# 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 1r5qA 102 2.51e-04 unknown_sccs -965 1v2zA 111 1.81e-03 1q6aA 107 2.28e-03 unknown_sccs -960 1dvpA 220 1.01e-01 1dvpA a.118.9.2 19216 g.50.1.1 45358 1moh 142 1.06e-01 1flp a.1.1.2 15012 1b0b 142 1.15e-01 2fal a.1.1.2 15010 1flp 142 1.41e-01 1flp a.1.1.2 15011 1dlyA 164 3.77e-01 1dlyA a.1.1.1 14983 1iqpA 327 4.32e-01 a.80.1.1 62649 c.37.1.20 62650 1a87 321 5.21e-01 1a87 f.1.1.1 43380 1gvhA 396 5.53e-01 a.1.1.2 70601 b.43.4.2 70602 c.25.1.5 70603 1p8cA 145 5.68e-01 unknown_sccs -1927 1tbmA 326 5.86e-01 1aj8A 371 7.25e-01 1aj8A a.103.1.1 18900 1tlqA 189 7.56e-01 1hz4A 373 8.28e-01 a.118.8.2 65960 1vkeA 133 9.44e-01 1jfiB 179 1.07e+00 1jfiB a.22.1.3 62937 1jdhA 529 1.11e+00 a.118.1.1 66549 1sxjE 354 1.18e+00 1gwiA 411 1.37e+00 a.104.1.1 76364 3bct 457 1.40e+00 3bct a.118.1.1 19112 1ufaA 520 1.42e+00 unknown_sccs -421 unknown_sccs -6065 1kmmA 424 1.59e+00 1adjA c.51.1.1 33174 d.104.1.1 40723 1fo3A 460 1.80e+00 1dl2A a.102.2.1 18845 1qusA 322 1.96e+00 1ltm d.2.1.6 36991 1ltm 320 2.00e+00 1ltm d.2.1.6 36992 1s9pA 227 2.53e+00 1i7wA 538 2.84e+00 3bct a.118.1.1 61909 1rfzA 168 3.09e+00 unknown_sccs -1206 1b0nB 57 3.11e+00 1b0nB a.34.1.1 17002 1g3jA 532 3.12e+00 3bct a.118.1.1 19114 1p49A 562 3.18e+00 c.76.1.2 -8432 1n2aA 201 3.21e+00 a.45.1.1 -938 c.47.1.5 -7463 1sctB 151 3.24e+00 3sdhA a.1.1.2 15003 1g73A 162 3.30e+00 1fewA a.7.4.1 16332 1rfmA 344 3.66e+00 c.122.1.1 -8032 1a0fA 201 3.79e+00 1a0fA a.45.1.1 17737 c.47.1.5 33031 1iomA 377 3.98e+00 a.103.1.1 83698 1arv 344 4.29e+00 1arv a.93.1.1 18590 1aru 344 4.30e+00 1arv a.93.1.1 18589 1o0uA 429 4.37e+00 c.118.1.1 80743 1kkhA 317 4.48e+00 d.14.1.5 72645 d.58.26.3 72646 1a28A 256 4.75e+00 1a28A a.123.1.1 19290 1f5xA 208 4.79e+00 1f5xA a.87.1.1 18516 1trlA 62 4.92e+00 1hyt j.78.1.1 18263 1qwlA 505 4.98e+00 e.5.1.1 -11823 1hr6A 475 5.07e+00 1hr6A d.185.1.1 61164 d.185.1.1 61165 1dlc 584 5.21e+00 1ciy b.18.1.3 23719 b.77.2.1 27976 f.1.3.1 43391 1s35A 214 5.26e+00 a.7.1.1 -391 a.7.1.1 -392 1hsr 344 5.38e+00 1arv a.93.1.1 18592 1gk4C 84 5.54e+00 h.1.20.1 70205 1rh5C 53 5.68e+00 unknown_sccs -12204 1qpaA 345 5.93e+00 1arv a.93.1.1 18585 1mi1A 414 5.97e+00 a.169.1.1 79137 b.55.1.6 79138 2ran 316 6.01e+00 1avc a.65.1.1 18170 1no4A 97 6.01e+00 