# List of top-scoring protein chains for t04-100-30-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.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 1vkeA 133 1.59e-07 a.152.1.2 108650 2q0tA 263 1.76e-06 3beyA 96 4.62e-06 2ouwA 138 1.31e-05 2qeuA 141 1.25e-04 1gu9A 177 7.64e-04 a.152.1.1 65540 1lw1A 177 3.20e-03 a.152.1.1 74290 2prrA 197 4.71e-03 3c1lA 188 7.06e-03 2gmyA 153 9.94e-03 a.152.1.3 135398 2o4dA 165 1.51e-02 a.152.1.3 138907 2oyoA 196 3.08e-02 2pfxA 191 3.73e-02 2ijcA 145 5.76e-02 a.152.1.3 137465 2b8nA 429 5.07e-01 c.118.1.1 128093 2gkmA 136 7.61e-01 1idrA 136 8.13e-01 1dlyA a.1.1.1 62301 1rd5A 262 9.93e-01 c.1.2.4 111772 2f2sA 406 1.15e+00 3b98A 475 1.35e+00 2b8eA 273 1.58e+00 c.108.1.7,d.220.1.1 128068,128069 2ebdA 309 1.67e+00 1vmiA 355 1.85e+00 c.77.1.5 113678 2i10A 202 2.00e+00 a.4.1.9,a.121.1.1 136960,136961 1txuA 273 2.01e+00 a.222.1.1 107439 3bnjA 485 2.22e+00 1ubkL 534 2.22e+00 e.18.1.1 88422 2aioA 269 2.27e+00 d.157.1.1 126829 1fs7A 485 2.30e+00 1qdbA a.138.1.3 19691 2ib8A 395 2.36e+00 2bsnA 145 2.45e+00 2ot3A 274 2.75e+00 a.222.1.1 139311 1wuiL 534 2.76e+00 e.18.1.1 121289 2ekcA 262 2.87e+00 1ujpA 271 3.12e+00 c.1.2.4 99462 1smlA 269 3.13e+00 1smlA d.157.1.1 42053 1h2rL 534 3.16e+00 1h2rL e.18.1.1 43298 2ahrA 259 3.64e+00 a.100.1.10,c.2.1.6 126775,126776 2nszA 129 3.66e+00 a.118.1.14 138560 2c9hA 444 4.09e+00 2v26A 784 4.90e+00 2ct8A 497 5.17e+00 1rxqA 178 5.95e+00 a.213.1.1 105118 2pefA 373 5.98e+00 1x3lA 440 6.24e+00 1f5qB 252 6.51e+00 1f5qB a.74.1.1,a.74.1.1 18362,18363 2rdzA 452 6.85e+00 1xsm 390 7.07e+00 1xsm 2bkhA 814 7.09e+00 2bnlA 136 7.57e+00 1qsaA 618 7.94e+00 1qsaA a.118.5.1,d.2.1.6 19182,36988 2ggtA 164 8.00e+00 c.47.1.10 135156 2iwzA 438 8.09e+00 1ydgA 211 8.55e+00 c.23.5.8 116614 1ztcA 221 8.65e+00 d.157.1.11 125635 2i62A 265 9.18e+00 1s5jA 847 9.28e+00 c.55.3.5,e.8.1.1 112040,112041 1ho1A 242 9.31e+00 1ho1A c.1.24.1 61097 1s5lU 134 9.43e+00 1aa7A 158 9.73e+00 1aa7A a.95.1.1 18741 1wz9A 375 9.99e+00 1ibrB 462 1.03e+01 1qgrA a.118.1.1 19120 1fc3A 120 1.04e+01 1fc3A a.4.6.3 16237 2hhjA 267 1.05e+01 c.60.1.1 136497 2gs5A 198 1.08e+01 d.310.1.1 135577 1ydmA 187 1.10e+01 1w68A 390 1.12e+01 a.25.1.2 109216 1q08A 99 1.12e+01 a.6.1.3 95497 2f82A 450 1.12e+01 1d0yA 761 1.14e+01 1lvk b.34.3.1,c.37.1.9 