# 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 1tljA 213 1.53e-36 1b65A 375 8.33e-02 1b65A d.154.1.1 42020 1kwkA 645 1.71e-01 b.71.1.1 77565 c.1.8.1 77566 c.23.16.5 77567 1kwgA 645 1.90e-01 b.71.1.1 77561 c.1.8.1 77562 c.23.16.5 77563 1t7pA 698 2.12e-01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1f0xA 571 2.32e-01 1f0xA d.58.32.2 39483 d.145.1.1 41746 1rkqA 282 2.35e-01 c.108.1.10 -6847 1j3mA 129 3.49e-01 1hv8A 367 3.57e-01 1hv8A c.37.1.19 32405 c.37.1.19 32406 1dkzA 219 3.95e-01 1dkzA unknown_sccs -445 unknown_sccs -3060 1dkxA 219 4.45e-01 1dkzA unknown_sccs -446 unknown_sccs -3061 1vaoA 560 4.65e-01 1qltA d.58.32.1 39461 d.145.1.1 41724 1g6sA 427 4.80e-01 1eps d.68.2.2 39584 1ayyA 151 5.27e-01 1apyA d.153.1.5 42016 1qysA 106 6.80e-01 unknown_sccs -13432 1eps 427 9.60e-01 1eps d.68.2.2 39586 1ftrA 296 1.01e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 1w1kA 560 1.01e+00 1ufkA 254 1.03e+00 unknown_sccs -8103 1j5yA 187 1.31e+00 a.4.5.1 71592 d.94.2.1 71593 1k2yX 463 1.33e+00 c.84.1.1 68063 c.84.1.1 68064 c.84.1.1 68065 d.129.2.1 68066 1e8gA 560 1.49e+00 1qltA d.58.32.1 39455 d.145.1.1 41718 1b8oA 284 1.52e+00 1b8oA c.56.2.1 33762 1qltA 560 1.73e+00 1qltA d.58.32.1 39457 d.145.1.1 41720 1brwA 433 1.73e+00 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1a3gA 308 1.99e+00 1daaA e.17.1.1 43286 1uouA 474 2.27e+00 a.46.2.1 -951 c.27.1.1 -6642 d.41.3.1 -9715 1ofuX 119 2.31e+00 c.37.1.22 86976 1mu5A 471 2.56e+00 a.156.1.3 79472 d.14.1.3 79473 d.122.1.2 79474 1n9eA 787 2.58e+00 b.30.2.1 -3529 d.17.2.1 -9278 d.17.2.1 -9279 1jeqB 565 2.69e+00 1jeqB unknown_sccs -4432 unknown_sccs -7996 1b3nA 412 2.74e+00 1dd8A c.95.1.1 35966 c.95.1.1 35967 1p5dX 463 2.83e+00 c.84.1.1 -8554 c.84.1.1 -8555 c.84.1.1 -8556 d.129.2.1 -11029 9gafA 295 2.86e+00 1apyA d.153.1.5 42008 1p4kA 295 2.93e+00 d.153.1.5 87772 1odkA 235 3.04e+00 c.56.2.1 86863 1f7uA 607 3.04e+00 1bs2A a.27.1.1 59673 c.26.1.1 59674 d.67.2.1 59675 1kas 412 3.40e+00 1dd8A c.95.1.1 35964 c.95.1.1 35965 1qwdA 177 3.47e+00 b.60.1.1 -4455 1bueA 265 3.55e+00 1btl e.3.1.1 42727 487dH 224 3.58e+00 1ad2 i.1.1.2 45835 1ad2 228 3.59e+00 1ad2 e.24.1.1 43353 1jetA 517 3.63e+00 1jevA c.94.1.1 35718 1ln1A 214 3.76e+00 d.129.3.2 74038 2ctb 307 4.03e+00 1aye c.56.5.1 33803 1mxa 383 4.16e+00 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1rg9A 383 4.28e+00 d.130.1.1 -11057 