# List of top-scoring protein chains for t06-100-30-stride-ebghtl-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 1vplA 256 4.48e-02 1brwA 433 2.02e-01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 2d2eA 250 2.09e-01 1tuaA 191 3.16e-01 d.51.1.1,d.51.1.1 107321,107322 1gtzA 156 4.12e-01 c.23.13.1 70539 1uqtA 482 4.62e-01 c.87.1.6 99794 1u1iA 392 5.42e-01 c.2.1.3,d.81.1.3 107582,107583 1uanA 227 6.12e-01 c.134.1.1 99135 1xyzA 347 8.15e-01 1taxA c.1.8.3 28804 1uqrA 154 8.29e-01 c.23.13.1 99779 1vbuA 328 8.51e-01 1y5eA 169 9.42e-01 1fzqA 181 1.13e+00 1hurA c.37.1.8 32060 1pujA 282 1.16e+00 c.37.1.8 88294 1pdo 135 1.31e+00 1pdo c.54.1.1 33376 1km4A 247 1.37e+00 c.1.2.3 72740 1r31A 428 1.45e+00 d.58.20.1,d.179.1.1 96897,96898 1x1zA 252 1.46e+00 1q9uA 130 1.50e+00 d.129.7.1 96314 1h05A 146 1.53e+00 c.23.13.1 76433 2gnoA 305 1.56e+00 2b0tA 738 1.78e+00 1vhwA 253 1.99e+00 c.56.2.1 100706 1mw9X 592 2.13e+00 e.10.1.1 91480 1d3vA 323 2.14e+00 1d3vA c.42.1.1 32559 1hkhA 279 2.44e+00 c.69.1.12 90628 1j0dA 341 2.50e+00 c.79.1.1 83902 2aebA 322 2.61e+00 2bsxA 253 2.62e+00 2fuvA 549 2.69e+00 1g8lA 411 2.74e+00 1g8lA b.85.6.1,b.103.1.1,c.57.1.2 60365,60366,60367 1pii 452 2.93e+00 1pii c.1.2.4,c.1.2.4 28559,28563 1tzjA 338 3.04e+00 1z15A 344 3.22e+00 1x9iA 302 3.54e+00 2bjvA 265 3.56e+00 1bn7A 294 3.64e+00 1bn6A c.69.1.8 34677 1khtA 192 3.70e+00 c.37.1.1 84401 1y0yA 353 3.76e+00 1vdkA 466 3.92e+00 a.127.1.1 100561 2f5xA 312 4.02e+00 1tv8A 340 4.16e+00 c.1.28.3 107352 1lzlA 323 4.37e+00 c.69.1.2 78306 1wozA 177 4.62e+00 1zxxA 319 4.68e+00 1p0kA 349 4.82e+00 c.1.4.1 87648 1o60A 292 5.19e+00 c.1.10.4 92532 1jkmB 361 5.44e+00 1jkmA c.69.1.2 34634 2b7kA 200 5.80e+00 1kv5A 250 5.90e+00 c.1.1.1 73052 1ituA 369 5.91e+00 c.1.9.7 71423 2b0lA 102 5.91e+00 1zavA 180 6.33e+00 1jl3A 139 6.37e+00 c.44.1.1 66826 1uz5A 402 6.61e+00 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 1ceo 343 6.81e+00 1ceo c.1.8.3 28808 2aq4A 434 6.91e+00 1oltA 457 6.99e+00 c.1.28.2 93334 1kamA 194 7.06e+00 c.26.1.3 72254 1f74A 293 7.12e+00 1nal3 c.1.10.1 29079 1t0hB 224 7.23e+00 c.37.1.1 106208 1mr3F 181 7.31e+00 c.37.1.8 79422 1ki9A 192 7.76e+00 c.37.1.1 84404 2gjlA 328 7.89e+00 1gudA 288 8.26e+00 c.93.1.1 83326 1v93A 296 8.48e+00 c.1.23.1 100532 2axpA 173 8.63e+00 1w44A 331 8.79e+00 2tpt 440 8.83e+00 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17759,31623,38621 1qf9A 194 8.84e+00 1zin c.37.1.1 31848 1lv7A 257 9.00e+00 c.37.1.20 78232 2pth 193 9.06e+00 2pth c.56.3.1 33793 2trcP 217 9.38e+00 1b9yC c.47.1.6 33051 1sqsA 242 9.45e+00 c.23.5.5 98968 1q2lA 939 