# List of top-scoring protein chains for t06-100-30-str2-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 2gj8A 172 8.97e-02 1f2tB 148 7.70e-01 1f2tB 1e9rA 437 8.60e-01 c.37.1.11 64827 1b8oA 284 9.56e-01 1b8oA c.56.2.1 33762 2dbbA 151 1.01e+00 1qo0D 196 1.40e+00 1qo0D c.23.1.3 31125 1xahA 354 1.42e+00 1wqaA 455 1.62e+00 1tcvA 287 1.74e+00 1yb0A 159 1.87e+00 2gzaA 361 1.99e+00 2fckA 181 2.43e+00 1vheA 373 2.62e+00 b.49.3.1,c.56.5.4 100669,100670 1cb0A 283 3.07e+00 1cb0A c.56.2.1 33790 2ffuA 501 3.19e+00 2bsxA 253 3.53e+00 1fcyA 236 3.82e+00 2lbd a.123.1.1 19282 1vp4A 425 3.84e+00 1odkA 235 4.36e+00 c.56.2.1 86863 1bqk 124 4.45e+00 1bqk b.6.1.1 22889 2cviA 83 4.58e+00 1s2dA 167 5.11e+00 c.23.14.1 98377 1twfK 120 5.34e+00 1yj7A 171 5.38e+00 1vjeA 166 5.46e+00 d.185.1.2 100807 1u7lA 392 5.53e+00 2f5gA 133 5.79e+00 1zpvA 91 6.93e+00 1wi1A 126 7.01e+00 1jysA 242 7.03e+00 c.56.2.1 77216 1xewY 172 7.30e+00 1pvvA 315 7.68e+00 c.78.1.1,c.78.1.1 95190,95191 1hzdA 272 8.14e+00 c.14.1.3 65969 2bfwA 200 8.50e+00 2cxcA 144 9.15e+00 2bj7A 138 9.52e+00 1wtaA 275 9.55e+00 2av4A 162 9.66e+00 2al2A 436 9.73e+00 2fuvA 549 1.03e+01 2al1A 436 1.04e+01 1r5tA 142 1.04e+01 c.97.1.1 104812 1oneA 436 1.06e+01 4enl c.1.11.1,d.54.1.1 29200,38844 2g5cA 281 1.06e+01 1g63A 181 1.07e+01 1g5qA c.34.1.1 60299 2akzA 439 1.08e+01 2c0nA 203 1.09e+01 1okgA 373 1.14e+01 c.46.1.2,c.46.1.2,d.26.1.3 93250,93251,93252 2g40A 224 1.15e+01 1in0A 163 1.15e+01 d.58.49.1,d.58.49.1 83694,83695 2a5dA 175 1.16e+01 1rq2A 382 1.19e+01 c.32.1.1,d.79.2.1 105048,105049 1r5lA 262 1.20e+01 a.5.3.1,c.13.1.1 97099,97100 1v60A 123 1.21e+01 1cl8A 276 1.24e+01 1ckqA c.52.1.1 33230 1v4pA 157 1.28e+01 1g66A 207 1.29e+01 1bs9 c.69.1.30 31329 1gd1O 334 1.30e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 2czcA 334 1.31e+01 1b3aA 67 1.37e+01 1b3aA d.9.1.1 37410 1yzfA 195 1.37e+01 1q2lA 939 1.38e+01 1ko6A 187 1.39e+01 b.119.1.1 77471 2arhA 203 1.40e+01 8abp 306 1.45e+01 8abp c.93.1.1 35647 1jndA 420 1.46e+01 c.1.8.5,d.26.3.1 71757,71758 1v8hA 107 1.46e+01 1d8wA 426 1.52e+01 1de5A c.1.15.2 29394 1hfc 169 1.53e+01 1hfc d.92.1.11 40335 1w77A 228 1.58e+01 2gcfA 73 1.58e+01 1vhwA 253 1.60e+01 c.56.2.1 100706 1fxlA 167 1.66e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1s3zA 165 1.67e+01 d.108.1.1 105250 1zd9A 188 1.71e+01 1uvqB 198 1.73e+01 b.1.1.2,d.19.1.1 100064,100065 1xc3A 302 1.76e+01 1ryiA 382 1.79e+01 2btzA 394 1.80e+01 1wj9A 211 1.81e+01 2ab5A 269 1.83e+01 1wduA 245 1.86e+01 d.151.1.1 109286 1ht6A 