24581,32178 1qopA 268 1.15e+01 2tysA c.1.2.4 28570 1xgwA 176 1.16e+01 1kfcA 268 1.17e+01 c.1.2.4 77371 1qgrA 876 1.20e+01 1qgrA a.118.1.1 19119 1ji0A 240 1.20e+01 c.37.1.12 71665 1n8vA 112 1.22e+01 a.118.21.1 85457 1ys4A 354 1.23e+01 2j01Q 141 1.25e+01 1y10A 407 1.27e+01 1vgoA 253 1.31e+01 1vkfA 188 1.34e+01 c.1.29.1 108656 1bd3A 243 1.38e+01 1bd3A c.61.1.1 34098 1zowA 313 1.39e+01 2tysA 268 1.39e+01 2tysA c.1.2.4 28572 2zceA 291 1.40e+01 1y5iB 512 1.42e+01 d.58.1.5 122641 2ev1A 222 1.43e+01 1u3eM 174 1.44e+01 d.4.1.3,d.285.1.1 107640,107641 1iktA 120 1.44e+01 d.106.1.1 66188 1tqyB 415 1.44e+01 c.95.1.1,c.95.1.1 107247,107248 1nn7A 105 1.44e+01 d.42.1.2 85894 1qhfA 240 1.47e+01 1qhfA c.60.1.1 33960 1szqA 483 1.51e+01 e.44.1.1 99045 1t3iA 420 1.51e+01 c.67.1.3 106354 2r48A 106 1.59e+01 2oixA 186 1.61e+01 2cq2A 114 1.70e+01 d.58.7.1 130713 2d59A 144 1.72e+01 c.2.1.8 131266 3cjpA 272 1.75e+01 1jpaA 312 1.75e+01 d.144.1.7 67011 1xfjA 261 1.75e+01 d.194.1.2 109585 2p8uA 478 1.76e+01 2akaA 776 1.78e+01 1epuA 591 1.80e+01 1dn1A e.25.1.1 43358 1lvk 762 1.86e+01 1lvk 1q7eA 428 1.88e+01 c.123.1.1 96035 1sl8A 191 1.89e+01 a.39.1.5 112099 1rkqA 282 1.91e+01 c.108.1.10 97621 1qvbA 481 1.93e+01 1qvbA c.1.8.4 28983 1m5wA 243 1.97e+01 c.1.24.1 84836 1vflA 356 1.99e+01 c.1.9.1 120041 1jf9A 408 2.06e+01 1c0nA c.67.1.3 62931 1pt7A 437 2.07e+01 c.123.1.1 95093 2r9gA 204 2.11e+01 1guxB 152 2.11e+01 1guxB a.74.1.3 18389 1kmkA 406 2.16e+01 c.67.1.3 68696 3by5A 155 2.19e+01 1fseA 74 2.22e+01 1fseA a.4.6.2 60000 1y0uA 96 2.24e+01 a.4.5.5 116310 1qb2A 109 2.26e+01 1qb2A a.36.1.1 17125 2o6lA 170 2.27e+01 2hy5B 136 2.29e+01 c.114.1.1 136866 2dpmA 284 2.29e+01 2dpmA c.66.1.28 34246 2h3gX 268 2.31e+01 1vhcA 224 2.31e+01 c.1.10.1 100661 1w9iA 770 2.34e+01 1rxwA 336 2.36e+01 a.60.7.1,c.120.1.2 98059,98060 1bykA 255 2.39e+01 1bykA c.93.1.1 35706 1p5hA 428 2.42e+01 c.123.1.1 87802 2q7eA 291 2.43e+01 2i5gA 325 2.43e+01 1pud 386 2.44e+01 1pud 2pkfA 334 2.45e+01 1yacA 208 2.45e+01 1yacA c.33.1.3 31757 2fsxA 148 2.46e+01 2o5hA 136 2.46e+01 2q3pA 112 2.46e+01 d.58.4.4 139798 1nbaA 264 2.48e+01 1nbaA c.33.1.3 31753 1jqoA 970 2.50e+01 c.1.12.3 77160 1k1vA 41 2.51e+01 a.37.1.1 71999 2d9sA 53 2.58e+01 1nigA 152 2.60e+01 a.25.2.1 85740 2dvtA 327 2.68e+01 c.1.9.15 131793 1f8yA 157 2.70e+01 