# List of top-scoring protein chains for t06-100-30-alpha-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 1.89e-02 1hzgA d.194.1.1 61122 2ap1A 327 8.47e-02 2bkrA 212 1.21e-01 5nul 138 5.41e-01 5nul c.23.5.1 31191 2az4A 429 5.49e-01 1y88A 199 6.27e-01 2b49A 287 7.23e-01 1zxfA 155 8.12e-01 1jx4A 352 8.57e-01 d.240.1.1,e.8.1.7 90378,90379 1t0iA 191 8.71e-01 c.23.5.4 106209 1p7gA 222 9.42e-01 a.2.11.1,d.44.1.1 94223,94224 1p57A 114 1.02e+00 d.170.1.2 94125 1pgs 314 1.10e+00 1pgs b.121.1.1,b.121.1.1 23653,23654 1y74A 57 1.26e+00 1lehA 364 1.26e+00 1bw9A c.2.1.7,c.58.1.1 30268,33916 1nw3A 416 1.37e+00 c.66.1.31 86288 1dc1A 323 1.46e+00 1dc1A c.52.1.11 33321 1jm1A 204 1.47e+00 b.33.1.1 71745 1r6wA 322 1.50e+00 c.1.11.2,d.54.1.1 97165,97166 1euvA 221 1.77e+00 1euvA d.3.1.7 37133 1qopA 268 2.04e+00 2tysA c.1.2.4 28570 2ag4A 164 2.08e+00 1n8fA 350 2.10e+00 c.1.10.4 85397 1vljA 407 2.40e+00 e.22.1.2 108832 1uptA 171 2.43e+00 c.37.1.8 99767 1o5kA 306 2.53e+00 c.1.10.1 92504 1jhgA 101 2.60e+00 1jhgA a.4.12.1 19009 1rlzA 369 2.61e+00 c.31.1.1 104989 1e8yA 966 2.82e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1q8yA 373 3.02e+00 d.144.1.7 96234 1tfr 305 3.05e+00 1tfr a.60.7.1,c.120.1.2 18081,33351 1x6oA 174 3.11e+00 b.34.5.2,b.40.4.5 109493,109494 1vicA 262 3.12e+00 c.68.1.13 100756 1m1hA 248 3.15e+00 b.114.1.1,d.58.42.1 78415,78416 1o4sA 389 3.22e+00 c.67.1.1 86620 1ofuX 119 3.36e+00 c.37.1.22 86976 2eu9A 355 3.44e+00 1p5dX 463 3.45e+00 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 1vpjA 192 3.48e+00 1k07A 263 3.61e+00 d.157.1.1 77218 1zo2A 129 3.67e+00 1vl4A 447 3.67e+00 d.283.1.1 108718 1gw5S 142 3.69e+00 d.110.4.2 70633 1w9cA 321 3.82e+00 1zgkA 308 3.85e+00 1nh8A 304 3.92e+00 c.94.1.1,d.58.5.3 80507,80508 1xwyA 264 3.97e+00 1hw6A 278 4.13e+00 1frb c.1.7.1 61296 1o2dA 371 4.20e+00 e.22.1.2 86591 1tuoA 464 4.26e+00 1rxdA 159 4.33e+00 1r31A 428 4.33e+00 d.58.20.1,d.179.1.1 96897,96898 1kfcA 268 4.40e+00 c.1.2.4 77371 1z8gA 372 4.59e+00 1k8kC 372 4.74e+00 b.69.4.1 68308 1yw5A 177 4.88e+00 1xb4A 202 5.18e+00 1vraB 215 5.42e+00 1lba 146 5.88e+00 1lba d.118.1.1 41062 1qfjA 232 5.95e+00 1qfjA b.43.4.2,c.25.1.1 25655,31545 2a5yB 549 5.97e+00 1gci 269 5.99e+00 1gci c.41.1.1 32503 1nrjA 158 6.04e+00 d.110.4.4 86124 2fn0A 437 6.34e+00 1wa3A 205 6.47e+00 1g291 372 6.53e+00 1g291 2gtrA 261 6.68e+00 1uheA 97 6.73e+00 2acaA 189 7.03e+00 1pinA 163 7.29e+00 1pinA b.72.1.1,d.26.1.1 27802,38431 1rjdA 334 7.43e+00 c.66.1.37 97558 3cla 213 7.59e+00 3cla c.43.1.1 32610 1id1A 153 7.59e+00 1id1A c.2.1.9 62286 1zkrA 153 7.66e+00 1u7zA 226 8.24e+00 