405 1.91e+01 b.71.1.1,c.1.8.1 83629,83630 1r6xA 395 1.92e+01 b.122.1.3,c.26.1.5 97167,97168 2b0jA 358 1.94e+01 1qe5A 266 1.95e+01 1b8oA c.56.2.1 33784 1wz8A 264 1.96e+01 1zzoA 136 1.96e+01 1b4bA 71 1.99e+01 1b4aA d.74.2.1 39718 1t13A 158 2.00e+01 1zdzA 302 2.00e+01 1bouB 302 2.01e+01 1bouB c.56.6.1 33859 2b7kA 200 2.03e+01 1us5A 314 2.03e+01 c.94.1.1 99856 1on0A 158 2.06e+01 d.108.1.1 87095 1tljA 213 2.06e+01 d.282.1.1 107126 1xwyA 264 2.07e+01 1jmtA 104 2.08e+01 d.58.7.3 63180 1eceA 358 2.10e+01 1eceA c.1.8.3 28813 1vkhA 273 2.13e+01 c.69.1.32 108662 1gegA 256 2.13e+01 1ybvA c.2.1.2 29888 1rkuA 206 2.15e+01 c.108.1.11 97627 1nzjA 298 2.17e+01 c.26.1.1 92377 1f3lA 321 2.19e+01 1g6q2 c.66.1.6 59630 1ztuA 341 2.20e+01 1iu8A 206 2.21e+01 c.56.4.1 71436 1x7oA 287 2.22e+01 1o1xA 155 2.23e+01 c.121.1.1 86553 1bdfA 235 2.25e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1eluA 390 2.26e+01 1elqA c.67.1.3 34434 1uk8A 282 2.27e+01 c.69.1.10 107907 1xo1A 291 2.28e+01 1exnA a.60.7.1,c.120.1.2 18086,33356 2oatA 439 2.29e+01 2dkb c.67.1.4 34452 1t64A 377 2.29e+01 c.42.1.2 106543 1o7nA 449 2.31e+01 b.33.1.2,d.129.3.3 81162,81163 1d3vA 323 2.31e+01 1d3vA c.42.1.1 32559 2cw5A 255 2.31e+01 2d00A 109 2.34e+01 2a8yA 270 2.38e+01 2b4aA 138 2.39e+01 1wjuA 100 2.46e+01 1o9gA 250 2.47e+01 c.66.1.29 86692 1r3sA 367 2.48e+01 c.1.22.1 96963 2choA 716 2.57e+01 1jztA 246 2.60e+01 c.104.1.1 63319 1erw 105 2.62e+01 1erv c.47.1.1 32745 1yp2A 451 2.62e+01 1e8cA 498 2.62e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1h6hA 143 2.63e+01 d.189.1.1 65681 1id1A 153 2.63e+01 1id1A c.2.1.9 62286 2faoA 309 2.67e+01 1erv 105 2.70e+01 1erv c.47.1.1 32743 1wstA 417 2.71e+01 1qo3C 137 2.72e+01 1qo3C d.169.1.1 42350 1y80A 210 2.74e+01 1tfr 305 2.75e+01 1tfr a.60.7.1,c.120.1.2 18081,33351 1sw6A 327 2.75e+01 1sw6A d.211.1.1 19176 2ffmA 91 2.77e+01 2fqxA 318 2.78e+01 2aebA 322 2.78e+01 1pu1A 94 2.81e+01 d.266.1.1 104307 1l2tA 235 2.82e+01 c.37.1.12 73514 1f9vA 347 2.84e+01 1bg2 c.37.1.9 59745 1j27A 102 2.86e+01 d.58.50.1 90778 1gadO 330 2.88e+01 1dssG c.2.1.3,d.81.1.1 29950,39865 1cl1A 395 2.88e+01 1cl2A c.67.1.3 34395 1ru3A 732 2.88e+01 e.26.1.3 97835 1zejA 293 2.88e+01 2dchX 216 2.89e+01 1c0pA 363 2.91e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 2ge3A 170 2.93e+01 1uirA 314 2.93e+01 c.66.1.17 99429 1sgwA 214 2.95e+01 c.37.1.12 105541 1bazA 53 2.98e+01 1bazA a.43.1.1 17421 1hfeL 421 3.00e+01 1fehA c.96.1.1,d.58.1.5 36018,39001 1wlsA 328 3.02e+01 1b5pA 385 3.02e+01 c.67.1.1 