1f8xA c.23.14.1 31395 1a4sA 503 2.71e+01 1bpwA c.82.1.1 35361 1clxA 347 2.73e+01 1taxA c.1.8.3 28899 2fhwA 24 2.74e+01 1dlwA 116 2.75e+01 1dlyA a.1.1.1 14982 2cbzA 237 2.75e+01 1zrnA 232 2.79e+01 c.108.1.1 43323 2dsjA 423 2.82e+01 3csvA 333 2.84e+01 2i2xB 258 2.86e+01 1u6eA 335 2.87e+01 c.95.1.2,c.95.1.2 119568,119569 8abp 306 2.88e+01 8abp 8abpA 306 2.88e+01 c.93.1.1 35647 2rcyA 262 2.90e+01 2csbA 519 2.93e+01 a.60.2.4,a.60.2.4,a.60.2.4,a.60.2.4,a.267.1.1 130751,130752,130753,130754,130755 1xw8A 252 2.95e+01 c.6.2.5 116111 1a4mA 349 2.96e+01 1a4mA c.1.9.1 29014 2o09A 189 2.96e+01 1tedA 393 2.98e+01 c.95.1.2 106807 1rypF 233 3.01e+01 1rypF d.153.1.4 41937 1bsgA 266 3.01e+01 e.3.1.1 42729 1hzpA 335 3.04e+01 1hn9A c.95.1.2,c.95.1.2 61455,61456 1ki1B 352 3.04e+01 a.87.1.1,b.55.1.1 72497,72498 1ow4A 129 3.07e+01 a.39.2.1 93628 2erbA 125 3.08e+01 1lj8A 493 3.10e+01 a.100.1.9,c.2.1.6 90392,90393 2a14A 263 3.21e+01 c.66.1.15 125972 2f02A 323 3.21e+01 c.72.1.1 132649 1vdzA 588 3.22e+01 2nnwA 376 3.26e+01 1uhkA 191 3.30e+01 a.39.1.5 119681 2g8yA 385 3.30e+01 2jbaA 127 3.34e+01 1dp4A 435 3.38e+01 1dp4A c.93.1.1 35710 2ez2A 456 3.50e+01 3ciwA 348 3.51e+01 1w32A 348 3.60e+01 c.1.8.3 114120 1ho8A 480 3.65e+01 1ho8A a.118.1.9 61107 2ot4A 525 3.66e+01 1vyqA 173 3.69e+01 b.85.4.1 120548 1nriA 306 3.73e+01 c.80.1.3 86123 1b9bA 255 3.75e+01 1amk c.1.1.1 28531 2axtB 510 3.75e+01 1i6wA 181 3.77e+01 1i6wA c.69.1.18 61859 2reiA 318 3.78e+01 2nq2C 253 3.81e+01 1rypJ 204 3.81e+01 d.153.1.4 41878 2q14A 410 3.81e+01 1frb 315 3.86e+01 1frb 1z85A 234 3.92e+01 1xesA 413 3.93e+01 1pxgA 382 3.96e+01 c.1.20.1 95287 1t9bA 677 4.00e+01 c.31.1.3,c.36.1.5,c.36.1.9 112334,112335,112336 2dejA 350 4.01e+01 2cw6A 298 4.02e+01 1e3dB 542 4.04e+01 1h2rL e.18.1.1 59189 2r6oA 294 4.05e+01 2dvyA 226 4.05e+01 1fxrA 64 4.05e+01 1fxd d.58.1.4 38993 2edmA 161 4.18e+01 1dlyA 164 4.18e+01 1dlyA a.1.1.1 14983 1xeoA 168 4.21e+01 d.167.1.1 121913 3cloA 258 4.25e+01 1mspA 126 4.31e+01 1mspA b.1.11.2 22333 2okuA 131 4.31e+01 2a3nA 355 4.32e+01 1yurA 98 4.32e+01 a.39.1.2 124062 2di3A 239 4.38e+01 1fkx 349 4.43e+01 1a4mA 1h6fA 193 4.44e+01 b.2.5.4 70901 1i7pA 274 4.44e+01 b.43.4.2,c.25.1.1 66048,66049 2cujA 108 4.45e+01 a.4.1.18 130812 1ybdA 239 4.57e+01 c.73.1.3 122884 1sekA 378 4.58e+01 e.1.1.1 42675 