# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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 1tljA 213 3.12e-31 1kwkA 645 1.97e-01 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1kwgA 645 2.18e-01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1hv8A 367 2.33e-01 1hv8A c.37.1.19 32405 c.37.1.19 32406 1f0xA 571 3.01e-01 1f0xA d.58.32.2 39483 d.145.1.1 41746 1rkqA 282 4.01e-01 c.108.1.10 -6847 1t7pA 698 4.60e-01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1b65A 375 4.67e-01 1b65A d.154.1.1 42020 1ofuX 119 6.04e-01 c.37.1.22 86976 1e8gA 560 7.58e-01 1qltA d.58.32.1 39455 d.145.1.1 41718 1w1kA 560 8.17e-01 1gz0A 253 8.48e-01 c.116.1.1 76391 d.79.3.3 76392 1vaoA 560 8.92e-01 1qltA d.58.32.1 39461 d.145.1.1 41724 1ayyA 151 9.82e-01 1apyA d.153.1.5 42016 2ctb 307 1.07e+00 1aye c.56.5.1 33803 2ctc 307 1.18e+00 1aye c.56.5.1 33802 1qltA 560 1.29e+00 1qltA d.58.32.1 39457 d.145.1.1 41720 1rpjA 288 1.41e+00 2dri c.93.1.1 35656 1a3gA 308 1.61e+00 1daaA e.17.1.1 43286 1fdyA 297 1.76e+00 1nal3 c.1.10.1 29071 1g6sA 427 1.82e+00 1eps d.68.2.2 39584 1ecfB 504 1.95e+00 1ecfB c.61.1.1 34054 d.153.1.1 41821 1i1kA 309 1.99e+00 1daaA e.17.1.1 61533 1yme 309 2.15e+00 1aye c.56.5.1 33804 1m4lA 307 2.15e+00 c.56.5.1 78604 1brwA 433 2.20e+00 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1j5yA 187 2.25e+00 a.4.5.1 71592 d.94.2.1 71593 1uouA 474 2.29e+00 a.46.2.1 -951 c.27.1.1 -6642 d.41.3.1 -9715 9gafA 295 2.33e+00 1apyA d.153.1.5 42008 1eps 427 2.34e+00 1eps d.68.2.2 39586 1b8oA 284 2.57e+00 1b8oA c.56.2.1 33762 6cpa 307 2.67e+00 1aye c.56.5.1 33816 1p4kA 295 2.71e+00 d.153.1.5 87772 1qysA 106 2.94e+00 unknown_sccs -13432 1iyeA 309 3.03e+00 e.17.1.1 83786 1s98A 107 3.03e+00 1gpjA 404 3.24e+00 a.151.1.1 65451 c.2.1.7 65452 d.58.39.1 65453 1bs2A 607 3.60e+00 1bs2A a.27.1.1 16930 c.26.1.1 31597 d.67.2.1 39563 1a8q 274 3.66e+00 1brt c.69.1.12 34702 1bd3A 243 3.74e+00 1bd3A c.61.1.1 34098 1hl2A 297 3.78e+00 c.1.10.1 83581 1aw7A 194 3.82e+00 1aw7A b.40.2.2 25164 d.15.6.1 37753 1ufkA 254 3.94e+00 unknown_sccs -8103 1ohvA 472 4.06e+00 c.67.1.4 -8181 1nal1 297 4.13e+00 1nal3 1ts3A 194 4.16e+00 1aw7A b.40.2.2 25168 d.15.6.1 37757 1gudA 288 4.81e+00 c.93.1.1 83326 1ecfA 504 4.82e+00 1ecfB c.61.1.1 34053 d.153.1.1 41820 1j3mA 129 4.85e+00 1k2yX 463 5.00e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1agi 125 6.02e+00 7rsa d.5.1.1 37303 3tss 194 6.12e+00 1aw7A b.40.2.2 25160 d.15.6.1 37749 1b7fA 168 6.28e+00 1b7fA d.58.7.1 39169 