# 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 1mq4A 272 2.77e-41 d.144.1.7 91391 1gz8A 299 3.95e-41 d.144.1.7 83405 1o6lA 337 5.51e-41 d.144.1.7 81092 1hcl 298 6.65e-41 1hcl d.144.1.7 41593 2bdwA 362 6.81e-41 1e1xA 299 1.11e-40 1hcl d.144.1.7 59157 1jvpP 298 1.30e-40 d.144.1.7 67371 1cdkA 350 2.11e-40 1cdkA d.144.1.7 41620 1xh9A 350 2.13e-40 2bfxA 284 2.29e-40 1xjdA 345 2.83e-40 1q8uA 350 3.38e-40 d.144.1.7 96230 1cmkE 350 3.58e-40 1cdkA d.144.1.7 41623 1phk 298 5.66e-40 1cdkA d.144.1.7 41635 1yhvA 297 1.07e-39 1apmE 350 1.30e-39 1cdkA d.144.1.7 41628 1rdqE 350 2.83e-39 d.144.1.7 97314 1uu3A 310 5.68e-39 d.144.1.7 99999 1f3mC 297 6.47e-39 1hcl d.144.1.7 41677 1h1wA 289 6.88e-39 d.144.1.7 83460 1jksA 294 7.09e-39 d.144.1.7 71710 2f57A 317 1.19e-38 1zrzA 364 2.42e-38 2eueA 279 3.83e-38 2c30A 321 7.62e-38 1p4fA 293 7.71e-38 d.144.1.7 104063 1kobA 387 1.07e-37 1tkiA d.144.1.7 41640 1blxA 326 2.93e-37 1hcl d.144.1.7 41596 1vzoA 355 3.80e-37 d.144.1.7 108971 1ia8A 289 3.91e-37 1ia8A d.144.1.7 62112 2bvaA 292 1.06e-36 2b9hA 353 1.61e-36 1s9jA 341 2.05e-36 3erk 364 2.28e-36 1hcl d.144.1.7 41654 1tvoA 368 2.88e-36 1zzlA 351 4.62e-36 1o6yA 299 5.53e-36 d.144.1.7 81106 1r3cA 366 8.57e-36 d.144.1.7 96906 1wbsA 360 9.03e-36 1pme 380 9.30e-36 1hcl d.144.1.7 41653 1ywrA 360 1.06e-35 1zz2A 360 1.70e-35 1pmnA 364 2.96e-35 d.144.1.7 94907 2gfsA 372 4.75e-35 1t4hA 290 1.13e-34 d.144.1.7 106420 2ac5A 316 1.26e-34 2ac3A 316 3.11e-34 1omwA 689 3.12e-34 a.91.1.1,b.55.1.1,d.144.1.7 87086,87087,87088 2evaA 307 4.82e-34 1tkiA 321 6.47e-34 1tkiA d.144.1.7 41638 1j1bA 420 7.41e-34 d.144.1.7 90758 1q41A 424 1.03e-33 d.144.1.7 95774 1opjA 293 2.03e-33 d.144.1.7 87230 1qpcA 279 3.54e-33 1fgkA d.144.1.7 41685 3lck 271 4.21e-33 1fmk d.144.1.7 41686 2b7aA 293 4.47e-33 2bikB 313 6.98e-33 1xwsA 313 7.55e-33 1zy4A 303 8.18e-33 2a19B 284 8.89e-33 1fmk 452 1.34e-32 1fmk b.34.2.1,d.93.1.1,d.144.1.7 24511,40436,41690 1mp8A 281 2.87e-32 d.144.1.7 91384 1ymiA 334 2.89e-32 1lp4A 332 2.94e-32 d.144.1.7 74170 1om1A 332 6.38e-32 d.144.1.7 93347 1a6o 332 7.12e-32 1a6o 1lpuA 332 7.49e-32 d.144.1.7 74177 1m2rA 327 9.54e-32 d.144.1.7 84760 1lufA 343 1.06e-31 d.144.1.7 78223 1fvrA 327 1.66e-31 d.144.1.7 60047 1xbbA 291 1.92e-31 1u46A 291 1.96e-31 d.144.1.7 107656 1jwhA 337 2.65e-31 d.144.1.7 71913 1ir3A 306 4.41e-31 1fmk d.144.1.7 41702 1jpaA 312 4.52e-31 d.144.1.7 