# List of top-scoring protein chains for t04-100-40-40-str2+CB_burial_14_7-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 1ufbA 127 7.16e-12 a.24.16.3 99331 1wolA 122 1.11e-11 1o3uA 135 1.86e-10 a.24.16.3 86615 1wwpA 119 3.82e-02 1ylmA 144 4.60e-01 1khyA 148 1.17e+00 a.174.1.1 77410 1xx1A 285 1.47e+00 1kq3A 376 1.50e+00 e.22.1.2 68790 1riqA 465 2.04e+00 a.203.1.1,d.104.1.1 97516,97517 1nbfA 353 2.20e+00 d.3.1.9 80387 1khoA 370 2.38e+00 a.124.1.1,b.12.1.3 72489,72490 2cmd 312 2.45e+00 2cmd c.2.1.5,d.162.1.1 30135,42102 1z8sA 146 2.51e+00 2cb5A 453 3.83e+00 3gcb d.3.1.1 37035 1fohA 664 3.86e+00 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 1nb8A 353 3.88e+00 d.3.1.9 80385 1jlwA 219 3.94e+00 a.45.1.1,c.47.1.5 71741,71742 1m2rA 327 4.20e+00 d.144.1.7 84760 1pn0A 665 4.48e+00 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1sz9A 144 4.70e+00 a.118.9.4 106139 2gmyA 153 5.37e+00 1ymiA 334 5.44e+00 1om1A 332 5.54e+00 d.144.1.7 93347 1jvsA 400 5.67e+00 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1q0qA 406 5.88e+00 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1yfsA 465 5.92e+00 1ta9A 450 6.24e+00 1jogA 146 6.30e+00 a.24.16.2 77142 1pv6A 417 6.44e+00 f.38.1.2 95151 1hl9A 449 6.54e+00 b.71.1.3,c.1.8.11 90650,90651 1r9kA 172 6.93e+00 a.168.1.1 104869 1qq5A 253 7.07e+00 1qq5A c.108.1.1 43327 1c1dA 355 7.36e+00 1bw9A c.2.1.7,c.58.1.1 30270,33918 1ovaA 386 7.65e+00 1ovaA e.1.1.1 42619 1t0qA 498 7.67e+00 a.25.1.2 106220 1uhgA 385 7.88e+00 e.1.1.1 88491 1lj9A 144 8.09e+00 a.4.5.28 78035 1jdpA 441 8.13e+00 c.93.1.1 62906 1sauA 115 8.46e+00 1qq7A 253 8.71e+00 1qq5A c.108.1.1 43329 1gzsB 165 8.95e+00 a.168.1.1 76425 1qhdA 398 9.21e+00 1qhdA a.115.1.2,b.19.1.1 63324,63325 1bif 469 9.65e+00 1bif c.37.1.7,c.60.1.4 31961,34003 2glfA 450 9.81e+00 1mhyD 521 9.88e+00 1mhyD a.25.1.2 16780 1guxA 218 1.01e+01 1guxA a.74.1.3 18388 1pxvA 183 1.10e+01 d.3.1.1 95301 1lqaA 346 1.11e+01 c.1.7.1 84674 1oshA 232 1.19e+01 a.123.1.1 93496 1bv1 159 1.21e+01 1bv1 d.129.3.1 41313 1y0kA 209 1.21e+01 1oapA 109 1.21e+01 d.79.7.1 92706 1v3wA 173 1.22e+01 b.81.1.5 100291 2fymA 431 1.25e+01 1moq 368 1.26e+01 1moq c.80.1.1 35302 1dwkA 156 1.28e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1rkbA 173 1.31e+01 1o5xA 248 1.31e+01 c.1.1.1 92528 1y4hA 188 1.36e+01 1ci4A 89 1.38e+01 1qckA a.60.5.1 17970 1o2dA 371 1.45e+01 e.22.1.2 86591 1dik 874 1.51e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1rzrA 