# List of top-scoring protein chains for t04-100-30-dssp-ehl2-scores 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 1bcfA 158 1.41e-04 1bcfA a.25.1.1 16648 1vjxA 157 2.17e-04 a.25.1.1 100837 2fkzA 155 3.60e-04 1nfvA 179 6.90e-03 a.25.1.1 85642 2fha 183 2.09e-02 2fha a.25.1.1 16674 1mojA 182 2.58e-02 a.25.1.1 91367 1tjoA 182 2.58e-02 1za0A 275 5.59e-02 1dat 174 9.36e-02 2fha a.25.1.1 16677 1rcd 173 2.21e-01 2fha a.25.1.1 16687 2gyqA 175 2.56e-01 1o9rA 162 2.65e-01 a.25.1.1 86706 1bgc 174 2.99e-01 1bgc a.26.1.1 16822 1r03A 182 3.81e-01 a.25.1.1 104675 1ru3A 732 4.08e-01 e.26.1.3 97835 1jigA 146 5.03e-01 a.25.1.1 71685 1jm0A 50 6.48e-01 k.8.1.1 66870 1e2uA 553 1.03e+00 1e1dA e.26.1.1 43362 1gntA 553 1.03e+00 e.26.1.1 70290 1ec5A 50 1.13e+00 1ec5A k.8.1.1 46421 1dpsA 167 1.32e+00 1dpsA a.25.1.1 16716 1q8iA 783 1.75e+00 c.55.3.5,e.8.1.1 96208,96209 1zpyA 95 1.80e+00 1ih8A 271 2.19e+00 2nsyA c.26.2.1 62377 2dchX 216 2.51e+00 1w7lA 422 2.54e+00 c.67.1.1 109226 1kqpA 271 2.58e+00 c.26.2.1 72883 2bl2A 156 2.66e+00 1qghA 156 2.71e+00 1qghA a.25.1.1 16728 1v2dA 381 3.05e+00 c.67.1.1 108281 1b5pA 385 3.17e+00 c.67.1.1 90403 1jt6A 188 3.33e+00 a.4.1.9,a.121.1.1 67247,67248 1o4sA 389 3.33e+00 c.67.1.1 86620 1au1A 166 3.59e+00 1ifa a.26.1.3 16889 1lucB 324 3.70e+00 1lucA c.1.16.1 29548 2trcP 217 3.78e+00 1b9yC c.47.1.6 33051 1vlgA 176 3.83e+00 a.25.1.1 108816 1u2eA 289 3.93e+00 1h96A 182 4.26e+00 2fha a.25.1.1 60811 1lb3A 182 4.26e+00 a.25.1.1 77873 1o9iA 266 4.41e+00 a.25.1.3 92671 1jkvA 266 4.53e+00 a.25.1.3 71719 1rcwA 231 4.56e+00 a.132.1.4 97299 2bidA 197 4.86e+00 2bidA f.1.4.1 43398 1uzeA 589 5.07e+00 d.92.1.5 108174 1rthA 560 5.14e+00 1rthA c.55.3.1,e.8.1.2 33576,43028 1vcsA 102 5.17e+00 1o86A 589 5.26e+00 d.92.1.5 81177 2cwlA 302 5.41e+00 1vjoA 393 5.57e+00 c.67.1.3 100827 1ux8A 132 5.93e+00 1bjwA 382 6.45e+00 1bjwA c.67.1.1 34349 1umnA 165 6.68e+00 a.25.1.1 99607 1gnlA 544 6.74e+00 e.26.1.1 70287 1afrA 345 6.87e+00 1afrA a.25.1.2 16805 1n1fA 159 6.97e+00 a.26.1.3 79803 1tx2A 297 7.66e+00 c.1.21.1 107420 1vrtA 560 7.84e+00 1rthA c.55.3.1,e.8.1.2 33574,43023 1lla 628 8.30e+00 1lla a.85.1.1,a.86.1.1,b.1.18.3 18485,18496,21861 1itwA 741 8.41e+00 c.77.1.2 76793 119l 164 8.45e+00 1l92 d.2.1.3 36622 1oq9A 363 8.63e+00 a.25.1.2 87257 1yuzA 202 8.86e+00 1li5A 461 9.26e+00 a.27.1.1,c.26.1.1 73912,73913 2a14A 263 9.53e+00 1csh 435 9.58e+00 1csh a.103.1.1 18880 1ru0A 