# List of top-scoring protein chains for t2k-100-30-near-backbone-11-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 1pvvA 315 4.39e-01 c.78.1.1,c.78.1.1 95190,95191 1a1s 314 5.55e-01 1othA c.78.1.1,c.78.1.1 35258,35259 1xc3A 302 5.98e-01 1df3A 162 6.39e-01 1mup b.60.1.1 27134 1i05A 180 8.81e-01 1mup b.60.1.1 27130 1i06A 180 9.87e-01 1mup b.60.1.1 27131 1jv4A 162 1.03e+00 b.60.1.1 67343 1qy1A 174 1.03e+00 b.60.1.1 96568 1wqaA 455 1.09e+00 1zndA 174 1.18e+00 1fps 348 1.86e+00 1uby a.128.1.1 19436 1aoxA 203 2.16e+00 1aoxA c.62.1.1 34151 1mup 166 2.31e+00 1mup b.60.1.1 27133 2lbd 267 2.55e+00 2lbd a.123.1.1 19287 1vjeA 166 3.70e+00 d.185.1.2 100807 1fcyA 236 3.70e+00 2lbd a.123.1.1 19282 1innA 166 3.74e+00 1j98A d.185.1.2 62608 1yseA 141 3.78e+00 1mylA 53 3.78e+00 1bazA a.43.1.1 17427 1gm6A 175 3.93e+00 b.60.1.1 70272 1uby 367 4.03e+00 1uby a.128.1.1 19435 1mykA 53 4.23e+00 1bazA a.43.1.1 17425 1parA 53 4.31e+00 1bazA a.43.1.1 17437 1bdtA 53 4.50e+00 1bazA a.43.1.1 17433 1v7pC 200 4.68e+00 c.62.1.1 108408 1k2fA 190 5.53e+00 b.8.1.2 68054 1bqbA 301 5.77e+00 1hyt d.92.1.2 58962 4lbd 267 5.81e+00 2lbd a.123.1.1 19289 1ws6A 171 6.17e+00 1hbq 183 6.38e+00 1aqb b.60.1.1 27078 1hbp 183 6.38e+00 1aqb b.60.1.1 27079 2gsq 202 6.47e+00 1pd21 a.45.1.1,c.47.1.5 17715,33009 1yemA 179 6.88e+00 1w44A 331 6.88e+00 1kx9A 112 7.35e+00 a.118.21.1 77602 2cpgA 45 7.47e+00 2cpgA a.43.1.3 17455 1z3eB 73 7.63e+00 1aqb 183 7.86e+00 1aqb b.60.1.1 27084 1q77A 138 8.14e+00 c.26.2.4 96023 1yv5A 374 8.23e+00 1kt6A 183 8.41e+00 b.60.1.1 84466 1nvmB 312 8.59e+00 c.2.1.3,d.81.1.1 86251,86252 2bj7A 138 9.30e+00 1bazA 53 9.45e+00 1bazA a.43.1.1 17421 1zpvA 91 9.92e+00 2dc4A 165 1.01e+01 1auiB 169 1.02e+01 1auiB a.39.1.5 17325 1a9r 282 1.07e+01 1b8oA c.56.2.1 33767 1a9s 289 1.08e+01 1b8oA c.56.2.1 33768 1yq7A 374 1.09e+01 2f94F 350 1.09e+01 1r45A 204 1.10e+01 1b01A 45 1.16e+01 2cpgA a.43.1.3 17458 2ivyA 101 1.20e+01 2aa1A 144 1.24e+01 1ri7A 171 1.24e+01 a.4.5.32,d.58.4.2 97504,97505 1odkA 235 1.26e+01 c.56.2.1 86863 2apoA 357 1.26e+01 1ew3A 159 1.32e+01 1mup b.60.1.1 27114 2a6sA 84 1.34e+01 2cunA 410 1.36e+01 1b8oA 284 1.37e+01 1b8oA c.56.2.1 33762 1a0i 348 1.39e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1lngA 87 1.53e+01 d.201.1.1 74045 3sdhA 146 1.64e+01 3sdhA a.1.1.2 14984 1ie9A 259 1.66e+01 1db1A a.123.1.1 62318 1iq8A 582 1.70e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1wj9A 211 1.71e+01 1op1A 82 1.76e+01 a.13.1.1 93396 8atcA 