d.58.7.1 39170 1ftrA 296 6.49e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 1r94A 118 6.61e+00 b.124.1.1 -4402 1f7uA 607 6.70e+00 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1lx7A 253 7.18e+00 c.56.2.1 74329 1q7sA 117 7.74e+00 unknown_sccs -7522 1odkA 235 7.94e+00 c.56.2.1 86863 1eqfA 280 8.38e+00 1eqfA a.29.2.1 16972 a.29.2.1 16973 1qupA 222 8.63e+00 1qupA b.1.8.1 22301 d.58.17.1 39352 1jeqB 565 9.31e+00 1jeqB unknown_sccs -4432 unknown_sccs -7996 1p5dX 463 9.47e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 1gnlA 544 9.85e+00 e.26.1.1 70287 1lc0A 294 9.89e+00 c.2.1.3 73823 d.81.1.4 73824 1gz6A 319 1.03e+01 c.2.1.2 76410 1kczA 413 1.03e+01 c.1.11.2 68451 d.54.1.1 68452 1iqpA 327 1.04e+01 a.80.1.1 62649 c.37.1.20 62650 487dH 224 1.05e+01 1ad2 i.1.1.2 45835 1ad2 228 1.05e+01 1ad2 e.24.1.1 43353 1hkhA 279 1.06e+01 c.69.1.12 -8342 1rcf 169 1.10e+01 1rcf c.23.5.1 31170 1nxiA 132 1.11e+01 d.58.47.1 86381 1b3nA 412 1.15e+01 1dd8A c.95.1.1 35966 c.95.1.1 35967 1eucB 396 1.17e+01 2scuB c.23.4.1 31149 d.142.1.4 41570 1gio 125 1.17e+01 7rsa d.5.1.1 37304 1l3iA 192 1.19e+01 c.66.1.22 77676 1mszA 86 1.20e+01 d.68.7.1 79428 1aye 401 1.22e+01 1aye c.56.5.1 33824 d.58.3.1 39065 1o5zA 442 1.23e+01 c.59.1.2 -7939 c.72.2.2 -8418 1eudB 396 1.24e+01 2scuB c.23.4.1 31150 d.142.1.4 41571 1gcuA 295 1.26e+01 1gcuA c.2.1.3 30063 d.81.1.4 39978 1dkzA 219 1.28e+01 1dkzA unknown_sccs -445 unknown_sccs -3060 1hl6A 165 1.30e+01 d.58.7.1 83609 1m5sA 297 1.31e+01 d.58.33.1 74511 d.58.33.1 74512 1rxyA 253 1.32e+01 c.56.2.1 -7834 3adk 195 1.33e+01 1zin c.37.1.1 31885 1kas 412 1.33e+01 1dd8A c.95.1.1 35964 c.95.1.1 35965 1oo0B 110 1.33e+01 d.58.7.1 87183 1dkxA 219 1.35e+01 1dkzA unknown_sccs -446 unknown_sccs -3061 1ykfA 352 1.37e+01 1pedA b.35.1.2 24757 c.2.1.1 29773 1qwdA 177 1.39e+01 b.60.1.1 -4455 1jetA 517 1.42e+01 1jevA c.94.1.1 35718 1rk8A 165 1.48e+01 d.58.7.1 -10018 1afb1 154 1.48e+01 1rtm1 1qo7A 394 1.51e+01 1qo7A c.69.1.11 34697 1dp4A 435 1.51e+01 1dp4A c.93.1.1 35710 1nal3 297 1.55e+01 1nal3 2irfG 113 1.60e+01 2irfG a.4.5.23 16185 1gw5S 142 1.63e+01 d.110.4.2 70633 1dxeA 256 1.63e+01 1dxeA c.1.12.5 29310 1v3hA 495 1.65e+01 1rhi3 236 1.67e+01 1aym3 1l9gA 192 1.68e+01 c.18.1.2 84568 1gntA 553 1.69e+01 e.26.1.1 70290 1mu5A 471 1.70e+01 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1g57A 217 1.70e+01 1g57A d.115.1.2 60253 1p1mA 406 1.71e+01 b.92.1.4 87696 c.1.9.9 87697 1r5jA 337 1.72e+01 unknown_sccs -8471 1o0xA 262 1.73e+01 