d.130.1.1 -11058 d.130.1.1 -11059 2ctc 307 4.42e+00 1aye c.56.5.1 33802 1jevA 517 4.46e+00 1jevA c.94.1.1 35720 1jeyB 565 4.56e+00 1jeqB unknown_sccs -4431 unknown_sccs -7995 1v3hA 495 4.57e+00 1m2oA 768 4.58e+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 1eqfA 280 4.61e+00 1eqfA a.29.2.1 16972 a.29.2.1 16973 2olbA 517 4.62e+00 1jevA c.94.1.1 35721 1korA 400 4.75e+00 c.26.2.1 72824 d.210.1.1 72825 1g57A 217 4.96e+00 1g57A d.115.1.2 60253 1mkeA 152 5.16e+00 b.55.1.4 79231 1mxb 383 5.34e+00 1mxb d.130.1.1 41329 d.130.1.1 41330 d.130.1.1 41331 1byb 495 5.37e+00 1byb c.1.8.1 28790 1gw5S 142 5.44e+00 d.110.4.2 70633 1clqA 903 5.51e+00 1clqA c.55.3.5 33717 e.8.1.1 43006 1qupA 222 5.64e+00 1qupA b.1.8.1 22301 d.58.17.1 39352 1up8A 598 6.09e+00 a.111.1.2 -1480 1s98A 107 6.14e+00 1o0xA 262 6.29e+00 d.127.1.1 80755 1q6cA 495 6.33e+00 c.1.8.1 -5300 1nxiA 132 6.68e+00 d.58.47.1 86381 1h0pA 182 6.79e+00 b.62.1.1 76450 1bs2A 607 7.24e+00 1bs2A a.27.1.1 16930 c.26.1.1 31597 d.67.2.1 39563 1hl6A 165 7.29e+00 d.58.7.1 83609 1bjt 793 7.32e+00 1bjt e.11.1.1 43249 1evhA 112 7.33e+00 1evhA b.55.1.4 26997 1eazA 125 7.41e+00 b.55.1.1 70113 1lc0A 294 7.63e+00 c.2.1.3 73823 d.81.1.4 73824 1agi 125 7.81e+00 7rsa d.5.1.1 37303 1dp4A 435 7.84e+00 1dp4A c.93.1.1 35710 1ih7A 903 7.91e+00 1clqA c.55.3.5 62375 e.8.1.1 62376 1ejhA 190 8.00e+00 1ejhA d.86.1.1 40147 1i1kA 309 8.08e+00 1daaA e.17.1.1 61533 1rpjA 288 8.18e+00 2dri c.93.1.1 35656 1m4lA 307 8.57e+00 c.56.5.1 78604 1yme 309 8.60e+00 1aye c.56.5.1 33804 2hnp 321 8.81e+00 1pty c.45.1.2 32678 1gio 125 8.92e+00 7rsa d.5.1.1 37304 1ohvA 472 9.06e+00 c.67.1.4 -8181 2sak 121 9.07e+00 2sak d.15.5.1 37711 1gz0A 253 9.13e+00 c.116.1.1 76391 d.79.3.3 76392 1hgeA 328 9.23e+00 1hgeA b.19.1.2 23816 1r3eA 309 9.56e+00 b.122.1.1 -5118 unknown_sccs -10146 1kv8A 216 9.67e+00 c.1.2.3 73054 2viuA 328 9.74e+00 1hgeA b.19.1.2 23797 1q6oA 216 9.75e+00 c.1.2.3 -5162 1e42A 258 9.85e+00 1e42A b.1.10.1 22316 d.105.1.1 40792 1avqA 228 9.85e+00 1avqA c.52.1.13 33326 1ptvA 321 1.02e+01 1pty c.45.1.2 32665 1mml 265 1.04e+01 1mml e.8.1.2 43015 1fmtB 314 1.05e+01 1fmtA b.46.1.1 25759 c.65.1.1 34175 1qtsA 247 1.07e+01 1qtsA b.1.10.1 22313 d.105.1.1 40789 1iu8A 206 1.10e+01 c.56.4.1 71436 1kyfA 247 1.11e+01 b.1.10.1 73220 d.105.1.1 73221 3hmgA 328 1.12e+01 1hgeA b.19.1.2 23825 1v7oA 165 1.13e+01 unknown_sccs -10249 1l9gA 192 1.14e+01 