90403 1hqz1 141 3.05e+01 1m7yA 435 3.14e+01 c.67.1.4 78761 1nrjB 218 3.15e+01 c.37.1.8 86125 1rkqA 282 3.20e+01 c.108.1.10 97621 2chnA 716 3.20e+01 1q45A 391 3.22e+01 c.1.4.1 95780 1nf2A 268 3.22e+01 c.108.1.10 91849 2c6qA 351 3.26e+01 1lc5A 364 3.27e+01 c.67.1.1 73827 1mzgA 146 3.27e+01 d.224.1.1 79696 1j0dA 341 3.29e+01 c.79.1.1 83902 3pmgA 561 3.32e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1f08A 148 3.32e+01 1f08A d.89.1.2 59564 1t0hB 224 3.33e+01 c.37.1.1 106208 2f51A 118 3.38e+01 2dc4A 165 3.43e+01 1g0cA 364 3.43e+01 7a3hA c.1.8.3 60165 1rxyA 253 3.47e+01 c.56.2.1 98065 2fiqA 420 3.49e+01 1zuoA 186 3.56e+01 1i76A 163 3.56e+01 1hfc d.92.1.11 61877 2bikB 313 3.60e+01 1h3fA 432 3.61e+01 c.26.1.1,d.66.1.4 76631,76632 1o58A 303 3.64e+01 c.79.1.1 92491 1iz6A 138 3.69e+01 b.34.5.2,b.40.4.5 76976,76977 1mwmA 320 3.70e+01 c.55.1.1,c.55.1.1 79580,79581 2glfA 450 3.70e+01 2fa8A 105 3.71e+01 1dbiA 280 3.74e+01 1gci c.41.1.1 32543 1ftrA 296 3.74e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1yacA 208 3.75e+01 1yacA c.33.1.3 31757 1qahA 136 3.81e+01 d.79.1.1 96338 1fcdA 401 3.82e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1sg4A 260 3.86e+01 1mg7A 417 3.88e+01 d.14.1.6,d.58.26.6 84954,84955 1pxfA 111 3.89e+01 b.40.4.4 88341 1fm0E 150 3.90e+01 1fmaE d.41.5.1 38629 1r62A 160 3.91e+01 d.122.1.3 104816 1itxA 419 3.91e+01 c.1.8.5,d.26.3.1 71425,71426 2aamA 309 3.91e+01 2eifA 136 3.92e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1ysrA 150 3.93e+01 2ao9A 155 3.97e+01 1ymqA 261 3.98e+01 1mzbA 136 4.02e+01 a.4.5.42 91497 1zin 217 4.10e+01 1zin c.37.1.1,g.41.2.1 31915,45178 1j5wA 298 4.11e+01 d.104.1.1 71589 2fsrA 195 4.11e+01 1xdpA 687 4.12e+01 1tqjA 230 4.13e+01 c.1.2.2 107228 1wcgA 464 4.14e+01 2ap1A 327 4.15e+01 1w8sA 263 4.16e+01 2ajrA 331 4.23e+01 1geqA 248 4.24e+01 2tysA c.1.2.4 28589 2a2pA 129 4.24e+01 2g2cA 167 4.25e+01 1i58A 189 4.28e+01 1b3qA d.122.1.3 61773 1oaa 259 4.30e+01 1oaa c.2.1.2 29829 2bycA 137 4.34e+01 1t4aA 84 4.34e+01 d.284.1.1 106404 2f1fA 164 4.43e+01 1sc6A 404 4.55e+01 2a0mA 316 4.57e+01 1vplA 256 4.58e+01 1k3rA 268 4.67e+01 b.40.4.10,c.116.1.2 72018,72019 1h6kZ 98 4.71e+01 d.58.7.1 60686 1np7A 489 4.73e+01 a.99.1.1,c.28.1.1 80677,80678 1oc2A 348 4.74e+01 c.2.1.2 92765 2erxA 172 4.75e+01 1nkqA 259 4.76e+01 d.177.1.1 103862 1ixcA 294 4.76e+01 a.4.5.37,c.94.1.1 83764,83765 2an9A 207 4.77e+01 1mqiA 263 4.79e+01 c.94.1.1 91398 1ws0A 156 4.84e+01 2a1iA 146 4.85e+01 1vkmA 297 4.86e+01 c.138.1.1 108670 1qtnA 164 