# 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.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 9.02e-07 a.152.1.2 108650 1p8cA 145 1.04e-06 a.152.1.2 94354 3beyA 96 2.50e-06 2q0tA 263 1.60e-05 2ouwA 138 7.62e-05 2qeuA 141 3.27e-04 1gu9A 177 3.47e-04 a.152.1.1 65540 1lw1A 177 1.21e-03 a.152.1.1 74290 2prrA 197 3.83e-03 3c1lA 188 7.77e-03 2pfxA 191 1.84e-02 2oyoA 196 3.86e-02 2o4dA 165 4.20e-02 a.152.1.3 138907 2gmyA 153 5.41e-02 a.152.1.3 135398 2ijcA 145 1.77e-01 a.152.1.3 137465 2b8nA 429 3.26e-01 c.118.1.1 128093 2b8eA 273 5.68e-01 c.108.1.7,d.220.1.1 128068,128069 3bnjA 485 1.37e+00 1dlyA 164 1.39e+00 1dlyA a.1.1.1 14983 1fs7A 485 1.58e+00 1qdbA a.138.1.3 19691 1y10A 407 1.90e+00 1qdbA 473 1.91e+00 1qdbA a.138.1.3 19688 1fc3A 120 1.92e+00 1fc3A a.4.6.3 16237 2nszA 129 2.01e+00 a.118.1.14 138560 2aioA 269 2.07e+00 d.157.1.1 126829 1vmiA 355 2.10e+00 c.77.1.5 113678 2ev1A 222 2.13e+00 1smlA 269 2.27e+00 1smlA d.157.1.1 42053 1ztcA 221 2.44e+00 d.157.1.11 125635 1txuA 273 2.64e+00 a.222.1.1 107439 1rd5A 262 2.84e+00 c.1.2.4 111772 2ekcA 262 3.04e+00 2gkmA 136 3.09e+00 1idrA 136 3.63e+00 1dlyA a.1.1.1 62301 1t3iA 420 4.08e+00 c.67.1.3 106354 2d9sA 53 5.60e+00 2ot3A 274 5.75e+00 a.222.1.1 139311 2f2sA 406 5.82e+00 2ebdA 309 6.02e+00 1kmkA 406 6.13e+00 c.67.1.3 68696 2nnwA 376 6.22e+00 1jf9A 408 6.50e+00 1c0nA c.67.1.3 62931 2fhwA 24 7.11e+00 1xfjA 261 7.24e+00 d.194.1.2 109585 1rxqA 178 7.26e+00 a.213.1.1 105118 1xhlA 297 7.39e+00 c.2.1.2 109591 1q08A 99 7.39e+00 a.6.1.3 95497 2rdzA 452 7.56e+00 2d59A 144 8.06e+00 c.2.1.8 131266 1gm6A 175 8.31e+00 b.60.1.1 70272 2j01Q 141 8.38e+00 1xkqA 280 8.41e+00 c.2.1.2 115417 1szqA 483 8.61e+00 e.44.1.1 99045 1y9kA 157 8.79e+00 d.108.1.1 122779 2i10A 202 8.79e+00 a.4.1.9,a.121.1.1 136960,136961 1rxwA 336 8.83e+00 a.60.7.1,c.120.1.2 98059,98060 3cneA 175 9.24e+00 2cq2A 114 9.44e+00 d.58.7.1 130713 1s5jA 847 9.57e+00 c.55.3.5,e.8.1.1 112040,112041 2ra6A 166 9.93e+00 2i5uA 83 1.01e+01 1vz0A 230 1.02e+01 a.4.14.1,d.268.1.1 108929,108930 1kfcA 268 1.02e+01 c.1.2.4 77371 2f82A 450 1.02e+01 1t0qA 498 1.03e+01 a.25.1.2 106220 1s69A 124 1.07e+01 a.1.1.1 105305 1mfqC 129 1.07e+01 a.36.1.1 79046 1jqoA 970 1.08e+01 c.1.12.3 77160 2dc4A 165 1.08e+01 1qopA 268 1.09e+01 2tysA c.1.2.4 28570 1rfzA 168 1.09e+01 a.195.1.1 97411 2ct8A 497 1.14e+01 1vgoA 253 1.15e+01 1vhcA 224 1.16e+01 c.1.10.1 100661 2gs5A 198 1.20e+01 d.310.1.1 135577 1ki1B 352 1.21e+01 a.87.1.1,b.55.1.1 72497,72498 1xk5A 204 1.21e+01 2ib8A 395 1.24e+01 2incA 491 1.25e+01 