# List of top-scoring protein chains for t06-100-30-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 1v2xA 194 6.25e-20 c.116.1.1 100274 1x7oA 287 8.53e-19 1zjrA 211 2.20e-18 1mxiA 160 5.26e-17 c.116.1.1 79646 1z85A 234 5.57e-04 1vbuA 328 5.42e-02 1zjjA 263 7.65e-02 1o6dA 163 8.15e-02 c.116.1.3 92567 1h1yA 228 8.39e-02 c.1.2.2 76506 1zxxA 319 1.86e-01 1vhyA 257 2.91e-01 b.122.1.2,c.116.1.5 100714,100715 1te2A 226 3.48e-01 c.108.1.6 106792 1wraA 308 4.81e-01 1ualA 274 4.85e-01 c.116.1.4 88383 1k3rA 268 5.02e-01 b.40.4.10,c.116.1.2 72018,72019 1uok 558 5.26e-01 1uok b.71.1.1,c.1.8.1 27801,28788 1ur1A 378 5.75e-01 c.1.8.3 99804 1zsyA 357 5.88e-01 1o1zA 234 6.28e-01 c.1.18.3 86555 1t9hA 307 6.39e-01 1othA 321 6.65e-01 1othA c.78.1.1,c.78.1.1 35260,35261 1kt6A 183 6.91e-01 b.60.1.1 84466 1v6zA 228 6.93e-01 2anuA 255 7.03e-01 1yzyA 413 7.97e-01 2as0A 396 8.22e-01 1j0hA 588 8.35e-01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1vmeA 410 8.48e-01 c.23.5.1,d.157.1.3 108893,108894 1dxeA 256 9.08e-01 1dxeA c.1.12.5 29310 1rreA 200 9.36e-01 d.14.1.10 97791 1iooA 196 9.65e-01 d.124.1.1 71250 1wjtA 103 1.01e+00 1xyzA 347 1.08e+00 1taxA c.1.8.3 28804 1j2rA 199 1.12e+00 c.33.1.3 90788 1m3sA 186 1.19e+00 c.80.1.3 78573 1d2nA 272 1.22e+00 1d2nA c.37.1.20 32428 2fi1A 190 1.33e+00 1g38A 393 1.35e+00 2admA c.66.1.27 60235 1o08A 221 1.36e+00 c.108.1.6 86525 2bibA 547 1.54e+00 1eokA 290 1.56e+00 1eokA c.1.8.5 28991 1ns5A 155 1.56e+00 c.116.1.3 80705 1zmtA 254 1.75e+00 2b8nA 429 1.78e+00 1aihA 170 1.91e+00 1aihA d.163.1.1 42149 1ecsA 126 1.96e+00 1ecsA d.32.1.2 59407 1yrtA 364 1.99e+00 2b0cA 206 1.99e+00 2f6uA 234 2.12e+00 2bneA 241 2.21e+00 1n82A 331 2.31e+00 c.1.8.3 91703 1w0mA 226 2.32e+00 c.1.1.1 109027 1im5A 180 2.38e+00 c.33.1.3 66211 1pwxA 254 2.43e+00 c.2.1.2 95262 1uc8A 280 2.43e+00 c.30.1.6,d.142.1.7 99165,99166 1t0bA 252 2.44e+00 c.23.16.6 106199 1qwgA 251 2.44e+00 c.1.27.1 96473 1o5zA 442 2.48e+00 c.59.1.2,c.72.2.2 92530,92531 1o4wA 147 2.53e+00 c.120.1.1 86629 1i60A 278 2.61e+00 c.1.15.4 71118 1d5rA 324 2.70e+00 1d5rA b.7.1.1,c.45.1.1 23181,32697 1e87A 118 2.73e+00 1b6e d.169.1.1 42327 1p4xA 250 2.73e+00 a.4.5.28,a.4.5.28 87784,87785 2a3nA 355 2.76e+00 1vi2A 300 2.79e+00 c.2.1.7,c.58.1.5 100726,100727 1gca 309 2.80e+00 1gca c.93.1.1 35659 1zrn 232 2.82e+00 1qq5A c.108.1.1 43323 1kfcA 268 2.83e+00 c.1.2.4 77371 1b77A 228 2.86e+00 1b77A d.131.1.2,d.131.1.2 