# 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.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 1uqrA 154 1.04e-01 c.23.13.1 99779 1o9rA 162 1.88e-01 a.25.1.1 86706 1ps9A 671 2.67e-01 c.1.4.1,c.3.1.1,c.4.1.1 95076,95077,95078 1yarA 233 3.63e-01 1to3A 304 3.68e-01 c.1.10.1 107161 1j0aA 325 5.79e-01 c.79.1.1 83871 1xr4A 509 6.57e-01 1z41A 338 7.39e-01 1wc9A 169 7.78e-01 1fzqA 181 8.21e-01 1hurA c.37.1.8 32060 2dhqA 146 9.07e-01 2dhqA c.23.13.1 31382 1vpgA 192 1.16e+00 1ki9A 192 1.25e+00 c.37.1.1 84404 1pii 452 1.58e+00 1pii c.1.2.4,c.1.2.4 28559,28563 1w1kA 560 1.68e+00 d.58.32.1,d.145.1.1 109059,109060 1b1cA 181 1.72e+00 1amoA c.23.5.2 31212 1yacA 208 1.95e+00 1yacA c.33.1.3 31757 1u9yA 284 1.96e+00 1h05A 146 1.97e+00 c.23.13.1 76433 1khtA 192 1.98e+00 c.37.1.1 84401 1p0kA 349 2.07e+00 c.1.4.1 87648 1mr3F 181 2.25e+00 c.37.1.8 79422 1e8gA 560 2.25e+00 1qltA d.58.32.1,d.145.1.1 39455,41718 2g8lA 299 2.33e+00 1vbuA 328 2.41e+00 1dosA 358 2.42e+00 1dosA c.1.10.2 29175 1dkuA 317 2.43e+00 1dkuA c.61.1.2,c.61.1.2 34118,34119 2chnA 716 2.47e+00 1mw9X 592 2.55e+00 e.10.1.1 91480 2b6hA 192 2.69e+00 1d0iA 156 2.71e+00 2dhqA c.23.13.1 31383 1sjqA 105 2.71e+00 d.58.7.1 105660 1l4uA 176 2.98e+00 c.37.1.2 73568 1hyeA 313 3.01e+00 2cmd c.2.1.5,d.162.1.1 61400,61401 1ypfA 336 3.29e+00 1gtzA 156 3.54e+00 c.23.13.1 70539 1t3gA 159 3.63e+00 2a0b 125 3.78e+00 2a0b a.24.10.1 16630 1sz7A 200 3.89e+00 2ad9A 119 4.06e+00 1i5nA 146 4.09e+00 1i5nA a.24.10.3 61805 1tzjA 338 4.18e+00 1wpoA 256 4.25e+00 1lay b.57.1.1 27012 1w0mA 226 4.32e+00 c.1.1.1 109027 1mdwA 328 4.42e+00 d.3.1.3 84934 1nw2A 105 4.53e+00 c.47.1.1 92215 1vdkA 466 4.71e+00 a.127.1.1 100561 1nswA 105 4.83e+00 c.47.1.1 92097 1sg6A 393 4.86e+00 e.22.1.1 105522 1mv8A 436 4.90e+00 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1dpsA 167 5.13e+00 1dpsA a.25.1.1 16716 1rk6A 496 5.44e+00 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 2f5xA 312 5.48e+00 1f2dA 341 5.97e+00 1f2dA c.79.1.1 35298 1m7jA 484 5.97e+00 b.92.1.6,b.92.1.6,c.1.9.11 78732,78733,78734 1h3nA 878 6.40e+00 a.27.1.1,b.51.1.1,c.26.1.1 76641,76642,76643 1erzA 303 6.42e+00 1erzA d.160.1.2 59498 2bvlA 543 6.57e+00 1uf5A 303 7.14e+00 d.160.1.2 107808 1jclA 260 7.32e+00 c.1.10.1 66501 1o5kA 306 7.66e+00 c.1.10.1 92504 1h2vC 771 7.98e+00 a.118.1.14,a.118.1.14,a.118.1.14 76592,76593,76594 1o3yA 166 8.05e+00 c.37.1.8 86618 1pa7A 130 8.07e+00 a.40.1.1 94410 1z83A 196 8.08e+00 1uf3A 228 8.33e+00 d.159.1.6 99317 1j0dA 341 8.45e+00 c.79.1.1 83902 2b06A 155 8.56e+00 1xyzA 347 8.56e+00 1taxA c.1.8.3 28804 