1svdM 110 8.35e+00 1oltA 457 8.43e+00 c.1.28.2 93334 1e19A 314 8.46e+00 1b7bA c.73.1.1 34967 2g8yA 385 8.48e+00 1q0pA 223 8.50e+00 c.62.1.1 95507 2a0mA 316 8.58e+00 1odzA 386 8.69e+00 c.1.8.3 86889 2a7kA 250 8.73e+00 2aioA 269 8.85e+00 1pbwA 216 8.90e+00 1pbwA a.116.1.1 19103 1z08A 170 8.99e+00 2dg5B 190 9.07e+00 1rliA 184 9.11e+00 c.23.5.6 97647 1kid 203 9.51e+00 1derA c.8.5.1 30771 2cayA 145 9.55e+00 1r0rE 274 9.66e+00 c.41.1.1 96735 2fm8A 135 9.74e+00 1u84A 90 1.02e+01 1mpxA 615 1.02e+01 b.18.1.13,c.69.1.21 85041,85042 1vg0A 650 1.03e+01 c.3.1.3,d.16.1.6 108596,108597 1nriA 306 1.05e+01 c.80.1.3 86123 2fmlA 273 1.07e+01 1e7uA 961 1.08e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1wxxA 382 1.08e+01 1ayoA 130 1.10e+01 1ayoA b.2.4.1 22431 2a4hA 126 1.11e+01 2f7tA 227 1.12e+01 1j7xA 302 1.16e+01 c.14.1.2 66425 2b0tA 738 1.17e+01 1e2kA 331 1.20e+01 1qhiA c.37.1.1 31854 2g6bA 180 1.20e+01 1r5mA 425 1.21e+01 1txoA 237 1.21e+01 1em8A 147 1.22e+01 c.128.1.1 90457 2a6hC 1119 1.23e+01 2a1vA 144 1.23e+01 1o5zA 442 1.25e+01 c.59.1.2,c.72.2.2 92530,92531 1ydgA 211 1.25e+01 1sk4A 163 1.25e+01 d.118.1.1 105664 1ckaA 57 1.26e+01 1ckaA b.34.2.1 24459 1yemA 179 1.28e+01 1vkyA 347 1.30e+01 e.53.1.1 108696 1w15A 153 1.30e+01 b.7.1.2 109041 1j0dA 341 1.31e+01 c.79.1.1 83902 1sz2A 332 1.34e+01 1ta9A 450 1.36e+01 2c46A 241 1.37e+01 1iwdA 215 1.39e+01 d.3.1.1 83756 1puoA 170 1.39e+01 a.101.1.1,a.101.1.1 95134,95135 1jlvA 209 1.40e+01 a.45.1.1,c.47.1.5 71729,71730 1g73C 121 1.49e+01 1g3fA g.52.1.1 45375 2ex3B 264 1.51e+01 1k2eA 156 1.53e+01 d.113.1.1 72010 1zy9A 564 1.53e+01 1spgA 144 1.53e+01 1abwA a.1.1.2 15409 1ob8A 135 1.54e+01 1bm4A 32 1.55e+01 1bm4A j.47.1.1 46325 1x88A 359 1.56e+01 1b5eA 246 1.59e+01 1b5eA d.117.1.1 41056 1pi1A 185 1.60e+01 a.29.7.1 94699 1wsrA 375 1.62e+01 1lzlA 323 1.65e+01 c.69.1.2 78306 1ptmA 329 1.66e+01 c.77.1.3 95104 1vbkA 307 1.67e+01 1wrjA 156 1.74e+01 2f9lA 199 1.75e+01 1b06A 210 1.77e+01 1avmA a.2.11.1,d.44.1.1 15740,38737 1ep3A 311 1.78e+01 2dorA c.1.4.1 28597 1bg1A 722 1.78e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17767,22461,40527 1x72A 334 1.82e+01 d.126.1.6 109495 1xvhA 129 1.82e+01 1lktA 104 1.85e+01 1lktA b.90.1.1 28398 1llnA 262 1.85e+01 d.165.1.1 84625 1g8kB 133 1.89e+01 1g8jB b.33.1.1 24435 1w2fA 276 1.90e+01 d.143.1.3 109125 1uj6A 227 1.93e+01 c.124.1.4,d.58.40.1 107898,107899 1ek9A 428 1.93e+01 1ek9A f.5.1.1 43809 1jhsA 188 1.94e+01 d.107.1.1 84172 1yaxA 153 1.94e+01 1kcqA 104 1.99e+01 d.109.1.1 68449 1hqz1 141 1.99e+01 1uanA 227 1.99e+01 c.134.1.1 99135 1epxA 370 2.00e+01 1fbaA c.1.10.1 