105 9.64e+00 1oe9A 795 9.73e+00 b.34.3.1,c.37.1.9 92792,92793 1n97A 389 1.02e+01 a.104.1.1 80335 1yiyA 429 1.04e+01 2ethA 154 1.08e+01 1pc6A 146 1.09e+01 d.262.1.1 94430 1gdeA 389 1.11e+01 c.67.1.1 60456 1li5B 461 1.13e+01 a.27.1.1,c.26.1.1 73914,73915 1ni3A 392 1.13e+01 c.37.1.8,d.15.10.2 80531,80532 1b67A 68 1.13e+01 1a7w a.22.1.2 16474 1yizA 429 1.13e+01 1x6mA 196 1.15e+01 1nxiA 132 1.16e+01 d.58.47.1 86381 1w7jA 795 1.17e+01 1wmwA 330 1.17e+01 1us7B 265 1.18e+01 a.205.1.1 99858 1u6tA 121 1.20e+01 1wtaA 275 1.32e+01 1nt4A 391 1.33e+01 c.60.1.2 92102 2auaA 224 1.36e+01 1kkoA 413 1.37e+01 c.1.11.2,d.54.1.1 68675,68676 1jetA 517 1.40e+01 1jevA c.94.1.1 35718 1h6gA 256 1.41e+01 1h6gA a.24.9.1,a.24.9.1 60669,60670 1xjuA 163 1.42e+01 1a0rP 245 1.43e+01 1b9yC c.47.1.6 33054 1p36A 164 1.46e+01 d.2.1.3 93978 2aqjA 538 1.47e+01 1j31A 262 1.47e+01 d.160.1.2 90808 1yhlA 362 1.49e+01 1b5l 172 1.49e+01 1b5l a.26.1.3 16900 1om1A 332 1.57e+01 d.144.1.7 93347 1m2rA 327 1.57e+01 d.144.1.7 84760 3sdhA 146 1.62e+01 3sdhA a.1.1.2 14984 2cb5A 453 1.66e+01 3gcb d.3.1.1 37035 1uw4B 248 1.70e+01 a.118.1.14 100072 1ug3A 339 1.75e+01 1orjA 130 1.79e+01 a.24.19.1 93456 6gsvA 217 1.80e+01 1b8xA a.45.1.1,c.47.1.5 17633,32925 1rw6A 210 1.80e+01 a.47.4.1 105113 1no7A 604 1.81e+01 e.48.1.1 92016 1ll7A 392 1.86e+01 c.1.8.5,d.26.3.1 78085,78086 2es4D 332 1.91e+01 1zynA 202 1.94e+01 1jltB 122 1.94e+01 a.133.1.2 66868 1x38A 602 1.99e+01 1oaoC 729 2.00e+01 e.26.1.3 86746 1aokB 122 2.02e+01 1poa a.133.1.2 19561 1zu0A 529 2.02e+01 1le6A 123 2.06e+01 a.133.1.2 73862 1izoA 417 2.08e+01 a.104.1.1 83851 1ug6A 431 2.09e+01 c.1.8.4 88490 2etsA 128 2.09e+01 1eswA 500 2.12e+01 1cwyA c.1.8.1 59500 1i36A 264 2.13e+01 a.100.1.8,c.2.1.6 71108,71109 1ofcX 304 2.13e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 1yucA 255 2.14e+01 1wwiA 148 2.14e+01 1dosA 358 2.15e+01 1dosA c.1.10.2 29175 1hzyA 332 2.16e+01 1pscA c.1.9.3 61468 2olbA 517 2.16e+01 1jevA c.94.1.1 35721 1m7vA 363 2.17e+01 d.174.1.1 78748 2dg5A 366 2.28e+01 1t2dA 322 2.28e+01 c.2.1.5,d.162.1.1 99084,99085 1s6bA 119 2.30e+01 a.133.1.2 98592 1otkA 249 2.31e+01 a.25.1.2 93521 1hyuA 521 2.34e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1nekD 115 2.34e+01 f.21.2.2 80432 2a5yA 204 2.36e+01 2d2jA 329 2.38e+01 1d2kA 392 2.46e+01 1d2kA c.1.8.5,d.26.3.1 29008,38442 1hwxA 501 2.47e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 1k0wA 