41362,41363 2aeuA 374 2.91e+00 1zx1A 231 2.98e+00 1xuuA 349 3.06e+00 1p7tA 731 3.19e+00 c.1.13.1 94319 2g09A 297 3.29e+00 1sg0A 230 3.29e+00 1m4jA 142 3.38e+00 d.109.1.2 78602 1zs9A 261 3.39e+00 1ymqA 261 3.40e+00 1ta3A 274 3.43e+00 c.1.8.5 106731 1geqA 248 3.54e+00 2tysA c.1.2.4 28589 1ht6A 405 3.58e+00 b.71.1.1,c.1.8.1 83629,83630 1pvvA 315 3.65e+00 c.78.1.1,c.78.1.1 95190,95191 1l6wA 220 3.67e+00 c.1.10.1 73632 2aamA 309 3.72e+00 1vizA 240 3.81e+00 c.1.4.1 100784 1mjfA 281 3.91e+00 c.66.1.17 79198 1kwgA 645 3.96e+00 b.71.1.1,c.1.8.1,c.23.16.5 77561,77562,77563 1tk9A 188 4.02e+00 c.80.1.3 107082 1st9A 143 4.22e+00 c.47.1.10 98987 1jae 471 4.40e+00 1smd b.71.1.1,c.1.8.1 27773,28760 1yvoA 172 4.47e+00 1lj9A 144 4.50e+00 a.4.5.28 78035 1v3vA 333 4.50e+00 b.35.1.2,c.2.1.1 108345,108346 1sl4A 155 4.57e+00 d.169.1.1 105710 1hdoA 206 4.58e+00 1he2A c.2.1.2 60965 1m1nB 522 4.59e+00 c.92.2.3 78418 1vd6A 224 4.66e+00 1w4rA 195 4.73e+00 1zp4A 304 5.06e+00 2pgd 482 5.16e+00 2pgd a.100.1.1,c.2.1.6 18778,30190 1lfpA 249 5.16e+00 e.39.1.1 73885 5nul 138 5.20e+00 5nul c.23.5.1 31191 1yf3A 259 5.28e+00 1jdw 423 5.34e+00 1jdw d.126.1.2 41129 2ceyA 306 5.42e+00 1jztA 246 5.52e+00 c.104.1.1 63319 1k4mA 213 5.56e+00 c.26.1.3 77258 2jdxA 385 5.57e+00 1jdw d.126.1.2 41139 1qo3C 137 5.65e+00 1qo3C d.169.1.1 42350 1xg5A 279 5.65e+00 1qyiA 384 5.68e+00 c.108.1.13 96595 1qopA 268 5.70e+00 2tysA c.1.2.4 28570 2a67A 167 5.70e+00 1ag9A 175 5.71e+00 1rcf c.23.5.1 31178 1rlmA 271 5.87e+00 1rliA 184 5.91e+00 c.23.5.6 97647 1sviA 195 5.94e+00 c.37.1.8 106048 1cjxA 357 5.99e+00 1cjxA d.32.1.3,d.32.1.3 38516,38517 2d0iA 333 6.01e+00 1u7pA 164 6.35e+00 1q8iA 783 6.36e+00 c.55.3.5,e.8.1.1 96208,96209 1ucnA 152 6.48e+00 d.58.6.1 99183 1m2kA 249 6.54e+00 c.31.1.5 84754 1ne2A 200 6.67e+00 c.66.1.32 85586 1tzjA 338 6.82e+00 1qo2A 241 7.02e+00 1qo2A c.1.2.1 28533 1u3wA 374 7.05e+00 1qipA 183 7.12e+00 1qipA d.32.1.1 38470 2gukA 120 7.37e+00 2b4jC 98 7.40e+00 1rxdA 159 7.43e+00 2cdcA 366 7.46e+00 1swvA 267 7.54e+00 1gci 269 7.66e+00 1gci c.41.1.1 32503 2go7A 207 7.93e+00 1vqtA 213 8.01e+00 1npyA 271 8.02e+00 c.2.1.7,c.58.1.5 85995,85996 1qf5A 431 8.17e+00 1adeA c.37.1.10 32212 1bqcA 302 8.17e+00 1bqcA c.1.8.3 28831 1t0yA 122 8.27e+00 d.15.1.1 99066 1b0uA 262 8.29e+00 1b0uA c.37.1.12 32370 2aeeA 211 8.30e+00 1gk9B 557 8.32e+00 1wdiA 345 8.40e+00 2ftbA 125 8.40e+00 1qe5A 266 8.54e+00 1b8oA c.56.2.1 33784 