# 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 2bo9A 308 1.04e-22 1z5rA 306 1.69e-22 1kwmA 402 2.18e-21 c.56.5.1,d.58.3.1 73079,73080 1dtdA 303 3.13e-21 1aye c.56.5.1 33823 1m4lA 307 2.84e-20 c.56.5.1 78604 1yw4A 341 2.85e-18 1h1nA 305 6.32e-02 c.1.8.3 70855 1w8sA 263 6.93e-02 1xb2B 291 2.14e-01 1tvnA 293 3.23e-01 1b8oA 284 3.78e-01 1b8oA c.56.2.1 33762 1im5A 180 4.37e-01 c.33.1.3 66211 1gqiA 708 4.51e-01 c.1.8.10,d.92.2.2 76279,76280 2freA 200 4.56e-01 1edg 380 5.40e-01 1edg c.1.8.3 28807 1pjr 724 5.56e-01 1pjr c.37.1.19,c.37.1.19 32391,32392 1t5bA 201 6.18e-01 c.23.5.3 106433 1vmaA 306 6.72e-01 a.24.13.1,c.37.1.10 108887,108888 2cygA 312 7.37e-01 1eceA 358 8.86e-01 1eceA c.1.8.3 28813 1tcvA 287 8.88e-01 1jwqA 179 1.12e+00 c.56.5.6 90921 1pe1A 267 1.12e+00 c.1.10.4 94591 1zhaA 267 1.17e+00 1vcoA 550 1.25e+00 c.23.16.1,c.37.1.10 108508,108509 1ki9A 192 1.27e+00 c.37.1.1 84404 1wkyA 464 1.36e+00 1o60A 292 1.46e+00 c.1.10.4 92532 1h4pA 408 1.63e+00 c.1.8.3 90617 1rtqA 299 1.74e+00 c.56.5.4 97819 1ur4A 399 1.82e+00 1t71A 281 2.11e+00 1gqnA 252 2.25e+00 c.1.10.1 90514 1khtA 192 2.30e+00 c.37.1.1 84401 1c3pA 375 2.41e+00 1c3pA c.42.1.2 32606 1wnaA 131 2.41e+00 1zemA 262 2.46e+00 1wf3A 301 2.48e+00 1r3dA 264 2.57e+00 1uuyA 167 2.65e+00 c.57.1.1 108059 1xmbA 418 2.99e+00 1vheA 373 3.23e+00 b.49.3.1,c.56.5.4 100669,100670 1w4xA 542 3.30e+00 c.3.1.5,c.3.1.5 109171,109172 1yvrA 538 3.50e+00 1sbyA 254 3.71e+00 1yh1A 359 3.77e+00 1zzmA 259 4.00e+00 1yq2A 1024 4.31e+00 1vjzA 341 4.39e+00 c.1.8.3 100838 1ht6A 405 4.49e+00 b.71.1.1,c.1.8.1 83629,83630 1yzyA 413 4.49e+00 1m22A 503 4.50e+00 c.117.1.1 78464 1shxA 138 4.59e+00 1tqyB 415 4.69e+00 c.95.1.1,c.95.1.1 107247,107248 1mj5A 302 4.74e+00 c.69.1.8 91285 1oaoA 674 4.76e+00 e.26.1.2 86744 1tzzA 392 5.05e+00 1h7eA 245 5.62e+00 c.68.1.13 60717 1vemA 516 5.74e+00 1k0fA 277 5.75e+00 c.92.2.2 71974 1vddA 228 6.01e+00 e.49.1.1 108519 1dozA 309 6.03e+00 1ak1 c.92.1.1 35592 1w96A 554 6.06e+00 1qd1A 325 6.28e+00 1qd1A d.58.34.1,d.58.34.1 39493,39494 2gl5A 410 6.46e+00 1j2rA 199 6.62e+00 c.33.1.3 90788 1j1iA 296 6.74e+00 c.69.1.10 83977 1hrkA 359 6.76e+00 1hrkA c.92.1.1 61228 1g0cA 364 6.77e+00 7a3hA c.1.8.3 60165 1ohtA 215 7.21e+00 d.118.1.1 87036 1xyzA 347 7.36e+00 