2obhA 143 4.62e+01 2r2dA 276 4.64e+01 1rfzA 168 4.67e+01 a.195.1.1 97411 1li4A 432 4.67e+01 c.2.1.4,c.23.12.3 84616,84617 2ieeA 271 4.72e+01 2bcgG 453 4.73e+01 c.3.1.3,c.3.1.3,d.16.1.6 128282,128283,128284 1qusA 322 4.76e+01 1ltm d.2.1.6 36991 1g6uA 48 4.77e+01 1g6uA k.9.1.1 46425 3c9fA 557 4.77e+01 2qk2A 242 4.80e+01 1om1A 332 4.85e+01 d.144.1.7 93347 2abqA 306 4.88e+01 c.72.1.1 126528 2pnwA 380 4.92e+01 1xwfA 431 4.94e+01 c.2.1.4,c.23.12.3 122392,122393 2ixaA 444 4.97e+01 1ispA 181 5.01e+01 c.69.1.18 76778 1r5yA 386 5.01e+01 c.1.20.1 97134 1ndh 272 5.03e+01 1ndh 2oqoA 200 5.04e+01 2tpsA 227 5.04e+01 2tpsA c.1.3.1 28591 2czvC 120 5.07e+01 2apoA 357 5.09e+01 b.122.1.1,d.265.1.2 127133,127134 1brwA 433 5.09e+01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1konA 249 5.11e+01 e.39.1.1 72823 1w1iE 357 5.14e+01 c.1.9.1 109051 2av5A 120 5.16e+01 1t3wA 148 5.19e+01 a.236.1.1 112233 3cb0A 173 5.23e+01 1wviA 257 5.25e+01 c.108.1.14 114915 1wdkC 390 5.27e+01 c.95.1.1,c.95.1.1 109258,109259 2bgsA 344 5.29e+01 1wwpA 119 5.30e+01 1lopA 164 5.34e+01 2cpl b.62.1.1 27510 2ie7A 318 5.34e+01 a.65.1.1 137293 2d51A 406 5.35e+01 2o8pA 227 5.36e+01 2p4zA 284 5.36e+01 1a8e 329 5.37e+01 1cb6A 1urvA 190 5.46e+01 a.1.1.2 113414 1x4pA 66 5.53e+01 2no4A 240 5.53e+01 1g67A 225 5.53e+01 c.1.3.1 60311 2uuuA 584 5.55e+01 1wueA 386 5.56e+01 c.1.11.2,d.54.1.1 114892,114893 1y88A 199 5.58e+01 a.60.4.3,c.52.1.30 116560,116561 2odmA 91 5.61e+01 1cvrA 435 5.65e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 3cqyA 370 5.65e+01 2g0wA 296 5.65e+01 c.1.15.4 134503 1h3nA 878 5.66e+01 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 2v2gA 233 5.70e+01 2bo5A 120 5.76e+01 1ak0A 270 5.77e+01 a.124.1.2 19345 1syyA 346 5.80e+01 a.25.1.2 106126 1wy6A 172 5.81e+01 a.118.20.1 121432 2nx9A 464 5.86e+01 2tpt 440 5.90e+01 1brwA 2q4oA 215 5.91e+01 c.129.1.1 139872 2p8tA 200 5.94e+01 1mzjA 339 5.97e+01 c.95.1.2,c.95.1.2 79700,79701 1bs4A 168 5.98e+01 1bs4A d.167.1.1 42287 3cjdA 198 5.99e+01 1x31B 404 6.07e+01 1qd9A 124 6.13e+01 1qu9A d.79.1.1 39758 3b9oA 440 6.13e+01 1vz0A 230 6.17e+01 a.4.14.1,d.268.1.1 108929,108930 1f4lA 551 6.18e+01 1qqtA a.27.1.1,c.26.1.1,g.41.1.1 59648,59649,59650 2fi0A 81 6.19e+01 a.248.1.1 133507 1t2dA 322 6.19e+01 c.2.1.5,d.162.1.1 99084,99085 1ak0 270 6.20e+01 