# 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 3.16e-01 c.78.1.1,c.78.1.1 95190,95191 1a1s 314 3.79e-01 1othA c.78.1.1,c.78.1.1 35258,35259 1wqaA 455 4.55e-01 1xc3A 302 7.50e-01 1df3A 162 1.30e+00 1mup b.60.1.1 27134 1fps 348 1.34e+00 1uby a.128.1.1 19436 1i05A 180 1.74e+00 1mup b.60.1.1 27130 2lbd 267 1.79e+00 2lbd a.123.1.1 19287 1i06A 180 2.05e+00 1mup b.60.1.1 27131 1qy1A 174 2.24e+00 b.60.1.1 96568 1jv4A 162 2.27e+00 b.60.1.1 67343 1fcyA 236 2.41e+00 2lbd a.123.1.1 19282 1zndA 174 2.46e+00 1uby 367 2.90e+00 1uby a.128.1.1 19435 4lbd 267 3.38e+00 2lbd a.123.1.1 19289 1aoxA 203 3.46e+00 1aoxA c.62.1.1 34151 1yseA 141 3.97e+00 2g5cA 281 4.08e+00 1yv5A 374 4.23e+00 1hbq 183 4.67e+00 1aqb b.60.1.1 27078 1hbp 183 4.83e+00 1aqb b.60.1.1 27079 2f94F 350 4.91e+00 2cpgA 45 4.93e+00 2cpgA a.43.1.3 17455 1ru3A 732 5.09e+00 e.26.1.3 97835 1mup 166 5.25e+00 1mup b.60.1.1 27133 1ja9A 274 5.26e+00 c.2.1.2 62817 1yq7A 374 5.32e+00 1zpvA 91 5.37e+00 1mykA 53 5.74e+00 1bazA a.43.1.1 17425 1k2fA 190 5.78e+00 b.8.1.2 68054 1aqb 183 5.80e+00 1aqb b.60.1.1 27084 1kt6A 183 5.93e+00 b.60.1.1 84466 1bqbA 301 5.99e+00 1hyt d.92.1.2 58962 1vjeA 166 6.34e+00 d.185.1.2 100807 1innA 166 6.44e+00 1j98A d.185.1.2 62608 1parA 53 6.48e+00 1bazA a.43.1.1 17437 1mylA 53 6.48e+00 1bazA a.43.1.1 17427 1bdtA 53 6.99e+00 1bazA a.43.1.1 17433 1v7pC 200 7.05e+00 c.62.1.1 108408 1w44A 331 7.16e+00 1b01A 45 7.29e+00 2cpgA a.43.1.3 17458 2aa1A 144 7.56e+00 1odkA 235 8.01e+00 c.56.2.1 86863 1gm6A 175 8.03e+00 b.60.1.1 70272 2bj7A 138 8.27e+00 1ng4A 390 8.60e+00 c.3.1.2,d.16.1.3 85666,85667 1kx9A 112 8.97e+00 a.118.21.1 77602 1d1dA 262 8.97e+00 1d1dA a.28.3.1,a.73.1.1 16958,18335 2gsq 202 9.11e+00 1pd21 a.45.1.1,c.47.1.5 17715,33009 1ws6A 171 9.13e+00 1z3eB 73 9.60e+00 2apoA 357 9.64e+00 1z8oA 404 9.64e+00 1ryiA 382 9.98e+00 2a6sA 84 1.07e+01 8atcA 310 1.09e+01 3csuA c.78.1.1,c.78.1.1 35132,35133 1jipA 403 1.10e+01 a.104.1.1 66748 2bjcA 62 1.10e+01 1ekxA 311 1.12e+01 3csuA c.78.1.1,c.78.1.1 35088,35089 1ew3A 159 1.18e+01 1mup b.60.1.1 27114 1q77A 138 1.20e+01 c.26.2.4 96023 1imuA 107 1.21e+01 d.204.1.1 66218 1wj9A 211 1.21e+01 1phk 298 1.21e+01 1cdkA d.144.1.7 