# List of top-scoring protein chains for t06-100-30-bys-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 1hq0A 295 3.22e-01 1hzgA d.194.1.1 61122 1vicA 262 5.16e-01 c.68.1.13 100756 1euvA 221 5.38e-01 1euvA d.3.1.7 37133 1p7gA 222 6.19e-01 a.2.11.1,d.44.1.1 94223,94224 2ap1A 327 7.75e-01 1g291 372 8.17e-01 1g291 1o5kA 306 1.19e+00 c.1.10.1 92504 1udxA 416 1.40e+00 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 2a6hC 1119 1.74e+00 2bkrA 212 1.75e+00 1y74A 57 1.78e+00 2eu9A 355 2.01e+00 1vljA 407 2.05e+00 e.22.1.2 108832 1gw5S 142 2.07e+00 d.110.4.2 70633 1mpxA 615 2.07e+00 b.18.1.13,c.69.1.21 85041,85042 1m1hA 248 2.11e+00 b.114.1.1,d.58.42.1 78415,78416 1nw3A 416 2.21e+00 c.66.1.31 86288 1dc1A 323 2.27e+00 1dc1A c.52.1.11 33321 1id1A 153 2.42e+00 1id1A c.2.1.9 62286 1n8fA 350 2.74e+00 c.1.10.4 85397 1e19A 314 2.83e+00 1b7bA c.73.1.1 34967 1tuoA 464 2.90e+00 1kcqA 104 2.97e+00 d.109.1.1 68449 1jhgA 101 3.08e+00 1jhgA a.4.12.1 19009 1t0iA 191 3.08e+00 c.23.5.4 106209 1yemA 179 3.22e+00 1z57A 339 3.49e+00 1jm1A 204 3.76e+00 b.33.1.1 71745 1y88A 199 3.76e+00 1xb4A 202 4.32e+00 1m2dA 110 4.46e+00 c.47.1.11 78476 3cla 213 4.51e+00 3cla c.43.1.1 32610 5nul 138 4.57e+00 5nul c.23.5.1 31191 1d7uA 433 4.70e+00 2dkb c.67.1.4 34439 1q8yA 373 4.89e+00 d.144.1.7 96234 1oltA 457 5.27e+00 c.1.28.2 93334 1h32A 261 5.68e+00 a.3.1.8,a.3.1.8 76618,76619 1vl4A 447 6.06e+00 d.283.1.1 108718 1nrjA 158 6.09e+00 d.110.4.4 86124 1wa3A 205 6.10e+00 1x6oA 174 6.18e+00 b.34.5.2,b.40.4.5 109493,109494 1zxfA 155 6.26e+00 1geeA 261 6.30e+00 c.2.1.2 90509 1nriA 306 6.32e+00 c.80.1.3 86123 1o4sA 389 6.59e+00 c.67.1.1 86620 1ydgA 211 6.71e+00 2gdjA 264 6.74e+00 1xruA 282 6.78e+00 2g8yA 385 6.85e+00 1iwdA 215 6.93e+00 d.3.1.1 83756 1jx4A 352 7.17e+00 d.240.1.1,e.8.1.7 90378,90379 1ohvA 472 7.28e+00 c.67.1.4 93031 1zkrA 153 7.33e+00 1w2fA 276 7.35e+00 d.143.1.3 109125 1ku0A 388 7.36e+00 c.69.1.18 72994 1rjdA 334 7.37e+00 c.66.1.37 97558 1rlzA 369 7.38e+00 c.31.1.1 104989 1u9cA 224 7.89e+00 1nh8A 304 8.06e+00 c.94.1.1,d.58.5.3 80507,80508 1vpjA 192 8.10e+00 2bibA 547 8.22e+00 2f7tA 227 8.24e+00 1qopA 268 8.35e+00 2tysA c.1.2.4 28570 1e8yA 966 8.72e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1sd4A 126 8.79e+00 a.4.5.39 105428 1rxdA 159 8.82e+00 1yw5A 177 8.91e+00 1jhsA 188 8.92e+00 d.107.1.1 84172 1u84A 90 9.09e+00 1uheA 97 9.15e+00 1oc2A 348 9.53e+00 c.2.1.2 92765 1kfcA 268 9.72e+00 