1taxA c.1.8.3 28804 1x8dA 104 7.44e+00 1qe5A 266 7.47e+00 1b8oA c.56.2.1 33784 2a9sA 171 7.55e+00 1qq9A 284 7.62e+00 1xjo c.56.5.4 33841 1xx1A 285 7.64e+00 1h4vB 421 7.64e+00 1adjA c.51.1.1,d.104.1.1 60624,60625 1jbkA 195 7.83e+00 c.37.1.20 71631 1zz1A 369 7.85e+00 1o7jA 327 7.92e+00 c.88.1.1 81140 1vp4A 425 8.04e+00 1o5zA 442 8.11e+00 c.59.1.2,c.72.2.2 92530,92531 1p6xA 334 8.41e+00 c.37.1.1 94195 1l0wA 580 8.43e+00 b.40.4.1,d.74.4.1,d.104.1.1 73426,73427,73428 1t64A 377 8.55e+00 c.42.1.2 106543 1ysjA 404 8.66e+00 2pia 321 8.76e+00 2pia b.43.4.2,c.25.1.2,d.15.4.2 25663,31553,37704 1uuqA 440 8.81e+00 c.1.8.3 100015 1ad2 228 8.92e+00 1ad2 e.24.1.1 43353 1m2oA 768 9.02e+00 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 78480,78481,78482,78483,78484 1bn7A 294 9.35e+00 1bn6A c.69.1.8 34677 2bjiA 277 9.39e+00 1x7oA 287 9.43e+00 1ctt 294 9.67e+00 1ctt c.97.1.1,c.97.1.1 36022,36023 1xwyA 264 9.86e+00 1xvwA 160 9.99e+00 2ew8A 249 1.02e+01 1fecA 490 1.02e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1iirA 415 1.03e+01 1iirA c.87.1.5 62453 1r3sA 367 1.03e+01 c.1.22.1 96963 1z5yE 149 1.05e+01 2bkkA 264 1.06e+01 1ynpA 317 1.06e+01 1k7hA 476 1.07e+01 c.76.1.1 72101 2b3yA 888 1.09e+01 1wv2A 265 1.09e+01 1kcfA 258 1.12e+01 a.140.2.1,c.55.3.7 68434,68435 1w4vA 119 1.22e+01 1j8mF 297 1.23e+01 1ng1 a.24.13.1,c.37.1.10 62742,62743 1nq6A 302 1.28e+01 c.1.8.3 92046 2cybA 323 1.32e+01 1gq6A 313 1.35e+01 c.42.1.1 70341 1vp8A 201 1.38e+01 1xovA 326 1.38e+01 1ls1A 295 1.39e+01 a.24.13.1,c.37.1.10 78170,78171 1vggA 161 1.42e+01 1lucA 355 1.43e+01 1lucA c.1.16.1 29547 1xjjA 644 1.43e+01 1ohlA 342 1.44e+01 c.1.10.3 87035 1x1rA 178 1.44e+01 1e0cA 271 1.46e+01 1e0cA c.46.1.2,c.46.1.2 32717,32718 1dp4A 435 1.47e+01 1dp4A c.93.1.1 35710 1tbd 134 1.47e+01 2tbd d.89.1.1 40240 1otjA 283 1.48e+01 b.82.2.5 93517 1xfkA 336 1.49e+01 1rvkA 382 1.50e+01 c.1.11.2,d.54.1.1 97928,97929 1kolA 398 1.50e+01 b.35.1.2,c.2.1.1 77474,77475 2gm3A 175 1.52e+01 1zhxA 438 1.56e+01 1pmmA 466 1.56e+01 c.67.1.6 94901 2ga9A 297 1.57e+01 1yloA 348 1.61e+01 1vhoA 346 1.62e+01 b.49.3.1,c.56.5.4 100694,100695 1yixA 265 1.62e+01 2ch4A 320 1.65e+01 1wz9A 375 1.69e+01 2c1iA 431 1.73e+01 1j8uA 325 1.75e+01 d.178.1.1 71611 1u9yA 284 1.78e+01 1a8s 273 