1p1xA 260 9.20e+00 c.1.10.1 104060 1vqoO 116 9.72e+00 1i60A 278 9.99e+00 c.1.15.4 71118 1zj6A 187 1.01e+01 1meoA 209 1.01e+01 c.65.1.1 79035 1f89A 291 1.03e+01 d.160.1.1 64988 1g2qA 187 1.03e+01 c.61.1.1 65117 1uuyA 167 1.07e+01 c.57.1.1 108059 1uptA 171 1.09e+01 c.37.1.8 99767 1bu7A 455 1.11e+01 1bu7A a.104.1.1 18937 1edt 271 1.12e+01 2ebn c.1.8.5 28993 1r4aA 165 1.14e+01 c.37.1.8 96986 1pdo 135 1.16e+01 1pdo c.54.1.1 33376 1ex1A 605 1.19e+01 1ex1A c.1.8.7,c.23.11.1 29013,31347 2aotA 292 1.20e+01 1qksA 567 1.20e+01 1qksA a.3.1.2,b.70.2.1 15951,27710 1c93A 265 1.20e+01 2ebn c.1.8.5 28998 4pgaA 337 1.22e+01 4pgaA c.88.1.1 35565 1xkrA 206 1.24e+01 2gnoA 305 1.25e+01 1uptC 170 1.28e+01 c.37.1.8 99769 2g62A 325 1.28e+01 1yzgA 179 1.28e+01 1s72O 116 1.31e+01 c.12.1.1 105334 2b4gA 317 1.31e+01 2f51A 118 1.34e+01 1xesA 413 1.40e+01 1ituA 369 1.42e+01 c.1.9.7 71423 1g8lA 411 1.43e+01 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 2f6hX 419 1.47e+01 1x38A 602 1.47e+01 1q1gA 276 1.52e+01 c.56.2.1 95574 1ug7A 128 1.59e+01 a.24.24.1 107824 1php 394 1.62e+01 16pk c.86.1.1 35452 1k32A 1045 1.63e+01 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1auoA 218 1.66e+01 1auoA c.69.1.14 34716 1bxkA 355 1.67e+01 1bxkA c.2.1.2 29803 1o60A 292 1.72e+01 c.1.10.4 92532 1h6kA 757 1.74e+01 a.118.1.14,a.118.1.14,a.118.1.14 60675,60676,60677 1r8sA 164 1.74e+01 c.37.1.8 97247 1jj2B 337 1.75e+01 1ffkB b.43.3.2 63086 1s72B 338 1.77e+01 b.43.3.2 105320 1izcA 339 1.81e+01 c.1.12.5 83838 1jqeA 292 1.82e+01 c.66.1.19 71789 1nfp 228 1.82e+01 1nfp c.1.16.2 29555 1jndA 420 1.85e+01 c.1.8.5,d.26.3.1 71757,71758 1zcoA 262 1.86e+01 1a4iA 301 1.91e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1mldA 314 1.91e+01 2cmd c.2.1.5,d.162.1.1 30122,42089 1qd1A 325 1.96e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1lehA 364 1.96e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1wy1A 172 1.98e+01 1i3dA 146 1.99e+01 a.1.1.2 61587 1mup 166 2.00e+01 1mup b.60.1.1 27133 2cw6A 298 2.01e+01 1vjgA 218 2.03e+01 c.23.10.6 100810 1c0pA 363 2.04e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1nf2A 268 2.07e+01 c.108.1.10 91849 1amuA 563 2.07e+01 1amuA e.23.1.1 43351 1h0oA 390 2.09e+01 a.25.1.2 70845 1rd5A 262 2.10e+01 1jv4A 162 2.12e+01 b.60.1.1 67343 1t0iA 191 2.14e+01 c.23.5.4 106209 1i06A 180 2.15e+01 1mup b.60.1.1 27131 2czdA 208 2.16e+01 1lxnA 99 2.17e+01 d.58.48.1 84737 1vizA 240 2.24e+01 c.1.4.1 100784 1i05A 180 2.24e+01 1mup b.60.1.1 27130 1zy9A 564 2.25e+01 1u2zA 433 2.26e+01 c.66.1.31 107626 2b3hA 329 2.26e+01 1dhn 121 2.26e+01 