a.25.1.2 137524 1mup 166 1.25e+01 1mup 1gvhA 396 1.26e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 2v26A 784 1.32e+01 1syyA 346 1.32e+01 a.25.1.2 106126 1t9bA 677 1.32e+01 c.31.1.3,c.36.1.5,c.36.1.9 112334,112335,112336 1ew3A 159 1.32e+01 1mup b.60.1.1 27114 2cztA 167 1.34e+01 1bd3A 243 1.35e+01 1bd3A c.61.1.1 34098 1i06A 180 1.38e+01 1mup b.60.1.1 27131 1qy1A 174 1.39e+01 b.60.1.1 96568 1jv4A 162 1.44e+01 b.60.1.1 67343 2hhjA 267 1.44e+01 c.60.1.1 136497 1ho8A 480 1.51e+01 1ho8A a.118.1.9 61107 2hekA 371 1.53e+01 a.211.1.1 136354 2tysA 268 1.53e+01 2tysA c.1.2.4 28572 1zndA 174 1.61e+01 b.60.1.1 125380 1s5lU 134 1.62e+01 1jpdX 324 1.62e+01 c.1.11.2,d.54.1.1 67014,67015 1qb2A 109 1.63e+01 1qb2A a.36.1.1 17125 2b5aA 77 1.63e+01 a.35.1.3 127882 1vqzA 341 1.64e+01 d.224.1.3,d.104.1.3 120426,120427 2fhzB 108 1.73e+01 d.243.1.2 133506 1yhlA 362 1.76e+01 2aq9A 262 1.77e+01 b.81.1.1 127167 1c9bA 207 1.78e+01 1tfb a.74.1.2,a.74.1.2 18372,18373 1x3lA 440 1.82e+01 2jf2A 264 1.85e+01 b.81.1.1 138289 1xgwA 176 1.86e+01 2bgsA 344 1.86e+01 3b9oA 440 1.86e+01 1reqB 637 1.87e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1dn1A 594 1.89e+01 1dn1A e.25.1.1 43357 2czvC 120 1.90e+01 1rk6A 496 1.99e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 2i2xB 258 1.99e+01 1m7jA 484 1.99e+01 b.92.1.6,b.92.1.6,c.1.9.11 78732,78733,78734 1ax4A 467 2.02e+01 1ax4A c.67.1.2 34391 1wvtA 172 2.04e+01 1iktA 120 2.07e+01 d.106.1.1 66188 2oo9A 46 2.09e+01 1xeoA 168 2.10e+01 d.167.1.1 121913 1zq1C 633 2.17e+01 a.182.1.2,d.74.4.1,d.128.1.5 125493,125494,125495 3b98A 475 2.17e+01 2qk2A 242 2.19e+01 1r3eA 309 2.20e+01 b.122.1.1,d.265.1.2 96907,96908 1tfb 208 2.24e+01 1tfb 2qdjA 304 2.25e+01 1schA 294 2.27e+01 1bgp a.93.1.1 18685 1a3yA 149 2.28e+01 1obpA b.60.1.1 27110 1g8kA 825 2.29e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1dzkA 157 2.31e+01 1obpA b.60.1.1 27096 2vg0A 227 2.32e+01 1lxa 262 2.33e+01 1lxa 1ez3A 127 2.37e+01 1dn1B a.47.2.1 17768 2qiaA 262 2.37e+01 1fxrA 64 2.37e+01 1fxd d.58.1.4 38993 2o6lA 170 2.41e+01 1sekA 378 2.42e+01 e.1.1.1 42675 1khyA 148 2.42e+01 a.174.1.1 77410 2pkfA 334 2.45e+01 2a8kA 108 2.45e+01 d.243.1.2 126404 1mtyD 512 2.47e+01 1mhyD a.25.1.2 16742 1guxB 152 2.49e+01 1guxB a.74.1.3 18389 1zcjA 463 2.49e+01 1q7eA 428 2.50e+01 c.123.1.1 96035 1ys4A 354 2.51e+01 1rkuA 206 2.56e+01 c.108.1.11 97627 1w8gA 234 2.58e+01 1spxA 278 2.58e+01 c.2.1.2 98958 1u9yA 284 2.60e+01 c.61.1.2,c.61.1.2 119655,119656 2av5A 120 2.62e+01 8abp 306 2.64e+01 8abp 8abpA 306 2.64e+01 