d.127.1.1 80755 1e2uA 553 1.74e+01 1e1dA e.26.1.1 43362 3hmgA 328 1.75e+01 1hgeA b.19.1.2 23825 1up8A 598 1.75e+01 a.111.1.2 -1480 1n9eA 787 1.77e+01 b.30.2.1 -3529 d.17.2.1 -9278 d.17.2.1 -9279 1vpwA 340 1.78e+01 1qpzA a.35.1.5 17087 c.93.1.1 35680 1gw9A 388 1.78e+01 c.1.15.3 70658 1npyA 271 1.78e+01 c.2.1.7 85995 c.58.1.5 85996 1l2rA 458 1.79e+01 1nthA 458 1.79e+01 c.1.25.1 80730 1hgeA 328 1.80e+01 1hgeA b.19.1.2 23816 1oboA 169 1.82e+01 c.23.5.1 86776 1clqA 903 1.82e+01 1clqA c.55.3.5 33717 e.8.1.1 43006 1bxnA 485 1.84e+01 1burA c.1.14.1 29376 d.58.9.1 39282 1jevA 517 1.85e+01 1jevA c.94.1.1 35720 2olbA 517 1.86e+01 1jevA c.94.1.1 35721 1tltA 319 1.87e+01 1hh1A 143 1.93e+01 1gefA c.52.1.18 61036 1byb 495 1.96e+01 1byb c.1.8.1 28790 1vc4A 254 1.98e+01 c.1.2.4 -5172 1ih7A 903 2.08e+01 1clqA c.55.3.5 62375 e.8.1.1 62376 1l2qA 458 2.08e+01 c.1.25.1 73510 2viuA 328 2.10e+01 1hgeA b.19.1.2 23797 1h1nA 305 2.10e+01 c.1.8.3 70855 1rg9A 383 2.13e+01 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 1mml 265 2.13e+01 1mml e.8.1.2 43015 1np3A 338 2.16e+01 a.100.1.2 85946 c.2.1.6 85947 1jeyB 565 2.18e+01 1jeqB unknown_sccs -4431 unknown_sccs -7995 1muwA 386 2.18e+01 c.1.15.3 79495 2dabA 282 2.19e+01 1daaA e.17.1.1 43274 1buuA 168 2.21e+01 1rtm1 d.169.1.1 42366 h.1.1.1 45388 2liv 344 2.24e+01 2liv c.93.1.1 35708 1ipiA 123 2.24e+01 c.52.1.18 66255 1q6cA 495 2.29e+01 c.1.8.1 -5300 1gox 370 2.29e+01 1gox c.1.4.1 28607 1tpt 440 2.29e+01 1brwA a.46.2.1 17763 c.27.1.1 31627 d.41.3.1 38625 1nf2A 268 2.32e+01 c.108.1.10 -6842 2oatA 439 2.38e+01 2dkb c.67.1.4 34452 1a53 247 2.38e+01 1a53 c.1.2.4 28564 1qpzA 340 2.41e+01 1qpzA a.35.1.5 17097 c.93.1.1 35673 1fjgJ 105 2.49e+01 1fjfJ d.58.15.1 39330 1e42A 258 2.53e+01 1e42A b.1.10.1 22316 d.105.1.1 40792 1igs 248 2.55e+01 1a53 c.1.2.4 28565 1kqfB 294 2.66e+01 d.58.1.5 75900 f.23.22.1 75901 1fmtB 314 2.68e+01 1fmtA b.46.1.1 25759 c.65.1.1 34175 1mxa 383 2.69e+01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1mxb 383 2.72e+01 1mxb d.130.1.1 41329 d.130.1.1 41330 d.130.1.1 41331 1l5jA 865 2.74e+01 a.118.15.1 73592 c.8.2.1 73593 c.83.1.1 73594 1daaA 282 2.79e+01 1daaA e.17.1.1 43270 1q6oA 216 2.80e+01 c.1.2.3 -5162 1fmtA 314 2.81e+01 1fmtA b.46.1.1 25758 c.65.1.1 34174 1kv8A 216 2.82e+01 c.1.2.3 73054 1ahjB 212 2.84e+01 2ahjB b.34.4.4 24601 1ejhA 190 2.84e+01 1ejhA d.86.1.1 40147 1fwrA 213 2.84e+01 1fwrA c.1.10.1 29164 2u1a 88 2.85e+01 2u1a d.58.7.1 39164 1wetA 340 2.86e+01 1qpzA a.35.1.5 17093 c.93.1.1 