9.56e+00 1gpjA 404 9.69e+00 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 2dri 271 1.02e+01 2dri c.93.1.1 35637 2fcr 173 1.05e+01 1rcf c.23.5.1 31151 1lxjA 104 1.05e+01 d.58.48.1 84736 1zp4A 304 1.06e+01 1o5zA 442 1.07e+01 c.59.1.2,c.72.2.2 92530,92531 1u9yA 284 1.11e+01 1g6hA 257 1.12e+01 1gajA c.37.1.12 60318 2chnA 716 1.13e+01 1jksA 294 1.13e+01 d.144.1.7 71710 1o0yA 260 1.14e+01 c.1.10.1 80756 1va4A 279 1.15e+01 c.69.1.12 108458 1dqzA 280 1.15e+01 1dqyA c.69.1.3 34638 1r8sA 164 1.16e+01 c.37.1.8 97247 1s99A 200 1.17e+01 1wwkA 307 1.18e+01 1snnA 227 1.19e+01 d.115.1.2 105821 1thfD 253 1.23e+01 1thfD c.1.2.1 28535 2trxA 108 1.23e+01 1thx c.47.1.1 32719 1np7A 489 1.25e+01 a.99.1.1,c.28.1.1 80677,80678 1yz7A 188 1.25e+01 2c1lA 358 1.26e+01 1wu7A 434 1.29e+01 1c93A 265 1.31e+01 2ebn c.1.8.5 28998 1sb8A 352 1.33e+01 c.2.1.2 105410 2plc 274 1.38e+01 2plc c.1.18.2 29614 1pa7A 130 1.39e+01 a.40.1.1 94410 1dkuA 317 1.41e+01 1dkuA c.61.1.2,c.61.1.2 34118,34119 1on3A 523 1.45e+01 c.14.1.4,c.14.1.4 87107,87108 1nswA 105 1.46e+01 c.47.1.1 92097 1jljA 189 1.50e+01 c.57.1.1 63169 1edt 271 1.51e+01 2ebn c.1.8.5 28993 1z83A 196 1.52e+01 1iab 200 1.52e+01 1iae d.92.1.8 40312 1u9iA 519 1.53e+01 1e4yA 214 1.53e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1x7yB 342 1.54e+01 1kshA 186 1.54e+01 c.37.1.8 72914 1udxA 416 1.60e+01 b.117.1.1,c.37.1.8,d.242.1.1 99228,99229,99230 2f6uA 234 1.61e+01 1o58A 303 1.64e+01 c.79.1.1 92491 1ypfA 336 1.66e+01 1cg2A 393 1.67e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 1zbqA 327 1.67e+01 1ll2A 333 1.68e+01 c.68.1.14 74005 2cmuA 342 1.69e+01 1a8s 273 1.74e+01 1brt c.69.1.12 34710 1mpxA 615 1.78e+01 b.18.1.13,c.69.1.21 85041,85042 1pyfA 312 1.80e+01 c.1.7.1 95334 1ku0A 388 1.83e+01 c.69.1.18 72994 1fnnA 389 1.85e+01 1fnnA a.4.5.11,c.37.1.20 16129,32426 2b06A 155 1.85e+01 2bfdB 345 1.86e+01 2bfwA 200 1.92e+01 1n9lA 109 1.94e+01 d.110.3.6 85468 1u94A 356 1.97e+01 c.37.1.11,d.48.1.1 107743,107744 1n55A 251 1.99e+01 c.1.1.1 80007 2ccjA 205 2.05e+01 1w0dA 337 2.07e+01 1drw 273 2.08e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1xffA 240 2.09e+01 d.153.1.1 109580 2bneA 241 2.10e+01 2fvgA 340 2.13e+01 1u2zA 433 2.18e+01 c.66.1.31 107626 1qgvA 142 2.20e+01 1qgvA c.47.1.8 33056 1uwkA 557 2.21e+01 e.51.1.1 108065 1fh9A 312 2.25e+01 1taxA c.1.8.3 28913 1ufoA 238 2.27e+01 c.69.1.27 99344 2c6cA 707 2.33e+01 1hf8A 289 2.35e+01 1hg5A a.7.8.2,a.118.9.3 90354,90355 1wstA 417 2.38e+01 1in4A 334 2.44e+01 1hqcA a.4.5.11,c.37.1.20 62597,62598 2c6qA 351 2.44e+01 1squA 155 2.45e+01 d.252.1.1 98971 1w36B 1180 