c.1.2.4 77371 1tfr 305 9.78e+00 1tfr a.60.7.1,c.120.1.2 18081,33351 1ofuX 119 1.03e+01 c.37.1.22 86976 2az4A 429 1.06e+01 1qysA 106 1.09e+01 k.41.1.1 96603 1k8kC 372 1.11e+01 b.69.4.1 68308 1g73C 121 1.11e+01 1g3fA g.52.1.1 45375 1qo3C 137 1.13e+01 1qo3C d.169.1.1 42350 1p57A 114 1.14e+01 d.170.1.2 94125 1gci 269 1.14e+01 1gci c.41.1.1 32503 1wy5A 317 1.15e+01 1puoA 170 1.16e+01 a.101.1.1,a.101.1.1 95134,95135 1v7pB 128 1.19e+01 d.169.1.1 108407 2fn0A 437 1.20e+01 1e9gA 286 1.21e+01 1wgjA b.40.5.1 59393 2a7kA 250 1.24e+01 2h1tA 188 1.26e+01 1wba 175 1.28e+01 1wba b.42.4.1 25591 2djkA 133 1.31e+01 2fm8A 135 1.32e+01 1tuaA 191 1.32e+01 d.51.1.1,d.51.1.1 107321,107322 1e7uA 961 1.35e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1spgA 144 1.37e+01 1abwA a.1.1.2 15409 1aop 497 1.37e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 2govA 195 1.37e+01 2ga9A 297 1.41e+01 1lba 146 1.46e+01 1lba d.118.1.1 41062 1w6vA 141 1.48e+01 1aj2 282 1.49e+01 1aj2 c.1.21.1 29665 1ob8A 135 1.52e+01 2ex3B 264 1.57e+01 1w9cA 321 1.57e+01 1uptA 171 1.58e+01 c.37.1.8 99767 1yqtA 538 1.58e+01 2c71A 216 1.61e+01 1jlvA 209 1.67e+01 a.45.1.1,c.47.1.5 71729,71730 1hw6A 278 1.68e+01 1frb c.1.7.1 61296 2b0tA 738 1.73e+01 1bt3A 345 1.76e+01 1bt3A a.86.1.2 18507 2fpmA 322 1.78e+01 1hywA 68 1.82e+01 1hywA d.186.1.1 61425 1jjtA 228 1.82e+01 1a7tA d.157.1.1 63139 2gtrA 261 1.83e+01 1r8oB 71 1.84e+01 1ylhA 560 1.91e+01 1qb5D 99 1.92e+01 b.40.2.1 88357 1xauA 122 1.93e+01 2b6nA 278 1.98e+01 1r6wA 322 2.02e+01 c.1.11.2,d.54.1.1 97165,97166 1svy 114 2.03e+01 1svy d.109.1.1 40831 1p5dX 463 2.04e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 2cvbA 188 2.05e+01 1mqeA 207 2.10e+01 d.113.1.1 91394 2bswA 146 2.12e+01 1r7cA 31 2.19e+01 j.35.1.1 104831 1hruA 188 2.21e+01 1hruA d.115.1.1 40926 2dg5B 190 2.33e+01 1b06A 210 2.33e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 2a1vA 144 2.35e+01 1zbqA 327 2.36e+01 1zgkA 308 2.38e+01 1pi1A 185 2.39e+01 a.29.7.1 94699 1oxkB 134 2.43e+01 c.23.1.1 93691 2bw4A 340 2.43e+01 1ad1A 266 2.44e+01 1aj2 c.1.21.1 29668 1odzA 386 2.45e+01 c.1.8.3 86889 1w66A 232 2.52e+01 1evhA 112 2.54e+01 1evhA b.55.1.4 26997 1xkzA 255 2.55e+01 1to2E 281 2.56e+01 1m4jA 142 2.62e+01 d.109.1.2 78602 1o2dA 371 2.62e+01 e.22.1.2 86591 1vg0A 650 2.65e+01 c.3.1.3,d.16.1.6 108596,108597 1ek9A 428 2.66e+01 1ek9A f.5.1.1 43809 1sk4A 163 2.68e+01 d.118.1.1 105664 2al1A 436 2.71e+01 2b5eA 