29150 1jl0A 334 2.04e+01 1jenA d.156.1.1 63155 2fhzA 109 2.04e+01 1oxkB 134 2.04e+01 c.23.1.1 93691 1in4A 334 2.07e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 2aebA 322 2.08e+01 1xi3A 215 2.13e+01 c.1.3.1 109601 1d7uA 433 2.15e+01 2dkb c.67.1.4 34439 2ak3A 226 2.15e+01 1zin c.37.1.1,g.41.2.1 31892,45193 1jjtA 228 2.17e+01 1a7tA d.157.1.1 63139 1x31C 206 2.20e+01 1e8cA 498 2.22e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 2bswA 146 2.24e+01 7odcA 424 2.25e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1xyzA 347 2.33e+01 1taxA c.1.8.3 28804 1oc2A 348 2.34e+01 c.2.1.2 92765 1ohvA 472 2.35e+01 c.67.1.4 93031 1svy 114 2.35e+01 1svy d.109.1.1 40831 1umdA 367 2.36e+01 c.36.1.11 99599 1geeA 261 2.36e+01 c.2.1.2 90509 1yb0A 159 2.40e+01 1nnwA 252 2.43e+01 d.159.1.5 80674 1ytqA 204 2.43e+01 1unqA 125 2.46e+01 b.55.1.1 107968 1o22A 170 2.47e+01 d.238.1.1 86557 1twdA 256 2.49e+01 c.1.30.1 107397 1ku0A 388 2.51e+01 c.69.1.18 72994 2b6nA 278 2.54e+01 1zud1 251 2.56e+01 1mp8A 281 2.57e+01 d.144.1.7 91384 1z57A 339 2.63e+01 1xd5A 112 2.64e+01 1to2E 281 2.70e+01 1azo 232 2.72e+01 1azo c.52.1.14 33329 1gqzA 274 2.72e+01 d.21.1.1,d.21.1.1 83311,83312 1uv7A 110 2.80e+01 d.67.4.1 100040 1zpyA 95 2.80e+01 1v58A 241 2.82e+01 c.47.1.9,d.17.3.1 108371,108372 1zvkA 358 2.83e+01 2govA 195 2.96e+01 1r7cA 31 2.99e+01 j.35.1.1 104831 2fr1A 486 2.99e+01 1qz9A 416 3.06e+01 c.67.1.3 96621 1xg8A 111 3.07e+01 1uqrA 154 3.08e+01 c.23.13.1 99779 1g0oA 283 3.11e+01 1ybvA c.2.1.2 60181 1zd8A 227 3.12e+01 1xfkA 336 3.12e+01 1wrmA 165 3.16e+01 1chd 203 3.16e+01 1chd c.40.1.1 32478 1in6A 334 3.17e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1za0A 275 3.19e+01 1yqeA 282 3.22e+01 1ppjA 446 3.22e+01 d.185.1.1,d.185.1.1 104252,104253 1pprM 312 3.22e+01 1pprM a.131.1.1,a.131.1.1 19502,19503 1s3aA 102 3.24e+01 1ymiA 334 3.28e+01 1e9gA 286 3.36e+01 1wgjA b.40.5.1 59393 1xfiA 367 3.39e+01 e.50.1.1 109584 2f22A 144 3.40e+01 1qzgA 187 3.42e+01 b.40.4.3 96643 1xyiA 66 3.44e+01 1gd0A 122 3.46e+01 1dptA d.80.1.3 39834 1w6vA 141 3.47e+01 1oneA 436 3.48e+01 4enl c.1.11.1,d.54.1.1 29200,38844 2bm3A 166 3.49e+01 2fj8A 125 3.52e+01 1t1gA 364 3.52e+01 c.41.1.2 106246 1tuaA 191 3.53e+01 d.51.1.1,d.51.1.1 107321,107322 1xruA 282 3.57e+01 1bjt 793 3.64e+01 1bjt e.11.1.1 43249 2cmuA 342 3.73e+01 1vlaA 150 3.73e+01 d.227.1.2 108735 1c8cA 64 3.76e+01 1azpA b.34.13.1 59084 1of8A 370 3.77e+01 c.1.10.4 92819 1vqoR 155 3.77e+01 1h2eA 207 3.80e+01 c.60.1.1 70857 3pmgA 561 3.82e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1yqzA 438 3.82e+01 2al2A 436 3.84e+01 