41635 1vd5A 377 1.23e+01 a.102.1.7 108518 1ri7A 171 1.23e+01 a.4.5.32,d.58.4.2 97504,97505 1at1A 310 1.25e+01 3csuA c.78.1.1,c.78.1.1 35168,35169 1yemA 179 1.29e+01 1tadA 324 1.37e+01 1cipA a.66.1.1,c.37.1.8 18194,32077 1auiB 169 1.37e+01 1auiB a.39.1.5 17325 1dxtB 147 1.44e+01 1abwA a.1.1.2 15450 1d7kA 421 1.45e+01 7odcA b.49.2.3,c.1.6.1 26486,28648 1a01B 146 1.45e+01 1abwA a.1.1.2 15448 3csuA 310 1.46e+01 3csuA c.78.1.1,c.78.1.1 35094,35095 1nvmB 312 1.48e+01 c.2.1.3,d.81.1.1 86251,86252 1kqqA 139 1.51e+01 a.4.3.1 72885 1acmA 310 1.51e+01 3csuA c.78.1.1,c.78.1.1 35180,35181 1ffkI 194 1.51e+01 1ffkI d.12.1.2 37494 1iwhB 146 1.51e+01 a.1.1.2 76883 1iq8A 582 1.52e+01 c.1.20.1,b.122.1.1,d.17.6.1 71270,83074,83075 1babB 146 1.59e+01 1abwA a.1.1.2 15414 1w1wA 430 1.62e+01 1lccA 51 1.62e+01 1pru a.35.1.5 17110 1bazA 53 1.63e+01 1bazA a.43.1.1 17421 1t3cA 421 1.64e+01 d.92.1.7 106343 2ah6A 208 1.70e+01 2arhA 203 1.70e+01 1etc 110 1.72e+01 1awcA a.4.5.21 16162 1tag 324 1.76e+01 1cipA a.66.1.1,c.37.1.8 18197,32080 1lqc 56 1.77e+01 1pru a.35.1.5 17109 1a0i 348 1.78e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1pt6A 213 1.78e+01 c.62.1.1 95091 1c0pA 363 1.79e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1ortA 335 1.82e+01 1othA c.78.1.1,c.78.1.1 35204,35205 2fv1A 377 1.84e+01 1rbp 182 1.85e+01 1aqb b.60.1.1 27085 1irdB 146 1.87e+01 a.1.1.2 66287 1gen 218 1.88e+01 1gen b.66.1.1 27536 1a9s 289 1.90e+01 1b8oA c.56.2.1 33768 2a7oA 112 1.94e+01 1op1A 82 1.94e+01 a.13.1.1 93396 1jnrA 643 1.95e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1aba 87 1.97e+01 1aba c.47.1.1 32760 1bjt 793 1.98e+01 1bjt e.11.1.1 43249 2d5xB 146 2.01e+01 1babA 143 2.03e+01 1abwA a.1.1.2 15235 1r45A 204 2.05e+01 1b4pA 217 2.06e+01 a.45.1.1,c.47.1.5 83158,83159 2di4A 238 2.06e+01 1a9r 282 2.13e+01 1b8oA c.56.2.1 33767 1a00B 146 2.16e+01 1abwA a.1.1.2 15469 1voqa 90 2.20e+01 1v2xA 194 2.24e+01 c.116.1.1 100274 1a6q 382 2.26e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1ie9A 259 2.27e+01 1db1A a.123.1.1 62318 1b8oA 284 2.34e+01 1b8oA c.56.2.1 33762 1lngA 87 2.35e+01 d.201.1.1 74045 1j7yB 146 2.38e+01 a.1.1.2 66427 1p4xA 250 2.42e+01 