2.48e+01 1uf3A 228 2.49e+01 d.159.1.6 99317 1ej0A 180 2.54e+01 1ej0A c.66.1.2 34179 1b0uA 262 2.54e+01 1b0uA c.37.1.12 32370 1z41A 338 2.55e+01 1p1jA 533 2.56e+01 c.2.1.3,d.81.1.3 87687,87688 1uwsA 489 2.57e+01 c.1.8.4 108073 1pea 385 2.59e+01 1pea c.93.1.1 35662 1geeA 261 2.61e+01 c.2.1.2 90509 2ftwA 521 2.62e+01 1nvmB 312 2.64e+01 c.2.1.3,d.81.1.1 86251,86252 1rz3A 201 2.65e+01 c.37.1.6 98132 1uu1A 335 2.68e+01 c.67.1.1 99993 1kqpA 271 2.69e+01 c.26.2.1 72883 1tuvA 114 2.73e+01 1m5q1 130 2.75e+01 1x72A 334 2.81e+01 d.126.1.6 109495 1kkhA 317 2.83e+01 d.14.1.5,d.58.26.3 72645,72646 1jx6A 342 2.84e+01 c.93.1.1 67406 1np6A 174 2.84e+01 c.37.1.10 85954 2auwA 170 2.89e+01 8abp 306 2.96e+01 8abp c.93.1.1 35647 2a5hA 416 2.96e+01 1o5xA 248 2.96e+01 c.1.1.1 92528 1xneA 113 2.96e+01 2a0b 125 3.00e+01 2a0b a.24.10.1 16630 1x38A 602 3.01e+01 1o97C 264 3.04e+01 c.26.2.3 81232 1wrjA 156 3.05e+01 1nrjB 218 3.05e+01 c.37.1.8 86125 1hzdA 272 3.07e+01 c.14.1.3 65969 1qv9A 283 3.07e+01 c.127.1.1 96356 1ujpA 271 3.13e+01 c.1.2.4 99462 1r3dA 264 3.13e+01 1ml4A 308 3.14e+01 c.78.1.1,c.78.1.1 79255,79256 2bg5A 324 3.14e+01 1jhsA 188 3.14e+01 d.107.1.1 84172 1l4uA 176 3.16e+01 c.37.1.2 73568 1mr7A 209 3.19e+01 b.81.1.3 91430 2f5gA 133 3.26e+01 1usgA 346 3.38e+01 c.93.1.1 99864 1s62A 106 3.40e+01 1o9rA 162 3.47e+01 a.25.1.1 86706 1meoA 209 3.51e+01 c.65.1.1 79035 1to6A 371 3.51e+01 c.141.1.1 107170 1goiA 499 3.52e+01 b.72.2.1,c.1.8.5,d.26.3.1 65413,65414,65415 1nu0A 138 3.56e+01 c.55.3.8 92165 2a2fX 325 3.57e+01 1j4aA 333 3.59e+01 c.2.1.4,c.23.12.1 71502,71503 1e8gA 560 3.63e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1wxiA 275 3.63e+01 1sbyA 254 3.67e+01 2d13A 227 3.70e+01 1zejA 293 3.72e+01 1tl9A 339 3.74e+01 1f60A 458 3.75e+01 1efcA b.43.3.1,b.44.1.1,c.37.1.8 25705,25745,32140 1bw0A 416 3.78e+01 1bw0A c.67.1.1 34385 1ua7A 422 3.86e+01 b.71.1.1,c.1.8.1 107759,107760 2b61A 377 3.93e+01 1fp3A 402 3.96e+01 1fp3A a.102.1.3 18842 1sg6A 393 3.99e+01 e.22.1.1 105522 1nkqA 259 4.08e+01 d.177.1.1 103862 2c7pA 327 4.13e+01 1i6pA 220 4.15e+01 1ddzA c.53.2.1 61848 1fkmA 396 4.17e+01 1fkmA a.69.2.1,a.69.2.1 18315,18316 1yc9A 442 4.18e+01 1q1fA 151 4.19e+01 a.1.1.2 104476 1jb7A 495 4.21e+01 1otcA b.40.4.3,b.40.4.3,b.40.4.3 62836,62837,62838 1sbp 310 4.22e+01 1sbp c.94.1.1 35760 1b8aA 438 4.23e+01 1b8aA b.40.4.1,d.104.1.1 25244,40765 1brt 277 4.24e+01 1brt c.69.1.12 34699 1vjpA 394 4.26e+01 c.2.1.3,d.81.1.3 100828,100829 1hqkA 154 4.41e+01 c.16.1.1 65902 1hy7A 173 4.44e+01 d.92.1.11 65957 1a0cA 438 4.62e+01 1a0cA c.1.15.3 29529 1guzA 310 4.62e+01 