67011 1u59A 287 4.87e-31 d.144.1.7 107681 1t46A 313 5.64e-31 d.144.1.7 106397 1fgkA 310 1.15e-30 1fgkA d.144.1.7 41693 1jqhA 308 8.05e-30 d.144.1.7 71793 1irk 306 8.81e-30 1fmk d.144.1.7 41703 1z57A 339 8.86e-30 1x8bA 289 1.27e-29 1p4oA 322 1.63e-29 d.144.1.7 87775 1r0pA 312 4.97e-29 d.144.1.7 96734 1ywnA 316 3.49e-28 2eu9A 355 9.49e-28 1q8yA 373 1.02e-27 d.144.1.7 96234 1howA 373 1.18e-27 1hcl d.144.1.7 41679 1wbpA 397 1.81e-26 1vjyA 303 4.31e-25 d.144.1.7 108633 1py5A 326 7.64e-25 d.144.1.7 104389 1b6cB 342 8.27e-25 1b6cB d.144.1.7 41673 1ckiA 317 6.93e-23 1csn d.144.1.7 41660 1csn 298 2.06e-20 1csn d.144.1.7 41664 1tqmA 282 5.23e-07 a.4.5.56,d.144.1.9 107236,107237 1zarA 282 6.69e-07 1zthA 258 6.48e-04 1j7lA 264 9.70e-02 d.144.1.6 62697 2bkkA 264 3.48e-01 1j7iA 264 4.85e-01 1j7iA d.144.1.6 62694 1e17A 150 8.92e-01 2hfh a.4.5.14 16143 1z5rA 306 9.55e-01 1nw1A 429 1.01e+00 d.144.1.8 86286 1e8xA 961 1.02e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19148,23183,37631,41711 1jb3A 131 1.15e+00 1jc7A b.40.3.2 62833 1e8yA 966 1.45e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19152,23187,37635,41715 1jc7A 131 1.55e+00 1jc7A b.40.3.2 62873 1e7uA 961 1.63e+00 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1wj7A 104 1.77e+00 1aipE 405 1.99e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25699,25739,32134 1dtdA 303 2.10e+00 1aye c.56.5.1 33823 2be4A 272 2.11e+00 2b7oA 464 2.61e+00 1uuzA 137 2.72e+00 d.233.1.1 100024 1aipA 405 2.74e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25697,25737,32132 1ha3A 405 3.02e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 60869,60870,60871 1v8aA 265 3.22e+00 c.72.1.2 100494 1oakA 196 3.59e+00 1auq c.62.1.1 34138 1ls1A 295 3.90e+00 a.24.13.1,c.37.1.10 78170,78171 1mgsA 73 3.94e+00 1tvxA d.9.1.1 37389 1fnsA 196 4.10e+00 1auq c.62.1.1 34136 1jpnA 296 4.22e+00 a.24.13.1,c.37.1.10 67039,67040 1wfxA 186 4.40e+00 1nd4A 264 4.68e+00 d.144.1.6 91815 1vcdA 126 4.76e+00 1ng1 294 4.86e+00 1ng1 a.24.13.1,c.37.1.10 16961,32272 1ffh 294 5.21e+00 1ng1 a.24.13.1,c.37.1.10 16960,32271 2bo9A 308 5.58e+00 1i7hA 111 5.64e+00 d.15.4.1 71122 1rro 108 5.94e+00 1a75A a.39.1.4 17195 1yixA 265 5.96e+00 1w2fA 276 6.21e+00 d.143.1.3 109125 2apoA 357 6.24e+00 1j6oA 268 6.30e+00 c.1.9.12 77088 1z7aA 308 7.47e+00 1fnoA 417 7.54e+00 d.58.19.1,c.56.5.4 70145,75841 1szhA 161 8.05e+00 