a.4.5.28,a.4.5.28 87784,87785 1y6hA 177 2.49e+01 1qc5A 192 2.51e+01 1aoxA c.62.1.1 34147 1l4sA 112 2.51e+01 d.204.1.1 77693 1h54B 754 2.54e+01 a.102.1.4,b.30.5.3 60636,60637 1i3dA 146 2.54e+01 a.1.1.2 61587 1urvA 190 2.58e+01 1ut0A 190 2.58e+01 a.1.1.2 108012 1cmyB 146 2.59e+01 1abwA a.1.1.2 15544 2cunA 410 2.69e+01 1k3xA 262 2.73e+01 a.156.1.2,b.113.1.1,g.39.1.8 77242,77243,77244 1aazA 87 2.74e+01 1aba c.47.1.1 32761 2fu2A 102 2.75e+01 3sdhA 146 2.82e+01 3sdhA a.1.1.2 14984 1uquA 482 2.88e+01 c.87.1.6 99796 1cye 129 2.91e+01 3chy c.23.1.1 31077 1h54A 754 2.91e+01 a.102.1.4,b.30.5.3 60634,60635 1qgdA 662 3.01e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 1vfgA 390 3.03e+01 a.173.1.1,d.218.1.4 108570,108571 1ilk 151 3.12e+01 2ilk a.26.1.3 16886 1rzuA 485 3.15e+01 c.87.1.8 105140 2aeeA 211 3.19e+01 1myo 118 3.23e+01 2myo d.211.1.1 19174 1x6mA 196 3.32e+01 2bt2A 161 3.33e+01 1lcdA 51 3.48e+01 1pru a.35.1.5 17111 3pnp 289 3.49e+01 1b8oA c.56.2.1 33763 2fjbA 643 3.51e+01 1o5kA 306 3.52e+01 c.1.10.1 92504 1uqtA 482 3.55e+01 c.87.1.6 99794 1othA 321 3.56e+01 1othA c.78.1.1,c.78.1.1 35260,35261 1xngA 268 3.58e+01 1bqg 451 3.61e+01 1bqg c.1.11.2,d.54.1.1 29217,38861 2bo3A 94 3.65e+01 1fsz 372 3.68e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1a9t 284 3.72e+01 1b8oA c.56.2.1 33765 1db1A 259 3.74e+01 1db1A a.123.1.1 19329 1q3iA 214 3.75e+01 d.220.1.1 104524 2myo 118 3.78e+01 2myo d.211.1.1 19175 1abwA 283 3.81e+01 1abwA a.1.1.2,a.1.1.2 15288,15289 1lj2A 110 3.82e+01 h.1.13.2 73926 1d3uB 201 3.85e+01 1aisB a.74.1.2,a.74.1.2 18386,18387 1ehkA 562 3.85e+01 1ehkA f.24.1.1 43624 1vrpA 381 3.88e+01 1xviA 275 3.91e+01 2cbiA 594 3.94e+01 1c20A 128 3.96e+01 1c20A a.4.3.1 16079 2gdm 153 4.02e+01 2gdm a.1.1.2 15212 1o6jA 150 4.07e+01 c.47.1.10 81089 2cyeA 133 4.07e+01 1a3yA 149 4.18e+01 1obpA b.60.1.1 27110 1wdtA 665 4.23e+01 1irdA 141 4.24e+01 a.1.1.2 66286 1svvA 359 4.28e+01 c.67.1.1 106054 1ne8A 117 4.29e+01 b.34.6.2 80424 1m2eA 135 4.32e+01 c.23.1.5 78478 1xmeA 568 4.34e+01 1qwdA 177 4.42e+01 b.60.1.1 96471 1cjgA 62 4.45e+01 1pru a.35.1.5 17112 1cg5A 141 4.47e+01 1abwA a.1.1.2 15406 1or4A 178 4.52e+01 a.1.1.2 93447 1ngr 85 4.55e+01 