# List of top-scoring protein chains for t06-100-40-40-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 2.24e-11 a.24.16.3 99331 1wolA 122 3.01e-11 1o3uA 135 2.77e-10 a.24.16.3 86615 1wwpA 119 2.43e-02 1ylmA 144 2.06e-01 1khyA 148 1.00e+00 a.174.1.1 77410 1oshA 232 1.58e+00 a.123.1.1 93496 1qhdA 398 1.67e+00 1qhdA a.115.1.2,b.19.1.1 63324,63325 1xx1A 285 1.84e+00 1kq3A 376 1.98e+00 e.22.1.2 68790 1lj9A 144 2.39e+00 a.4.5.28 78035 1gzsB 165 2.47e+00 a.168.1.1 76425 1z8sA 146 2.71e+00 1r9kA 172 3.68e+00 a.168.1.1 104869 1y2mA 716 4.21e+00 1yfsA 465 4.58e+00 1ta9A 450 4.59e+00 1pxvA 183 4.62e+00 d.3.1.1 95301 1a76 326 4.88e+00 1a76 a.60.7.1,c.120.1.2 18091,33361 1w7jA 795 5.13e+00 2gmyA 153 6.20e+00 1v58A 241 6.64e+00 c.47.1.9,d.17.3.1 108371,108372 2gk9A 426 6.85e+00 1nb8A 353 6.89e+00 d.3.1.9 80385 1jogA 146 6.93e+00 a.24.16.2 77142 1sz9A 144 6.93e+00 a.118.9.4 106139 1y4hA 188 7.01e+00 2cw8A 537 7.19e+00 1q0qA 406 7.27e+00 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1rkbA 173 7.68e+00 1oapA 109 7.76e+00 d.79.7.1 92706 1q2lA 939 7.85e+00 1o2dA 371 8.36e+00 e.22.1.2 86591 1ng6A 148 8.43e+00 a.182.1.1 85670 1khoA 370 8.96e+00 a.124.1.1,b.12.1.3 72489,72490 2bl8A 103 9.40e+00 1mtyB 384 9.44e+00 1mtyB a.25.1.2 16740 1e5dA 402 9.72e+00 1e5dA c.23.5.1,d.157.1.3 31208,42061 1hl9A 449 9.84e+00 b.71.1.3,c.1.8.11 90650,90651 2fymA 431 1.01e+01 1bif 469 1.01e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1cv8 174 1.01e+01 1cv8 d.3.1.1 37089 1uhgA 385 1.02e+01 e.1.1.1 88491 1rrmA 386 1.02e+01 e.22.1.2 105081 1v3wA 173 1.05e+01 b.81.1.5 100291 1nv8A 284 1.10e+01 c.66.1.30 86224 1r85A 379 1.10e+01 c.1.8.3 104839 1mtyD 512 1.10e+01 1mhyD a.25.1.2 16742 2cb5A 453 1.12e+01 3gcb d.3.1.1 37035 2bikB 313 1.13e+01 1qq5A 253 1.13e+01 1qq5A c.108.1.1 43327 1jdpA 441 1.14e+01 c.93.1.1 62906 1r71A 178 1.15e+01 a.4.14.1 104823 1o5xA 248 1.16e+01 c.1.1.1 92528 1t0qA 498 1.19e+01 a.25.1.2 106220 1ci4A 89 1.25e+01 1qckA a.60.5.1 17970 1sflA 238 1.26e+01 1r2rA 248 1.27e+01 c.1.1.1 96875 451c 82 1.28e+01 451c a.3.1.1 15904 1sauA 115 1.29e+01 1vljA 407 1.30e+01 e.22.1.2 108832 1g4wR 383 1.31e+01 1g4uS a.24.11.1,c.45.1.2 16644,32692 1myt 146 1.32e+01 1a6m a.1.1.2 15207 2c71A 216 1.33e+01 1y0kA 209 1.36e+01 1om1A 332 1.37e+01 d.144.1.7 93347 1c1dA 355 1.39e+01 1bw9A c.2.1.7,c.58.1.1 30270,33918 1usyA 275 1.40e+01 1jrrA 382 1.53e+01 e.1.1.1 63256 1knyA 253 1.54e+01 1knyA a.24.16.1,d.218.1.1 75896,75897 1lddA 74 1.55e+01 a.4.5.34 73841 1kutA 230 1.57e+01 