332 1.52e+01 1mtyD 512 1.55e+01 1mhyD a.25.1.2 16742 1r71A 178 1.55e+01 a.4.14.1 104823 1a76 326 1.55e+01 1a76 a.60.7.1,c.120.1.2 18091,33361 1r2rA 248 1.57e+01 c.1.1.1 96875 1ofcX 304 1.60e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 1q2lA 939 1.60e+01 1p5zB 263 1.65e+01 c.37.1.1 87815 1mldA 314 1.71e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1vdkA 466 1.78e+01 a.127.1.1 100561 3sdhA 146 1.79e+01 3sdhA a.1.1.2 14984 1m6jA 261 1.92e+01 c.1.1.1 78693 1lyxA 248 1.94e+01 c.1.1.1 78304 1kutA 230 1.97e+01 d.143.1.1 73017 1dvkA 173 1.99e+01 1dvkA a.72.1.1 18319 1np8A 159 1.99e+01 a.39.1.8 92022 1kblA 873 1.99e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1m48A 133 2.03e+01 a.26.1.2 74443 1ur5A 309 2.05e+01 c.2.1.5,d.162.1.1 99807,99808 1ezvC 385 2.06e+01 1be3C f.32.1.1,f.21.1.2 75833,75834 1j5wA 298 2.06e+01 d.104.1.1 71589 1z23A 163 2.08e+01 2cybA 323 2.10e+01 1nhyA 219 2.10e+01 a.45.1.1,c.47.1.5 80520,80521 1ui5A 215 2.10e+01 a.4.1.9,a.121.1.1 107856,107857 1nogA 177 2.12e+01 a.25.2.2 85923 1kb9C 385 2.13e+01 f.32.1.1,f.21.1.2 77315,77316 1nv8A 284 2.15e+01 c.66.1.30 86224 1bob 320 2.18e+01 1bob d.108.1.1 40816 1z6oM 191 2.19e+01 2bl8A 103 2.24e+01 1tpfA 250 2.24e+01 1amk c.1.1.1 28467 1qj2B 809 2.25e+01 1qj2B 1usyA 275 2.32e+01 1xwsA 313 2.35e+01 2cw8A 537 2.35e+01 1tqhA 247 2.38e+01 c.69.1.29 107225 1ivyA 452 2.40e+01 1ivyA c.69.1.5 34654 1i6wA 181 2.42e+01 1i6wA c.69.1.18 61859 1sxgA 280 2.45e+01 1m98A 317 2.45e+01 a.175.1.1,d.17.4.6 78866,78867 2gk9A 426 2.46e+01 2aw5A 541 2.51e+01 1ispA 181 2.51e+01 c.69.1.18 76778 1qr6A 584 2.55e+01 1qr6A c.2.1.7,c.58.1.3 30293,33941 1u00A 227 2.55e+01 1u2pA 163 2.58e+01 1yeyA 444 2.60e+01 2iu1A 208 2.62e+01 2c71A 216 2.62e+01 1n62B 809 2.76e+01 d.41.1.1,d.133.1.1 80092,80093 3gcb 470 2.79e+01 3gcb d.3.1.1 37032 1bpyA 335 2.81e+01 1bpyA a.60.6.1,a.60.12.1,d.218.1.2 17980,75819,75820 1ah7 245 2.82e+01 1ah7 a.124.1.1 19339 2fmlA 273 2.83e+01 2aplA 157 2.87e+01 1mwmA 320 2.87e+01 c.55.1.1,c.55.1.1 79580,79581 1lnwA 147 2.89e+01 a.4.5.28 78104 1xfrA 128 2.89e+01 1eexA 554 2.90e+01 1dioA c.1.19.3 29650 4crxA 322 2.92e+01 4crxA a.60.9.1,d.163.1.1 18095,42155 1k3rA 268 2.97e+01 b.40.4.10,c.116.1.2 72018,72019 1xrsA 516 3.00e+01 351c 82 3.01e+01 451c a.3.1.1 15905 1vqwA 457 3.04e+01 1ks9A 291 3.08e+01 a.100.1.7,c.2.1.6 68857,68858 1pinA 163 3.09e+01 1pinA b.72.1.1,d.26.1.1 27802,38431 2bikB 313 3.11e+01 451c 82 3.18e+01 