1ngr a.77.1.2 18422 2ac4A 309 4.58e+01 1iktA 120 4.65e+01 d.106.1.1 66188 1mit 69 4.79e+01 1hymA d.40.1.1 38582 1b4cA 92 4.79e+01 1b4cA a.39.1.2 17169 1azsC 388 4.82e+01 1cipA a.66.1.1,c.37.1.8 18203,32086 1spgA 144 4.83e+01 1abwA a.1.1.2 15409 1tin 69 4.90e+01 2sniI d.40.1.1 38580 1lh1 153 4.91e+01 2gdm a.1.1.2 15222 1jmtA 104 4.93e+01 d.58.7.3 63180 1m2oB 190 4.99e+01 c.37.1.8 78485 3chy 128 5.02e+01 3chy c.23.1.1 31038 1dzkA 157 5.03e+01 1obpA b.60.1.1 27096 1e6mA 128 5.07e+01 3chy c.23.1.1 31039 1x71A 178 5.08e+01 1n3gA 113 5.12e+01 d.204.1.1 79962 2a25A 193 5.12e+01 1agjA 242 5.13e+01 1agjA b.47.1.1 25827 1jbeA 128 5.15e+01 3chy c.23.1.1 62845 1gdj 153 5.20e+01 2gdm a.1.1.2 15213 1gkpA 458 5.22e+01 b.92.1.3,c.1.9.6 70231,70232 1em8A 147 5.24e+01 c.128.1.1 90457 2b1xA 470 5.31e+01 1vkhA 273 5.35e+01 c.69.1.32 108662 1wozA 177 5.36e+01 2ac2A 309 5.37e+01 1ynfA 458 5.39e+01 1i21A 159 5.41e+01 1i21A d.108.1.1 61549 1ov2A 99 5.45e+01 a.13.1.1 93580 1zljA 78 5.48e+01 1a3oA 141 5.52e+01 1abwA a.1.1.2 15274 1bj7 156 5.54e+01 1bj7 b.60.1.1 27113 1n9lA 109 5.60e+01 d.110.3.6 85468 1vp8A 201 5.62e+01 1fhjB 146 5.63e+01 1abwA a.1.1.2 59838 1s4kA 120 5.65e+01 a.35.1.6 105254 1xouB 95 5.68e+01 1chuA 540 5.70e+01 1chuA a.7.3.1,c.3.1.4,d.168.1.1 16325,30424,42307 1dekA 241 5.73e+01 1dekA c.37.1.1 31842 2ilk 160 5.80e+01 2ilk a.26.1.3 16885 1a4fB 146 5.85e+01 1abwA a.1.1.2 15573 1zud1 251 5.86e+01 2dc3A 193 5.86e+01 1vbkA 307 5.89e+01 1j7yA 141 5.92e+01 a.1.1.2 66426 1x89A 178 5.96e+01 1h1nA 305 5.97e+01 c.1.8.3 70855 1wh5A 80 5.97e+01 1xqiA 195 6.04e+01 1c25 161 6.06e+01 1c25 c.46.1.1 32698 1ez1A 392 6.07e+01 1ez1A b.84.2.1,c.30.1.1,d.142.1.2 28248,31655,41500 1psqA 163 6.08e+01 c.47.1.10 88283 2lh2 153 6.10e+01 2gdm a.1.1.2 15220 1e5mA 416 6.12e+01 1dd8A c.95.1.1,c.95.1.1 58973,58974 1wy1A 172 6.18e+01 1fseA 74 6.18e+01 1fseA a.4.6.2 60000 1l5wA 796 6.21e+01 c.87.1.4 73605 1rp4A 389 6.24e+01 a.227.1.1 105027 1epxA 370 6.25e+01 1fbaA c.1.10.1 29150 1vehA 92 6.33e+01 1vmeA 410 6.35e+01 c.23.5.1,d.157.1.3 108893,108894 1y2mA 716 6.36e+01 1delA 241 6.41e+01 1dekA c.37.1.1 31844 1tr8A 102 6.48e+01 1q18A 332 6.51e+01 c.55.1.7,c.55.1.7 