1aj2 282 3.88e+01 1aj2 c.1.21.1 29665 2gi3A 476 3.90e+01 1mtzA 293 3.91e+01 c.69.1.7 79467 1uwzA 136 3.91e+01 c.97.1.1 108081 2al1A 436 3.93e+01 1lk5A 229 3.97e+01 c.124.1.4,d.58.40.1 73960,73961 2gkeA 274 3.97e+01 1j5pA 253 4.00e+01 d.81.1.3,c.2.1.3 71577,83092 1ua4A 455 4.03e+01 c.72.1.3 99128 1pwgA 349 4.03e+01 e.3.1.1 104340 1nd4A 264 4.08e+01 d.144.1.6 91815 1xqwA 293 4.10e+01 1nni1 174 4.11e+01 1l1eA 287 4.12e+01 c.66.1.18 73454 2bmeA 186 4.17e+01 1qlwA 328 4.20e+01 1qlwA c.69.1.15 34722 1kzlA 208 4.23e+01 b.43.4.3,b.43.4.3 77635,77636 1dyoA 160 4.23e+01 1dyoA b.18.1.7 23771 1lqaA 346 4.24e+01 c.1.7.1 84674 2ahmA 88 4.24e+01 3bamA 213 4.27e+01 1bam c.52.1.3 33288 1t7rA 269 4.32e+01 a.123.1.1 106635 1rypA 243 4.33e+01 1pmaA d.153.1.4 41932 1r8sE 203 4.34e+01 a.118.3.1 97248 1vjzA 341 4.34e+01 c.1.8.3 100838 1qc7A 101 4.39e+01 1qc7A a.118.14.1 18456 2gdjA 264 4.42e+01 1rz2A 254 4.42e+01 b.100.1.1 105130 1z2mA 155 4.43e+01 1thg 544 4.44e+01 1thg c.69.1.17 34763 2ajrA 331 4.45e+01 1zxuA 217 4.46e+01 1ec7A 446 4.46e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1zg2A 107 4.47e+01 1wruA 379 4.51e+01 1lam 484 4.64e+01 1lam c.50.1.1,c.56.5.3 33166,33829 1xjuA 163 4.68e+01 1auk 489 4.69e+01 1auk c.76.1.2 35030 1kjkA 64 4.72e+01 d.10.1.4 72613 2fpmA 322 4.73e+01 1hn0A 1021 4.75e+01 a.102.3.2,b.18.1.17,b.24.1.1,b.30.5.2 83616,83617,83618,83619 1pc3A 350 4.77e+01 c.94.1.1 104102 1cz6A 25 4.78e+01 j.3.1.3 46072 1zbqA 327 4.81e+01 1wjgA 137 4.84e+01 1usgA 346 4.86e+01 c.93.1.1 99864 2fkiA 126 4.87e+01 1wvgA 359 4.87e+01 1qb5D 99 4.90e+01 b.40.2.1 88357 2f7fA 494 4.92e+01 1yqtA 538 4.92e+01 1aop 497 4.97e+01 2aop d.58.36.1,d.58.36.1,d.134.1.1,d.134.1.1 39501,39502,41425,41426 1k4mA 213 4.99e+01 c.26.1.3 77258 1zvaA 77 5.01e+01 1sd4A 126 5.02e+01 a.4.5.39 105428 1k0wA 231 5.02e+01 c.74.1.1 77220 2f2hA 773 5.03e+01 1z6nA 167 5.03e+01 1pa1A 310 5.05e+01 c.45.1.2 94404 1lnsA 763 5.06e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1yz7A 188 5.07e+01 1r1hA 696 5.08e+01 d.92.1.4 104756 2cvbA 188 5.12e+01 1jy2P 48 5.20e+01 h.1.8.1 67442 1xw8A 252 5.20e+01 1b7yA 350 5.21e+01 1pysA d.104.1.1 40776 1ustA 93 5.24e+01 a.4.5.13 99884 1rkxA 357 5.25e+01 c.2.1.2 97631 1zchA 255 5.26e+01 1gjwA 637 5.30e+01 b.71.1.1,c.1.8.1 60582,60583 1s2wA 295 5.33e+01 c.1.12.7 98407 2ai4A 119 5.40e+01 1xviA 275 5.40e+01 1qo3C 137 5.44e+01 1qo3C d.169.1.1 42350 1tksA 204 5.46e+01 d.115.1.2 107114 2cfuA 658 5.47e+01 1u02A 239 5.50e+01 c.108.1.15 107538 2g39A 497 5.51e+01 1n13A 52 5.56e+01 d.155.1.2 85248 2afbA 351 5.58e+01 1iqrA 420 5.61e+01 a.99.1.1,c.28.1.1 