d.143.1.1 73017 1pn0A 665 1.59e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 1rtwA 220 1.59e+01 a.132.1.3 97823 1dvkA 173 1.62e+01 1dvkA a.72.1.1 18319 1z6oM 191 1.65e+01 1wzuA 300 1.68e+01 1tu9A 134 1.73e+01 a.1.1.2 107320 1yovA 537 1.73e+01 1ymiA 334 1.75e+01 1zs3A 182 1.77e+01 2bcqA 335 1.80e+01 1jq5A 370 1.81e+01 e.22.1.2 67084 2fsjA 346 1.86e+01 1e3oC 160 1.87e+01 1au7A a.4.1.1,a.35.1.1 59197,59198 1w2lA 99 1.89e+01 1u00A 227 1.89e+01 1qwgA 251 1.89e+01 c.1.27.1 96473 1lnwA 147 1.91e+01 a.4.5.28 78104 1chkA 238 1.98e+01 1chkA d.2.1.7 36999 1xfrA 128 1.99e+01 1tqgA 105 2.04e+01 a.24.10.3 107224 2gv8A 447 2.04e+01 1j5wA 298 2.10e+01 d.104.1.1 71589 1zgyA 272 2.12e+01 2cxaA 256 2.13e+01 1urvA 190 2.14e+01 1pme 380 2.15e+01 1hcl d.144.1.7 41653 1m48A 133 2.16e+01 a.26.1.2 74443 1o20A 427 2.17e+01 c.82.1.1 86556 1z23A 163 2.21e+01 1pu6A 218 2.24e+01 a.96.1.5 95123 1ui5A 215 2.29e+01 a.4.1.9,a.121.1.1 107856,107857 1xrsA 516 2.32e+01 2c1iA 431 2.34e+01 1fh9A 312 2.36e+01 1taxA c.1.8.3 28913 1eexA 554 2.39e+01 1dioA c.1.19.3 29650 1ofcX 304 2.39e+01 a.4.1.3,a.4.1.13,a.187.1.1 92826,92827,92828 1kb9B 352 2.40e+01 d.185.1.1,d.185.1.1 77313,77314 1n0qA 93 2.43e+01 k.37.1.1 79754 1ps1A 337 2.46e+01 1ps1A a.128.1.4 19450 1ee8A 266 2.47e+01 1ee8A a.156.1.2,b.113.1.1,g.39.1.8 75823,75824,75825 2iu1A 208 2.52e+01 1m6jA 261 2.53e+01 c.1.1.1 78693 1tzzA 392 2.55e+01 1ezfA 340 2.56e+01 1ezfA a.128.1.2 19440 1jpaA 312 2.59e+01 d.144.1.7 67011 2pvbA 107 2.61e+01 1a75A a.39.1.4 17205 2pth 193 2.64e+01 2pth c.56.3.1 33793 3sdhA 146 2.64e+01 3sdhA a.1.1.2 14984 1h05A 146 2.64e+01 c.23.13.1 76433 1u09A 476 2.67e+01 e.8.1.4 107545 1lvaA 258 2.70e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 1t33A 224 2.72e+01 a.4.1.9,a.121.1.1 106295,106296 2aplA 157 2.81e+01 1yqyA 523 2.90e+01 1khtA 192 2.90e+01 c.37.1.1 84401 2fbhA 146 2.94e+01 1co6A 107 2.96e+01 1ycc a.3.1.1 15894 1qlpA 394 2.97e+01 1ovaA e.1.1.1 42628 1bed 181 2.99e+01 1fvkA c.47.1.13 90330 1i4dA 224 3.01e+01 h.4.7.1 61682 1sedA 117 3.01e+01 a.219.1.1 105449 1hb6A 86 3.06e+01 a.11.1.1 70959 1pinA 163 3.07e+01 1pinA b.72.1.1,d.26.1.1 27802,38431 1qc7A 101 3.10e+01 1qc7A a.118.14.1 18456 1pmnA 364 3.14e+01 d.144.1.7 94907 2a65A 519 3.16e+01 1wznA 252 3.18e+01 1mtpA 323 3.23e+01 e.1.1.1 85107 1dk0A 188 3.24e+01 1b2vA d.35.1.1 38530 1rt8A 513 3.24e+01 a.40.1.1 105095 1jmsA 381 3.26e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1ivyA 452 3.27e+01 1ivyA c.69.1.5 34654 1mldA 314 