# List of top-scoring protein chains for t2k.w0.5 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.soe.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 2w01A 208 1.84e-26 3et6A 190 8.44e-25 1yk9A 204 1.33e-24 1wc3A 219 4.72e-23 d.58.29.1 114495 1wc1A 226 5.66e-23 d.58.29.1 114492 2wz1A 219 3.00e-21 1culA 217 8.87e-20 1azsA d.58.29.1 39417 1cs4A 225 8.93e-20 1azsA d.58.29.1 39418 1azsA 220 9.68e-20 1azsA d.58.29.1 39416 1ybtA 184 4.65e-19 1fx4A 231 1.97e-18 1fx2A d.58.29.1 39431 1fx2A 235 2.31e-18 1fx2A d.58.29.1 39430 1y10A 407 1.74e-17 1ab8A 220 9.73e-17 1azsA d.58.29.1 39414 1culB 208 1.18e-16 1azsA d.58.29.1 39424 1azsB 212 1.20e-16 1azsA d.58.29.1 39423 3iclA 171 1.16e-02 3l0qA 554 6.18e-01 3gg4A 554 6.18e-01 2hkxA 221 1.21e+00 2aydA 76 1.48e+00 2fmyA 220 1.69e+00 1pl5A 142 1.71e+00 h.1.23.1 104186 3cx5E 185 1.75e+00 b.33.1.1 157084 f.23.12.1 157085 2qv6A 268 2.11e+00 3lmbA 165 2.11e+00 1xaxA 154 2.16e+00 3l70A 446 2.16e+00 2dskA 311 2.22e+00 1x52A 124 2.28e+00 d.79.3.2 145854 2f2bA 246 2.50e+00 1nyhA 166 3.35e+00 h.1.23.1 86403 2qjpC 179 3.56e+00 2biiA 424 4.01e+00 2bihA 474 4.20e+00 2jjhA 449 4.35e+00 3i5aA 334 4.50e+00 2numA 141 4.76e+00 2nukA 141 5.03e+00 2nwfA 141 5.10e+00 2jjeA 449 5.16e+00 2cjgA 449 5.17e+00 2jjfA 449 5.27e+00 2r9vA 515 5.72e+00 1q15A 503 7.40e+00 c.26.2.1 95538 d.153.1.1 95539 2nveA 141 7.71e+00 1g66A 207 8.21e+00 1bs9 c.69.1.30 31329 1o75A 415 8.26e+00 b.1.20.1 81117 b.1.20.1 81118 b.120.1.1 81119 1lehA 364 8.37e+00 1bw9A c.2.1.7 30268 c.58.1.1 33916 2nvgA 141 8.48e+00 2iyeA 263 8.52e+00 3ezuA 342 8.59e+00 2isbA 192 8.76e+00 c.8.9.1 137601 3cmuA 2050 9.42e+00 3cmwA 1706 9.51e+00 1wj2A 78 9.60e+00 g.79.1.1 114689 2o1bA 404 9.65e+00 3cmvA 1357 9.69e+00 1skyB 502 9.89e+00 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1m41A 380 9.95e+00 c.1.16.4 78595 1nqkA 381 9.96e+00 c.1.16.4 92050 2rebA 352 1.00e+01 c.37.1.11 32282 d.48.1.1 38767 2recA 353 1.00e+01 2reb i.2.1.1 45879 3gmgA 170 1.00e+01 1u94A 356 1.01e+01 c.37.1.11 107743 d.48.1.1 107744 1hy8A 76 1.01e+01 a.28.1.1 65959 2x2bA 78 1.05e+01 1f80D 81 1.12e+01 1acp a.28.1.1 59686 3eh8A 254 1.16e+01 2cgqA 113 1.17e+01 1o66A 275 1.20e+01 c.1.12.8 92547 3hheA 255 1.31e+01 1xcgA 368 1.31e+01 a.87.1.1 115120 b.55.1.1 115121 2ausA 334 1.33e+01 1u1iA 392 1.35e+01 c.2.1.3 107582 d.81.1.3 107583 1kzlA 208 1.37e+01 b.43.4.3 77635 b.43.4.3 77636 1f0kA 364 1.39e+01 1f0kA c.87.1.2 35465 3e4bA 452 1.43e+01 2b81A 323 1.43e+01 1ldmA 329 1.55e+01 c.2.1.5 30160 d.162.1.1 42127 6ldhA 330 1.55e+01 c.2.1.5 30161 d.162.1.1 42128 3fnlA 595 1.58e+01 2bjkA 516 1.61e+01 1uzbA 516 1.64e+01 c.82.1.1 100220 2o5aA 125 1.65e+01 d.218.1.12 148593 2d4aA 308 1.69e+01 