c.93.1.1 35647 2di0A 71 2.70e+01 a.5.2.4 131521 1g8jA 825 2.73e+01 1g8jA b.52.2.2,c.81.1.1 26924,35332 1xa3A 437 2.77e+01 c.123.1.1 115025 2hy5B 136 2.78e+01 c.114.1.1 136866 1tz9A 367 2.83e+01 c.1.15.6 107466 1c75A 71 2.87e+01 451c a.3.1.1 15796 2pnwA 380 2.87e+01 1lwjA 441 2.92e+01 b.71.1.1,c.1.8.1 74303,74304 1a4sA 503 2.94e+01 1bpwA c.82.1.1 35361 1jscA 630 2.95e+01 c.31.1.3,c.36.1.5,c.36.1.9 67224,67225,67226 1lopA 164 2.97e+01 2cpl b.62.1.1 27510 2ot4A 525 2.99e+01 1y9iA 178 2.99e+01 a.195.1.1 116586 1g0uI 205 3.00e+01 d.153.1.4 41891 2cbiA 594 3.06e+01 a.246.1.1,c.1.8.10,d.92.2.3 130179,130180,130181 2fsxA 148 3.08e+01 2rn7A 108 3.11e+01 1ezwA 349 3.12e+01 1ezwA c.1.16.3 29558 2r2dA 276 3.15e+01 1g6uA 48 3.16e+01 1g6uA k.9.1.1 46425 1dekA 241 3.16e+01 1dekA c.37.1.1 31842 1kblA 873 3.17e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 3bhqA 211 3.21e+01 1xk7A 408 3.21e+01 c.123.1.1 122071 2af4C 333 3.23e+01 c.77.1.5 126656 1xxaA 78 3.23e+01 1xxaA d.74.2.1 39700 1omiA 248 3.29e+01 b.82.3.3,a.4.5.4 87079,87080 1ceqA 316 3.31e+01 1ceqA c.2.1.5,d.162.1.1 30163,42130 2h28A 130 3.33e+01 d.110.8.1 135995 2bkhA 814 3.35e+01 1wkbA 810 3.38e+01 1rypJ 204 3.43e+01 d.153.1.4 41878 1bs4A 168 3.44e+01 1bs4A d.167.1.1 42287 2a6aA 218 3.45e+01 c.55.1.9,c.55.1.9 126231,126232 2gm5A 139 3.47e+01 1wmiB 67 3.48e+01 a.137.13.1 121046 2edmA 161 3.50e+01 1x31B 404 3.53e+01 2inwA 133 3.54e+01 d.110.8.1 137533 1pgyA 47 3.54e+01 a.5.2.1 94696 2nwvA 114 3.55e+01 d.326.1.1 138720 1epaA 164 3.55e+01 1epaA b.60.1.1 27128 1y0uA 96 3.56e+01 a.4.5.5 116310 1z85A 234 3.58e+01 1y88A 199 3.61e+01 a.60.4.3,c.52.1.30 116560,116561 2fb2A 340 3.61e+01 1mqsA 671 3.65e+01 e.25.1.1 79414 1uf3A 228 3.71e+01 d.159.1.6 99317 2g0wA 296 3.71e+01 c.1.15.4 134503 1w4xA 542 3.73e+01 c.3.1.5,c.3.1.5 109171,109172 1i6wA 181 3.82e+01 1i6wA c.69.1.18 61859 2hzcA 87 3.86e+01 1epuA 591 3.86e+01 1dn1A e.25.1.1 43358 2vccA 891 3.87e+01 2q3pA 112 3.89e+01 d.58.4.4 139798 1rhcA 330 3.91e+01 c.1.16.3 97468 2dkoA 146 3.98e+01 1t5jA 313 3.99e+01 a.209.1.1 99125 1nmsA 249 4.00e+01 c.17.1.1 85879 1lycA 343 4.01e+01 a.93.1.1 74344 1jx6A 342 4.05e+01 c.93.1.1 67406 2gscA 128 4.11e+01 1lj8A 493 4.12e+01 a.100.1.9,c.2.1.6 90392,90393 2fxaA 207 4.20e+01 a.4.5.28 134304 1br2A 791 4.23e+01 1lvk b.34.3.1,c.37.1.9 24558,32155 1wwpA 119 4.24e+01 1vr6A 350 4.25e+01 c.1.10.4 120439 1vkfA 188 4.25e+01 c.1.29.1 108656 1cf2O 337 4.27e+01 1b7gO c.2.1.3,d.81.1.1 29994,39909 2ibdA 204 4.32e+01 1j32A 388 4.33e+01 c.67.1.1 77067 2bgcA 238 4.33e+01 