1dhn d.96.1.3 40663 1b16A 254 2.27e+01 1b16A c.2.1.2 29875 1cg5A 141 2.27e+01 1abwA a.1.1.2 15406 1c02A 166 2.28e+01 1qspA a.24.10.2 16633 1xm3A 264 2.29e+01 1hrhA 136 2.31e+01 1rthA c.55.3.1 33577 1gudA 288 2.33e+01 c.93.1.1 83326 2bsxA 253 2.34e+01 1gefA 123 2.34e+01 1gefA c.52.1.18 60465 1lvaA 258 2.37e+01 a.4.5.35,a.4.5.35,a.4.5.35,a.4.5.35 74276,74277,74278,74279 2ffcA 353 2.39e+01 1liiA 363 2.39e+01 c.72.1.1 73921 2tpsA 227 2.47e+01 2tpsA c.1.3.1 28591 1dorA 311 2.48e+01 2dorA c.1.4.1 28595 1zndA 174 2.49e+01 2cbiA 594 2.50e+01 1i36A 264 2.52e+01 a.100.1.8,c.2.1.6 71108,71109 1u0fA 564 2.54e+01 1qy1A 174 2.58e+01 b.60.1.1 96568 1sbyA 254 2.60e+01 1lxjA 104 2.60e+01 d.58.48.1 84736 1p80A 753 2.62e+01 c.23.16.3,e.5.1.1 94337,94338 2gx9A 129 2.65e+01 1km4A 247 2.66e+01 c.1.2.3 72740 1cf9A 753 2.69e+01 1cf9A c.23.16.3,e.5.1.1 31441,42815 2dorA 311 2.70e+01 2dorA c.1.4.1 28593 1t6cA 315 2.81e+01 c.55.1.8,c.55.1.8 106558,106559 1ubeA 349 2.81e+01 c.37.1.11,d.48.1.1 88412,88413 1c7gA 456 2.85e+01 c.67.1.2 90415 1v1rB 342 2.85e+01 c.36.1.7,c.48.1.2 108273,108274 1qxhA 167 2.87e+01 c.47.1.10 96528 1hurA 180 2.94e+01 1hurA c.37.1.8 32052 1gewA 356 2.94e+01 1gewA c.67.1.1 60470 2a2fX 325 2.97e+01 7odcA 424 2.97e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1pnsC 206 3.07e+01 i.1.1.1 88170 1vqoB 338 3.07e+01 1hyuA 521 3.09e+01 1hyuA c.3.1.5,c.3.1.5,c.47.1.2,c.47.1.2 30547,30548,32779,32780 1w68A 390 3.12e+01 a.25.1.2 109216 1v4aA 440 3.12e+01 a.24.16.4,d.218.1.9 108350,108351 2gq1A 332 3.13e+01 1pj5A 830 3.14e+01 b.44.2.1,c.3.1.2,d.16.1.5,d.250.1.1 94742,94743,94744,94745 1q0sA 259 3.15e+01 c.66.1.28 95509 1vr6A 350 3.16e+01 1sfjA 238 3.18e+01 1qghA 156 3.18e+01 1qghA a.25.1.1 16728 2plc 274 3.19e+01 2plc c.1.18.2 29614 1zzmA 259 3.21e+01 2cmuA 342 3.23e+01 1x1nA 524 3.30e+01 2cxnA 557 3.31e+01 1olsB 342 3.32e+01 c.36.1.7,c.48.1.2 93332,93333 1ii7A 333 3.32e+01 1ii7A d.159.1.4 62415 1ib2A 349 3.32e+01 1ib2A a.118.1.8 62141 1xg7A 250 3.33e+01 2fymA 431 3.36e+01 1x7yB 342 3.39e+01 1fjgC 239 3.41e+01 1fjfC d.52.3.1,d.53.1.1 38831,38839 1rzmA 338 3.45e+01 c.1.10.4 105137 1ej1A 190 3.46e+01 1ejhA d.86.1.1 40144 1txvB 440 3.49e+01 1ji8A 111 3.50e+01 d.203.1.1 66733 1lucA 355 3.57e+01 1lucA c.1.16.1 29547 1jfuA 186 3.60e+01 c.47.1.10 62940 1ir6A 424 3.62e+01 c.107.1.2 71342 1tjoA 182 3.64e+01 1k1xA 659 3.65e+01 a.8.3.2,b.30.5.8,c.6.2.2 84279,84280,84281 1yf3A 259 3.68e+01 1wndA 495 3.71e+01 1kafA 108 3.74e+01 d.199.1.1 68372 1lw7A 365 3.74e+01 c.26.1.3,c.37.1.1 74295,74296 1iv8A 720 3.75e+01 b.71.1.1,c.1.8.1 76842,76843 