1ak0 1wr8A 231 6.20e+01 c.108.1.10 114836 2ivnA 330 6.23e+01 1mi3A 322 6.34e+01 c.1.7.1 91274 1nvmA 345 6.35e+01 a.5.7.1,c.1.10.5 86249,86250 1k5dB 201 6.46e+01 b.55.1.3 68169 3bg1B 442 6.46e+01 1uedA 406 6.47e+01 a.104.1.1 99256 1uj0A 62 6.58e+01 b.34.2.1 99449 1xx7A 184 6.58e+01 a.211.1.1 116143 1xhlA 297 6.61e+01 c.2.1.2 109591 2ondA 308 6.61e+01 1g2yA 32 6.65e+01 a.34.2.1 17003 1o3uA 135 6.66e+01 a.24.16.3 86615 1tc1A 220 6.69e+01 1tc1A c.61.1.1 34083 2v82A 212 6.70e+01 2v0cA 878 6.72e+01 1v6tA 255 6.72e+01 c.6.2.5 113550 1jx6A 342 6.79e+01 c.93.1.1 67406 1khyA 148 6.80e+01 a.174.1.1 77410 1u9yA 284 6.83e+01 c.61.1.2,c.61.1.2 119655,119656 1pbyA 489 6.84e+01 a.3.1.7,a.3.1.7,b.1.18.14,b.1.18.14,b.61.4.1 94417,94418,94419,94420,94421 2r7gA 347 6.85e+01 2zhgA 154 6.86e+01 1ku2A 241 6.88e+01 a.4.13.1,a.177.1.1 83096,83097 2yxbA 161 6.92e+01 2b1eA 564 6.93e+01 2oo9A 46 6.95e+01 1m2rA 327 6.97e+01 d.144.1.7 84760 2vjqA 428 7.08e+01 2fb2A 340 7.14e+01 1tvnA 293 7.19e+01 c.1.8.3 119360 1ux8A 132 7.19e+01 a.1.1.1 113449 1qsmA 152 7.19e+01 1qsmA d.108.1.1 40808 1w7lA 422 7.19e+01 c.67.1.1 109226 2a1vA 144 7.20e+01 d.198.3.1 126019 1ni4A 365 7.25e+01 c.36.1.11 85728 2di0A 71 7.25e+01 a.5.2.4 131521 1o5oA 221 7.27e+01 c.61.1.1 92509 3bruA 222 7.30e+01 2gx9A 129 7.38e+01 d.299.1.1 135828 1iowA 306 7.38e+01 c.30.1.2,d.142.1.1 31713,41481 1hjsA 332 7.39e+01 c.1.8.3 83492 1iow 306 7.39e+01 1iow 1pfvA 551 7.47e+01 a.27.1.1,c.26.1.1,g.41.1.1 94660,94661,94662 2hekA 371 7.48e+01 a.211.1.1 136354 1umkA 275 7.48e+01 b.43.4.2,c.25.1.1 113312,113313 1t5jA 313 7.51e+01 a.209.1.1 99125 2g3fA 421 7.53e+01 2jg2A 422 7.54e+01 1gwiA 411 7.55e+01 a.104.1.1 76364 1g57A 217 7.57e+01 1g57A d.115.1.2 60253 2h2kA 106 7.61e+01 1epwA 1290 7.61e+01 b.29.1.6,b.42.4.2,d.92.1.7,h.4.2.1 24269,25614,40305,45785 1uwsA 489 7.62e+01 c.1.8.4 108073 2a67A 167 7.63e+01 2oc5A 244 7.66e+01 1na3A 91 7.68e+01 k.38.1.1 85481 1rhcA 330 7.70e+01 c.1.16.3 97468 1r3eA 309 7.70e+01 b.122.1.1,d.265.1.2 96907,96908 2hfsA 332 7.81e+01 2iu1A 208 7.83e+01 2dfaA 250 7.85e+01 c.6.2.5 131469 2ehsA 77 7.90e+01 1i0lA 221 7.93e+01 c.61.1.1 71096 2jg1A 330 7.95e+01 1allA 160 7.95e+01 1qgwC a.1.1.3 15647 1nh1A 330 7.96e+01 e.45.1.1 91871 1k1xA 659 8.00e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281