310 1.76e+01 3csuA c.78.1.1,c.78.1.1 35132,35133 2g5cA 281 1.80e+01 1a3yA 149 1.80e+01 1obpA b.60.1.1 27110 2a7oA 112 1.82e+01 1ru3A 732 1.83e+01 e.26.1.3 97835 1iwhB 146 1.84e+01 a.1.1.2 76883 1rbp 182 1.84e+01 1aqb b.60.1.1 27085 1d7kA 421 1.84e+01 7odcA b.49.2.3,c.1.6.1 26486,28648 1gen 218 1.86e+01 1gen b.66.1.1 27536 1ja9A 274 1.88e+01 c.2.1.2 62817 1dxtB 147 1.93e+01 1abwA a.1.1.2 15450 1tadA 324 2.00e+01 1cipA a.66.1.1,c.37.1.8 18194,32077 1a9t 284 2.01e+01 1b8oA c.56.2.1 33765 1at1A 310 2.05e+01 3csuA c.78.1.1,c.78.1.1 35168,35169 1ng4A 390 2.05e+01 c.3.1.2,d.16.1.3 85666,85667 2aeeA 211 2.07e+01 1a6q 382 2.08e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1a01B 146 2.11e+01 1abwA a.1.1.2 15448 3pnp 289 2.14e+01 1b8oA c.56.2.1 33763 2arhA 203 2.16e+01 1ekxA 311 2.22e+01 3csuA c.78.1.1,c.78.1.1 35088,35089 1dzkA 157 2.23e+01 1obpA b.60.1.1 27096 1babB 146 2.26e+01 1abwA a.1.1.2 15414 1ortA 335 2.27e+01 1othA c.78.1.1,c.78.1.1 35204,35205 1t3cA 421 2.28e+01 d.92.1.7 106343 1v2xA 194 2.30e+01 c.116.1.1 100274 2bjcA 62 2.36e+01 2d5xB 146 2.45e+01 1y6hA 177 2.46e+01 1c0pA 363 2.46e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 2ah6A 208 2.47e+01 1acmA 310 2.48e+01 3csuA c.78.1.1,c.78.1.1 35180,35181 2di4A 238 2.54e+01 1ffkI 194 2.56e+01 1ffkI d.12.1.2 37494 1db1A 259 2.56e+01 1db1A a.123.1.1 19329 1ryiA 382 2.57e+01 1tag 324 2.57e+01 1cipA a.66.1.1,c.37.1.8 18197,32080 1d1dA 262 2.59e+01 1d1dA a.28.3.1,a.73.1.1 16958,18335 1z8oA 404 2.65e+01 3csuA 310 2.75e+01 3csuA c.78.1.1,c.78.1.1 35094,35095 2bjiA 277 2.76e+01 1irdB 146 2.81e+01 a.1.1.2 66287 1k3xA 262 2.83e+01 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1q18A 332 2.84e+01 c.55.1.7,c.55.1.7 104470,104471 1imuA 107 2.87e+01 d.204.1.1 66218 1dekA 241 2.88e+01 1dekA c.37.1.1 31842 1othA 321 2.97e+01 1othA c.78.1.1,c.78.1.1 35260,35261 1lccA 51 2.98e+01 1pru a.35.1.5 17110 1g24A 211 3.00e+01 1g24A d.166.1.1 42270 1etc 110 3.00e+01 1awcA a.4.5.21 16162 1qwdA 177 3.04e+01 b.60.1.1 96471 1rzuA 485 3.04e+01 c.87.1.8 105140 1delA 241 3.06e+01 1dekA c.37.1.1 31844 1wdtA 665 3.06e+01 1a00B 146 3.09e+01 1abwA a.1.1.2 15469 1i3dA 146 3.18e+01 a.1.1.2 61587 1u96A 69 3.19e+01 1h54B 754 3.19e+01 a.102.1.4,b.30.5.3 60636,60637 1j7yB 146 3.23e+01 a.1.1.2 66427 1w1wA 430 3.27e+01 1phk 298 3.30e+01 1cdkA d.144.1.7 41635 1pt6A 213 3.31e+01 c.62.1.1 95091 1m2oB 190 3.31e+01 c.37.1.8 78485 2a9kB 223 3.31e+01 1bj7 156 3.35e+01 1bj7 b.60.1.1 27113 1jipA 403 3.39e+01 