a.226.1.1 106157 1eft 405 8.11e+00 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25688,25728,32123 2gq1A 332 8.24e+00 6cpa 307 8.40e+00 1aye c.56.5.1 33816 1upkA 341 8.46e+00 a.118.1.15 99758 1yme 309 9.99e+00 1aye c.56.5.1 33804 2ctc 307 1.02e+01 1aye c.56.5.1 33802 1bavA 309 1.02e+01 1aye c.56.5.1 33806 1wkbA 810 1.08e+01 2ng1 293 1.13e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1txqA 93 1.15e+01 1pcs 98 1.15e+01 1plc b.6.1.1 22871 1x92A 199 1.19e+01 1kwmA 402 1.20e+01 c.56.5.1,d.58.3.1 73079,73080 2ctb 307 1.21e+01 1aye c.56.5.1 33803 2ftzA 284 1.21e+01 1ijbA 202 1.28e+01 c.62.1.1 71229 1f0jA 377 1.29e+01 1f0jA a.211.1.2 19346 1wgwA 99 1.30e+01 1exmA 405 1.35e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25696,25736,32131 1auq 208 1.36e+01 1auq c.62.1.1 34137 1pgvA 197 1.36e+01 c.10.1.1 88073 1lm5A 214 1.41e+01 d.211.2.1 74029 1z63A 500 1.50e+01 1vixA 420 1.58e+01 c.56.5.4,d.58.19.1 100777,100778 1r89A 437 1.59e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 1rliA 184 1.70e+01 c.23.5.6 97647 1uu1A 335 1.73e+01 c.67.1.1 99993 1qusA 322 1.73e+01 1ltm d.2.1.6 36991 2etvA 346 1.75e+01 1ltm 320 1.77e+01 1ltm d.2.1.6 36992 2fsp 124 1.79e+01 1dz3A c.23.1.1 31119 1m4lA 307 1.79e+01 c.56.5.1 78604 1g8iA 190 1.79e+01 1rec a.39.1.5 60363 487dH 224 1.81e+01 1ad2 i.1.1.2 45835 1d1qA 161 1.82e+01 1dg9A c.44.1.1 32642 1ad2 228 1.85e+01 1ad2 e.24.1.1 43353 1x6iA 91 1.86e+01 1uetA 437 1.89e+01 a.160.1.3,d.218.1.7,d.58.16.2 99272,99273,99274 1wznA 252 1.92e+01 1twdA 256 1.93e+01 c.1.30.1 107397 1yqtA 538 1.98e+01 1qczA 169 2.00e+01 1qczA c.23.8.1 31276 1bncA 449 2.03e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28236,31643,41488 1nmeA 146 2.04e+01 c.17.1.1 85874 1iu8A 206 2.08e+01 c.56.4.1 71436 2c78A 405 2.12e+01 2bwvA 440 2.35e+01 2aeuA 374 2.47e+01 1uebA 184 2.48e+01 b.34.5.2,b.40.4.5,b.40.4.5 107782,107783,107784 1ksfX 758 2.58e+01 a.174.1.1,c.37.1.20,c.37.1.20 77522,77523,77524 1wl9A 440 2.60e+01 1esc 306 2.62e+01 1esc c.23.10.1 31334 1fepA 724 2.69e+01 1fepA f.4.3.3 43808 1g6hA 257 2.71e+01 1gajA c.37.1.12 60318 1aye 401 2.83e+01 1aye c.56.5.1,d.58.3.1 33824,39065 1zkoA 136 2.87e+01 2ccjA 205 2.89e+01 2cygA 312 2.89e+01 1rwiA 270 2.89e+01 b.68.9.1 97987 1lre 81 2.90e+01 1lre a.13.1.1 16376 1fezA 256 2.92e+01 1fezA c.108.1.3 43343 1aj8A 371 2.93e+01 1aj8A a.103.1.1 18900 1a16 440 2.96e+01 1az9 