104470,104471 1o54A 277 6.58e+01 c.66.1.13 92482 1myt 146 6.60e+01 1a6m a.1.1.2 15207 2d2mC 147 6.65e+01 1gajA 257 6.69e+01 1gajA c.37.1.12 60416 1wduA 245 6.70e+01 d.151.1.1 109286 2gasA 307 6.71e+01 1uxd 65 6.71e+01 1uxc a.35.1.5 17118 1ixmA 192 6.94e+01 1ixmA d.123.1.1 41114 1i1dA 161 7.04e+01 1i21A d.108.1.1 61526 1x1oA 286 7.04e+01 1avqA 228 7.04e+01 1avqA c.52.1.13 33326 7odcA 424 7.04e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1y6nL 145 7.15e+01 1yqdA 366 7.15e+01 1g24A 211 7.28e+01 1g24A d.166.1.1 42270 1v30A 124 7.37e+01 1w41A 101 7.41e+01 1aj9A 141 7.42e+01 1abwA a.1.1.2 15332 1bqk 124 7.49e+01 1bqk b.6.1.1 22889 1m6iA 493 7.53e+01 c.3.1.5,c.3.1.5,d.87.1.1 74533,74534,74535 1v9sA 208 7.57e+01 2bjiA 277 7.62e+01 2evaA 307 7.74e+01 1mx4A 168 7.79e+01 d.211.1.1 79640 1aab 83 7.80e+01 1cktA a.21.1.1 16420 1q67A 231 7.82e+01 b.55.1.7 95960 1jfuA 186 7.82e+01 c.47.1.10 62940 2a9kB 223 7.83e+01 1vbiA 344 7.90e+01 1b77A 228 7.93e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 1v6tA 255 7.94e+01 1spgB 147 8.08e+01 1cg5B a.1.1.2 15588 1nrjB 218 8.16e+01 c.37.1.8 86125 1mzbA 136 8.19e+01 a.4.5.42 91497 1tx4B 178 8.19e+01 1ctqA c.37.1.8 32045 1dm5A 315 8.20e+01 1avc a.65.1.1 18186 1emy 153 8.23e+01 1a6m a.1.1.2 15204 1wuiS 267 8.26e+01 1uujA 88 8.27e+01 a.221.1.1 108046 1g291 372 8.32e+01 1g291 1i12A 160 8.34e+01 1i21A d.108.1.1 61515 1rwyA 109 8.35e+01 a.39.1.4 98002 1ys7A 233 8.35e+01 1rfmA 344 8.38e+01 c.122.1.1 97385 1cfpA 92 8.39e+01 1b4cA a.39.1.2 17172 1hcqA 84 8.39e+01 2nllB g.39.1.2 45117 2dbbA 151 8.42e+01 1q7hA 153 8.43e+01 b.122.1.1,d.17.6.2 96042,96043 1xvjA 109 8.46e+01 1w8iA 156 8.49e+01 1ak1 310 8.52e+01 1ak1 c.92.1.1 35594 1xhbA 472 8.57e+01 1vkkA 154 8.59e+01 d.109.1.2 108669 3pbgA 468 8.63e+01 1e70M c.1.8.4 28951 1e3dA 266 8.68e+01 2frvA e.19.1.1 59188 1ztdA 133 8.70e+01 1v95A 130 8.71e+01 c.51.1.1 108435 1wrvA 308 8.74e+01 1otcA 495 8.83e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 25307,25308,25309 1aisB 200 8.88e+01 1aisB a.74.1.2,a.74.1.2 18384,18385 2d5xA 141 8.90e+01 1r1dA 247 8.90e+01 c.69.1.29 96813 1ob8A 135 8.93e+01 2ffuA 501 8.95e+01 1g71A 347 8.97e+01 1g71A d.264.1.1 43268