c.18.1.2 84568 1fmtA 314 1.14e+01 1fmtA b.46.1.1 25758 c.65.1.1 34174 1gcuA 295 1.15e+01 1gcuA c.2.1.3 30063 d.81.1.4 39978 1pyaB 228 1.15e+01 1pyaB 1gudA 288 1.19e+01 c.93.1.1 83326 1bpr 191 1.20e+01 1dkzA unknown_sccs 43319 1i50B 1224 1.21e+01 e.29.1.1 61755 1iyeA 309 1.21e+01 e.17.1.1 83786 1qipA 183 1.25e+01 1qipA d.32.1.1 38470 1cl2A 395 1.25e+01 1cl2A c.67.1.3 34397 1qm4A 396 1.26e+01 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1o63A 219 1.27e+01 c.94.1.1 -8691 1pa1A 310 1.29e+01 c.45.1.2 -7332 1r94A 118 1.29e+01 b.124.1.1 -4402 1ibvB 229 1.30e+01 6cpa 307 1.35e+01 1aye c.56.5.1 33816 1gajA 257 1.36e+01 1gajA c.37.1.12 60416 1bh5A 183 1.39e+01 1qipA d.32.1.1 38476 2irfG 113 1.41e+01 2irfG a.4.5.23 16185 1kczA 413 1.41e+01 c.1.11.2 68451 d.54.1.1 68452 1ytn 306 1.42e+01 1ytw c.45.1.2 32688 1vc4A 254 1.43e+01 c.1.2.4 -5172 1lyvA 306 1.44e+01 c.45.1.2 74348 1pty 321 1.45e+01 1pty c.45.1.2 32656 1eeoA 321 1.47e+01 1pty c.45.1.2 32655 1b9kA 238 1.49e+01 1qtsA b.1.10.1 22315 d.105.1.1 40791 1oltA 457 1.51e+01 unknown_sccs -5688 1yts 278 1.51e+01 1ytw c.45.1.2 32690 1yptA 305 1.52e+01 1ytw c.45.1.2 32686 1rxyA 253 1.52e+01 c.56.2.1 -7834 1st0A 337 1.52e+01 unknown_sccs -9014 unknown_sccs -9474 1mdoA 393 1.52e+01 c.67.1.4 79013 1lx7A 253 1.56e+01 c.56.2.1 74329 1cl1A 395 1.58e+01 1cl2A c.67.1.3 34395 1kay 381 1.58e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1hyeA 313 1.59e+01 2cmd c.2.1.5 61400 d.162.1.1 61401 1riqA 465 1.62e+01 unknown_sccs -1295 d.104.1.1 -10769 1ecfB 504 1.63e+01 1ecfB c.61.1.1 34054 d.153.1.1 41821 1rlhA 173 1.67e+01 unknown_sccs -10786 1gpjA 404 1.67e+01 a.151.1.1 65451 c.2.1.7 65452 d.58.39.1 65453 1ytw 306 1.71e+01 1ytw c.45.1.2 32689 1pujA 282 1.79e+01 c.37.1.8 88294 1a53 247 1.79e+01 1a53 c.1.2.4 28564 1igs 248 1.85e+01 1a53 c.1.2.4 28565 1bupA 386 1.86e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1e2uA 553 1.86e+01 1e1dA e.26.1.1 43362 1rfzA 168 1.87e+01 unknown_sccs -1206 1vdeA 454 1.89e+01 1vdeA b.86.1.2 28378 d.95.2.2 40581 d.95.2.2 40582 1k5dB 201 1.89e+01 b.55.1.3 68169 1gntA 553 1.97e+01 e.26.1.1 70290 1l8bA 190 2.00e+01 d.86.1.1 73683 1ba1 386 2.02e+01 1ba1 c.55.1.1 33387 c.55.1.1 33388 1iz1A 294 2.05e+01 a.4.5.37 83823 c.94.1.1 83824 1iqpA 327 2.06e+01 a.80.1.1 62649 c.37.1.20 62650 1kp0A 402 2.10e+01 c.55.2.1 72834 d.127.1.1 72835 1l3aA 228 2.10e+01 d.18.1.2 73531 1epaA 