# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1y1xA 191 3.30e-01 1u4bA 580 4.47e-01 c.55.3.5,e.8.1.1 107664,107665 2awiA 317 4.67e-01 1f45B 197 6.34e-01 1f45B a.26.1.1 59642 1ywfA 296 6.56e-01 1v4eA 299 7.31e-01 a.128.1.1 100296 1nk4A 580 7.75e-01 c.55.3.5,e.8.1.1 91923,91924 1ihgA 370 1.43e+00 2cpl a.118.8.1,b.62.1.1 62380,62381 1l3sA 580 1.44e+00 c.55.3.5,e.8.1.1 84521,84522 1f5nA 592 1.48e+00 1dg3A a.114.1.1,c.37.1.8 19077,32152 1ewqA 765 1.51e+00 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1oxjA 173 1.75e+00 a.60.1.2,a.118.1.13 87517,87518 1xwl 580 2.08e+00 1xwl c.55.3.5,e.8.1.1 33708,43001 1ybdA 239 2.25e+00 2grrB 170 2.26e+00 1f60A 458 2.54e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 2al6A 375 2.57e+00 1huxA 270 2.60e+00 1huxA c.55.1.5 61278 1yt3A 375 2.67e+00 1h96A 182 3.16e+00 2fha a.25.1.1 60811 1alvA 173 3.31e+00 1alvA a.39.1.8 17370 4tmkA 213 3.41e+00 5tmpA c.37.1.1 31930 2gyqA 175 3.48e+00 1ylmA 144 3.82e+00 1au1A 166 4.13e+00 1ifa a.26.1.3 16889 1u5tB 169 4.23e+00 a.4.5.54,a.4.5.54 107686,107687 2fgeA 995 4.34e+00 1sz9A 144 4.40e+00 a.118.9.4 106139 1lb3A 182 4.96e+00 a.25.1.1 77873 1z77A 200 5.11e+00 1dat 174 5.15e+00 2fha a.25.1.1 16677 1ykuA 136 5.15e+00 1xg7A 250 5.74e+00 1paqA 189 5.82e+00 a.118.1.14 94413 1ry6A 360 5.86e+00 c.37.1.9 98090 2anxA 146 6.15e+00 1k94A 165 6.24e+00 a.39.1.8 68333 1k07A 263 6.74e+00 d.157.1.1 77218 1b79A 119 7.07e+00 1b79A a.81.1.1 18451 2aehA 369 7.37e+00 2g3kA 94 7.43e+00 1rcwA 231 7.44e+00 a.132.1.4 97299 1t3wA 148 7.52e+00 1po5A 476 7.57e+00 a.104.1.1 94963 1puoA 170 7.62e+00 a.101.1.1,a.101.1.1 95134,95135 1v7bA 185 7.66e+00 1nfvA 179 7.93e+00 a.25.1.1 85642 1m8jA 181 8.43e+00 c.26.1.3 84875 1d8bA 81 8.47e+00 1d8bA a.60.8.1 18094 1b3uA 588 9.15e+00 1b3uA a.118.1.2 19135 2bnxA 386 9.43e+00 1rw1A 114 9.55e+00 5eau 548 9.56e+00 5eat a.102.4.1,a.128.1.3 18851,19443 1jykA 254 9.77e+00 c.68.1.13 67458 1colA 204 9.81e+00 1a87 f.1.1.1 43378 1dmtA 696 1.01e+01 1dmtA d.92.1.4 40296 2genA 197 1.03e+01 1ho8A 480 1.06e+01 1ho8A a.118.1.9 61107 1trkA 680 1.09e+01 1trkA c.36.1.10,c.36.1.6,c.48.1.1 31803,31804,33090 1b5tA 275 1.10e+01 1b5tA c.1.23.1 29676 1eg3A 261 1.14e+01 1eg3A a.39.1.7,a.39.1.7,b.72.1.1 17376,17377,27805 1l8nA 679 1.16e+01 c.1.8.10,d.92.2.2 84564,84565 1wudA 89 1.17e+01 2guhA 214 1.21e+01 2fha 183 1.23e+01 2fha a.25.1.1 16674 1w8iA 156 1.25e+01 1wtyA 119 1.29e+01 1gpuA 680 1.31e+01 c.36.1.10,c.36.1.6,c.48.1.1 65454,65455,65456 2choA 716 1.32e+01 1fm9D 272 1.36e+01 2prgA a.123.1.1 19313 1sqnA 261 1.40e+01 a.123.1.1 105944 2a84A 300 1.43e+01 1sr7A 259 1.43e+01 a.123.1.1 105957 2auwA 170 1.44e+01 2h1rA 299 