c.55.2.1,d.127.1.1 33548,41165 1m1lA 236 3.03e+01 d.260.1.1 91166 3vtk 343 3.09e+01 1qhiA c.37.1.1 31884 1fsz 372 3.15e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1jfrA 262 3.17e+01 1jfrA c.69.1.16 34724 1wlzA 105 3.19e+01 1vdxA 184 3.22e+01 2ct9A 208 3.44e+01 1na3A 91 3.54e+01 k.38.1.1 85481 1uddA 226 3.59e+01 a.132.1.3 107776 1q67A 231 3.60e+01 b.55.1.7 95960 1az9 457 3.67e+01 1az9 c.55.2.1,d.127.1.1 33547,41164 1syyA 346 3.69e+01 a.25.1.2 106126 2hddA 61 3.70e+01 2hddA a.4.1.1 15971 1rdfA 267 3.73e+01 c.108.1.3 104884 1gsoA 431 3.77e+01 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1rr7A 129 3.78e+01 a.4.1.14 105075 1f39A 101 3.82e+01 1umuA b.87.1.1 28386 1p99A 295 3.82e+01 c.94.1.1 94384 1kutA 230 3.91e+01 d.143.1.1 73017 1tcoA 375 3.91e+01 1auiA d.159.1.3 42084 1uouA 474 3.93e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1ddt 535 3.97e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22379,42241,43384 1seiA 130 3.97e+01 1seiA d.140.1.1 41463 1rom 403 4.01e+01 1rom a.104.1.1 18963 2dfkA 402 4.05e+01 2b2hA 399 4.08e+01 1jfbA 404 4.12e+01 a.104.1.1 66624 1tzvA 142 4.15e+01 a.79.1.1 107526 1cojA 212 4.19e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1k3sA 113 4.20e+01 d.198.1.1 68120 2bv9A 290 4.22e+01 2coeA 120 4.31e+01 1t2bA 397 4.34e+01 1a03A 90 4.43e+01 4icb a.39.1.2 17157 1feuA 206 4.61e+01 1feuA b.53.1.1 59801 1swvA 267 4.61e+01 1zr5A 214 4.63e+01 2ahqA 76 4.65e+01 1zxkA 98 4.68e+01 1odeA 122 4.74e+01 d.79.1.2 86846 1ejdA 419 4.74e+01 1uae d.68.2.2 39576 1zw0A 66 4.78e+01 1tv8A 340 4.78e+01 c.1.28.3 107352 1cp3A 277 4.90e+01 1pauA c.17.1.1 30992 1b48A 221 4.91e+01 1pgtA a.45.1.1,c.47.1.5 17703,32997 1du0A 57 4.91e+01 2hddA a.4.1.1 15974 1sro 76 4.95e+01 1sro b.40.4.5 25327 1mfiA 114 5.00e+01 1dptA d.80.1.3 39856 2gauA 232 5.01e+01 1pauA 147 5.05e+01 1pauA c.17.1.1 30994 1pxfA 111 5.05e+01 b.40.4.4 88341 1wgzA 510 5.07e+01 2b43A 526 5.22e+01 1rqlA 267 5.26e+01 c.108.1.3 97750 1or4A 178 5.27e+01 a.1.1.2 93447 1cjdA 394 5.32e+01 1cjdA b.121.2.1,b.121.2.1 58963,58964 1w33A 181 5.32e+01 1y63A 184 5.34e+01 1z7wA 322 5.37e+01 2atjA 308 5.46e+01 1bgp a.93.1.1 18675 1a3h 300 5.53e+01 7a3hA c.1.8.3 28819 1nnlA 225 5.57e+01 c.108.1.4 85906 1tadA 324 5.63e+01 1cipA a.66.1.1,c.37.1.8 18194,32077 1ns1A 73 5.67e+01 1ail a.16.1.1 16382 1nm2A 317 5.67e+01 c.19.1.1,d.58.23.1 80654,80655 1op1A 82 5.72e+01 