a.4.5.4,b.82.3.3 128458,128459 1wz9A 375 4.33e+01 2ggtA 164 4.37e+01 c.47.1.10 135156 1br0A 120 4.37e+01 a.47.2.1 17772 1pt7A 437 4.37e+01 c.123.1.1 95093 1qtnA 164 4.39e+01 1pauA c.17.1.1 30999 1a4mA 349 4.39e+01 1a4mA c.1.9.1 29014 1dik 874 4.41e+01 1dik 1t90A 486 4.43e+01 1cp3A 277 4.44e+01 1pauA c.17.1.1 30992 1tv8A 340 4.44e+01 c.1.28.3 107352 1f5qB 252 4.44e+01 1f5qB a.74.1.1,a.74.1.1 18362,18363 1fkx 349 4.46e+01 1a4mA 3cjpA 272 4.47e+01 1wdvA 152 4.51e+01 d.116.1.1 114539 1y56B 382 4.54e+01 1c0nA 406 4.56e+01 1c0nA c.67.1.3 34433 1tzvA 142 4.57e+01 a.79.1.1 107526 2bgxA 261 4.59e+01 a.20.1.1,d.118.1.1 128504,128505 1eh9A 558 4.61e+01 1ehaA b.1.18.2,b.71.1.1,c.1.8.1 21858,27785,28772 1dp4A 435 4.62e+01 1dp4A c.93.1.1 35710 1dszA 86 4.63e+01 2nllB g.39.1.2 45129 2g7rA 117 4.65e+01 2fbdA 122 4.65e+01 1wy5A 317 4.67e+01 c.26.2.5,d.229.1.1 121428,121429 1g2yA 32 4.71e+01 a.34.2.1 17003 1arv 344 4.71e+01 1arv 1xx7A 184 4.71e+01 a.211.1.1 116143 1t2dA 322 4.73e+01 c.2.1.5,d.162.1.1 99084,99085 2cmgA 262 4.76e+01 2c9oA 456 4.79e+01 1ifyA 49 4.87e+01 a.5.2.1 71207 1xdiA 499 4.89e+01 c.3.1.5,d.87.1.1 115160,115161 2e3bA 344 4.90e+01 a.93.1.1 132024 2q0lA 311 4.90e+01 3bjdA 332 4.91e+01 2eq9C 41 4.92e+01 1rovA 857 4.94e+01 a.119.1.1,b.12.1.1 97674,97675 2nq2C 253 4.96e+01 2z0xA 158 4.96e+01 1aru 344 4.96e+01 1arv 1hwxA 501 4.98e+01 1hwyA c.2.1.7,c.58.1.1 30250,33898 2rslA 140 4.98e+01 2rslA c.53.1.1 33345 2d2jA 329 5.01e+01 c.1.9.3 131175 2cx5A 158 5.02e+01 1p90A 145 5.02e+01 c.55.5.2 94377 1vgyA 393 5.06e+01 c.56.5.4,d.58.19.1 100620,100621 1k1vA 41 5.09e+01 a.37.1.1 71999 1izmA 184 5.10e+01 a.199.1.1 90725 1vflA 356 5.12e+01 c.1.9.1 120041 2gk4A 232 5.12e+01 1byiA 224 5.37e+01 c.37.1.10 32199 2eh6A 375 5.38e+01 2jg2A 422 5.39e+01 2h56A 233 5.40e+01 1byi 224 5.41e+01 1byi 2vc7A 314 5.43e+01 3ciwA 348 5.43e+01 1xw8A 252 5.45e+01 c.6.2.5 116111 3b49A 211 5.46e+01 1u3eM 174 5.47e+01 d.4.1.3,d.285.1.1 107640,107641 2o8pA 227 5.47e+01 1uddA 226 5.53e+01 a.132.1.3 107776 1h4gA 207 5.54e+01 b.29.1.11 70863 2h3hA 313 5.54e+01 3clqA 421 5.60e+01 1ydmA 187 5.65e+01 1ujpA 271 5.71e+01 c.1.2.4 99462 2a3nA 355 5.72e+01 2p8tA 200 5.73e+01 1gpjA 404 5.74e+01 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 2c9hA 444 5.75e+01 1ispA 181 5.75e+01 c.69.1.18 76778 1tedA 393 5.79e+01 c.95.1.2 106807 1yrnA 61 5.81e+01 1akhA a.4.1.1 15981 1ghtA 105 5.81e+01 2rslA c.53.1.1 60526 1p4wA 99 5.82e+01 a.4.6.2 87783 1yukA 103 5.87e+01 1avqA 228 5.87e+01 1avqA c.52.1.13 33326 1dc7A 124 5.88e+01 