1x1zA 252 3.82e+01 1h09A 338 3.82e+01 b.109.1.1,c.1.8.8 83420,83421 1d2zB 153 3.85e+01 1d2zB a.77.1.2 18439 1xtaA 221 3.91e+01 2bfdB 345 3.97e+01 1wwkA 307 4.01e+01 2a19B 284 4.02e+01 1xi3A 215 4.03e+01 c.1.3.1 109601 2aeeA 211 4.09e+01 1sazA 381 4.10e+01 1wyzA 242 4.12e+01 2c07A 285 4.14e+01 1sflA 238 4.14e+01 1jubA 311 4.16e+01 c.1.4.1 90908 1k0wA 231 4.19e+01 c.74.1.1 77220 2absA 383 4.21e+01 1t3lA 337 4.21e+01 b.34.2.1,c.37.1.1 106358,106359 1hnjA 317 4.29e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 2ghpA 292 4.30e+01 1khyA 148 4.30e+01 a.174.1.1 77410 1nf1A 333 4.30e+01 1nf1A a.116.1.2 19110 1gdhA 320 4.43e+01 1gdhA c.2.1.4,c.23.12.1 30095,31355 1lyxA 248 4.48e+01 c.1.1.1 78304 1s95A 333 4.49e+01 d.159.1.3 105375 1j96A 323 4.54e+01 c.1.7.1 71616 1xsm 390 4.55e+01 1xsm a.25.1.2 16804 1bolA 222 4.60e+01 1bolA d.124.1.1 41120 1yb2A 275 4.64e+01 1fmjA 351 4.66e+01 c.37.1.5 59879 1tl9A 339 4.71e+01 1x9iA 302 4.75e+01 1jyaA 130 4.81e+01 d.198.1.1 67453 1pq4A 291 4.83e+01 c.92.2.2 94995 1eemA 241 4.91e+01 1eemA a.45.1.1,c.47.1.5 17717,33011 1pbgA 468 4.94e+01 1e70M c.1.8.4 28946 1vl2A 421 4.96e+01 c.26.2.1,d.210.1.1 108708,108709 1mojA 182 4.99e+01 a.25.1.1 91367 1y5eA 169 5.01e+01 1dxy 333 5.06e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 1nrlA 316 5.11e+01 a.123.1.1 92091 1ywfA 296 5.14e+01 1v4xB 146 5.17e+01 a.1.1.2 108364 1dtwB 342 5.23e+01 1qs0B c.36.1.7,c.48.1.2 31828,33102 8abp 306 5.23e+01 8abp c.93.1.1 35647 1zbqA 327 5.28e+01 1mkmA 249 5.42e+01 a.4.5.33,d.110.2.2 79242,79243 1l1qA 186 5.44e+01 c.61.1.1 77653 1yt8A 539 5.47e+01 1kshA 186 5.55e+01 c.37.1.8 72914 1z2lA 423 5.56e+01 1a8i 842 5.58e+01 1a8i c.87.1.4 35490 1x42A 232 5.61e+01 1vplA 256 5.63e+01 1nekA 588 5.63e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1o5xA 248 5.66e+01 c.1.1.1 92528 1dofA 403 5.69e+01 1c3cA a.127.1.1 19429 1yhtA 367 5.70e+01 2pth 193 5.75e+01 2pth c.56.3.1 33793 1tqjA 230 5.79e+01 c.1.2.2 107228 1w41A 101 5.81e+01 1byi 224 5.83e+01 1byi c.37.1.10 32199 1wd5A 208 5.86e+01 1vhnA 318 5.86e+01 c.1.4.1 100693 1rz3A 201 5.89e+01 c.37.1.6 98132 1l6wA 220 5.89e+01 c.1.10.1 73632 2bhoA 130 5.93e+01 1e6cA 173 5.93e+01 1shkA c.37.1.2 59296 1pbe 394 5.94e+01 1pbe c.3.1.2,d.16.1.2 30338,37869 1o6zA 303 5.97e+01 c.2.1.5,d.162.1.1 81107,81108 2cu3A 64 5.99e+01 1qs0B 338 6.01e+01 1qs0B c.36.1.7,c.48.1.2 31830,33103 1jayA 212 6.05e+01 c.2.1.6 66478 1of8A 370 6.15e+01 c.1.10.4 92819 1vp8A 201 6.16e+01 1l8bA 190 6.21e+01 d.86.1.1 73683 1womA 271 6.24e+01 1mmsA 140 6.26e+01 1mmsA a.4.7.1,d.47.1.1 16247,38766 1ceo 