h.1.24.1 85918 1kyqA 274 6.04e+00 c.2.1.11 73281 e.37.1.1 73282 1omwA 689 6.25e+00 a.91.1.1 87086 b.55.1.1 87087 d.144.1.7 87088 1uzxA 169 6.25e+00 d.20.1.2 -9409 1sr7A 259 6.57e+00 1e5rA 290 6.75e+00 1e5rA b.82.2.4 59276 1a8b 318 6.84e+00 1avc a.65.1.1 18171 1gakA 141 6.95e+00 1gakA a.19.1.1 16415 1lycA 343 7.13e+00 a.93.1.1 74344 1qc7A 101 7.29e+00 1qc7A a.118.14.1 18456 1hvd 319 7.50e+00 1avc a.65.1.1 18154 1a4mA 349 7.65e+00 1a4mA c.1.9.1 29014 1k8eA 345 7.77e+00 1o17A 345 7.77e+00 a.46.2.1 80765 c.27.1.1 80766 1kktA 511 7.78e+00 a.102.2.1 68687 1gk4D 84 7.97e+00 h.1.20.1 70206 5csmA 256 8.05e+00 5csmA a.130.1.2 19494 1fkx 349 8.19e+00 1a4mA c.1.9.1 29018 1llp 343 8.25e+00 1arv a.93.1.1 18578 1m12A 84 8.33e+00 a.64.1.1 84745 1a8a 318 8.34e+00 1avc a.65.1.1 18169 1s3jA 155 8.37e+00 a.4.5.28 -227 1huw 166 8.41e+00 1huw a.26.1.1 16831 1fzaB 328 8.81e+00 3fib d.171.1.1 42480 h.1.8.1 45621 1c3wA 222 9.11e+00 1c3wA f.13.1.1 43405 1gntA 553 9.31e+00 e.26.1.1 70290 1anxA 319 9.42e+00 1avc a.65.1.1 18161 2mhr 118 9.56e+00 2mhr a.24.4.1 16581 7timA 247 9.80e+00 1amk c.1.1.1 28457 1neyA 247 9.87e+00 c.1.1.1 80449 1e2uA 553 9.91e+00 1e1dA e.26.1.1 43362 1cqxA 403 9.95e+00 1cqxA a.1.1.2 15635 b.43.4.2 25667 c.25.1.5 31562 1q4mA 221 1.00e+01 unknown_sccs -1910 1or7A 194 1.02e+01 a.4.13.2 87332 a.177.1.1 87333 1jmeA 455 1.05e+01 a.104.1.1 66885 1bvsB 203 1.06e+01 1hjp a.5.1.1 16281 a.60.2.1 17956 b.40.4.2 25275 1add 349 1.10e+01 1a4mA c.1.9.1 29020 1i45A 248 1.11e+01 1amk c.1.1.1 61665 1pbwA 216 1.13e+01 1pbwA a.116.1.1 19103 1k04A 162 1.22e+01 a.24.14.1 67904 1kpsB 171 1.23e+01 a.118.12.1 68787 1ihp 438 1.26e+01 1ihp c.60.1.2 33993 1i27A 73 1.28e+01 1i27A a.4.5.30 61555 1keiA 316 1.32e+01 d.92.1.2 77349 1np3A 338 1.36e+01 a.100.1.2 85946 c.2.1.6 85947 1r71A 178 1.36e+01 1on0A 158 1.40e+01 d.108.1.1 87095 1hq3D 103 1.40e+01 1aoiB a.22.1.1 16464 2cyp 294 1.41e+01 1ryc a.93.1.1 18600 1dynA 125 1.41e+01 1dynA b.55.1.1 26955 1mroA 548 1.44e+01 1mroA a.89.1.1 18525 d.58.31.2 39443 1bjt 793 1.44e+01 1bjt e.11.1.1 43249 1jdrA 294 1.45e+01 1ryc a.93.1.1 62908 1hbnA 549 1.45e+01 1mroA a.89.1.1 60898 d.58.31.2 60899 1hyt 316 1.46e+01 1hyt d.92.1.2 59005 1lkvX 232 1.47e+01 a.118.14.1 73980 1m7vA 363 1.48e+01 d.174.1.1 78748 1axn 323 1.49e+01 1avc