4.87e+01 1pauA c.17.1.1 30999 1oo0B 110 4.90e+01 d.58.7.1 87183 3sdhA 146 4.92e+01 3sdhA a.1.1.2 14984 1xq6A 253 5.05e+01 2a5hA 416 5.05e+01 1m2oA 768 5.11e+01 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1yloA 348 5.14e+01 1ta3A 274 5.14e+01 c.1.8.5 106731 1obfO 335 5.16e+01 c.2.1.3,d.81.1.1 86768,86769 1o66A 275 5.17e+01 c.1.12.8 92547 1jcfA 344 5.19e+01 c.55.1.1,c.55.1.1 62878,62879 1jmkC 230 5.19e+01 c.69.1.22 71747 1em8B 112 5.22e+01 c.126.1.1 90458 1vefA 395 5.22e+01 1g3qA 237 5.29e+01 1hyqA c.37.1.10 60237 1kicA 339 5.35e+01 c.70.1.1 72510 1j1lA 290 5.40e+01 b.82.1.12 90766 1wf3A 301 5.46e+01 1w3oA 216 5.51e+01 1r7aA 504 5.56e+01 b.71.1.1,c.1.8.1 97192,97193 1d3yA 301 5.58e+01 1d3yA e.12.1.1 43252 1xubA 298 5.61e+01 1zu4A 320 5.63e+01 1nvmB 312 5.67e+01 c.2.1.3,d.81.1.1 86251,86252 2c82A 413 5.69e+01 1z47A 355 5.69e+01 1zbsA 291 5.69e+01 1y93A 159 5.71e+01 2ch4A 320 5.72e+01 1xrtA 467 5.74e+01 1svy 114 5.76e+01 1svy d.109.1.1 40831 1qgvA 142 5.78e+01 1qgvA c.47.1.8 33056 2bitX 165 5.82e+01 1xo0A 324 5.86e+01 1n4qB 377 5.87e+01 a.102.4.3 91636 1d2mA 665 5.92e+01 1d2mA c.37.1.19,c.37.1.19 32417,32418 1oqvA 192 5.93e+01 d.24.1.2 87320 1eu1A 780 6.00e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1z08A 170 6.00e+01 1i4uA 181 6.02e+01 b.60.1.1 61732 1zndA 174 6.04e+01 1vr4A 103 6.07e+01 1efpB 252 6.08e+01 1efvB c.26.2.3 31636 1qh8B 519 6.10e+01 1qguB c.92.2.3 35634 2ivyA 101 6.11e+01 1qwdA 177 6.12e+01 b.60.1.1 96471 1ja9A 274 6.12e+01 c.2.1.2 62817 1y0zA 330 6.16e+01 1ursA 402 6.23e+01 c.94.1.1 99833 1avqA 228 6.25e+01 1avqA c.52.1.13 33326 1st9A 143 6.28e+01 c.47.1.10 98987 1pyoA 167 6.29e+01 c.17.1.1 95370 1ppjB 439 6.39e+01 d.185.1.1,d.185.1.1 104254,104255 1senA 164 6.41e+01 c.47.1.1 105465 1sviA 195 6.44e+01 c.37.1.8 106048 1ofuX 119 6.48e+01 c.37.1.22 86976 1lvwA 295 6.51e+01 c.68.1.6 84723 2c2nA 339 6.61e+01 2f4nA 273 6.67e+01 1w2fA 276 6.69e+01 d.143.1.3 109125 1wy2A 351 6.69e+01 1wdiA 345 6.78e+01 1gefA 123 6.89e+01 1gefA c.52.1.18 60465 1qjcA 158 6.89e+01 1b6tA c.26.1.3 63328 2d0oA 610 6.89e+01 1nqkA 381 6.89e+01 c.1.16.4 92050 2a97A 439 6.90e+01 1qh4A 380 6.92e+01 1qh4A a.83.1.1,d.128.1.2 18462,41197 1xppA 115 6.93e+01 1iukA 140 6.95e+01 c.2.1.8 83712 1iuz 98 6.95e+01 1plc b.6.1.1 22861 1xaoA 121 6.95e+01 1zosA 230 6.96e+01 1hm9A 468 7.02e+01 b.81.1.4,c.68.1.5 65866,65867 1y42X 392 7.02e+01 1wy7A 207 7.03e+01 1fvgA 199 7.07e+01 1fvaA d.58.28.1 39408 2gzxA 265 7.08e+01 1nu4A 97 7.12e+01 d.58.7.1 80731 1fjgP 88 7.15e+01 1emwA