a.104.1.1 66748 1lqc 56 3.45e+01 1pru a.35.1.5 17109 1kqqA 139 3.45e+01 a.4.3.1 72885 1or4A 178 3.52e+01 a.1.1.2 93447 1qc5A 192 3.55e+01 1aoxA c.62.1.1 34147 1b4cA 92 3.61e+01 1b4cA a.39.1.2 17169 1h54A 754 3.64e+01 a.102.1.4,b.30.5.3 60634,60635 1b4pA 217 3.65e+01 a.45.1.1,c.47.1.5 83158,83159 1jnrA 643 3.74e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1vd5A 377 3.77e+01 a.102.1.7 108518 1cmyB 146 3.77e+01 1abwA a.1.1.2 15544 1o5kA 306 3.83e+01 c.1.10.1 92504 1p4xA 250 3.85e+01 a.4.5.28,a.4.5.28 87784,87785 1vkhA 273 3.86e+01 c.69.1.32 108662 1uquA 482 3.87e+01 c.87.1.6 99796 1x71A 178 3.96e+01 2ac4A 309 4.03e+01 1imbA 277 4.13e+01 1imbA e.7.1.1 42957 1vmeA 410 4.13e+01 c.23.5.1,d.157.1.3 108893,108894 1tzzA 392 4.20e+01 1babA 143 4.24e+01 1abwA a.1.1.2 15235 1xviA 275 4.25e+01 2gj8A 172 4.28e+01 1uqtA 482 4.30e+01 c.87.1.6 99794 2fu2A 102 4.36e+01 2gsaA 432 4.37e+01 2gsaA c.67.1.4 34446 1tin 69 4.40e+01 2sniI d.40.1.1 38580 1em8A 147 4.49e+01 c.128.1.1 90457 2hhmA 276 4.54e+01 1imbA e.7.1.1 42955 1x89A 178 4.55e+01 1mit 69 4.55e+01 1hymA d.40.1.1 38582 1vbkA 307 4.56e+01 2bt2A 161 4.63e+01 2cyeA 133 4.67e+01 1yj7A 171 4.80e+01 1ehkA 562 4.89e+01 1ehkA f.24.1.1 43624 1yqfA 203 4.89e+01 1vehA 92 4.92e+01 1o54A 277 4.94e+01 c.66.1.13 92482 1qgdA 662 4.96e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 1ilk 151 4.97e+01 2ilk a.26.1.3 16886 1psqA 163 4.99e+01 c.47.1.10 88283 1urvA 190 5.15e+01 1ut0A 190 5.15e+01 a.1.1.2 108012 1avqA 228 5.17e+01 1avqA c.52.1.13 33326 2ac2A 309 5.18e+01 1w8iA 156 5.21e+01 1h1nA 305 5.25e+01 c.1.8.3 70855 1mzbA 136 5.25e+01 a.4.5.42 91497 1q3iA 214 5.25e+01 d.220.1.1 104524 1h91A 180 5.28e+01 b.60.1.1 60805 1cg5A 141 5.33e+01 1abwA a.1.1.2 15406 1iktA 120 5.38e+01 d.106.1.1 66188 2d0eA 407 5.41e+01 1voqa 90 5.42e+01 1i21A 159 5.44e+01 1i21A d.108.1.1 61549 1ne8A 117 5.44e+01 b.34.6.2 80424 1q7hA 153 5.46e+01 b.122.1.1,d.17.6.2 96042,96043 1xmeA 568 5.49e+01 1n9lA 109 5.54e+01 d.110.3.6 85468 1azo 232 5.55e+01 1azo c.52.1.14 33329 1sz2A 332 5.63e+01 1rfmA 344 5.67e+01 c.122.1.1 97385 2cviA 83 5.79e+01 1azsC 388 5.81e+01 1cipA a.66.1.1,c.37.1.8 18203,32086 1nrjB 218 5.81e+01 c.37.1.8 86125 1i4uA 181 5.81e+01 b.60.1.1 61732 1aba 87 5.86e+01 1aba c.47.1.1 32760 2d09A 407 5.88e+01 2fv1A 377 5.95e+01 1myt 146 5.97e+01 1a6m a.1.1.2 15207 1lj2A 110 6.04e+01 h.1.13.2 73926 1uaaA 673 6.07e+01 1pjr c.37.1.19,c.37.1.19 32401,32402 1uirA 314 6.09e+01 c.66.1.17 99429 1ov2A 99 6.09e+01 