343 6.31e+01 1ceo c.1.8.3 28808 1tzbA 302 6.33e+01 c.80.1.1 107470 1yzfA 195 6.34e+01 1fl2A 310 6.36e+01 1hyuA c.3.1.5,c.3.1.5 59869,59870 1im8A 244 6.43e+01 c.66.1.14 66212 2f9dA 125 6.43e+01 2d13A 227 6.47e+01 1lqaA 346 6.51e+01 c.1.7.1 84674 1hx0A 496 6.51e+01 b.71.1.1,c.1.8.1 61346,61347 1zowA 313 6.56e+01 1dvjA 246 6.72e+01 1dvjA c.1.2.3 28546 1ql0A 241 6.74e+01 1qaeA d.4.1.2 37139 1v98A 140 6.79e+01 1ixh 321 6.79e+01 1ixh c.94.1.1 35761 2ew8A 249 6.81e+01 1j8yF 297 6.81e+01 1ng1 a.24.13.1,c.37.1.10 62747,62748 1ccwA 137 6.87e+01 1be1 c.23.6.1 31238 1uwmA 106 6.88e+01 1qqeA 292 6.93e+01 1qqeA a.118.8.1 19210 1jigA 146 7.01e+01 a.25.1.1 71685 1obr 326 7.03e+01 1aye c.56.5.2 33828 1ihjA 98 7.03e+01 1pdr b.36.1.1 62382 1aqm 453 7.06e+01 1smd b.71.1.1,c.1.8.1 27717,28704 1qwgA 251 7.46e+01 c.1.27.1 96473 2fug7 129 7.48e+01 1lm4A 194 7.54e+01 d.167.1.1 84626 1on2A 142 7.57e+01 a.4.5.24,a.76.1.1 87103,87104 1hcuA 503 7.61e+01 a.102.2.1 65796 1jx2B 315 7.63e+01 c.37.1.8 67404 1rypF 233 7.74e+01 1rypF d.153.1.4 41937 1j6oA 268 7.76e+01 c.1.9.12 77088 1midA 91 7.81e+01 a.52.1.1 91280 1pgtA 210 7.87e+01 1pgtA a.45.1.1,c.47.1.5 17515,32809 1o94A 729 7.90e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 1ub3A 220 7.94e+01 c.1.10.1 88395 1fds 327 7.97e+01 1fds c.2.1.2 29838 1zn8A 180 8.02e+01 1gc5A 467 8.05e+01 1gc5A c.72.1.3 60429 1bueA 265 8.08e+01 1btl e.3.1.1 42727 1gg4A 452 8.12e+01 1gg4A c.59.1.1,c.98.1.1,c.72.2.1 33957,58985,58986 2a5dA 175 8.14e+01 1fiy 883 8.20e+01 1fiy c.1.12.3 29307 1o4sA 389 8.23e+01 c.67.1.1 86620 1cy9A 264 8.28e+01 1ecl e.10.1.1 43236 2igd 61 8.31e+01 2igd d.15.7.1 37821 2trxA 108 8.35e+01 1thx c.47.1.1 32719 1c9kA 180 8.35e+01 1c9kB c.37.1.11 32363 1va4A 279 8.36e+01 c.69.1.12 108458 1ykjA 394 8.40e+01 1mxmA 254 8.44e+01 b.38.1.3,d.58.43.1,f.34.1.1 79647,79648,79649 1e9mA 106 8.44e+01 1ayfA d.15.4.1 59397 1r7aA 504 8.44e+01 b.71.1.1,c.1.8.1 97192,97193 1nbaA 264 8.44e+01 1nbaA c.33.1.3 31753 1ta0A 197 8.46e+01 c.108.1.16 106729 1hzdA 272 8.50e+01 c.14.1.3 65969 1z77A 200 8.57e+01 1zkdA 387 8.59e+01 5abp 306 8.61e+01 8abp c.93.1.1 35651 1ezwA 349 8.62e+01 1ezwA c.1.16.3 29558 1vhcA 224 8.65e+01 c.1.10.1 100661 1f9vA 347 8.69e+01 1bg2 c.37.1.9 59745 1uroA 367 8.70e+01 1uroA c.1.22.1 29675 1r3sA 367 8.71e+01 c.1.22.1 96963 1k2xB 143 8.74e+01 1uxy 340 8.80e+01 2mbr d.145.1.2,d.146.1.1 41748,41761 1wi0A 113 8.85e+01 1ep3A 311 8.97e+01 2dorA c.1.4.1 28597 1mzjA 339 8.97e+01 c.95.1.2,c.95.1.2 79700,79701 1gsa 316 8.97e+01 1gsa c.30.1.3,d.142.1.1 31718,41477 1rxxA 421 8.98e+01 d.126.1.4 98061