504 2.72e+01 2acaA 189 2.73e+01 1unqA 125 2.75e+01 b.55.1.1 107968 2irfG 113 2.78e+01 2irfG a.4.5.23 16185 1ppjJ 62 2.78e+01 f.23.14.1 104266 1uwzA 136 2.79e+01 c.97.1.1 108081 1x31C 206 2.81e+01 2gi3A 476 2.81e+01 1sg4A 260 2.84e+01 1jq5A 370 2.84e+01 e.22.1.2 67084 1pgs 314 2.85e+01 1pgs b.121.1.1,b.121.1.1 23653,23654 1xg0A 76 2.87e+01 1xg8A 111 2.89e+01 1pfvA 551 2.96e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 2cvjA 180 2.96e+01 2f57A 317 2.97e+01 2f7fA 494 3.03e+01 1lnsA 763 3.10e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1nrzA 164 3.10e+01 c.38.1.1 86131 1ihuA 589 3.12e+01 c.37.1.10,c.37.1.10 62394,62395 1vraB 215 3.17e+01 2c30A 321 3.17e+01 1uqrA 154 3.18e+01 c.23.13.1 99779 1k3yA 221 3.20e+01 a.45.1.1,c.47.1.5 77245,77246 1ckaA 57 3.20e+01 1ckaA b.34.2.1 24459 1wkbA 810 3.20e+01 1zvaA 77 3.22e+01 1sfxA 109 3.24e+01 a.4.5.50 105505 1wguA 136 3.25e+01 1zpyA 95 3.26e+01 1b5eA 246 3.27e+01 1b5eA d.117.1.1 41056 1kjkA 64 3.27e+01 d.10.1.4 72613 1xvhA 129 3.30e+01 1wu7A 434 3.32e+01 1twdA 256 3.32e+01 c.1.30.1 107397 1z8gA 372 3.33e+01 2al2A 436 3.33e+01 1n97A 389 3.35e+01 a.104.1.1 80335 1xg0B 67 3.36e+01 1p5fA 189 3.36e+01 c.23.16.2 94142 2f2hA 773 3.38e+01 1q0pA 223 3.43e+01 c.62.1.1 95507 1p90A 145 3.51e+01 c.55.5.2 94377 1oneA 436 3.53e+01 4enl c.1.11.1,d.54.1.1 29200,38844 2abqA 306 3.56e+01 2ebn 289 3.59e+01 2ebn c.1.8.5 28990 1b8zA 90 3.61e+01 1huuA a.55.1.1 17902 1x72A 334 3.61e+01 d.126.1.6 109495 1g0oA 283 3.64e+01 1ybvA c.2.1.2 60181 1h09A 338 3.67e+01 b.109.1.1,c.1.8.8 83420,83421 1ituA 369 3.70e+01 c.1.9.7 71423 1pinA 163 3.72e+01 1pinA b.72.1.1,d.26.1.1 27802,38431 2g2cA 167 3.77e+01 1qauA 112 3.79e+01 1qauA b.36.1.1 24779 1mzbA 136 3.80e+01 a.4.5.42 91497 1azo 232 3.82e+01 1azo c.52.1.14 33329 1ptmA 329 3.82e+01 c.77.1.3 95104 1if1A 113 3.82e+01 2irfG a.4.5.23 16183 2fhzA 109 3.84e+01 1vpt 348 3.86e+01 3mag c.66.1.25 34207 1k07A 263 3.91e+01 d.157.1.1 77218 1z1nX 560 3.95e+01 1cl1A 395 3.95e+01 1cl2A c.67.1.3 34395 2a5yB 549 3.96e+01 1umdA 367 4.00e+01 c.36.1.11 99599 1zud1 251 4.05e+01 1s2wA 295 4.10e+01 c.1.12.7 98407 1qc7A 101 4.11e+01 1qc7A a.118.14.1 18456 1zin 217 4.11e+01 1zin c.37.1.1,g.41.2.1 31915,45178 2ajrA 331 4.26e+01 1e2kA 331 4.26e+01 1qhiA c.37.1.1 31854 1h6pA 203 4.30e+01 a.146.1.1 60690 1f53A 84 4.37e+01 1f53A b.11.1.4 23632 1j3aA 142 4.39e+01 c.21.1.1 77070 2cvzA 289 4.40e+01 1vqoR 155 4.42e+01 1yb0A 159 