1tqjA 230 8.54e+00 c.1.2.2 107228 1j31A 262 8.57e+00 d.160.1.2 90808 1vzwA 244 8.58e+00 1jc4A 148 8.66e+00 1jc4A d.32.1.4 62863 1iukA 140 8.68e+00 c.2.1.8 83712 1vk3A 615 8.83e+00 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 2ez9A 603 8.84e+00 1ef8A 261 8.88e+00 1ef8A c.14.1.3 30921 1wzlA 585 9.04e+00 2f9lA 199 9.17e+00 1rdfA 267 9.32e+00 c.108.1.3 104884 1fh9A 312 9.43e+00 1taxA c.1.8.3 28913 2c4nA 250 9.60e+00 2c6cA 707 9.72e+00 1hdcA 253 9.73e+00 1e6wA c.2.1.2 29862 2d0oA 610 9.87e+00 1tf1A 198 9.92e+00 d.110.2.2 106826 1nnlA 225 9.97e+00 c.108.1.4 85906 2fr1A 486 1.01e+01 1vhh 162 1.01e+01 1vhh d.65.1.2 39550 1svdA 473 1.01e+01 2d5xA 141 1.01e+01 1c93A 265 1.01e+01 2ebn c.1.8.5 28998 1y8qA 346 1.01e+01 1nrwA 288 1.01e+01 c.108.1.10 86128 1ydiA 263 1.03e+01 1ypfA 336 1.06e+01 1oflA 481 1.06e+01 b.80.1.4 103934 2ebn 289 1.09e+01 2ebn c.1.8.5 28990 1js8A 394 1.09e+01 a.86.1.1,b.112.1.1 67219,67220 1p7gA 222 1.09e+01 a.2.11.1,d.44.1.1 94223,94224 1wohA 305 1.09e+01 c.42.1.1 109446 1ym3A 215 1.10e+01 1f8fA 371 1.11e+01 b.35.1.2,c.2.1.1 83246,83247 2dri 271 1.12e+01 2dri c.93.1.1 35637 1mhqA 148 1.15e+01 a.118.9.2 84973 1pe1A 267 1.15e+01 c.1.10.4 94591 1sqiA 393 1.15e+01 d.32.1.3,d.32.1.3 105914,105915 2f9sA 151 1.18e+01 1hqsA 423 1.21e+01 1iso c.77.1.1 61154 1pne 140 1.21e+01 1pne d.110.1.1 40866 1ybdA 239 1.22e+01 1edt 271 1.25e+01 2ebn c.1.8.5 28993 1uayA 242 1.26e+01 c.2.1.2 88390 1qczA 169 1.27e+01 1qczA c.23.8.1 31276 1n8kA 374 1.27e+01 b.35.1.2,c.2.1.1 80298,80299 1vimA 200 1.29e+01 c.80.1.3 100758 1np6A 174 1.31e+01 c.37.1.10 85954 8rucI 123 1.32e+01 1rboC d.73.1.1 39629 1r45A 204 1.33e+01 1vemA 516 1.33e+01 1w9gA 104 1.34e+01 1xx6A 191 1.34e+01 2g7uA 257 1.34e+01 1g5aA 628 1.35e+01 b.71.1.1,c.1.8.1 65152,65153 2ftwA 521 1.35e+01 1g60A 260 1.35e+01 c.66.1.11 70151 1pl8A 356 1.35e+01 b.35.1.2,c.2.1.1 94878,94879 1e43A 483 1.36e+01 1bli b.71.1.1,c.1.8.1 59217,59218 1qtwA 285 1.36e+01 1qumA c.1.15.1 29392 1ptmA 329 1.38e+01 c.77.1.3 95104 1nq6A 302 1.40e+01 c.1.8.3 92046 1wq3A 322 1.40e+01 1o4sA 389 1.42e+01 c.67.1.1 86620 1pt6A 213 1.43e+01 c.62.1.1 95091 1efpB 252 1.43e+01 1efvB c.26.2.3 31636 1ls1A 295 1.44e+01 a.24.13.1,c.37.1.10 78170,78171 1ikpA 613 1.44e+01 b.29.1.7,d.166.1.1,f.1.5.1 66182,66183,66184 2c0hA 353 1.45e+01 1wddS 128 1.48e+01 1v2dA 381 1.49e+01 c.67.1.1 108281 1yb5A 351 1.51e+01 2ae2A 260 1.52e+01 1bdb c.2.1.2 29945 1it2A 146 