a.65.1.1 18149 6tmnE 316 1.51e+01 1hyt d.92.1.2 59071 1k5hA 398 1.52e+01 a.69.3.1 68192 c.2.1.3 68193 d.81.1.3 68194 1m6kA 251 1.52e+01 e.3.1.1 78695 1aoiB 87 1.55e+01 1aoiB a.22.1.1 16470 1hm5A 558 1.56e+01 c.80.1.2 76717 1gk4A 84 1.66e+01 h.1.20.1 70203 1knvA 293 1.66e+01 c.52.1.7 68707 1csc 433 1.68e+01 1csh a.103.1.1 18886 1fioA 196 1.74e+01 1fioA a.47.2.1 17773 1idrA 136 1.75e+01 1dlyA a.1.1.1 62301 1ccg 291 1.77e+01 1ryc a.93.1.1 18627 1dqrA 557 1.79e+01 1dqrA c.80.1.2 35305 1jgtA 513 1.79e+01 c.26.2.1 66684 d.153.1.1 66685 6gsvA 217 1.79e+01 1b8xA a.45.1.1 17633 c.47.1.5 32925 1eqcA 394 1.80e+01 1cz1A c.1.8.3 28811 1cz1A 394 1.81e+01 1cz1A c.1.8.3 28839 1ryc 294 1.87e+01 1ryc a.93.1.1 18601 1aoiF 87 1.88e+01 1aoiB a.22.1.1 16471 6cts 433 1.89e+01 1csh a.103.1.1 18891 1pf5A 131 1.90e+01 d.79.1.1 -10368 1nogA 177 1.90e+01 a.25.2.2 85923 1ufhA 180 1.91e+01 d.108.1.1 88485 1jvsA 400 1.94e+01 a.69.3.1 77187 c.2.1.3 77188 d.81.1.3 77189 1n5dA 288 1.94e+01 c.2.1.2 80030 1hu4A 288 1.94e+01 1hu4A 1mijA 152 1.96e+01 a.4.1.1 79150 1ofcX 304 1.97e+01 a.4.1.3 -195 unknown_sccs -199 unknown_sccs -978 1r9dA 787 1.98e+01 1o1yA 239 1.99e+01 c.23.16.1 86554 1j7iA 264 2.00e+01 1j7iA d.144.1.6 62694 1rjdA 334 2.01e+01 unknown_sccs -8079 1uedA 406 2.02e+01 a.104.1.1 -1459 1j7lA 264 2.04e+01 d.144.1.6 62697 2ccyA 128 2.06e+01 2ccyA a.24.3.2 16544 1odoA 408 2.06e+01 a.104.1.1 -1463 1h6zA 913 2.11e+01 c.1.12.2 70906 c.8.1.1 70907 d.142.1.5 70908 2dynA 122 2.12e+01 1dynA b.55.1.1 26957 1j8yF 297 2.13e+01 1ng1 a.24.13.1 62747 c.37.1.10 62748 1dd5A 185 2.17e+01 1dd5A d.67.3.1 39564 1dseA 292 2.20e+01 1ryc a.93.1.1 59130 1j8mF 297 2.20e+01 1ng1 a.24.13.1 62742 c.37.1.10 62743 1em9A 154 2.20e+01 1d1dA a.73.1.1 18333 1nd4A 264 2.21e+01 d.144.1.6 -11381 1ei1A 391 2.21e+01 1aj6 d.14.1.3 37570 d.122.1.2 41104 1f24A 402 2.22e+01 1rom a.104.1.1 18953 1d9cA 121 2.23e+01 1d9cA a.26.1.3 16901 1a27 289 2.23e+01 1fds c.2.1.2 29839 8tlnE 316 2.24e+01 1hyt d.92.1.2 59075 1nw1A 429 2.27e+01 d.144.1.8 86286 1kx5B 102 2.32e+01 a.22.1.1 77594 1iatA 557 2.33e+01 1dqrA c.80.1.2 62123 1i5rA 327 2.40e+01 c.2.1.2 83668 1or0A 160 2.41e+01 d.153.1.2 -11415 1j2jB 45 2.46e+01 a.7.8.1 84017 2a0b 125 2.51e+01 2a0b a.24.10.1 16630 1dm5A 315 2.54e+01 1avc a.65.1.1 18186 1fdt 327 