1dbwA c.23.1.1 31093 2o09A 189 5.93e+01 1bsgA 266 5.95e+01 e.3.1.1 42729 1sgmA 191 5.96e+01 a.4.1.9,a.121.1.1 105537,105538 1hwyA 501 6.01e+01 1hwyA c.2.1.7,c.58.1.1 30262,33910 1dt1A 129 6.03e+01 1c52 a.3.1.1 15811 2gduA 504 6.05e+01 b.71.1.1,c.1.8.1 135032,135033 2vd6A 503 6.08e+01 1zybA 232 6.09e+01 a.4.5.4,b.82.3.2 125815,125816 1y56A 493 6.10e+01 3c6qA 311 6.17e+01 1fjcA 96 6.17e+01 1fjcA d.58.7.1 39212 2bw8A 227 6.24e+01 b.29.1.11 129324 1jyeA 349 6.27e+01 c.93.1.1 67455 1irxA 523 6.32e+01 a.97.1.2,c.26.1.1 71378,71379 1qhfA 240 6.35e+01 1qhfA c.60.1.1 33960 2pefA 373 6.36e+01 1ji0A 240 6.37e+01 c.37.1.12 71665 2p8uA 478 6.39e+01 1bpwA 503 6.40e+01 1bpwA c.82.1.1 35365 1svdA 473 6.43e+01 c.1.14.1,d.58.9.1 119057,119058 2qvcA 313 6.44e+01 1j58A 385 6.49e+01 b.82.1.2 71531 1ydgA 211 6.53e+01 c.23.5.8 116614 3b4dA 96 6.57e+01 2cvjA 180 6.59e+01 2gx9A 129 6.69e+01 d.299.1.1 135828 1ltm 320 6.75e+01 1ltm 1y5iB 512 6.77e+01 d.58.1.5 122641 1cvrA 435 6.77e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1aa7A 158 6.80e+01 1aa7A a.95.1.1 18741 1k1xA 659 6.83e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1f07A 321 6.86e+01 1ezwA c.1.16.3 59560 2ce0A 105 6.96e+01 1i7pA 274 6.97e+01 b.43.4.2,c.25.1.1 66048,66049 1h0bA 256 6.99e+01 b.29.1.11 83422 2egzA 219 6.99e+01 2c7yA 404 7.07e+01 1qoiA 177 7.08e+01 2cpl b.62.1.1 27490 1qgpA 77 7.09e+01 1qbjA a.4.5.19 16158 1wgnA 63 7.10e+01 a.5.2.1 114617 1c52 131 7.11e+01 1c52 1c52A 131 7.11e+01 a.3.1.1 15810 2yyyA 343 7.14e+01 2dxcC 243 7.18e+01 1uj0A 62 7.22e+01 b.34.2.1 99449 1orjA 130 7.26e+01 a.24.19.1 93456 1h67A 108 7.32e+01 a.40.1.1 65643 1b0nB 57 7.35e+01 1b0nB a.34.1.1 17002 2gsmB 262 7.36e+01 b.6.1.2,f.17.2.1 135590,135591 1rcwA 231 7.38e+01 a.132.1.4 97299 1r7aA 504 7.41e+01 b.71.1.1,c.1.8.1 97192,97193 1oi7A 288 7.42e+01 c.2.1.8,c.23.4.1 87049,87050 2ahrA 259 7.43e+01 a.100.1.10,c.2.1.6 126775,126776 1b0nA 111 7.43e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1o89A 345 7.43e+01 b.35.1.2,c.2.1.1 92644,92645 2ywlA 180 7.47e+01 1ubi 76 7.54e+01 1ubi 1oltA 457 7.56e+01 c.1.28.2 93334 1pytC 253 7.57e+01 5ptp b.47.1.2 26233 1mioA 534 7.67e+01 1qguA c.92.2.3 35601 2eq7C 40 7.67e+01 2pulA 397 7.77e+01 2k29A 53 7.80e+01 2cosA 54 7.82e+01 a.5.2.1 130683 2cb5A 453 7.83e+01 3gcb d.3.1.1 37035 1whzA 70 7.87e+01 d.50.3.2 114656 1liaA 164 7.88e+01 1cpcA a.1.1.3 15661 1lj9A 144 7.89e+01 a.4.5.28 78035 1cqxA 403 7.91e+01 1cqxA a.1.1.2,b.43.4.2,c.25.1.5 15635,25667,31562 2nvaA 372 7.93e+01 1qusA 322 8.00e+01 1ltm d.2.1.6 36991