231 2.48e+01 c.74.1.1 77220 1i0dA 332 2.48e+01 1pscA c.1.9.3 61487 1vapA 123 2.56e+01 1poa a.133.1.2 19548 2cxbA 124 2.59e+01 1ycc a.3.1.1 15891 1jk0B 345 2.62e+01 a.25.1.2 63143 1e4mM 501 2.63e+01 1e70M c.1.8.4 59226 1lw9A 164 2.63e+01 d.2.1.3 84727 1v02A 565 2.67e+01 c.1.8.4 108194 1jlvA 209 2.68e+01 a.45.1.1,c.47.1.5 71729,71730 1ee8A 266 2.69e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1cxc 124 2.69e+01 1ycc a.3.1.1 15890 1fds 327 2.69e+01 1fds c.2.1.2 29838 2avuE 192 2.69e+01 1j77A 209 2.72e+01 1j77A a.132.1.2 62674 1z0sA 278 2.77e+01 1w9yA 319 2.81e+01 1a7w 69 3.02e+01 1a7w a.22.1.2 16477 5abp 306 3.04e+01 8abp c.93.1.1 35651 1ex1A 605 3.05e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 1a76 326 3.05e+01 1a76 a.60.7.1,c.120.1.2 18091,33361 1i1iP 681 3.07e+01 1i1iP d.92.1.5 40297 2f22A 144 3.08e+01 1h3lA 87 3.12e+01 a.177.1.1 76639 1xwmA 217 3.13e+01 1a5t 334 3.13e+01 1a5t a.80.1.1,c.37.1.20 18450,32423 1ireA 204 3.14e+01 d.149.1.1 76769 1igwA 434 3.16e+01 c.1.12.7 62370 1h4vB 421 3.17e+01 1adjA c.51.1.1,d.104.1.1 60624,60625 1ugpA 203 3.17e+01 d.149.1.1 107831 1r6fA 310 3.32e+01 e.46.1.1 97149 1wryA 121 3.37e+01 1zq4A 693 3.41e+01 1r6xA 395 3.43e+01 b.122.1.3,c.26.1.5 97167,97168 2h3bA 494 3.47e+01 8abp 306 3.54e+01 8abp c.93.1.1 35647 4xis 387 3.55e+01 4xis c.1.15.3 29421 1yovA 537 3.59e+01 3xis 387 3.60e+01 4xis c.1.15.3 29423 1qv9A 283 3.63e+01 c.127.1.1 96356 1vqrA 297 3.65e+01 1w9pA 433 3.65e+01 1jsdB 176 3.72e+01 h.3.1.1 63259 1jpzA 473 3.74e+01 a.104.1.1 67069 1dmhA 311 3.76e+01 1dmhA b.3.6.1 22633 2bg5A 324 3.77e+01 1xqaA 113 3.78e+01 2f1kA 279 3.81e+01 1huw 166 3.83e+01 1huw a.26.1.1 16831 1h0oA 390 3.84e+01 a.25.1.2 70845 1c7gA 456 3.93e+01 c.67.1.2 90415 1mxgA 435 3.94e+01 b.71.1.1,c.1.8.1 85193,85194 1f1eA 154 4.09e+01 a.22.1.2 64927 1wzdA 215 4.12e+01 2c1vA 338 4.19e+01 1zgmA 248 4.23e+01 2fnoA 248 4.23e+01 1suwA 249 4.24e+01 e.52.1.1 106027 1jflA 228 4.27e+01 c.78.2.1,c.78.2.1 71656,71657 1nd6A 354 4.30e+01 c.60.1.2 80407 1fp3A 402 4.35e+01 1fp3A a.102.1.3 18842 1vhcA 224 4.37e+01 c.1.10.1 100661 1tk1A 260 4.37e+01 d.248.1.1 107066 1jhfA 202 4.50e+01 a.4.5.2,b.87.1.1 63057,63058 1qr0A 228 4.52e+01 1qr0A d.150.1.1,d.150.1.1 59038,59039 1px5A 349 4.53e+01 a.160.1.2,d.218.1.6 95277,95278 1bkdS 439 4.56e+01 1bkdS a.117.1.1 19111 1o58A 303 4.56e+01 c.79.1.1 92491 1mswD 883 4.56e+01 e.8.1.3 79427 1gnxA 479 4.62e+01 c.1.8.4 