4.44e+01 4tmkA 213 4.46e+01 5tmpA c.37.1.1 31930 1cy5A 97 4.47e+01 1cy5A a.77.1.3 18430 1vlgA 176 4.48e+01 a.25.1.1 108816 1rdqE 350 4.52e+01 d.144.1.7 97314 1w0dA 337 4.54e+01 2bjbA 462 4.60e+01 1epxA 370 4.62e+01 1fbaA c.1.10.1 29150 1ta9A 450 4.62e+01 3thiA 371 4.63e+01 2thiA c.94.1.1 35792 1mp8A 281 4.65e+01 d.144.1.7 91384 1pbwA 216 4.67e+01 1pbwA a.116.1.1 19103 2ahmA 88 4.67e+01 1bm4A 32 4.68e+01 1bm4A j.47.1.1 46325 2a10A 125 4.68e+01 1s3cA 141 4.70e+01 1wbeA 209 4.71e+01 1z83A 196 4.73e+01 1yqeA 282 4.78e+01 1wvgA 359 4.78e+01 2cvhA 220 4.81e+01 1brwA 433 4.81e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1s1pA 331 4.84e+01 c.1.7.1 98350 1vjzA 341 4.89e+01 c.1.8.3 100838 1g8kB 133 4.95e+01 1g8jB b.33.1.1 24435 1vkyA 347 4.98e+01 e.53.1.1 108696 2bmeA 186 5.06e+01 1zd8A 227 5.11e+01 1v6tA 255 5.13e+01 1wxxA 382 5.14e+01 1xngA 268 5.20e+01 1jjfA 268 5.20e+01 c.69.1.2 66765 1jz8A 1023 5.22e+01 b.1.4.1,b.1.4.1,b.18.1.5,b.30.5.1,c.1.8.3 67830,67831,67832,67833,67834 1u7bA 261 5.26e+01 1swxA 209 5.29e+01 a.224.1.1 106075 1qlwA 328 5.45e+01 1qlwA c.69.1.15 34722 1poiB 260 5.48e+01 1poiB c.124.1.3 34155 1ua4A 455 5.58e+01 c.72.1.3 99128 1zupA 315 5.59e+01 1nd6A 354 5.59e+01 c.60.1.2 80407 1wrmA 165 5.62e+01 2atrA 138 5.65e+01 3pviA 157 5.68e+01 3pviA c.52.1.6 33300 1mtzA 293 5.71e+01 c.69.1.7 79467 1auk 489 5.74e+01 1auk c.76.1.2 35030 2cmuA 342 5.74e+01 1hqkA 154 5.80e+01 c.16.1.1 65902 1ja9A 274 5.86e+01 c.2.1.2 62817 2afbA 351 5.90e+01 1o1yA 239 5.97e+01 c.23.16.1 86554 1ia9A 280 6.02e+01 1ia9A d.144.1.5 62113 1ec7A 446 6.04e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1pg4A 652 6.08e+01 e.23.1.1 88067 1k4mA 213 6.09e+01 c.26.1.3 77258 1yaxA 153 6.09e+01 2ftrA 108 6.09e+01 1gqpA 221 6.13e+01 b.18.1.9 70372 1zsoA 164 6.14e+01 1zy9A 564 6.16e+01 1em8A 147 6.22e+01 c.128.1.1 90457 2gn4A 344 6.22e+01 1rypA 243 6.24e+01 1pmaA d.153.1.4 41932 1ytqA 204 6.25e+01 1dv1A 449 6.27e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1uv4A 293 6.33e+01 1vbkA 307 6.36e+01 1jy2P 48 6.38e+01 h.1.8.1 67442 1t95A 240 6.40e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1qjtA 99 6.40e+01 1eh2 a.39.1.6 17335 1h2eA 207 6.42e+01 c.60.1.1 70857 1od6A 160 6.44e+01 c.26.1.3 86836 1c93A 265 6.46e+01 2ebn c.1.8.5 28998 1vlaA 150 6.49e+01 d.227.1.2 108735 1hssA 124 6.51e+01 1bea a.52.1.2 17819 1uj6A 227 6.59e+01 c.124.1.4,d.58.40.1 107898,107899 1in6A 334 