164 2.10e+01 1epaA b.60.1.1 27128 1n7zA 334 2.12e+01 b.127.1.1 85380 1h1nA 305 2.15e+01 c.1.8.3 70855 1hh1A 143 2.15e+01 1gefA c.52.1.18 61036 1epbA 164 2.17e+01 1epaA b.60.1.1 27126 1psdA 409 2.17e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1dywA 173 2.21e+01 2cpl b.62.1.1 27505 1d1gA 168 2.23e+01 1d1gA c.71.1.1 34889 7taa 478 2.26e+01 7taa b.71.1.1 27778 c.1.8.1 28765 1fa0B 537 2.27e+01 1fa0B a.160.1.1 75839 d.218.1.3 75840 d.58.16.1 39336 1hd8A 363 2.29e+01 b.105.1.1 65803 e.3.1.1 65804 1uwvA 433 2.31e+01 unknown_sccs -3950 unknown_sccs -8107 1gd1O 334 2.31e+01 1dssG c.2.1.3 29962 d.81.1.1 39877 1o7jA 327 2.34e+01 c.88.1.1 81140 2napA 723 2.36e+01 2napA b.52.2.2 26926 c.81.1.1 35334 1fa0A 537 2.41e+01 1fa0B a.160.1.1 75837 d.218.1.3 75838 d.58.16.1 39335 1oo0B 110 2.42e+01 d.58.7.1 87183 1pl5A 142 2.43e+01 1f1oA 431 2.44e+01 1f1oA a.127.1.1 19433 1khcA 147 2.44e+01 b.34.9.2 68608 1rhi3 236 2.47e+01 1aym3 1e9iA 431 2.49e+01 c.1.11.1 64818 d.54.1.1 64819 1m5sA 297 2.55e+01 d.58.33.1 74511 d.58.33.1 74512 1juk 248 2.56e+01 1a53 c.1.2.4 28567 1ahjB 212 2.56e+01 2ahjB b.34.4.4 24601 1ni4A 365 2.59e+01 c.36.1.7 85728 1b7gO 340 2.59e+01 1b7gO c.2.1.3 29992 d.81.1.1 39907 1konA 249 2.60e+01 e.39.1.1 72823 1jsrA 327 2.63e+01 c.88.1.1 67237 1kfiA 572 2.63e+01 c.84.1.1 68555 c.84.1.1 68556 c.84.1.1 68557 d.129.2.1 68558 1gqyA 475 2.69e+01 c.5.1.1 83305 c.59.1.1 83306 c.72.2.1 83307 1jiwP 470 2.73e+01 1sat unknown_sccs 63079 d.92.1.6 63080 1ubeA 349 2.74e+01 c.37.1.11 88412 d.48.1.1 88413 1oatA 439 2.76e+01 2dkb c.67.1.4 34461 1ipcA 217 2.79e+01 d.86.1.1 71257 1fu1B 203 2.80e+01 1fu1B b.59.1.1 27077 h.1.11.1 45631 1ccwB 483 2.81e+01 1cb7B c.1.19.2 29646 1dbqA 289 2.81e+01 1qpzA c.93.1.1 35666 1gnlA 544 2.84e+01 e.26.1.1 70287 1c1lA 136 2.89e+01 1c1lA b.29.1.3 24219 1nbwB 117 2.90e+01 c.51.3.2 80396 1jslA 327 2.95e+01 c.88.1.1 67233 3pnp 289 2.96e+01 1b8oA c.56.2.1 33763 1vk3A 615 2.97e+01 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1c76A 136 2.97e+01 2sak d.15.5.1 37718 1sczA 233 2.98e+01 c.43.1.1 -7326 2ahjB 212 2.99e+01 2ahjB b.34.4.4 24599 1f1zA 273 3.03e+01 1f1zA a.4.5.27 16081 c.52.1.16 33334 1a58 177 3.09e+01 2cpl b.62.1.1 27495 1nyhA 166 3.10e+01 h.1.23.1 86403 1scmA 60 3.10e+01 1wdcA 1mszA 86 3.11e+01 d.68.7.1 79428 1qhdA 398 3.12e+01 1qhdA a.115.1.2 63324 b.19.1.1 63325 1a04A 215 3.12e+01 1a04A a.4.6.2 16234 