2.55e+01 1fds c.2.1.2 29841 1ca1 370 2.55e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1ds4A 292 2.56e+01 1ryc a.93.1.1 59129 1fyhA 258 2.57e+01 1d9cA a.26.1.3 16907 a.26.1.3 16908 1fds 327 2.62e+01 1fds c.2.1.2 29838 1fs1B 141 2.64e+01 1vcbB a.157.1.1 19252 d.42.1.1 38664 1us6A 102 2.67e+01 3sdhA 146 2.71e+01 3sdhA a.1.1.2 14984 1i37A 260 2.75e+01 1a28A a.123.1.1 61583 1h2rL 534 2.80e+01 1h2rL e.18.1.1 43298 1jfbA 404 2.83e+01 a.104.1.1 66624 2abk 211 2.86e+01 2abk a.96.1.1 18743 1go3F 107 2.92e+01 a.60.8.2 65407 1q4rA 112 2.92e+01 d.58.4.4 -9943 1fm2A 169 2.93e+01 1fm2A d.153.1.2 59877 1r1dA 247 2.95e+01 unknown_sccs -8335 1rp4A 389 2.95e+01 1l9hA 349 2.96e+01 f.13.1.2 73720 3tmkA 216 2.99e+01 3tmkA c.37.1.1 31920 1ukfA 188 3.02e+01 unknown_sccs -8886 1csh 435 3.08e+01 1csh a.103.1.1 18880 5eat 548 3.10e+01 5eat a.102.4.1 18853 a.128.1.3 19445 1ev7B 317 3.11e+01 1ev7B c.52.1.9 33316 1l4aD 87 3.11e+01 h.1.15.1 73562 1lfb 99 3.11e+01 1lfb a.4.1.1 15989 1cmnA 402 3.15e+01 1rom a.104.1.1 18958 1jtvA 327 3.19e+01 c.2.1.2 84230 1iznA 286 3.19e+01 e.43.1.1 83847 1tgoA 773 3.29e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1amz 435 3.32e+01 1csh a.103.1.1 18884 1gcuA 295 3.33e+01 1gcuA c.2.1.3 30063 d.81.1.4 39978 1csmA 256 3.33e+01 5csmA a.130.1.2 19495 1lucA 355 3.37e+01 1lucA c.1.16.1 29547 1ks9A 291 3.39e+01 a.100.1.7 68857 c.2.1.6 68858 2tmnE 316 3.42e+01 1hyt d.92.1.2 59055 1keaA 221 3.44e+01 a.96.1.2 68491 1o5hA 214 3.49e+01 unknown_sccs -1078 1us7B 265 3.51e+01 unknown_sccs -1518 1rw2A 152 3.54e+01 unknown_sccs -1645 1lmeA 176 3.56e+01 d.167.1.1 84629 1hzxA 349 3.62e+01 1f88A f.13.1.2 61466 1b4pA 217 3.65e+01 a.45.1.1 83158 c.47.1.5 83159 1cg5B 141 3.66e+01 1cg5B a.1.1.2 15585 1ubkL 534 3.71e+01 e.18.1.1 88422 1jqaA 370 3.75e+01 e.22.1.2 67085 1q53A 112 3.75e+01 d.58.4.4 -9944 1e1dA 553 3.86e+01 1e1dA e.26.1.1 43363 1qdbA 473 3.88e+01 1qdbA a.138.1.3 19688 1jq5A 370 3.90e+01 e.22.1.2 67084 1lc0A 294 3.90e+01 c.2.1.3 73823 d.81.1.4 73824 1f88A 348 3.91e+01 1f88A f.13.1.2 43429 2tmkA 216 3.92e+01 3tmkA c.37.1.1 31928 1ornA 226 3.94e+01 a.96.1.1 87342 1epwA 1290 3.96e+01 b.29.1.6 24269 b.42.4.2 25614 d.92.1.7 40305 h.4.2.1 45785 1m1zA 513 3.97e+01 c.26.2.1 78457 d.153.1.1 78458 1i6pA 220 3.97e+01 1ddzA c.53.2.1 61848