a.13.1.1 93396 1hx6A 394 5.78e+01 1cjdA b.121.2.1,b.121.2.1 58995,58996 1zkeA 83 5.79e+01 2e2c 156 5.83e+01 1u9aA d.20.1.1 38336 2bfwA 200 5.83e+01 2gaiA 633 5.84e+01 1souA 194 5.91e+01 c.124.1.6 105858 1jf3A 147 5.92e+01 a.1.1.2 71642 1lmeA 176 6.01e+01 d.167.1.1 84629 1hb5A 394 6.06e+01 i.6.1.1 65752 1uuqA 440 6.07e+01 c.1.8.3 100015 1qwgA 251 6.11e+01 c.1.27.1 96473 1n25A 368 6.14e+01 c.37.1.20 85264 1avpA 204 6.14e+01 1avpA d.3.1.7 37132 1mkmA 249 6.14e+01 a.4.5.33,d.110.2.2 79242,79243 1b5tA 275 6.17e+01 1b5tA c.1.23.1 29676 2citA 282 6.23e+01 2gtrA 261 6.23e+01 1ur3M 319 6.24e+01 c.1.7.1 99806 1z6aA 500 6.34e+01 1gvzA 237 6.35e+01 b.47.1.2 76360 1qnoA 344 6.39e+01 1qnoA c.1.8.3 28838 1zp4A 304 6.44e+01 1sd4A 126 6.61e+01 a.4.5.39 105428 2cqeA 98 6.65e+01 1xmpA 170 6.67e+01 1vgjA 184 6.73e+01 2cxxA 190 6.75e+01 1hddC 61 6.75e+01 2hddA a.4.1.1 15978 1og6A 298 6.78e+01 c.1.7.1 86984 1yioA 208 6.83e+01 1tme3 236 6.83e+01 1qqp3 1ail 73 7.02e+01 1ail a.16.1.1 16381 1f07A 321 7.06e+01 1ezwA c.1.16.3 59560 1ufyA 122 7.10e+01 d.79.1.2 88489 1f6oA 219 7.12e+01 1bnkA b.46.1.2 25763 1f2hA 169 7.16e+01 1f3vA d.58.22.1 59612 1gwuA 309 7.23e+01 a.93.1.1 83351 1q1vA 70 7.29e+01 a.159.4.1 104479 1z7yA 322 7.33e+01 1g0hA 252 7.37e+01 1dk4A e.7.1.1 60171 1cpt 412 7.37e+01 1cpt a.104.1.1 18968 1iapA 211 7.42e+01 a.91.1.1 62119 1qvzA 237 7.46e+01 c.23.16.2 96453 1l2uA 245 7.47e+01 c.1.2.3 73516 1enh 54 7.54e+01 2hddA a.4.1.1 15973 1z8uA 102 7.54e+01 1fvzA 271 7.55e+01 1fvzA 1mldA 314 7.56e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1sig 339 7.60e+01 1sig a.177.1.1 19068 1ycqA 107 7.81e+01 1ycqA a.42.1.1 17419 1f24A 402 7.90e+01 1rom a.104.1.1 18953 1yh2A 175 8.08e+01 3adk 195 8.08e+01 1zin c.37.1.1 31885 1xhfA 123 8.09e+01 1i27A 73 8.18e+01 1i27A a.4.5.30 61555 1dk4A 252 8.19e+01 1dk4A e.7.1.1 42970 2aifA 135 8.19e+01 1nlnA 204 8.20e+01 d.3.1.7 91962 1dar 691 8.23e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1qnrA 344 8.25e+01 1qnoA c.1.8.3 28834 1z82A 335 8.33e+01 1y01A 102 8.38e+01 1pot 325 8.48e+01 1pot c.94.1.1 35807 1sheA 103 8.52e+01 d.274.1.1 105551 1am4A 199 8.62e+01 1tx4A a.116.1.1 19100 1ff9A 450 8.71e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1svmA 377 8.78e+01 1w3iA 293 8.80e+01 c.1.10.1 109152 1ajqB 557 8.85e+01 1ajqB 1ra0A 430 8.86e+01 1y8aA 332 8.90e+01 7a3hA 303 8.94e+01 7a3hA c.1.8.3 28817