451c a.3.1.1 15904 2fsjA 346 3.19e+01 1yovA 537 3.19e+01 1rrmA 386 3.19e+01 e.22.1.2 105081 2ah5A 210 3.19e+01 1qqcA 773 3.24e+01 1tgoA c.55.3.5,e.8.1.1 33724,43013 1g4wR 383 3.27e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1fit 147 3.34e+01 1fit d.13.1.1 37499 2a0b 125 3.35e+01 2a0b a.24.10.1 16630 1ezfA 340 3.36e+01 1ezfA a.128.1.2 19440 1gcb 454 3.37e+01 3gcb d.3.1.1 37034 1e3oC 160 3.38e+01 1au7A a.4.1.1,a.35.1.1 59197,59198 1v58A 241 3.42e+01 c.47.1.9,d.17.3.1 108371,108372 1jq5A 370 3.45e+01 e.22.1.2 67084 1qpcA 279 3.45e+01 1fgkA d.144.1.7 41685 1ca1 370 3.45e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1nksA 194 3.49e+01 1nksA c.37.1.1 31886 1cv8 174 3.50e+01 1cv8 d.3.1.1 37089 1n0qA 93 3.51e+01 k.37.1.1 79754 1khtA 192 3.55e+01 c.37.1.1 84401 2fhi 147 3.57e+01 1fit d.13.1.1 37505 1w33A 181 3.62e+01 1lj8A 493 3.65e+01 a.100.1.9,c.2.1.6 90392,90393 2db0A 253 3.66e+01 2gv8A 447 3.67e+01 1i45A 248 3.69e+01 1amk c.1.1.1 61665 1zcbA 362 3.70e+01 1i50B 1224 3.71e+01 e.29.1.1 61755 1fw1A 216 3.73e+01 a.45.1.1,c.47.1.5 60051,60052 1zxiB 809 3.76e+01 3ertA 261 3.77e+01 3erdA a.123.1.1 19292 2fd5A 180 3.77e+01 1pulA 125 3.78e+01 1wznA 252 3.78e+01 1vljA 407 3.83e+01 e.22.1.2 108832 1xo0A 324 3.87e+01 1w2lA 99 3.91e+01 1xsnA 335 3.92e+01 2c1iA 431 4.00e+01 1lo7A 141 4.00e+01 d.38.1.1 74144 1pa7A 130 4.01e+01 a.40.1.1 94410 3erk 364 4.03e+01 1hcl d.144.1.7 41654 2gs8A 317 4.05e+01 2iu5A 195 4.05e+01 2a6hD 1524 4.12e+01 2mnr 357 4.20e+01 2mnr c.1.11.2,d.54.1.1 29245,38889 1ezvB 352 4.21e+01 1ezvB d.185.1.1,d.185.1.1 59543,59544 2a2cA 478 4.21e+01 2c1gA 431 4.24e+01 1r1dA 247 4.25e+01 c.69.1.29 96813 1sedA 117 4.34e+01 a.219.1.1 105449 1pgjA 478 4.43e+01 2pgd a.100.1.1,c.2.1.6 18783,30195 1w7jA 795 4.44e+01 1pme 380 4.44e+01 1hcl d.144.1.7 41653 1bvqA 141 4.47e+01 1bvqA d.38.1.1 38542 2a19A 175 4.47e+01 1txgA 335 4.50e+01 1uxjA 309 4.53e+01 c.2.1.5,d.162.1.1 108112,108113 1neyA 247 4.57e+01 c.1.1.1 80449 2fckA 181 4.59e+01 1fezA 256 4.62e+01 1fezA c.108.1.3 43343 2cfuA 658 4.66e+01 1fh9A 312 4.67e+01 1taxA c.1.8.3 28913 1u3aA 189 4.69e+01 1itwA 741 4.69e+01 c.77.1.2 76793 1a17 166 4.73e+01 1a17 a.118.8.1 19206 1ka1A 357 4.75e+01 e.7.1.1 68369 1iv3A 152 4.81e+01 d.79.5.1 76828 1jdlA 121 4.85e+01 a.3.1.1 66557 1y0zA 330 4.87e+01 1ee8A 266 4.98e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 1oe9A 795 5.00e+01 b.34.3.1,c.37.1.9 92792,92793 1myt 146 5.00e+01 1a6m a.1.1.2 