c.2.1.5,d.162.1.1 65586,65587 1o4vA 183 4.65e+01 c.23.8.1 86628 1w5tA 412 4.66e+01 1txgA 335 4.69e+01 1d3gA 367 4.74e+01 1d3gA c.1.4.1 28600 1kicA 339 4.74e+01 c.70.1.1 72510 1ja1A 622 4.76e+01 1amoA b.43.4.1,c.23.5.2,c.25.1.4 62803,62804,62805 1pb1A 416 4.76e+01 c.77.1.1 88014 1g8pA 350 4.77e+01 1g8pA c.37.1.20 60376 1krhA 338 4.78e+01 b.43.4.2,c.25.1.2,d.15.4.2 72891,72892,72893 1ixkA 315 4.78e+01 c.66.1.38 90716 1yacA 208 4.82e+01 1yacA c.33.1.3 31757 1xklA 273 4.86e+01 1jsdB 176 4.86e+01 h.3.1.1 63259 1qhtA 775 4.87e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1h7eA 245 4.88e+01 c.68.1.13 60717 1j6oA 268 4.93e+01 c.1.9.12 77088 1pzgA 331 4.94e+01 c.2.1.5,d.162.1.1 95425,95426 1vjgA 218 4.95e+01 c.23.10.6 100810 1ykdA 398 4.96e+01 1hnjA 317 4.99e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 2av4A 162 5.01e+01 2b9eA 303 5.04e+01 2agaA 190 5.10e+01 1lehA 364 5.10e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1xdpA 687 5.12e+01 1o3uA 135 5.13e+01 a.24.16.3 86615 1om4A 422 5.13e+01 d.174.1.1 87067 1yarO 237 5.13e+01 2af4C 333 5.16e+01 2bd0A 244 5.20e+01 1ltzA 297 5.21e+01 d.178.1.1 74254 2ga9A 297 5.23e+01 1o5kA 306 5.25e+01 c.1.10.1 92504 1mp9A 198 5.26e+01 d.129.1.1,d.129.1.1 91385,91386 1vp8A 201 5.26e+01 1o3yA 166 5.30e+01 c.37.1.8 86618 1rm6A 769 5.32e+01 1vmhA 144 5.33e+01 1m8jA 181 5.38e+01 c.26.1.3 84875 1pq4A 291 5.39e+01 c.92.2.2 94995 1xr4A 509 5.43e+01 1lzjA 292 5.48e+01 c.68.1.9 74352 1t6cA 315 5.49e+01 c.55.1.8,c.55.1.8 106558,106559 1cnzA 363 5.51e+01 1cnzA c.77.1.1 35061 2cvhA 220 5.52e+01 1rh9A 373 5.53e+01 2f62A 161 5.57e+01 2br9A 234 5.60e+01 1yx1A 264 5.65e+01 2cxcA 144 5.71e+01 1whsB 153 5.71e+01 1whtB 1xkpB 124 5.73e+01 1o1yA 239 5.75e+01 c.23.16.1 86554 1gr0A 367 5.79e+01 c.2.1.3,d.81.1.3 70379,70380 1s2oA 244 5.81e+01 1z6fA 363 5.82e+01 1ej2A 181 5.85e+01 1f9aA c.26.1.3 59414 1i88A 389 5.86e+01 c.95.1.2,c.95.1.2 66070,66071 2bvlA 543 5.90e+01 1sviA 195 5.93e+01 c.37.1.8 106048 1jf9A 408 5.93e+01 1c0nA c.67.1.3 62931 2gm3A 175 5.97e+01 1f6yA 262 5.98e+01 1f6yA c.1.21.2 29673 1muwA 386 6.02e+01 c.1.15.3 79495 1fg7A 356 6.05e+01 1gewA c.67.1.1 59819 1xi3A 215 6.05e+01 c.1.3.1 109601 1hyeA 313 6.14e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1hrhA 136 6.19e+01 1rthA c.55.3.1 33577 1t4nA 94 6.20e+01 d.50.1.1 106424 1aisA 182 6.22e+01 1ytbA d.129.1.1,d.129.1.1 41288,41289 1g8sA 230 6.29e+01 c.66.1.3 90507 1m1nA 491 6.30e+01 c.92.2.3 78417 2fn0A 437 6.31e+01 1or4A 178 6.34e+01 a.1.1.2 93447 1noyA 388 6.40e+01 1clqA c.55.3.5 33713 2czcA 334 6.42e+01 1w19A 160 6.47e+01 2c3mA 1231 6.47e+01 