1.46e+01 1gg1A 350 1.47e+01 1qr7A c.1.10.4 29187 1jeyA 609 1.47e+01 1jeqA b.131.1.1,c.62.1.3 90370,90371 1mqsA 671 1.49e+01 e.25.1.1 79414 1ovlA 271 1.50e+01 a.123.1.1 87455 1va6A 518 1.53e+01 1zgyA 272 1.56e+01 1a6i 217 1.58e+01 2tct a.4.1.9,a.121.1.1 16066,19243 1aisB 200 1.61e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 1aua 296 1.61e+01 1aua a.5.3.1,c.13.1.1 16290,30882 1yoyA 175 1.68e+01 1a28A 256 1.74e+01 1a28A a.123.1.1 19290 2ff4A 388 1.76e+01 1ow4A 129 1.82e+01 a.39.2.1 93628 1tp4A 97 1.82e+01 a.189.1.1 107183 1bm9A 122 1.85e+01 1bm9A a.4.5.7 16116 1ei7A 158 1.85e+01 1rmvA a.24.5.1 16584 1xjzA 233 1.89e+01 1jpzA 473 1.90e+01 a.104.1.1 67069 1ef1A 294 1.91e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16368,27003,37611 1mhqA 148 1.95e+01 a.118.9.2 84973 1oe9A 795 1.96e+01 b.34.3.1,c.37.1.9 92792,92793 1un8A 552 2.02e+01 c.119.1.2,a.208.1.1 103806,99661 1q4mA 221 2.02e+01 a.132.1.3 95805 1afrA 345 2.03e+01 1afrA a.25.1.2 16805 2ahqA 76 2.06e+01 1em9A 154 2.10e+01 1d1dA a.73.1.1 18333 1eumA 165 2.15e+01 1eumA a.25.1.1 59507 1ks9A 291 2.15e+01 a.100.1.7,c.2.1.6 68857,68858 1w7jA 795 2.19e+01 1ej5A 107 2.21e+01 1ej5A a.68.1.1 18268 1htjF 210 2.22e+01 1htjF a.91.1.1 61254 2gtqA 867 2.22e+01 2chnA 716 2.23e+01 1zb1A 392 2.25e+01 1r1hA 696 2.30e+01 d.92.1.4 104756 1np7A 489 2.37e+01 a.99.1.1,c.28.1.1 80677,80678 1n45A 233 2.38e+01 a.132.1.1 79981 1sqgA 429 2.38e+01 a.79.1.3,c.66.1.38 105912,105913 1us7B 265 2.40e+01 a.205.1.1 99858 2f2gA 221 2.41e+01 1w33A 181 2.46e+01 2gwxA 267 2.49e+01 2prgA a.123.1.1 19323 1xiuA 230 2.50e+01 1foeA 377 2.50e+01 1foeA a.87.1.1,b.55.1.1 18517,26969 1t13A 158 2.51e+01 1di0A 158 2.60e+01 1di0A c.16.1.1 30957 1ois 223 2.61e+01 1a36A e.15.1.1 43267 1nksA 194 2.63e+01 1nksA c.37.1.1 31886 1n46A 258 2.83e+01 a.123.1.1 85315 1qq8A 214 2.87e+01 1qq8A 2dfkA 402 2.89e+01 1i27A 73 2.92e+01 1i27A a.4.5.30 61555 1zavA 180 3.03e+01 1w36C 1122 3.04e+01 1p4xA 250 3.08e+01 a.4.5.28,a.4.5.28 87784,87785 1nogA 177 3.09e+01 a.25.2.2 85923 1wdcC 156 3.11e+01 1wdcC a.39.1.5 17317 1bu7A 455 3.12e+01 1bu7A a.104.1.1 18937 1yqgA 263 3.13e+01 1hw1A 239 3.13e+01 1e2xA a.4.5.6,a.78.1.1 16111,18441 1jr5A 90 3.17e+01 a.150.1.1 67113 1or7A 194 3.20e+01 a.4.13.2,a.177.1.1 87332,87333 1qs0A 407 3.23e+01 1qs0A c.36.1.11 31829 1o17A 345 3.30e+01 a.46.2.1,c.27.1.1 80765,80766 1oq9A 363 3.31e+01 a.25.1.2 87257 2evwX 166 3.31e+01 1ej2A 181 3.33e+01 1f9aA c.26.1.3 59414 1lqtA 456 3.34e+01 c.3.1.1,c.4.1.1 74198,74199 1a17 166 3.35e+01 1a17 a.118.8.1 19206 1s4bP 674 3.39e+01 d.92.1.5 105252 1oyzA 280 3.39e+01 a.118.1.16 93775 1v5eA 590 3.41e+01 1nqkA 381 3.42e+01 c.1.16.4 