76241 1eg5A 384 4.64e+01 1ecxA c.67.1.3 34429 2myr 501 4.70e+01 1wdyA 285 4.72e+01 1epuA 591 4.79e+01 1dn1A e.25.1.1 43358 1m3uA 264 4.84e+01 c.1.12.8 84784 1vkuA 100 4.86e+01 a.28.1.1 108690 1yi8A 351 4.89e+01 1t56A 216 4.91e+01 a.4.1.9,a.121.1.1 106428,106429 1lngA 87 4.93e+01 d.201.1.1 74045 1jtvA 327 4.93e+01 c.2.1.2 84230 1rss 151 4.95e+01 1rss a.75.1.1 18392 1v54L 47 4.98e+01 f.23.6.1 100333 2occL 47 5.01e+01 2occL f.23.6.1 43526 1p1jA 533 5.02e+01 c.2.1.3,d.81.1.3 87687,87688 1zq1C 633 5.02e+01 1h1nA 305 5.10e+01 c.1.8.3 70855 1u2xA 474 5.11e+01 c.72.1.3 107622 1y75A 118 5.16e+01 1q35A 320 5.27e+01 c.94.1.1 95661 1hxhA 253 5.31e+01 c.2.1.2 76725 1j5kA 89 5.34e+01 d.51.1.1 71565 1owqA 361 5.40e+01 c.1.8.5,d.26.3.1 104041,104042 1l2lA 457 5.44e+01 c.72.1.3 77656 2anxA 146 5.50e+01 1uedA 406 5.50e+01 a.104.1.1 99256 2hpaA 342 5.51e+01 1cviA c.60.1.2 33985 1zd0A 150 5.52e+01 1fjgM 126 5.57e+01 1fjfM a.156.1.1 16293 2g7jA 124 5.57e+01 1bd8 156 5.61e+01 1bd8 d.211.1.1 19157 1ct9A 553 5.65e+01 1ct9A c.26.2.1,d.153.1.1 31616,41834 1w68A 390 5.72e+01 a.25.1.2 109216 2bw3A 534 5.79e+01 1p2xA 159 5.87e+01 a.40.1.1 104062 1nlwA 80 5.87e+01 a.38.1.1 80633 2ccyA 128 5.97e+01 2ccyA a.24.3.2 16544 1regX 122 6.03e+01 1regX d.58.27.1 39406 1dxrM 323 6.03e+01 6prcM f.26.1.1 43432 1tf4A 605 6.04e+01 1tf4A a.102.1.2,b.2.2.2 18827,22393 1re9A 414 6.06e+01 1evsA 187 6.08e+01 1evsA a.26.1.1 16845 2f4qA 346 6.13e+01 1dcoA 104 6.14e+01 1dcpA d.74.1.1 39680 1vls 146 6.17e+01 1vls a.24.2.1 16532 1t6uA 117 6.25e+01 a.24.22.1 106584 1uz1A 468 6.26e+01 1qgrA 876 6.27e+01 1qgrA a.118.1.1 19119 1lkoA 191 6.27e+01 a.25.1.1,g.41.5.1 78063,78064 1g8fA 511 6.29e+01 1g8fA b.122.1.3,c.26.1.5,c.37.1.15 60348,60349,60350 1e19A 314 6.37e+01 1b7bA c.73.1.1 34967 2dpiA 420 6.38e+01 1vpdA 299 6.45e+01 1czaN 917 6.49e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33463,33464,33465,33466 1zetA 388 6.49e+01 1rzhM 307 6.51e+01 f.26.1.1 98165 1b71A 191 6.54e+01 1ryt a.25.1.1,g.41.5.1 16647,45246 2cohA 202 6.54e+01 1swyA 164 6.58e+01 1sx7A 164 6.58e+01 1r0vA 305 6.60e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 2a0iA 330 6.60e+01 1js3A 486 6.61e+01 c.67.1.6 67215 1t6jA 714 6.64e+01 1r5yA 386 6.67e+01 c.1.20.1 97134 1musA 477 6.76e+01 c.55.3.4 79494 2hekA 371 6.77e+01 1lvwA 295 6.82e+01 c.68.1.6 84723 1pxgA 382 6.91e+01 c.1.20.1 95287 1e4iA 447 6.92e+01 1e70M c.1.8.4 59225 1xzoA 174 