35670 1n7zA 334 2.88e+01 b.127.1.1 85380 1vkbA 161 2.88e+01 1kyqA 274 2.88e+01 c.2.1.11 73281 e.37.1.1 73282 1huvA 380 2.92e+01 c.1.4.1 61277 1tplA 426 2.92e+01 1ax4A c.67.1.2 34387 1p4cA 380 2.93e+01 c.1.4.1 -5201 1ln1A 214 2.93e+01 d.129.3.2 74038 1va4A 279 2.94e+01 1irf 112 2.96e+01 2irfG a.4.5.23 16192 3daaA 277 2.99e+01 1daaA e.17.1.1 43272 1gefA 123 3.00e+01 1gefA c.52.1.18 60465 1evhA 112 3.03e+01 1evhA b.55.1.4 26997 1mnzA 388 3.03e+01 c.1.15.3 79328 1j5vA 351 3.09e+01 c.72.1.1 71585 1riqA 465 3.10e+01 unknown_sccs -1295 d.104.1.1 -10769 1b7gO 340 3.11e+01 1b7gO c.2.1.3 29992 d.81.1.1 39907 1bouB 302 3.11e+01 1bouB c.56.6.1 33859 1jkfA 533 3.13e+01 c.2.1.3 71700 d.81.1.3 71701 1iz0A 302 3.14e+01 b.35.1.2 83821 c.2.1.1 83822 1k6dA 220 3.21e+01 unknown_sccs 72082 1xis 387 3.22e+01 4xis c.1.15.3 29422 1rfzA 168 3.23e+01 unknown_sccs -1206 1lucB 324 3.23e+01 1lucA c.1.16.1 29548 4xis 387 3.23e+01 4xis c.1.15.3 29421 1pl5A 142 3.23e+01 2xis 387 3.24e+01 4xis c.1.15.3 29427 1ytbA 180 3.25e+01 1ytbA d.129.1.1 41276 d.129.1.1 41277 1ni4A 365 3.29e+01 c.36.1.7 85728 1gxlA 213 3.31e+01 d.215.1.1 70713 1euaA 213 3.36e+01 1fwrA c.1.10.1 29155 1ci9A 392 3.37e+01 e.3.1.1 64767 1rtm1 149 3.39e+01 1rtm1 1juk 248 3.39e+01 1a53 c.1.2.4 28567 1lgtA 297 3.39e+01 d.32.1.3 77956 d.32.1.3 77957 1han 297 3.42e+01 1han d.32.1.3 38506 d.32.1.3 38507 1gtxA 472 3.42e+01 1gtxA 2ahjB 212 3.43e+01 2ahjB b.34.4.4 24599 1hd8A 363 3.44e+01 b.105.1.1 65803 e.3.1.1 65804 1k5dB 201 3.45e+01 b.55.1.3 68169 1oatA 439 3.50e+01 2dkb c.67.1.4 34461 1v7oA 165 3.51e+01 unknown_sccs -10249 1qhdA 398 3.55e+01 1qhdA a.115.1.2 63324 b.19.1.1 63325 1g99A 408 3.56e+01 1g99A c.55.1.2 33457 c.55.1.2 33458 1e1dA 553 3.57e+01 1e1dA e.26.1.1 43363 1p27B 106 3.58e+01 d.58.7.1 -10020 1oi2A 366 3.59e+01 c.32.1.2 87039 d.79.2.2 87040 1lkdA 297 3.60e+01 d.32.1.3 78059 d.32.1.3 78060 1oltA 457 3.65e+01 unknown_sccs -5688 1dywA 173 3.71e+01 2cpl b.62.1.1 27505 1r3eA 309 3.72e+01 b.122.1.1 -5118 unknown_sccs -10146 1knwA 425 3.75e+01 b.49.2.3 -4274 c.1.6.1 -5229 1fxlA 167 3.76e+01 1b7fA d.58.7.1 39183 d.58.7.1 39184 1mai 131 3.78e+01 1mai b.55.1.1 26951 1lylA 504 3.78e+01 1lylA b.40.4.1 25261 d.104.1.1 40717 1i9sA 210 3.80e+01 1i9sA c.45.1.1 62099 1d1gA 168 3.82e+01 1d1gA c.71.1.1 34889 1rlhA 173 3.84e+01 unknown_sccs -10786 1o63A 219 3.88e+01 c.94.1.1 -8691 2scuB 388 3.96e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 1p3wA 404 3.99e+01 c.67.1.3 87752 1o7jA 327 4.00e+01 c.88.1.1 81140