c.23.1.1 31089 1bwzA 274 3.13e+01 1bwzA d.21.1.1 38337 d.21.1.1 38338 1cb7B 483 3.14e+01 1cb7B c.1.19.2 29648 1p3wA 404 3.16e+01 c.67.1.3 87752 1fdyA 297 3.16e+01 1nal3 c.1.10.1 29071 1k6dA 220 3.17e+01 unknown_sccs 72082 1dkgD 383 3.17e+01 1ba1 c.55.1.1 33427 c.55.1.1 33428 1vkbA 161 3.20e+01 2oatA 439 3.22e+01 2dkb c.67.1.4 34452 1fc4A 401 3.23e+01 1bs0A c.67.1.4 59760 1e2o 233 3.23e+01 1eaf c.43.1.1 32631 1hyuA 521 3.26e+01 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1kijA 390 3.28e+01 d.14.1.3 72514 d.122.1.2 72515 1oaoC 729 3.29e+01 e.26.1.3 86746 1pot 325 3.30e+01 1pot c.94.1.1 35807 7at1B 154 3.30e+01 8atcB d.58.2.1 39053 g.41.7.1 45305 1tpt 440 3.36e+01 1brwA a.46.2.1 17763 c.27.1.1 31627 d.41.3.1 38625 1k92A 455 3.39e+01 c.26.2.1 68325 d.210.1.1 68326 1gefA 123 3.39e+01 1gefA c.52.1.18 60465 1pzgA 331 3.39e+01 c.2.1.5 -5931 d.162.1.1 -11498 1afb1 154 3.43e+01 1rtm1 1mai 131 3.45e+01 1mai b.55.1.1 26951 1fu1A 203 3.45e+01 1fu1B b.59.1.1 27076 h.1.11.1 45630 1g7fA 298 3.47e+01 1pty c.45.1.2 60330 1ut7A 171 3.52e+01 unknown_sccs -4724 1eokA 290 3.53e+01 1eokA c.1.8.5 28991 1ci9A 392 3.54e+01 e.3.1.1 64767 1h7sA 365 3.54e+01 d.14.1.3 65705 d.122.1.2 65706 1cz3A 168 3.56e+01 1d1gA c.71.1.1 34891 1gqzA 274 3.57e+01 d.21.1.1 83311 d.21.1.1 83312 1l5jA 865 3.61e+01 a.118.15.1 73592 c.8.2.1 73593 c.83.1.1 73594 1d0yA 761 3.61e+01 1lvk b.34.3.1 24581 c.37.1.9 32178 1gz6A 319 3.62e+01 c.2.1.2 76410 1kapP 479 3.62e+01 1sat unknown_sccs 28012 d.92.1.6 40298 2u1a 88 3.63e+01 2u1a d.58.7.1 39164 1lucB 324 3.63e+01 1lucA c.1.16.1 29548 1ixcA 294 3.68e+01 a.4.5.37 83764 c.94.1.1 83765 1c3oG 1073 3.70e+01 a.92.1.1 18565 c.24.1.1 31494 c.30.1.1 31687 c.30.1.1 31688 d.142.1.2 41532 d.142.1.2 41533 1qo7A 394 3.71e+01 1qo7A c.69.1.11 34697 1gm6A 175 3.71e+01 b.60.1.1 70272 1k2xA 177 3.74e+01 d.153.1.5 -11450 1e1dA 553 3.75e+01 1e1dA e.26.1.1 43363 1aw7A 194 3.83e+01 1aw7A b.40.2.2 25164 d.15.6.1 37753 1np3A 338 3.84e+01 a.100.1.2 85946 c.2.1.6 85947 1ecfA 504 3.84e+01 1ecfB c.61.1.1 34053 d.153.1.1 41820 1g0hA 252 3.87e+01 1dk4A e.7.1.1 60171 1p65A 73 3.88e+01 unknown_sccs -10331 1kqfB 294 3.90e+01 d.58.1.5 75900 f.23.22.1 75901 1b7fA 168 3.91e+01 1b7fA d.58.7.1 39169 d.58.7.1 39170 2dabA 282 3.92e+01 1daaA e.17.1.1 43274 1o12A 376 3.94e+01 b.92.1.5 80758 c.1.9.10 80759 1l3iA 192 3.94e+01 c.66.1.22 77676 1ipiA 123 3.96e+01 c.52.1.18 66255