e4iA 447 2.18e+01 1e70M c.1.8.4 59225 1a17 166 2.18e+01 1a17 a.118.8.1 19206 1k30A 368 2.19e+01 c.112.1.1 68067 1a8h 500 2.21e+01 1a8h a.27.1.1 16922 c.26.1.1 31589 1j77A 209 2.24e+01 1j77A a.132.1.2 62674 1efvA 315 2.24e+01 1efvA c.26.2.3 31633 c.31.1.2 31728 1qcwA 410 2.25e+01 1gox c.1.4.1 28622 1jf0A 195 2.26e+01 1ej3A a.39.1.5 62926 1eu8A 409 2.27e+01 1eu8A c.94.1.1 59502 1gwcA 230 2.28e+01 a.45.1.1 70660 c.47.1.5 70661 1kkjA 419 2.28e+01 c.67.1.4 72647 1rjdA 334 2.29e+01 unknown_sccs -8079 1fchA 368 2.30e+01 1fchA a.118.8.1 19212 3tmkA 216 2.30e+01 3tmkA c.37.1.1 31920 1v54E 109 2.31e+01 a.118.11.1 -1652 1jgsA 138 2.35e+01 a.4.5.28 66683 2tmkA 216 2.36e+01 3tmkA c.37.1.1 31928 1ps1A 337 2.41e+01 1ps1A a.128.1.4 19450 1k1vA 41 2.42e+01 a.37.1.1 71999 1fcbA 511 2.45e+01 1gox c.1.4.1 28620 d.120.1.1 41087 1bk6A 422 2.45e+01 1bk5A a.118.1.1 19133 5eat 548 2.45e+01 5eat a.102.4.1 18853 a.128.1.3 19445 1jdhA 529 2.48e+01 a.118.1.1 66549 1gox 370 2.50e+01 1gox c.1.4.1 28607 1a7w 69 2.50e+01 1a7w a.22.1.2 16477 1tgoA 773 2.51e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1lc0A 294 2.52e+01 c.2.1.3 73823 d.81.1.4 73824 1otkA 249 2.56e+01 a.25.1.2 -695 4rnpA 883 2.56e+01 1cezA e.8.1.3 43113 1rqjA 299 2.58e+01 a.128.1.1 -1774 1sedA 117 2.58e+01 1i37A 260 2.61e+01 1a28A a.123.1.1 61583 1dseA 292 2.62e+01 1ryc a.93.1.1 59130 1go3F 107 2.62e+01 a.60.8.2 65407 1dmhA 311 2.64e+01 1dmhA b.3.6.1 22633 1qhtA 775 2.64e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1kw4A 89 2.66e+01 a.60.1.2 73077 1owcA 427 2.66e+01 1kbjA 412 2.71e+01 c.1.4.1 72280 1q59A 172 2.74e+01 f.1.4.1 -12062 1l4aD 87 2.75e+01 h.1.15.1 73562 1qhbA 596 2.76e+01 1qhbA a.111.1.2 19055 1q3eA 207 2.77e+01 b.82.3.2 -4922 1mhqA 148 2.78e+01 a.118.9.2 84973 1mba 147 2.80e+01 2fal a.1.1.2 15149 1g59A 468 2.80e+01 a.97.1.1 60257 c.26.1.1 60258 5eau 548 2.80e+01 5eat a.102.4.1 18851 a.128.1.3 19443 1ng6A 148 2.82e+01 a.182.1.1 85670 1dkxA 219 2.84e+01 1dkzA unknown_sccs -446 unknown_sccs -3061 1tr1A 447 2.85e+01 1e70M c.1.8.4 28957 1ifl 53 2.86e+01 1ifi h.1.4.1 45566 1i5rA 327 2.88e+01 c.2.1.2 83668 1qjbA 245 2.91e+01 1qjaA a.118.7.1 19202 1nnwA 252 2.92e+01 d.159.1.5 80674 1r3nA 462 2.92e+01 c.56.5.4 -7872 d.58.19.1 -10096 1us6A 102 2.93e+01 1gcuA 295 2.94e+01 1gcuA c.2.1.3 30063 d.81.1.4 39978 1dar 691 3.04e+01 1dar b.43.3.1 25707 c.37.1.8 32142 d.14.1.1 37547 d.58.11.1 39300 1jtvA 327 3.06e+01 c.2.1.2 84230 1fpkA 335 3.09e+01 1frpA e.7.1.1 42930 1fdt 327 3.09e+01 1fds c.2.1.2 29841 1kf6D 119 3.16e+01 f.21.2.2 72400 1or7A 194 3.18e+01 a.4.13.2 87332 a.177.1.1 87333 1i6pA 220 3.19e+01 1ddzA c.53.2.1 61848 2abk 211 3.21e+01 2abk a.96.1.1 18743 1neyA 247 3.23e+01 c.1.1.1 80449 1iwhA 141 3.28e+01 a.1.1.2 76882 7timA 247 3.31e+01 1amk c.1.1.1 28457 1fs1B 141 3.33e+01 1vcbB a.157.1.1 19252 d.42.1.1 38664 1i45A 248 3.35e+01 1amk c.1.1.1 61665 1hu3A 260 3.37e+01 1hu3A unknown_sccs 19137 1f88A 348 3.42e+01 1f88A f.13.1.2 43429 5fbpA 335 3.45e+01 1frpA e.7.1.1 42873 1imvA 398 3.45e+01 e.1.1.1 62591 1ic8A 194 3.47e+01 a.4.1.1 76740 a.35.1.1 76741 1ryc 294 3.49e+01 1ryc a.93.1.1 18601 1ds4A 292 3.51e+01 1ryc a.93.1.1 59129 1d9cA 121 3.51e+01 1d9cA a.26.1.3 16901 1id3B 102 3.52e+01 a.22.1.1 66113 1bjt 793 3.54e+01 1bjt e.11.1.1 43249 1bfmA 69 3.56e+01 1a7w a.22.1.2 16479 1qcrG 70 3.57e+01 1be3G f.23.13.1 43677 1nogA 177 3.61e+01 a.25.2.2 85923 1fds 327 3.62e+01 1fds c.2.1.2 29838 1q4rA 112 3.62e+01 d.58.4.4 -9943 1j09A 468 3.63e+01 a.97.1.1 77025 c.26.1.1 77026 1ea1A 455 3.63e+01 1ea1A a.104.1.1 18970 1hzxA 349 3.64e+01 1f88A f.13.1.2 61466 1hh2P 344 3.68e+01 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1lfkA 398 3.68e+01 a.104.1.1 77926 1dvkA 173 3.69e+01 1dvkA a.72.1.1 18319 1ah7 245 3.70e+01 1ah7 a.124.1.1 19339 1l9hA 349 3.73e+01 f.13.1.2 73720 1llp 343 3.74e+01 1arv a.93.1.1 18578 1i4sA 147 3.78e+01 a.149.1.1 66026 1oe8A 211 3.79e+01 a.45.1.1 86905 c.47.1.5 86906 1g3jA 532 3.88e+01 3bct a.118.1.1 19114 1nxhA 126 3.90e+01 unknown_sccs -1239 1h2vC 771 3.95e+01 unknown_sccs 76592 unknown_sccs 76593 unknown_sccs 76594 1bx4A 345 3.98e+01 1bx4A c.72.1.1 34935 1fioA 196 3.98e+01 1fioA a.47.2.1 17773