15207 1o20A 427 5.11e+01 c.82.1.1 86556 1nq7A 244 5.11e+01 a.123.1.1 92047 1qlpA 394 5.15e+01 1ovaA e.1.1.1 42628 1u24A 337 5.20e+01 1mdl 359 5.31e+01 2mnr c.1.11.2,d.54.1.1 29247,38891 2a2dA 478 5.32e+01 2gdnA 267 5.34e+01 1i5nA 146 5.36e+01 1i5nA a.24.10.3 61805 1l5wA 796 5.36e+01 c.87.1.4 73605 1u09A 476 5.37e+01 e.8.1.4 107545 1qv1A 195 5.37e+01 a.39.1.5 96347 1qq8A 214 5.40e+01 1qq8A 1qmqA 414 5.44e+01 1phd a.104.1.1 18907 1n45A 233 5.48e+01 a.132.1.1 79981 1t9kA 347 5.53e+01 c.124.1.5 106721 1i4dA 224 5.53e+01 h.4.7.1 61682 1ct5A 256 5.53e+01 1ct5A c.1.6.2 28663 2auwA 170 5.53e+01 1tvoA 368 5.54e+01 1xpcA 248 5.55e+01 1dk0A 188 5.59e+01 1b2vA d.35.1.1 38530 1zs3A 182 5.65e+01 1paqA 189 5.69e+01 a.118.1.14 94413 1mtyB 384 5.73e+01 1mtyB a.25.1.2 16740 1ockA 412 5.74e+01 c.117.1.1 86802 1f6vA 91 5.74e+01 1f6vA a.49.1.1 17791 1pujA 282 5.76e+01 c.37.1.8 88294 2apjA 260 5.85e+01 1qwgA 251 5.91e+01 c.1.27.1 96473 1lngA 87 5.96e+01 d.201.1.1 74045 2btoA 473 5.98e+01 1gg3A 279 6.00e+01 1ef1A a.11.2.1,b.55.1.5,d.15.1.4 16372,27007,37615 1tph1 247 6.01e+01 1amk 2blkA 122 6.04e+01 1vg5A 73 6.08e+01 1twfB 1224 6.11e+01 1nrfA 262 6.18e+01 e.3.1.1 92086 1hyhA 309 6.18e+01 1hyhA c.2.1.5,d.162.1.1 30150,42117 2bcqA 335 6.18e+01 1dgnA 89 6.20e+01 1dgnA a.77.1.3 18436 1u59A 287 6.21e+01 d.144.1.7 107681 1ihoA 283 6.23e+01 1ihoA c.26.1.4 62390 1xzoA 174 6.28e+01 1ohlA 342 6.37e+01 c.1.10.3 87035 1pzgA 331 6.38e+01 c.2.1.5,d.162.1.1 95425,95426 1lddA 74 6.39e+01 a.4.5.34 73841 2fmpA 335 6.46e+01 1ddf 127 6.47e+01 1ddf a.77.1.2 18423 2ew2A 316 6.48e+01 2a61A 145 6.48e+01 1yt8A 539 6.49e+01 1qgxA 357 6.53e+01 1qgxA e.7.1.1 42973 1ro7A 259 6.53e+01 c.130.1.1 97667 1j98A 157 6.57e+01 1j98A d.185.1.2 62755 2d2sA 235 6.58e+01 1bed 181 6.62e+01 1fvkA c.47.1.13 90330 1or4A 178 6.64e+01 a.1.1.2 93447 2ffjA 300 6.66e+01 1dj8A 89 6.72e+01 1bg8A a.57.1.1 17919 1wtyA 119 6.77e+01 2avpA 70 6.82e+01 1v4xB 146 6.83e+01 a.1.1.2 108364 1rpyA 114 6.92e+01 d.93.1.1 97718 1oafA 261 6.92e+01 a.93.1.1 86734 1mkmA 249 6.94e+01 a.4.5.33,d.110.2.2 79242,79243 1aihA 170 6.94e+01 1aihA d.163.1.1 42149 1jnrA 643 6.96e+01 a.7.3.1,c.3.1.4,d.168.1.1 66966,66967,66968 1y10A 407 7.02e+01 1apxA 249 7.05e+01 1ryc a.93.1.1 18669 1ykuA 136 7.06e+01 1hq0A 295 7.06e+01 1hzgA d.194.1.1 61122 1z6mA 175 7.10e+01 1z47A 355 7.12e+01 1otvA 259 7.13e+01 a.132.1.4 93526 1e6yB 433 7.18e+01 1mroB a.89.1.1,d.58.31.2 18535,39453 1sfjA 238 7.20e+01 1n55A 