1.81e+01 1brt c.69.1.12 34710 1je0A 236 1.81e+01 c.56.2.1 66581 1uwkA 557 1.86e+01 e.51.1.1 108065 1wloA 136 1.92e+01 1nf9A 207 1.95e+01 c.33.1.3 85631 1x1zA 252 1.95e+01 1d7oA 297 2.01e+01 1enp c.2.1.2 29907 1y8qB 640 2.04e+01 1wpnA 188 2.07e+01 1tkjA 284 2.09e+01 1yb0A 159 2.11e+01 1sf8A 126 2.12e+01 d.271.1.1 105472 1gpmA 525 2.15e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1umkA 275 2.17e+01 1ji6A 589 2.17e+01 b.18.1.3,b.77.2.1,f.1.3.1 63066,63067,63068 1vmjA 151 2.18e+01 2fytA 340 2.20e+01 1xqwA 293 2.22e+01 1z41A 338 2.26e+01 1azsA 220 2.32e+01 1azsA d.58.29.1 39416 1cojA 212 2.33e+01 1avmA a.2.11.1,d.44.1.1 15737,38734 1uwsA 489 2.37e+01 c.1.8.4 108073 1x7vA 99 2.37e+01 d.58.4.11 109501 1vpt 348 2.41e+01 3mag c.66.1.25 34207 1toaA 313 2.45e+01 1toaA c.92.2.2 35598 1gen 218 2.51e+01 1gen b.66.1.1 27536 1zrn 232 2.58e+01 1qq5A c.108.1.1 43323 1cb8A 678 2.61e+01 1cb8A a.102.3.2,b.24.1.1,b.30.5.2 18849,23898,24422 1fjgE 162 2.62e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1byrA 155 2.63e+01 1byrA d.136.1.1 41450 1t0hB 224 2.65e+01 c.37.1.1 106208 1ijbA 202 2.66e+01 c.62.1.1 71229 1yk3A 210 2.69e+01 1qwoA 442 2.70e+01 c.60.1.2 104620 1sflA 238 2.70e+01 1el5A 389 2.74e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 1p7gA 222 2.74e+01 a.2.11.1,d.44.1.1 94223,94224 1nd4A 264 2.74e+01 d.144.1.6 91815 1wlsA 328 2.76e+01 2fp4B 395 2.78e+01 1hc7A 477 2.78e+01 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 1mi3A 322 2.78e+01 c.1.7.1 91274 1qo7A 394 2.80e+01 1qo7A c.69.1.11 34697 2dri 271 2.80e+01 2dri c.93.1.1 35637 1lzlA 323 2.80e+01 c.69.1.2 78306 1edqA 540 2.82e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1w4rA 195 2.83e+01 1vgyA 393 2.84e+01 c.56.5.4,d.58.19.1 100620,100621 1m0dA 138 2.84e+01 c.52.1.17 74354 1km4A 247 2.89e+01 c.1.2.3 72740 1ceo 343 2.89e+01 1ceo c.1.8.3 28808 1f89A 291 2.92e+01 d.160.1.1 64988 1yr2A 741 2.92e+01 1svdA 473 2.99e+01 2d1yA 256 3.02e+01 1rlzA 369 3.04e+01 c.31.1.1 104989 1hyvA 166 3.05e+01 1b9dA c.55.3.2 61424 1xjvA 294 3.13e+01 1ufoA 238 3.13e+01 c.69.1.27 99344 2fo3A 125 3.16e+01 1vd5A 377 3.18e+01 a.102.1.7 108518 1rjoA 646 3.21e+01 1y0kA 209 3.21e+01 2c6qA 351 3.23e+01 1nv8A 284 3.24e+01 c.66.1.30 86224 1rmwA 212 3.25e+01 1vkcA 158 