1jfrA 262 6.47e+01 1jfrA c.69.1.16 34724 1ylhA 560 6.51e+01 1t4oA 117 6.52e+01 d.50.1.1 106425 1dv1A 449 6.53e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1g60A 260 6.55e+01 c.66.1.11 70151 1uuyA 167 6.56e+01 c.57.1.1 108059 1ra6A 461 6.58e+01 e.8.1.4 104879 2c4nA 250 6.62e+01 1t4hA 290 6.64e+01 d.144.1.7 106420 1j0hA 588 6.66e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1ib2A 349 6.72e+01 1ib2A a.118.1.8 62141 1ff9A 450 6.72e+01 1ff9A c.2.1.3,d.81.1.2 30039,39954 1i4fA 275 6.77e+01 1agdA b.1.1.2,d.19.1.1 61687,61688 1e6yA 569 6.87e+01 1mroA a.89.1.1,d.58.31.2 18529,39447 1cfzA 162 6.91e+01 1cfzA c.56.1.1 33754 1dozA 309 6.92e+01 1ak1 c.92.1.1 35592 1n7kA 234 6.94e+01 c.1.10.1 85374 1g5aA 628 6.95e+01 b.71.1.1,c.1.8.1 65152,65153 1ynpA 317 6.96e+01 1rkbA 173 6.96e+01 1zrn 232 6.96e+01 1qq5A c.108.1.1 43323 1eg2A 319 6.98e+01 1eg2A c.66.1.11 34249 1j3bA 529 6.98e+01 c.91.1.1,c.109.1.1 77071,77072 1s9jA 341 7.01e+01 2cokA 113 7.04e+01 1wf3A 301 7.10e+01 1ir6A 424 7.10e+01 c.107.1.2 71342 1ewkA 490 7.25e+01 1ewkA c.93.1.1 35712 1wz3A 96 7.27e+01 2fa8A 105 7.30e+01 1xkyA 301 7.33e+01 1oruA 195 7.47e+01 b.58.1.2 93464 4uagA 437 7.51e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1a4iA 301 7.51e+01 1a4iA c.2.1.7,c.58.1.2 30278,33926 1z6bA 154 7.53e+01 1vqoB 338 7.56e+01 1yrbA 262 7.56e+01 1r0mA 375 7.58e+01 c.1.11.2,d.54.1.1 104747,104748 1s7zA 117 7.61e+01 a.159.3.1 98715 2flsA 132 7.68e+01 2d00A 109 7.70e+01 1dd9A 338 7.73e+01 1dd9A e.13.1.1 43254 2asbA 251 7.85e+01 1uwcA 261 7.86e+01 c.69.1.17 100101 1xppA 115 7.98e+01 1kq3A 376 8.02e+01 e.22.1.2 68790 1o08A 221 8.03e+01 c.108.1.6 86525 1xp8A 366 8.08e+01 1o50A 157 8.12e+01 d.37.1.1,d.37.1.1 92478,92479 1r8gA 372 8.17e+01 d.128.1.3 104845 2c43A 323 8.20e+01 1o98A 511 8.27e+01 c.105.1.1,c.76.1.3 86684,86685 1wwiA 148 8.35e+01 1fm0D 81 8.36e+01 1fmaD d.15.3.1 37642 2bibA 547 8.40e+01 1i1wA 303 8.42e+01 c.1.8.3 76732 1bg4 302 8.48e+01 1taxA c.1.8.3 28806 1i60A 278 8.49e+01 c.1.15.4 71118 2gokA 429 8.54e+01 1jr2A 286 8.61e+01 c.113.1.1 67111 2eu9A 355 8.69e+01 1gk9A 260 8.69e+01 d.153.1.2 65246 1wpnA 188 8.70e+01 1ddwA 120 8.70e+01 1evhA b.55.1.4 27001 2bbeA 108 8.72e+01 1y13A 181 8.77e+01 1reqA 727 8.77e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1w0mA 226 8.78e+01 c.1.1.1 109027 2f6rA 281 8.83e+01 1yueA 427 8.87e+01 1budA 197 8.88e+01 1atlA d.92.1.9 40328 1atlA 202 8.88e+01 1atlA d.92.1.9 40322 1qnaA 200 8.91e+01 1ytbA d.129.1.1,d.129.1.1 41226,41227 1wraA 308 8.91e+01 1bdb 277 8.95e+01 1bdb c.2.1.2 29874 1oxxK 353 8.95e+01 b.40.6.3,c.37.1.12 93715,93716