251 7.25e+01 c.1.1.1 80007 1rtwA 220 7.29e+01 a.132.1.3 97823 2anxA 146 7.33e+01 1f45B 197 7.36e+01 1f45B a.26.1.1 59642 1octC 156 7.38e+01 1au7A a.4.1.1,a.35.1.1 15991,17017 1uu3A 310 7.42e+01 d.144.1.7 99999 1h3fA 432 7.44e+01 c.26.1.1,d.66.1.4 76631,76632 1h1wA 289 7.44e+01 d.144.1.7 83460 1mo0A 275 7.47e+01 c.1.1.1 79329 1knyA 253 7.52e+01 1knyA a.24.16.1,d.218.1.1 75896,75897 1aoa 275 7.56e+01 1aoa a.40.1.1,a.40.1.1 17396,17397 1t8tA 271 7.58e+01 c.37.1.5 106685 1ojaA 520 7.61e+01 c.3.1.2,d.16.1.5 93096,93097 1rqlA 267 7.65e+01 c.108.1.3 97750 1p3jA 217 7.65e+01 c.37.1.1,g.41.2.1 94022,94023 2a11A 242 7.67e+01 1wy1A 172 7.70e+01 2bmaA 470 7.72e+01 1j1uA 306 7.73e+01 c.26.1.1 83980 1vjvA 415 7.79e+01 d.3.1.9 108632 1tzzA 392 7.79e+01 1lldA 319 7.82e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 2akzA 439 7.89e+01 1dz4A 414 7.92e+01 1phd a.104.1.1 18903 1yqyA 523 7.92e+01 1ujnA 348 7.94e+01 e.22.1.1 99460 1y2mA 716 7.94e+01 1kb9B 352 7.94e+01 d.185.1.1,d.185.1.1 77313,77314 1rxwA 336 7.99e+01 a.60.7.1,c.120.1.2 98059,98060 2bryA 497 8.03e+01 1qkmA 255 8.06e+01 3erdA a.123.1.1 19309 1v9dA 340 8.09e+01 a.207.1.1 100535 1v7zA 260 8.11e+01 c.125.1.1 100488 2eu8A 216 8.12e+01 1uspA 139 8.15e+01 d.227.1.1 99879 1mla 309 8.15e+01 1mla c.19.1.1,d.58.23.1 31031,39383 1g1eB 89 8.19e+01 1g1eB a.59.1.1 17931 1alvA 173 8.20e+01 1alvA a.39.1.8 17370 1zrzA 364 8.21e+01 1oj7A 408 8.26e+01 e.22.1.2 103971 1qnxA 209 8.28e+01 1qnxA d.111.1.1 40914 1jpaA 312 8.33e+01 d.144.1.7 67011 1li5B 461 8.34e+01 a.27.1.1,c.26.1.1 73914,73915 1vpbA 451 8.35e+01 1h6gA 256 8.38e+01 1h6gA a.24.9.1,a.24.9.1 60669,60670 2cxaA 256 8.38e+01 1t8qA 336 8.38e+01 c.1.18.3 106669 1amk 251 8.39e+01 1amk c.1.1.1 28503 1j6rA 214 8.43e+01 d.173.1.2 71598 1e5dA 402 8.43e+01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1f3iA 481 8.44e+01 1b7eA 1r0kA 388 8.47e+01 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 1mo9A 523 8.51e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1olsA 400 8.51e+01 c.36.1.11 93331 1ji7A 89 8.54e+01 a.60.1.1 71682 2d0tA 406 8.55e+01 2f42A 179 8.58e+01 1x7yA 400 8.61e+01 1q8yA 373 8.61e+01 d.144.1.7 96234 1chkA 238 8.65e+01 1chkA d.2.1.7 36999 1howA 373 8.65e+01 1hcl d.144.1.7 41679 1ux8A 132 8.76e+01 2his 312 8.79e+01 1taxA c.1.8.3 28918 1te6A 439 8.81e+01 c.1.11.1,d.54.1.1 106797,106798 2anpA 291 8.87e+01 2ghcX 261 8.90e+01 1svdM 110 8.92e+01 1g0cA 364 8.94e+01 7a3hA c.1.8.3 60165