3.26e+01 1j7xA 302 3.26e+01 c.14.1.2 66425 1xm3A 264 3.28e+01 2f6uA 234 3.28e+01 1wcgA 464 3.29e+01 2bklA 695 3.29e+01 2fcr 173 3.31e+01 1rcf c.23.5.1 31151 1whsB 153 3.36e+01 1whtB 1w4tA 299 3.36e+01 1gvfA 286 3.37e+01 c.1.10.2 70599 2bcgG 453 3.45e+01 1ejdA 419 3.46e+01 1uae d.68.2.2 39576 1hw6A 278 3.49e+01 1frb c.1.7.1 61296 1zxxA 319 3.53e+01 1f5mA 180 3.54e+01 1f5mB d.110.2.1 40895 1fyeA 229 3.57e+01 1fyeA c.23.16.4 31477 1ni4B 341 3.57e+01 c.36.1.7,c.48.1.2 85729,85730 3gcb 470 3.58e+01 3gcb d.3.1.1 37032 1l6rA 227 3.60e+01 c.108.1.10 77768 1mdoA 393 3.60e+01 c.67.1.4 79013 1w6gA 646 3.62e+01 2fuvA 549 3.62e+01 2c2nA 339 3.64e+01 2asbA 251 3.69e+01 1qyaA 307 3.75e+01 d.21.1.2,d.21.1.2 104653,104654 1a9xA 1058 3.76e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1mtzA 293 3.77e+01 c.69.1.7 79467 1g94A 448 3.80e+01 b.71.1.1,c.1.8.1 65169,65170 1z7aA 308 3.85e+01 1iuqA 367 3.86e+01 c.112.1.1 90703 1fobA 334 3.87e+01 c.1.8.3 83255 1hd7A 318 3.90e+01 1bix d.151.1.1 41780 2dpmA 284 3.90e+01 2dpmA c.66.1.28 34246 1fx2A 235 3.92e+01 1fx2A d.58.29.1 39430 1f6yA 262 3.92e+01 1f6yA c.1.21.2 29673 2ghpA 292 3.92e+01 1n9eA 787 3.93e+01 b.30.2.1,d.17.2.1,d.17.2.1 91708,91709,91710 2b82A 211 3.93e+01 1bn8A 420 4.09e+01 1pcl b.80.1.1 28022 1dbwA 126 4.12e+01 1dbwA c.23.1.1 31095 1f46A 140 4.15e+01 1f46A d.129.4.1 59643 2bpqA 373 4.15e+01 2f46A 156 4.21e+01 1vmfA 145 4.21e+01 1xszA 356 4.22e+01 1lnsA 763 4.26e+01 a.40.2.1,b.18.1.13,c.69.1.21 78101,78102,78103 1k3sA 113 4.30e+01 d.198.1.1 68120 1dbxA 158 4.43e+01 1dbuA d.116.1.1 40928 1rybA 212 4.44e+01 c.56.3.1 98098 1khoA 370 4.45e+01 a.124.1.1,b.12.1.3 72489,72490 1sdjA 310 4.50e+01 d.21.1.2,d.21.1.2 98807,98808 1auk 489 4.55e+01 1auk c.76.1.2 35030 2b0cA 206 4.60e+01 1g5tA 196 4.60e+01 1g5rA c.37.1.11 32366 1ylhA 560 4.61e+01 1vquA 374 4.62e+01 1r9jA 673 4.65e+01 1rifA 282 4.66e+01 c.37.1.23 97507 1rwzA 245 4.66e+01 d.131.1.2,d.131.1.2 98005,98006 1g2oA 268 4.69e+01 1b8oA c.56.2.1 60228 1hdcA 253 4.69e+01 1e6wA c.2.1.2 29862 1b7yA 350 4.70e+01 1pysA d.104.1.1 40776 2ebn 289 4.72e+01 2ebn c.1.8.5 28990 2cwkA 160 4.72e+01 1bf5A 545 4.73e+01 1bg1A a.47.1.1,b.2.5.5,d.93.1.1 17766,22460,40526 1oe4A 247 4.77e+01 c.18.1.3 86895 1jv1A 505 4.78e+01 c.68.1.5 71892 