a.13.1.1 93580 1bjt 793 6.15e+01 1bjt e.11.1.1 43249 1s1fA 406 6.20e+01 1vfgA 390 6.26e+01 a.173.1.1,d.218.1.4 108570,108571 1l4sA 112 6.26e+01 d.204.1.1 77693 1svvA 359 6.26e+01 c.67.1.1 106054 1jmtA 104 6.29e+01 d.58.7.3 63180 1wh5A 80 6.33e+01 1fsz 372 6.33e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1gajA 257 6.34e+01 1gajA c.37.1.12 60416 1x1oA 286 6.35e+01 1ghhA 81 6.37e+01 1ghhA d.57.1.1 38940 1m2eA 135 6.42e+01 c.23.1.5 78478 1x1eA 239 6.46e+01 1zljA 78 6.46e+01 1spgA 144 6.47e+01 1abwA a.1.1.2 15409 1q67A 231 6.50e+01 b.55.1.7 95960 2cbiA 594 6.53e+01 1x6mA 196 6.54e+01 1cye 129 6.56e+01 3chy c.23.1.1 31077 2fjbA 643 6.57e+01 1rzrA 332 6.59e+01 1w77A 228 6.61e+01 1pbn 289 6.62e+01 1b8oA c.56.2.1 33771 1a41 234 6.62e+01 1a41 d.163.1.2 42174 1o6jA 150 6.64e+01 c.47.1.10 81089 1ztdA 133 6.66e+01 1ez1A 392 7.06e+01 1ez1A b.84.2.1,c.30.1.1,d.142.1.2 28248,31655,41500 1i1dA 161 7.12e+01 1i21A d.108.1.1 61526 1kjlA 146 7.17e+01 1uujA 88 7.33e+01 a.221.1.1 108046 1jnyA 435 7.36e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1lcdA 51 7.45e+01 1pru a.35.1.5 17111 1jjuA 489 7.50e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 66774,66775,66776,66777,66778 1c25 161 7.54e+01 1c25 c.46.1.1 32698 2a25A 193 7.56e+01 2bo3A 94 7.61e+01 1wozA 177 7.62e+01 1aab 83 7.66e+01 1cktA a.21.1.1 16420 1bqg 451 7.66e+01 1bqg c.1.11.2,d.54.1.1 29217,38861 2evaA 307 7.73e+01 1ak1 310 7.74e+01 1ak1 c.92.1.1 35594 1agjA 242 7.74e+01 1agjA b.47.1.1 25827 1abwA 283 7.80e+01 1abwA a.1.1.2,a.1.1.2 15288,15289 1vrpA 381 7.95e+01 1qxhA 167 8.13e+01 c.47.1.10 96528 1xyzA 347 8.19e+01 1taxA c.1.8.3 28804 1aazA 87 8.23e+01 1aba c.47.1.1 32761 1a3wA 500 8.28e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27060,29288,33142 1hcqA 84 8.29e+01 2nllB g.39.1.2 45117 1bebA 162 8.34e+01 1bebA b.60.1.1 27115 1tr8A 102 8.39e+01 7odcA 424 8.45e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1g6hA 257 8.47e+01 1gajA c.37.1.12 60318 1qqsA 174 8.48e+01 1nglA b.60.1.1 27143 2f5gA 133 8.56e+01 1wduA 245 8.58e+01 d.151.1.1 109286 1xqiA 195 8.61e+01 1l5wA 796 8.68e+01 c.87.1.4 73605 1wy1A 172 8.72e+01 1xouB 95 8.72e+01 1jfuA 186 8.74e+01 c.47.1.10 62940 1i12A 160 8.77e+01 1i21A d.108.1.1 61515 1irdA 141 8.78e+01 a.1.1.2 66286 1qhuA 460 8.80e+01 1qhuA b.66.1.1,b.66.1.1 27530,27531 1ys7A 233 8.89e+01 1ju2A 536 8.90e+01 c.3.1.2,d.16.1.1 77169,77170 1a9nB 96 8.91e+01 1urnA d.58.7.1 39165 1xngA 268 8.96e+01 5ukdA 194 9.00e+01 1zin c.37.1.1 31851