1.52e+01 a.1.1.2 66365 1yz1A 174 1.52e+01 1dbiA 280 1.53e+01 1gci c.41.1.1 32543 1p0fA 373 1.53e+01 b.35.1.2,c.2.1.1 87642,87643 1d3yA 301 1.55e+01 1d3yA e.12.1.1 43252 1nofA 383 1.55e+01 b.71.1.2,c.1.8.3 92020,92021 2czdA 208 1.55e+01 1jbeA 128 1.56e+01 3chy c.23.1.1 62845 1gudA 288 1.56e+01 c.93.1.1 83326 2fcr 173 1.57e+01 1rcf c.23.5.1 31151 1ny1A 240 1.58e+01 c.6.2.3 86395 1sflA 238 1.58e+01 1pswA 348 1.58e+01 c.87.1.7 88287 1prxA 224 1.59e+01 1prxA c.47.1.10 33076 1y0nA 78 1.59e+01 1frb 315 1.62e+01 1frb c.1.7.1 28665 1irdA 141 1.63e+01 a.1.1.2 66286 1f1xA 322 1.65e+01 d.32.1.3,d.32.1.3 83208,83209 1szqA 483 1.65e+01 e.44.1.1 99045 1zhaA 267 1.66e+01 1uufA 369 1.68e+01 b.35.1.2,c.2.1.1 100006,100007 1r85A 379 1.68e+01 c.1.8.3 104839 1m5wA 243 1.69e+01 c.1.24.1 84836 1sjdA 368 1.71e+01 c.1.11.2,d.54.1.1 105632,105633 1v4xB 146 1.73e+01 a.1.1.2 108364 1bvoA 175 1.74e+01 1a3qA b.2.5.3 22457 1m15A 357 1.75e+01 a.83.1.1,d.128.1.2 78368,78369 1rkuA 206 1.77e+01 c.108.1.11 97627 2fhpA 187 1.78e+01 1vkmA 297 1.78e+01 c.138.1.1 108670 1xkrA 206 1.80e+01 1oi7A 288 1.80e+01 c.2.1.8,c.23.4.1 87049,87050 1ijbA 202 1.83e+01 c.62.1.1 71229 1qh8B 519 1.83e+01 1qguB c.92.2.3 35634 1ep3A 311 1.84e+01 2dorA c.1.4.1 28597 1qf9A 194 1.85e+01 1zin c.37.1.1 31848 1rkd 309 1.86e+01 1rkd c.72.1.1 34928 1us0A 316 1.87e+01 c.1.7.1 99850 1x2iA 75 1.87e+01 1m65A 245 1.89e+01 c.6.3.1 84847 1yviA 149 1.90e+01 1kw4A 89 1.91e+01 a.60.1.2 73077 2b81A 323 1.93e+01 2a5jA 191 1.93e+01 1v71A 323 1.94e+01 1epuA 591 1.94e+01 1dn1A e.25.1.1 43358 1u5hA 273 1.95e+01 1mvoA 136 1.96e+01 c.23.1.1 79513 2d13A 227 1.96e+01 1o98A 511 1.97e+01 c.105.1.1,c.76.1.3 86684,86685 1ii7A 333 1.99e+01 1ii7A d.159.1.4 62415 1u5vA 273 2.01e+01 1w8sA 263 2.03e+01 1ss4A 153 2.07e+01 d.32.1.6 105976 1uslA 170 2.08e+01 c.121.1.1 99871 1i6aA 219 2.08e+01 c.94.1.1 61827 1drw 273 2.09e+01 1drw c.2.1.3,d.81.1.3 30057,39972 1h75A 81 2.09e+01 1h75A c.47.1.1 60716 1eg2A 319 2.10e+01 1eg2A c.66.1.11 34249 1kngA 156 2.10e+01 c.47.1.10 72777 1f9zA 135 2.11e+01 1qipA d.32.1.1 38484 1zczA 464 2.12e+01 1m6jA 261 2.15e+01 c.1.1.1 78693 1w1oA 534 2.18e+01 d.58.32.4,d.145.1.1 109071,109072 1khdA 345 2.19e+01 a.46.2.1,c.27.1.1 77400,77401 1jftA 340 2.20e+01 a.35.1.5,c.93.1.1 66652,66653 1x3lA 440 2.22e+01 2bz1A 196 2.23e+01 1vqoC 246 2.24e+01 1v0lA 313 2.24e+01 c.1.8.3 108207 1wr2A 238 2.26e+01 1vpqA 273 2.26e+01 2a4hA 126 2.27e+01 2d5xB 