d.27.1.1 38444 1zxtA 76 7.16e+01 2cbzA 237 7.17e+01 2c1lA 358 7.18e+01 1auiB 169 7.21e+01 1auiB a.39.1.5 17325 1puiA 210 7.23e+01 c.37.1.8 88292 1qy1A 174 7.23e+01 b.60.1.1 96568 1wxiA 275 7.25e+01 1qysA 106 7.27e+01 k.41.1.1 96603 1kt6A 183 7.30e+01 b.60.1.1 84466 1g2rA 100 7.33e+01 1g2rA d.192.1.1 60231 2cpgA 45 7.35e+01 2cpgA a.43.1.3 17455 1pc6A 146 7.42e+01 d.262.1.1 94430 1d7uA 433 7.44e+01 2dkb c.67.1.4 34439 1r8sA 164 7.44e+01 c.37.1.8 97247 1rhs 296 7.46e+01 1rhs c.46.1.2,c.46.1.2 32703,32704 2ffeA 311 7.48e+01 1xvaA 292 7.49e+01 1xvaA c.66.1.5 34183 2au3A 407 7.52e+01 2vhbA 146 7.54e+01 2vhbA a.1.1.2 15629 7odcA 424 7.58e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1zud1 251 7.61e+01 1wa3A 205 7.64e+01 1c4oA 664 7.65e+01 1d2mA c.37.1.19,c.37.1.19 32415,32416 2g7jA 124 7.65e+01 1hjsA 332 7.66e+01 c.1.8.3 83492 1z41A 338 7.66e+01 1i60A 278 7.67e+01 c.1.15.4 71118 1yirA 408 7.68e+01 1augA 215 7.69e+01 1a2zA c.56.4.1 33798 1yzvA 204 7.69e+01 1dbqA 289 7.76e+01 1qpzA c.93.1.1 35666 1iu4A 331 7.78e+01 d.3.1.8 71430 1ng6A 148 7.80e+01 a.182.1.1 85670 1u8fO 335 7.82e+01 1cseI 71 7.82e+01 1egpA d.40.1.1 38559 1y9aA 360 7.83e+01 1oz9A 150 7.84e+01 d.92.1.15 93808 1jksA 294 7.87e+01 d.144.1.7 71710 1guzA 310 7.88e+01 c.2.1.5,d.162.1.1 65586,65587 1zz1A 369 7.90e+01 2d1sA 548 7.90e+01 1m1hA 248 7.94e+01 b.114.1.1,d.58.42.1 78415,78416 1e6yC 247 7.98e+01 1mroC d.58.31.1 39441 1cvrA 435 8.01e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1nrzA 164 8.09e+01 c.38.1.1 86131 1s4iA 175 8.10e+01 1m8aA 70 8.11e+01 d.9.1.1 74579 1jftA 340 8.13e+01 a.35.1.5,c.93.1.1 66652,66653 1vbkA 307 8.13e+01 1rybA 212 8.15e+01 c.56.3.1 98098 1uozA 315 8.15e+01 2f96A 224 8.20e+01 1g5cA 170 8.20e+01 1g5cA c.53.2.1 60264 1tzjA 338 8.21e+01 1osdA 72 8.22e+01 d.58.17.1 104022 2akoA 251 8.22e+01 1y81A 138 8.23e+01 1ppjA 446 8.26e+01 d.185.1.1,d.185.1.1 104252,104253 1vggA 161 8.27e+01 1vjlA 164 8.34e+01 d.257.1.1 100822 1b25A 619 8.35e+01 1b25A a.110.1.1,d.152.1.1 19044,41796 2bkrA 212 8.36e+01 1u53A 196 8.42e+01 2dcnA 311 8.43e+01 1s12A 94 8.46e+01 2f9sA 151 8.52e+01 1epxA 370 8.52e+01 1fbaA c.1.10.1 29150 1l5xA 280 8.52e+01 c.106.1.1 77718 1xtmA 175 8.52e+01 1nd4A 264 8.53e+01 d.144.1.6 91815 2bwvA 440 8.54e+01 1e5pA 151 8.55e+01 1bj7 b.60.1.1 59272 1o0iA 138 8.58e+01 d.38.1.5 86532 1xdfA 157 8.64e+01 1ys7A 233 8.64e+01 2erfA 209 8.79e+01 1lq9A 112 8.82e+01 d.58.4.3 78129 1rm8A 169 8.84e+01 d.92.1.11 97660 1tr9A 341 8.85e+01 1wexA 104 8.91e+01 1vqsA 116 8.96e+01