2arjA 211 1.73e+01 b.1.1.1 144829 b.1.1.2 144830 2nvfA 141 1.77e+01 1e0cA 271 1.87e+01 1e0cA c.46.1.2 32717 c.46.1.2 32718 2w6jD 528 1.93e+01 2qojZ 254 1.94e+01 1p8kZ 254 1.94e+01 d.95.2.1 94361 d.95.2.1 94362 1p3hA 99 1.94e+01 b.35.1.1 87734 2p6rA 702 1.96e+01 a.4.5.43 149270 a.289.1.2 149271 c.37.1.19 149272 c.37.1.19 149273 1nbmD 480 2.01e+01 1skyE a.69.1.1 18290 b.49.1.1 26455 c.37.1.11 32335 2jdiD 482 2.02e+01 a.69.1.1 138263 b.49.1.1 138264 c.37.1.11 138265 1e79D 482 2.04e+01 1skyE a.69.1.1 18272 b.49.1.1 26437 c.37.1.11 32317 2qjkC 179 2.06e+01 2qjyC 187 2.10e+01 2c63A 247 2.15e+01 2d69A 430 2.17e+01 c.1.14.1 131292 d.58.9.1 131293 2f93B 122 2.22e+01 f.17.4.1 145151 1zakA 222 2.23e+01 1zin c.37.1.1 31913 g.41.2.1 45202 1skyE 473 2.24e+01 1skyE a.69.1.1 18314 b.49.1.1 26479 c.37.1.11 32359 1ocxA 182 2.27e+01 b.81.1.3 86814 1lepA 99 2.35e+01 1lepA b.35.1.1 24649 1ywtA 248 2.43e+01 3bypA 94 2.43e+01 d.52.9.1 155726 3lw1A 253 2.46e+01 2o02A 230 2.55e+01 a.118.7.1 148541 1qw2A 102 2.56e+01 d.249.1.1 96456 1gnyA 153 2.56e+01 b.18.1.11 65404 1qjbA 245 2.57e+01 1qjaA a.118.7.1 19202 1qjaA 245 2.57e+01 1qjaA a.118.7.1 19204 3gjzA 336 2.57e+01 2v7dA 247 2.59e+01 a.118.7.1 152717 3he7D 242 2.60e+01 1rieA 129 2.65e+01 b.33.1.1 24427 2c1nA 258 2.67e+01 a.118.7.1 129640 1pmiA 440 2.68e+01 b.82.1.3 28114 3busA 273 2.83e+01 1tisA 286 2.86e+01 d.117.1.1 41040 2rcnA 358 2.92e+01 2pgnA 589 2.98e+01 1bccE 196 3.10e+01 1rie b.33.1.1 24431 f.23.12.1 43699 1uhkA 191 3.11e+01 a.39.1.5 119681 1ej3A 191 3.11e+01 1ej3A a.39.1.5 17259 2w2jA 291 3.13e+01 3l70E 196 3.13e+01 3hjwA 327 3.15e+01 2ey4A 333 3.15e+01 b.122.1.1 132578 d.265.1.2 132579 3haxA 346 3.15e+01 2wmkA 606 3.16e+01 1mabB 479 3.20e+01 1skyE a.69.1.1 18312 b.49.1.1 26477 c.37.1.11 32357 1mx3A 347 3.20e+01 c.2.1.4 79638 c.23.12.1 79639 2f95B 163 3.20e+01 f.17.4.1 145152 2wmiB 606 3.23e+01 2wmiA 606 3.23e+01 3hrdD 160 3.25e+01 3i5cA 206 3.28e+01 1ppjE 196 3.30e+01 b.33.1.1 104260 f.23.12.1 104261 1bgyE 196 3.30e+01 1bgyE f.23.12.1 43683 3e1sA 574 3.31e+01 2cmtA 172 3.34e+01 3i5bA 179 3.34e+01 2rfkA 334 3.39e+01 b.122.1.1 151996 d.265.1.2 151997 1zvcA 189 3.44e+01 b.159.1.1 125705 2ge4A 177 3.46e+01 f.4.1.1 135048 1g90A 176 3.47e+01 1bxwA f.4.1.1 60388 1vlmA 219 3.54e+01 c.66.1.41 108836 2cr9A 139 3.58e+01 d.297.1.1 130735 1vkwA 218 3.70e+01 d.90.1.2 108695 1r8gA 372 3.73e+01 d.128.1.3 104845 2apoA 357 3.77e+01 b.122.1.1 127133 d.265.1.2 127134 2pqcA 445 3.79e+01 2gg6A 455 3.84e+01 2q4iA 193 3.85e+01 b.159.1.1 139857 1z8kA 193 3.85e+01 b.159.1.1 124703 2v6gA 364 3.85e+01 3kqfA 265 3.88e+01 3hmuA 472 3.94e+01 1unlD 208 3.96e+01 a.74.1.1 113326 2brjA 188 3.99e+01 b.159.1.1 146213