66275,66276 2bf6A 449 5.61e+01 2bw0A 329 5.62e+01 1vclA 432 5.63e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1i1qA 520 5.63e+01 1qdlA d.161.1.1 61543 1wnaA 131 5.72e+01 1ufyA 122 5.75e+01 d.79.1.2 88489 2djkA 133 5.75e+01 1ukuA 102 5.78e+01 d.58.5.2 99533 1ooeA 236 5.79e+01 c.2.1.2 87196 1npiA 61 5.79e+01 g.3.7.1 80685 1lldA 319 5.81e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 3fapB 94 5.81e+01 1nsgB a.24.7.1 16612 1zsoA 164 5.82e+01 2bywA 418 5.83e+01 1dabA 539 5.88e+01 1dabA b.80.1.7 28049 1qy1A 174 5.88e+01 b.60.1.1 96568 1r5iD 216 5.89e+01 a.202.1.1 97091 1v7pB 128 5.90e+01 d.169.1.1 108407 2d00A 109 5.90e+01 1v5vA 401 5.92e+01 1zjkA 403 5.98e+01 1xknA 355 5.99e+01 1molA 94 5.99e+01 1molA d.17.1.1 37988 2b81A 323 6.03e+01 2h1tA 188 6.13e+01 1zczA 464 6.19e+01 256bA 106 6.23e+01 256bA a.24.3.1 16539 2ccmA 191 6.26e+01 1mqeA 207 6.26e+01 d.113.1.1 91394 1bt3A 345 6.27e+01 1bt3A a.86.1.2 18507 2bibA 547 6.28e+01 1poiB 260 6.29e+01 1poiB c.124.1.3 34155 1wz8A 264 6.32e+01 2bkfA 87 6.33e+01 1qj4A 257 6.37e+01 1qj4A c.69.1.20 34796 1tl9A 339 6.38e+01 1xg0B 67 6.42e+01 1j3wA 163 6.48e+01 d.110.7.1 90833 1usmA 80 6.50e+01 d.74.1.1 99876 1uoyA 64 6.50e+01 g.3.19.1 99709 4dpvZ 584 6.51e+01 2cas b.121.5.2 23377 2fb6A 117 6.52e+01 1wqaA 455 6.53e+01 1k3yA 221 6.53e+01 a.45.1.1,c.47.1.5 77245,77246 1gyhA 318 6.58e+01 b.67.2.1 70757 2dcnA 311 6.60e+01 1meoA 209 6.61e+01 c.65.1.1 79035 2cvjA 180 6.67e+01 1zndA 174 6.70e+01 1vhxA 150 6.76e+01 c.55.3.8 100712 1p2fA 220 6.77e+01 a.4.6.1,c.23.1.1 87720,87721 1x3sA 195 6.81e+01 1t95A 240 6.87e+01 a.5.8.1,d.235.1.2,d.58.11.3 106705,106706,106707 1j3aA 142 6.87e+01 c.21.1.1 77070 1wdtA 665 6.88e+01 1hqkA 154 6.89e+01 c.16.1.1 65902 1ur1A 378 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b.92.1.7,c.1.9.13 87172,87173 1vlgA 176 8.41e+01 a.25.1.1 108816 1nvpB 57 8.41e+01 a.32.1.1 92211 1tffA 234 8.49e+01 d.3.1.11 106854 1v25A 541 8.55e+01 e.23.1.1 108275 2gkpA 167 8.58e+01 1yd9A 193 8.61e+01 1zkpA 268 8.61e+01 1n8vA 112 8.64e+01 a.118.21.1 85457 1jeoA 180 8.67e+01 c.80.1.3 66611 1tr8A 102 8.67e+01 1wdnA 226 8.71e+01 1lst c.94.1.1 35816 4tmkA 213 8.73e+01 5tmpA c.37.1.1 31930 2bo9A 308 8.74e+01 1vm0A 130 8.75e+01 d.68.6.2 108873 1d3bB 91 8.76e+01 1d3bB b.38.1.1 24804 1wi0A 113 8.77e+01 1q7zA 566 8.80e+01 c.1.21.2,c.1.26.1 96090,96091 2a10A 125 8.81e+01 1zd7A 159 8.84e+01 1vjpA 394 8.85e+01 c.2.1.3,d.81.1.3 100828,100829 1uj0A 62 8.94e+01 b.34.2.1 99449 1fj2A 232 8.95e+01 1auoA c.69.1.14 34720 1ub9A 100 8.95e+01 a.4.5.28 99159 1fs0E 138 8.96e+01 1aqt a.2.10.1,b.93.1.1 59997,59998