6.61e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1j7xA 302 6.62e+01 c.14.1.2 66425 2ccmA 191 6.63e+01 1nnwA 252 6.67e+01 d.159.1.5 80674 1vqvA 306 6.75e+01 1u7zA 226 6.80e+01 1xwyA 264 6.82e+01 1pa1A 310 6.97e+01 c.45.1.2 94404 1zgyA 272 6.98e+01 1q7zA 566 6.99e+01 c.1.21.2,c.1.26.1 96090,96091 1w9pA 433 7.00e+01 2g39A 497 7.01e+01 1ois 223 7.03e+01 1a36A e.15.1.1 43267 1yz7A 188 7.03e+01 1ep3A 311 7.04e+01 2dorA c.1.4.1 28597 1onwA 390 7.12e+01 b.92.1.7,c.1.9.13 87172,87173 1wlmA 151 7.14e+01 1x9uA 116 7.14e+01 256bA 106 7.16e+01 256bA a.24.3.1 16539 1tffA 234 7.17e+01 d.3.1.11 106854 2aplA 157 7.19e+01 1z6oM 191 7.20e+01 1u4gA 301 7.21e+01 d.92.1.2 107670 1cz6A 25 7.25e+01 j.3.1.3 46072 1wrjA 156 7.26e+01 2f5tX 233 7.27e+01 1reqB 637 7.29e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 2csgA 424 7.33e+01 1tuzA 118 7.35e+01 1lf7A 182 7.39e+01 b.60.1.1 73878 1gqnA 252 7.42e+01 c.1.10.1 90514 1uanA 227 7.44e+01 c.134.1.1 99135 1txoA 237 7.47e+01 1in4A 334 7.48e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1u59A 287 7.50e+01 d.144.1.7 107681 1tl9A 339 7.56e+01 1q3iA 214 7.60e+01 d.220.1.1 104524 1wzlA 585 7.64e+01 1c75A 71 7.66e+01 451c a.3.1.1 15796 2bywA 418 7.68e+01 2fpnA 216 7.69e+01 1wsrA 375 7.70e+01 1g5tA 196 7.70e+01 1g5rA c.37.1.11 32366 1pprM 312 7.72e+01 1pprM a.131.1.1,a.131.1.1 19502,19503 2ak3A 226 7.75e+01 1zin c.37.1.1,g.41.2.1 31892,45193 1u46A 291 7.76e+01 d.144.1.7 107656 1vcvA 226 7.77e+01 1m93B 245 7.79e+01 2f71A 298 7.80e+01 1kolA 398 7.83e+01 b.35.1.2,c.2.1.1 77474,77475 1ayoA 130 7.86e+01 1ayoA b.2.4.1 22431 2dlbA 80 8.05e+01 3cms 323 8.05e+01 1smrA b.50.1.2 26865 1c3pA 375 8.06e+01 1c3pA c.42.1.2 32606 2as0A 396 8.07e+01 2dri 271 8.11e+01 2dri c.93.1.1 35637 1hqz1 141 8.11e+01 2dcnA 311 8.13e+01 2a0mA 316 8.13e+01 3fapB 94 8.17e+01 1nsgB a.24.7.1 16612 1zaiA 363 8.21e+01 2fb6A 117 8.25e+01 2gkeA 274 8.33e+01 1t46A 313 8.36e+01 d.144.1.7 106397 1vmbA 140 8.39e+01 1xi3A 215 8.48e+01 c.1.3.1 109601 1z2mA 155 8.50e+01 1qj4A 257 8.57e+01 1qj4A c.69.1.20 34796 1gqzA 274 8.62e+01 d.21.1.1,d.21.1.1 83311,83312 1jsdB 176 8.66e+01 h.3.1.1 63259 1khbA 625 8.72e+01 c.91.1.1,c.109.1.1 68606,68607 1xfkA 336 8.74e+01 2bw0A 329 8.80e+01 1l1eA 287 8.86e+01 c.66.1.18 73454 1r5iD 216 8.90e+01 a.202.1.1 97091 1j09A 468 8.93e+01 a.97.1.1,c.26.1.1 77025,77026 1u0kA 288 8.93e+01 d.21.1.2,d.21.1.2 107547,107548 1r31A 428 8.94e+01 d.58.20.1,d.179.1.1 96897,96898