92050 1b8dA 164 3.43e+01 1cpcA a.1.1.3 15665 1ftkA 279 3.46e+01 1gr2A c.94.1.1 35819 1e17A 150 3.52e+01 2hfh a.4.5.14 16143 1e2aA 105 3.56e+01 1e2aA a.7.2.1 16322 1vdyA 140 3.59e+01 1mkmA 249 3.60e+01 a.4.5.33,d.110.2.2 79242,79243 1f9aA 168 3.62e+01 1f9aA c.26.1.3 31602 2bg5A 324 3.64e+01 1oe4A 247 3.65e+01 c.18.1.3 86895 1rxqA 178 3.74e+01 a.213.1.1 105118 2a9uA 144 3.76e+01 5csmA 256 3.81e+01 5csmA a.130.1.2 19494 2a65A 519 3.81e+01 1mho 88 3.82e+01 1b4cA a.39.1.2 17171 2h21A 440 3.89e+01 1wixA 164 3.91e+01 1iw0A 215 3.92e+01 a.132.1.1 83720 1qjcA 158 4.03e+01 1b6tA c.26.1.3 63328 1zrzA 364 4.04e+01 1n8fA 350 4.12e+01 c.1.10.4 85397 1ummA 172 4.15e+01 a.3.1.1 107958 1jyeA 349 4.21e+01 c.93.1.1 67455 1q8fA 313 4.25e+01 c.70.1.1 96203 2aq8A 269 4.26e+01 1h6zA 913 4.26e+01 c.1.12.2,c.8.1.1,d.142.1.5 70906,70907,70908 1p36A 164 4.27e+01 d.2.1.3 93978 2c8sA 172 4.31e+01 1rcd 173 4.31e+01 2fha a.25.1.1 16687 1i0vA 104 4.45e+01 9rnt d.1.1.4 36054 1rvgA 305 4.48e+01 c.1.10.2 97920 1ki9A 192 4.49e+01 c.37.1.1 84404 1o2dA 371 4.55e+01 e.22.1.2 86591 2etdA 171 4.58e+01 1fgs 428 4.66e+01 1fgs c.59.1.2,c.72.2.2 33959,34962 1jtvA 327 4.68e+01 c.2.1.2 84230 1in4A 334 4.68e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 1m32A 366 4.70e+01 c.67.1.3 78508 1lvfA 110 4.71e+01 a.47.2.1 74280 1j77A 209 4.72e+01 1j77A a.132.1.2 62674 1uhnA 189 4.78e+01 a.39.1.5 99399 1a9xA 1058 4.80e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1cf9A 753 4.88e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 1ctqA 166 4.91e+01 1ctqA c.37.1.8 31965 1m45A 148 4.95e+01 a.39.1.5 78598 1zp4A 304 5.01e+01 1qkrA 188 5.05e+01 1qkrA a.24.9.1 16628 1jeyB 565 5.07e+01 1jeqB b.131.1.2,c.62.1.4 90372,90373 1umdA 367 5.09e+01 c.36.1.11 99599 1omhA 293 5.11e+01 d.89.1.5 93348 1yvhA 329 5.12e+01 1wzdA 215 5.13e+01 1rlzA 369 5.13e+01 c.31.1.1 104989 1c1kA 217 5.14e+01 1c1kA a.120.1.1 19239 1zm7A 230 5.15e+01 1ujkA 147 5.18e+01 a.118.9.2 99457 1gqiA 708 5.25e+01 c.1.8.10,d.92.2.2 76279,76280 1dhpA 292 5.29e+01 1dhpA c.1.10.1 29097 1pk1B 89 5.37e+01 1in6A 334 5.40e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 2lisA 136 5.42e+01 1lis a.19.1.1 16405 1zl8A 53 5.44e+01 1i2oA 316 5.58e+01 1onrA c.1.10.1 61574 1xqoA 256 5.60e+01 1xk4A 93 5.79e+01 1e19A 314 5.80e+01 1b7bA c.73.1.1 34967 1iqrA 420 5.92e+01 a.99.1.1,c.28.1.1 66275,66276 1gvnB 287 6.06e+01 c.37.1.21 76354 1hb6A 86 6.08e+01 a.11.1.1 70959 1r0vA 305 6.12e+01 c.52.2.1,c.52.2.1,d.75.1.1 96742,96743,96744 1jbwA 428 6.17e+01 c.59.1.2,c.72.2.2 62860,62861 1o3uA 135 6.17e+01 a.24.16.3 86615 1fds 327 6.18e+01 1fds c.2.1.2 29838 1mr8A 93 6.21e+01 1b4cA a.39.1.2 17186 