6.93e+01 1bea 127 6.93e+01 1bea a.52.1.2 17826 1ryt 190 6.94e+01 1ryt a.25.1.1,g.41.5.1 16646,45245 1ax4A 467 6.94e+01 1ax4A c.67.1.2 34391 1xxsA 122 6.95e+01 1rr7A 129 6.95e+01 a.4.1.14 105075 1pud 386 6.97e+01 1pud c.1.20.1 29658 1ithA 141 6.98e+01 1ithA a.1.1.2 15623 1xg7A 250 6.99e+01 1nogA 177 7.02e+01 a.25.2.2 85923 1mtyB 384 7.05e+01 1mtyB a.25.1.2 16740 1yiiA 320 7.09e+01 1y10A 407 7.18e+01 1iw0A 215 7.18e+01 a.132.1.1 83720 1muwA 386 7.29e+01 c.1.15.3 79495 1ub0A 258 7.36e+01 c.72.1.2 88394 2cbuA 468 7.37e+01 1ltqA 301 7.39e+01 c.108.1.9,c.37.1.1 78208,78209 2alzA 390 7.41e+01 1rylA 167 7.43e+01 d.276.1.1 105124 1zrn 232 7.48e+01 1qq5A c.108.1.1 43323 1uf2A 1019 7.57e+01 e.28.1.2 99289 1kqqA 139 7.58e+01 a.4.3.1 72885 1z6oM 191 7.64e+01 1utg 70 7.65e+01 1utg a.101.1.1 18813 1keaA 221 7.67e+01 a.96.1.2 68491 1v74B 87 7.76e+01 a.24.20.1 100443 1l8dA 112 7.83e+01 h.4.12.1 73687 1yxhA 126 7.83e+01 3c2c 112 7.86e+01 1ycc a.3.1.1 15885 1zlbA 122 7.88e+01 1ldg 316 7.88e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1pw4A 451 7.91e+01 f.38.1.1 95198 2g2dA 193 8.00e+01 1uj6A 227 8.00e+01 c.124.1.4,d.58.40.1 107898,107899 2awiA 317 8.03e+01 1yrcA 414 8.10e+01 1hruA 188 8.14e+01 1hruA d.115.1.1 40926 1pvtA 238 8.17e+01 c.74.1.1 95189 2utgA 70 8.19e+01 1utg a.101.1.1 18814 1jli 112 8.27e+01 1jli a.26.1.2 16884 1dc1A 323 8.28e+01 1dc1A c.52.1.11 33321 1urfA 81 8.33e+01 a.2.6.1 99827 1t3nA 388 8.33e+01 d.240.1.1,e.8.1.7 106363,106364 1yxlA 119 8.36e+01 1e3pA 757 8.38e+01 1e3hA a.4.9.1,b.40.4.5,d.14.1.4,d.14.1.4,d.52.3.1,d.101.1.1,d.101.1.1 16258,25328,37574,37575,38811,40697,40698 1jipA 403 8.40e+01 a.104.1.1 66748 1kv9A 668 8.42e+01 a.3.1.6,b.70.1.1 73056,73057 1k7jA 206 8.43e+01 d.115.1.1 72103 1pprM 312 8.44e+01 1pprM a.131.1.1,a.131.1.1 19502,19503 1y6nL 145 8.47e+01 1n9dA 199 8.50e+01 a.26.1.1 85464 1y2mA 716 8.52e+01 1xsm 390 8.55e+01 1xsm a.25.1.2 16804 2akaB 299 8.58e+01 1pbgA 468 8.60e+01 1e70M c.1.8.4 28946 1t5bA 201 8.61e+01 c.23.5.3 106433 2bh7A 261 8.67e+01 1txuA 273 8.68e+01 a.222.1.1 107439 1umvX 122 8.69e+01 a.133.1.2 99630 1s8iA 121 8.71e+01 a.133.1.2 98735 2c46A 241 8.72e+01 2bgxA 261 8.78e+01 1lhpA 312 8.78e+01 c.72.1.5 77960 1zwwA 256 8.79e+01 1hf2A 210 8.81e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 1wu4A 396 8.85e+01 2au3A 407 8.90e+01 1mpgA 282 8.95e+01 1mpgA a.96.1.3,d.129.1.2 18747,41296 1rh5A 436 8.95e+01 f.41.1.1 97464