3.29e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1p5zB 263 3.29e+01 c.37.1.1 87815 1rh5A 436 3.29e+01 f.41.1.1 97464 1i5nA 146 3.31e+01 1i5nA a.24.10.3 61805 1pujA 282 3.32e+01 c.37.1.8 88294 1ga3A 113 3.34e+01 1ga3A a.26.1.2 60411 1rxwA 336 3.41e+01 a.60.7.1,c.120.1.2 98059,98060 1vdkA 466 3.41e+01 a.127.1.1 100561 2b0tA 738 3.45e+01 1gnwA 211 3.46e+01 1gnwA a.45.1.1,c.47.1.5 17727,33021 1lj8A 493 3.47e+01 a.100.1.9,c.2.1.6 90392,90393 2fmpA 335 3.47e+01 1ujnA 348 3.48e+01 e.22.1.1 99460 1y0zA 330 3.48e+01 1csn 298 3.49e+01 1csn d.144.1.7 41664 1t6uA 117 3.53e+01 a.24.22.1 106584 1d9uA 154 3.66e+01 1am7A d.2.1.4 59111 1n45A 233 3.66e+01 a.132.1.1 79981 2fmlA 273 3.67e+01 1a6m 151 3.70e+01 1a6m a.1.1.2 15018 2cfqA 417 3.71e+01 2furA 209 3.72e+01 1xg0C 177 3.75e+01 1uxjA 309 3.75e+01 c.2.1.5,d.162.1.1 108112,108113 1oq9A 363 3.79e+01 a.25.1.2 87257 1otvA 259 3.79e+01 a.132.1.4 93526 1fit 147 3.83e+01 1fit d.13.1.1 37499 1qnxA 209 3.84e+01 1qnxA d.111.1.1 40914 1dj8A 89 3.84e+01 1bg8A a.57.1.1 17919 1u6zA 513 3.85e+01 1hyeA 313 3.89e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1qmgA 524 3.95e+01 1qmgA a.100.1.2,c.2.1.6 18785,30182 1fs7A 485 4.03e+01 1qdbA a.138.1.3 19691 1f6vA 91 4.04e+01 1f6vA a.49.1.1 17791 1mkmA 249 4.04e+01 a.4.5.33,d.110.2.2 79242,79243 1ppjC 379 4.05e+01 f.32.1.1,f.21.1.2 104256,104257 2a0b 125 4.10e+01 2a0b a.24.10.1 16630 2bcgG 453 4.10e+01 1jr8A 117 4.18e+01 a.24.15.1 67115 1e7uA 961 4.19e+01 1e8xA a.118.1.6,b.7.1.1,d.15.1.5,d.144.1.4 19147,23182,37630,41710 1f45B 197 4.19e+01 1f45B a.26.1.1 59642 1yeyA 444 4.19e+01 2apjA 260 4.22e+01 1oafA 261 4.23e+01 a.93.1.1 86734 2gdnA 267 4.23e+01 1paqA 189 4.27e+01 a.118.1.14 94413 2dh4A 340 4.28e+01 1fecA 490 4.31e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 2a2cA 478 4.31e+01 1r0dA 206 4.33e+01 a.216.1.1 104715 1dcs 311 4.33e+01 1dcs b.82.2.1 28124 1j7xA 302 4.35e+01 c.14.1.2 66425 2fckA 181 4.35e+01 1hrkA 359 4.37e+01 1hrkA c.92.1.1 61228 1u24A 337 4.37e+01 1lqaA 346 4.38e+01 c.1.7.1 84674 2a7oA 112 4.43e+01 1j5sA 463 4.47e+01 c.1.9.8 71580 2b9hA 353 4.48e+01 1e6wA 260 4.53e+01 1e6wA c.2.1.2 59326 2a11A 242 4.55e+01 1sgmA 191 4.56e+01 a.4.1.9,a.121.1.1 105537,105538 1hq0A 295 4.56e+01 1hzgA d.194.1.1 61122 1qpcA 279 4.58e+01 1fgkA d.144.1.7 41685 1zzpA 130 4.58e+01 1pa7A 130 4.58e+01 a.40.1.1 94410 1z6mA 175 4.65e+01 1sbxA 106 4.66e+01 a.6.1.4 105414 1dm5A 315 4.75e+01 1avc a.65.1.1 18186 1w2xA 758 4.76e+01 c.14.1.4,c.14.1.4 109134,109135 1ispA 181 4.80e+01 