146 2.29e+01 2cc0A 195 2.32e+01 1kaeA 434 2.33e+01 c.82.1.2 72247 1nvvS 481 2.35e+01 a.117.1.1 86279 1gs5A 258 2.35e+01 c.73.1.2 70395 1mpxA 615 2.37e+01 b.18.1.13,c.69.1.21 85041,85042 1ii5A 233 2.41e+01 c.94.1.1 62412 1a53 247 2.42e+01 1a53 c.1.2.4 28564 1tmy 120 2.44e+01 1dbwA c.23.1.1 31083 2basA 431 2.48e+01 1k77A 260 2.48e+01 c.1.15.5 72096 1wa3A 205 2.49e+01 1j75A 67 2.53e+01 a.4.5.19 62673 1tz9A 367 2.53e+01 c.1.15.6 107466 1q3eA 207 2.53e+01 b.82.3.2 95669 1xf1A 926 2.54e+01 2aefA 234 2.55e+01 2fv7A 331 2.60e+01 1g63A 181 2.62e+01 1g5qA c.34.1.1 60299 1thx 115 2.62e+01 1thx c.47.1.1 32732 1km4A 247 2.63e+01 c.1.2.3 72740 1yqdA 366 2.64e+01 1zybA 232 2.65e+01 1nzjA 298 2.67e+01 c.26.1.1 92377 1xrtA 467 2.68e+01 1xdwA 331 2.71e+01 1tn3 137 2.71e+01 1htn d.169.1.1 42423 2agaA 190 2.73e+01 1xi3A 215 2.74e+01 c.1.3.1 109601 1wy1A 172 2.74e+01 1xg8A 111 2.74e+01 1jixA 351 2.75e+01 1c3jA c.87.1.1 63081 1y1oA 203 2.75e+01 2f2hA 773 2.75e+01 1ykiA 217 2.76e+01 1bli 483 2.76e+01 1bli b.71.1.1,c.1.8.1 27715,28702 1rkqA 282 2.77e+01 c.108.1.10 97621 1u4nA 310 2.79e+01 1s4cA 155 2.80e+01 1xphA 150 2.81e+01 1c30B 382 2.83e+01 c.8.3.1,c.23.16.1 30736,31413 1ovlA 271 2.85e+01 a.123.1.1 87455 1duvG 333 2.88e+01 1othA c.78.1.1,c.78.1.1 35228,35229 1s69A 124 2.93e+01 a.1.1.1 105305 1qnrA 344 2.95e+01 1qnoA c.1.8.3 28834 1rvkA 382 2.96e+01 c.1.11.2,d.54.1.1 97928,97929 2fu2A 102 2.96e+01 1j0dA 341 3.00e+01 c.79.1.1 83902 1gxrA 337 3.00e+01 b.69.4.1 70722 1xmpA 170 3.04e+01 1fcqA 350 3.06e+01 c.1.8.9 65006 1vhvA 268 3.07e+01 c.90.1.1 100704 1lddA 74 3.07e+01 a.4.5.34 73841 1d2zB 153 3.08e+01 1d2zB a.77.1.2 18439 1vb3A 428 3.11e+01 1j79A 347 3.12e+01 1j79A c.1.9.4 62675 1j4aA 333 3.13e+01 c.2.1.4,c.23.12.1 71502,71503 1zq6A 359 3.15e+01 1yemA 179 3.16e+01 1mzhA 225 3.18e+01 c.1.10.1 79698 1em2A 229 3.20e+01 1em2A d.129.3.2 41321 1ezfA 340 3.24e+01 1ezfA a.128.1.2 19440 1dusA 194 3.27e+01 1dusA c.66.1.4 34182 1va4A 279 3.29e+01 c.69.1.12 108458 1p3dA 475 3.30e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 2fliA 220 3.32e+01 2csbA 519 3.33e+01 2fywA 267 3.36e+01 1g3qA 237 3.37e+01 1hyqA c.37.1.10 60237 2gfhA 260 3.38e+01 1o17A 345 3.40e+01 a.46.2.1,c.27.1.1 80765,80766 1v95A 130 3.41e+01 c.51.1.1 108435 1z0wA 207 3.43e+01 1js3A 486 3.43e+01 c.67.1.6 67215 1l7mA 211 3.46e+01 c.108.1.4 73664 2axoA 270 3.46e+01 2fbhA 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