1od6A 160 6.25e+01 c.26.1.3 86836 1wsrA 375 6.27e+01 1cs0A 1073 6.38e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 2gi3A 476 6.38e+01 1qhlA 227 6.44e+01 1qhlA c.37.1.12 32382 1tlfA 301 6.45e+01 1tlfA c.93.1.1 35687 2an3A 289 6.48e+01 1iqvA 218 6.48e+01 1rss a.75.1.1 62661 2ayvA 166 6.49e+01 1z5hA 780 6.51e+01 1lis 136 6.59e+01 1lis a.19.1.1 16406 1y1nA 291 6.65e+01 1qv9A 283 6.66e+01 c.127.1.1 96356 1lw9A 164 6.73e+01 d.2.1.3 84727 2a6nA 292 6.75e+01 1szqA 483 6.76e+01 e.44.1.1 99045 1yxcA 292 6.81e+01 1z9hA 290 6.90e+01 2bbhA 269 6.91e+01 1p0yA 444 6.91e+01 a.166.1.1,b.85.7.3 87654,87655 1orsC 132 6.96e+01 f.14.1.1 87353 1q0qA 406 6.98e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1mvwC 147 6.98e+01 i.15.1.1 79525 1b7yB 785 7.12e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16301,16302,25312,39311,40780,41456 1eny 268 7.12e+01 1eny c.2.1.2 29910 1qgtA 149 7.24e+01 1qgtA a.62.1.1 18135 1yovA 537 7.25e+01 1rtxA 123 7.30e+01 a.1.1.1 97827 1ll2A 333 7.33e+01 c.68.1.14 74005 1np8A 159 7.36e+01 a.39.1.8 92022 1wy2A 351 7.38e+01 1ekeA 230 7.41e+01 1ekeA c.55.3.1 33572 1sx7A 164 7.47e+01 1mixA 206 7.47e+01 a.11.2.1,b.55.1.5 79166,79167 1onrA 316 7.50e+01 1onrA c.1.10.1 29169 1re9A 414 7.50e+01 2h58A 330 7.51e+01 1u3dA 509 7.52e+01 a.99.1.1,c.28.1.1 107638,107639 2cbiA 594 7.53e+01 1yfsA 465 7.58e+01 1i7kA 179 7.59e+01 1u9aA d.20.1.1 61889 2grrA 161 7.60e+01 2kfnA 605 7.61e+01 1xwl c.55.3.5,e.8.1.1 33682,42975 1a6s 87 7.63e+01 1a6s a.61.1.4 18134 1y74A 57 7.63e+01 1vf1A 229 7.71e+01 1kkhA 317 7.71e+01 d.14.1.5,d.58.26.3 72645,72646 1dik 874 7.87e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 119l 164 7.88e+01 1l92 d.2.1.3 36622 1ryp2 233 7.89e+01 1ryp2 1a8b 318 7.89e+01 1avc a.65.1.1 18171 2b3hA 329 7.89e+01 2a0iA 330 7.92e+01 1ehkA 562 7.93e+01 1ehkA f.24.1.1 43624 1jwgA 147 8.01e+01 a.118.9.2 71911 2fbqA 235 8.05e+01 1swyA 164 8.10e+01 1f44A 324 8.20e+01 a.60.9.1,d.163.1.1 64982,64983 1sv0C 82 8.26e+01 a.60.1.1 106037 1nowA 507 8.30e+01 c.1.8.6,d.92.2.1 85936,85937 1fc3A 120 8.39e+01 1fc3A a.4.6.3 16237 1vhzA 198 8.41e+01 d.113.1.1 100718 1o9iA 266 8.43e+01 a.25.1.3 92671 2a6lA 292 8.45e+01 1dhs 344 8.45e+01 1dhs c.31.1.1 31727 2akaB 299 8.46e+01 2tct 207 8.54e+01 2tct a.4.1.9,a.121.1.1 16063,19240 1sheA 103 8.58e+01 d.274.1.1 105551 2ge7A 108 8.59e+01 1om2A 95 8.63e+01 1om2A a.23.4.1 16520 1f9vA 347 8.64e+01 1bg2 c.37.1.9 59745 1yh6A 179 8.73e+01 1r9jA 673 8.75e+01 1khtA 192 8.77e+01 c.37.1.1 84401 1dpe 507 8.80e+01 1dpe c.94.1.1 35799 1zbmA 280 8.85e+01 1ynbA 173 8.85e+01 1w5cF 44 8.89e+01 1jfbA 404 8.96e+01 a.104.1.1 66624 1ksoA 101 8.97e+01 a.39.1.2 72926