c.69.1.18 76778 2a19A 175 4.80e+01 1xo0A 324 4.81e+01 1yi8A 351 4.84e+01 2ftzA 284 4.85e+01 1tuzA 118 4.85e+01 1e29A 135 4.86e+01 1e29A a.3.1.1 59161 1kblA 873 4.87e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1ct5A 256 4.87e+01 1ct5A c.1.6.2 28663 1x3kA 152 4.88e+01 2c43A 323 4.93e+01 1dgnA 89 4.96e+01 1dgnA a.77.1.3 18436 1ijyA 130 4.97e+01 1ijxA a.141.1.1 62517 1jdlA 121 4.98e+01 a.3.1.1 66557 2a61A 145 4.98e+01 1tw9A 206 5.04e+01 a.45.1.1,c.47.1.5 107381,107382 1eteA 134 5.12e+01 1eteA a.26.1.2 16869 1neyA 247 5.13e+01 c.1.1.1 80449 1m98A 317 5.13e+01 a.175.1.1,d.17.4.6 78866,78867 2ah5A 210 5.13e+01 4tmkA 213 5.14e+01 5tmpA c.37.1.1 31930 1azo 232 5.15e+01 1azo c.52.1.14 33329 1k6kA 143 5.15e+01 a.174.1.1 77274 2c3nA 247 5.15e+01 2iu5A 195 5.19e+01 2btoA 473 5.30e+01 2frfA 153 5.42e+01 1xzoA 174 5.47e+01 1l5xA 280 5.52e+01 c.106.1.1 77718 2gs8A 317 5.53e+01 1w33A 181 5.56e+01 1b0uA 262 5.61e+01 1b0uA c.37.1.12 32370 1n82A 331 5.70e+01 c.1.8.3 91703 1dmuA 299 5.72e+01 1dmuA c.52.1.4 33294 1kyqA 274 5.72e+01 c.2.1.11,e.37.1.1 73281,73282 1qv1A 195 5.75e+01 a.39.1.5 96347 1js1X 324 5.76e+01 c.78.1.1,c.78.1.1 71834,71835 1sr2A 116 5.78e+01 1ymtA 246 5.79e+01 1alvA 173 5.85e+01 1alvA a.39.1.8 17370 1mw7A 240 5.86e+01 e.39.1.1 79557 1brt 277 5.88e+01 1brt c.69.1.12 34699 1zk8A 183 5.88e+01 1n71A 180 5.90e+01 d.108.1.1 85370 1hr6A 475 5.92e+01 1hr6A d.185.1.1,d.185.1.1 61164,61165 1z72A 225 5.92e+01 1dwkA 156 5.96e+01 1dw9A a.35.1.4,d.72.1.1 17075,39606 1v74A 107 5.98e+01 d.243.1.1 100442 1d1qA 161 6.04e+01 1dg9A c.44.1.1 32642 1c52 131 6.04e+01 1c52 a.3.1.1 15810 1kb9A 431 6.06e+01 d.185.1.1,d.185.1.1 77311,77312 2ghcX 261 6.12e+01 1j8uA 325 6.17e+01 d.178.1.1 71611 1sxvA 172 6.19e+01 1fnnA 389 6.19e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 1z77A 200 6.27e+01 2d2sA 235 6.27e+01 1lvwA 295 6.34e+01 c.68.1.6 84723 1guxA 218 6.40e+01 1guxA a.74.1.3 18388 1v4xB 146 6.42e+01 a.1.1.2 108364 1x9zA 188 6.49e+01 1olmA 403 6.52e+01 a.5.3.1,b.132.1.1,c.13.1.1 104008,104009,104010 1xyzA 347 6.55e+01 1taxA c.1.8.3 28804 1ux8A 132 6.56e+01 1jgsA 138 6.56e+01 a.4.5.28 66683 1keaA 221 6.56e+01 a.96.1.2 68491 2fkcA 247 6.57e+01 1mwmA 320 6.58e+01 c.55.1.1,c.55.1.1 79580,79581 1xjdA 345 6.59e+01 2gsfA 373 6.62e+01 1tjoA 182 6.62e+01 1v4pA 157 6.65e+01 1ro7A 259 6.65e+01 c.130.1.1 97667 2glfA 450 6.67e+01 2auwA 170 6.72e+01 1axn 323 6.72e+01 1avc a.65.1.1 18149 1ka1A 357 6.73e+01 e.7.1.1 68369 1pe9A 361 6.76e+01 b.80.1.1 94595 1su0B 159 6.77e+01 d.224.1.2 106015 1u2pA 163 6.78e+01 1g0cA 364 6.80e+01 7a3hA c.1.8.3 60165 1pvaA 110 6.83e+01 1a75A a.39.1.4 17207 2dc3A 193 6.88e+01 1r45A 204 6.89e+01 1bob 320 6.89e+01 1bob d.108.1.1 40816 1ykuA 136 6.93e+01 1svdM 110 6.93e+01 1lo7A 141 6.93e+01 d.38.1.1 74144 1vfrA 218 6.96e+01 1vfrA d.90.1.1 40247 1p68A 102 6.96e+01 k.8.1.1 94158 1pjcA 361 7.01e+01 1sayA c.2.1.4,c.23.12.2 30101,31361 1txgA 335 7.02e+01 1ca1 370 7.03e+01 1ca1 a.124.1.1,b.12.1.3 19340,23648 1xnzA 264 7.03e+01 1wteA 272 7.07e+01 1e4yA 214 7.08e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1opjA 293 7.08e+01 d.144.1.7 87230 1tt7A 330 7.08e+01 2aa1B 146 7.14e+01 1dqeA 137 7.14e+01 1dqeA a.39.2.1 17388 1wd5A 208 7.14e+01 1tkeA 224 7.18e+01 1zsxA 347 7.22e+01 1gjnA 153 7.28e+01 a.1.1.2 70191 1dqzA 280 7.29e+01 1dqyA c.69.1.3 34638 1ewkA 490 7.30e+01 1ewkA c.93.1.1 35712 1l8rA 101 7.32e+01 a.6.1.4 73700 1yozA 116 7.35e+01 1w07A 659 7.43e+01 2g9zA 348 7.43e+01 2f4qA 346 7.47e+01 2genA 197 7.48e+01 2cdnA 201 7.56e+01 1yviA 149 7.56e+01 2dbnA 461 7.57e+01 1rylA 167 7.59e+01 d.276.1.1 105124 1jmuB 666 7.63e+01 1ihoA 283 7.63e+01 1ihoA c.26.1.4 62390 1h6gA 256 7.66e+01 1h6gA a.24.9.1,a.24.9.1 60669,60670 1zchA 255 7.70e+01 2gauA 232 7.72e+01 1xd8A 289 7.72e+01 1sz7A 200 7.73e+01 2cujA 108 7.75e+01 1epuA 591 7.77e+01 1dn1A e.25.1.1 43358 2blkA 122 7.78e+01 1ccwB 483 7.80e+01 1cb7B c.1.19.2 29646 1yz7A 188 7.82e+01 1s3eA 520 7.83e+01 c.3.1.2,d.16.1.5 98426,98427 1w4xA 542 7.93e+01 c.3.1.5,c.3.1.5 109171,109172 1gnxA 479 7.96e+01 c.1.8.4 76241 1ryiA 382 8.00e+01 1wc3A 219 8.02e+01 1w5fA 353 8.02e+01 2eu8A 216 8.04e+01 1g6aA 271 8.05e+01 1btl e.3.1.1 42704 1moq 368 8.08e+01 1moq c.80.1.1 35302 1rqwA 207 8.10e+01 b.25.1.1 97781 1pl4A 198 8.17e+01 a.2.11.1,d.44.1.1 94854,94855 1u55A 188 8.30e+01 d.278.1.1 107677 1tdpA 111 8.37e+01 a.29.8.1 106781 1rxqA 178 8.39e+01 a.213.1.1 105118 2es9A 115 8.39e+01 2b5aA 77 8.42e+01 1wtjA 343 8.44e+01 1mla 309 8.46e+01 1mla c.19.1.1,d.58.23.1 31031,39383 1m6sA 347 8.47e+01 c.67.1.1 78701 1bqbA 301 8.51e+01 1hyt d.92.1.2 58962 1f20A 435 8.60e+01 b.43.4.1,c.25.1.4 64932,64933 1uhvA 500 8.62e+01 b.71.1.2,c.1.8.3 99402,99403 1ynfA 458 8.66e+01 1ixkA 315 8.69e+01 c.66.1.38 90716 1jihA 531 8.72e+01 d.240.1.1,e.8.1.7 90374,90375 2fulA 178 8.73e+01 1u14A 172 8.74e+01 c.51.4.3 107579 1b5qA 472 8.85e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 2fswA 107 8.93e+01 2cmwA 310 8.95e+01 1eu1A 780 8.95e+01 1dmr b.52.2.2,c.81.1.1 26903,35311