1p5zB 263 4.82e+01 c.37.1.1 87815 1odzA 386 4.84e+01 c.1.8.3 86889 1s3rA 535 4.84e+01 1vzwA 244 4.88e+01 1cnzA 363 4.94e+01 1cnzA c.77.1.1 35061 1knvA 293 4.96e+01 c.52.1.7 68707 1h2wA 710 5.00e+01 b.69.7.1,c.69.1.4 76596,76597 1sxrA 183 5.00e+01 d.118.1.1 106101 2ajgA 196 5.01e+01 2czdA 208 5.03e+01 1euhA 475 5.05e+01 1euhA c.82.1.1 35369 1cxqA 162 5.10e+01 1cxqA c.55.3.2 33621 1l6sA 323 5.10e+01 c.1.10.3 73627 1cs0A 1073 5.11e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1gnlA 544 5.13e+01 e.26.1.1 70287 1vpbA 451 5.13e+01 1ag9A 175 5.15e+01 1rcf c.23.5.1 31178 1gd0A 122 5.15e+01 1dptA d.80.1.3 39834 1s5pA 235 5.20e+01 c.31.1.5 98569 1cg2A 393 5.23e+01 1cg2A c.56.5.4,d.58.19.1 33844,39360 2gfoA 396 5.27e+01 1bqcA 302 5.28e+01 1bqcA c.1.8.3 28831 1mdl 359 5.29e+01 2mnr c.1.11.2,d.54.1.1 29247,38891 1zvkA 358 5.29e+01 1ituA 369 5.30e+01 c.1.9.7 71423 2f7tA 227 5.37e+01 1t0qA 498 5.45e+01 a.25.1.2 106220 1whsA 255 5.47e+01 1ivyA c.69.1.5 34649 1nvmA 345 5.47e+01 a.5.7.1,c.1.10.5 86249,86250 1yeyA 444 5.48e+01 1cvl 319 5.49e+01 1cvl c.69.1.18 34786 1u4nA 310 5.50e+01 1hjsA 332 5.53e+01 c.1.8.3 83492 1knwA 425 5.53e+01 b.49.2.3,c.1.6.1 90969,90970 1vhrA 184 5.57e+01 1vhrA c.45.1.1 32651 1bw0A 416 5.64e+01 1bw0A c.67.1.1 34385 2gdzA 267 5.66e+01 1dzfA 215 5.67e+01 1dzfA c.52.3.1,d.78.1.1 33344,39753 1j24A 143 5.69e+01 c.52.1.20 84008 1g60A 260 5.71e+01 c.66.1.11 70151 2b0jA 358 5.71e+01 1d3vA 323 5.72e+01 1d3vA c.42.1.1 32559 1chd 203 5.74e+01 1chd c.40.1.1 32478 1kao 167 5.75e+01 1ctqA c.37.1.8 32014 1qnrA 344 5.76e+01 1qnoA c.1.8.3 28834 2a67A 167 5.78e+01 1gvhA 396 5.78e+01 a.1.1.2,b.43.4.2,c.25.1.5 70601,70602,70603 1jkmB 361 5.80e+01 1jkmA c.69.1.2 34634 1e4mM 501 5.83e+01 1e70M c.1.8.4 59226 1e4yA 214 5.83e+01 1zin c.37.1.1,g.41.2.1 31901,45181 1gmuA 143 5.83e+01 b.107.1.1,d.58.38.1 65335,65336 2b8nA 429 5.86e+01 1ym5A 300 5.86e+01 1kb9D 246 5.89e+01 a.3.1.3,f.23.11.1 77317,77318 1x8gA 227 5.92e+01 2a1fA 247 5.95e+01 1tx2A 297 5.97e+01 c.1.21.1 107420 1fh9A 312 5.99e+01 1taxA c.1.8.3 28913 2cx1A 187 6.00e+01 1mdc 133 6.02e+01 1hmt b.60.1.2 27198 2an1A 292 6.04e+01 1uqtA 482 6.05e+01 c.87.1.6 99794 2a0mA 316 6.05e+01 1ttuA 477 6.13e+01 b.1.18.1,b.2.5.8,b.42.7.1 107305,107306,107307 1y0yA 353 6.14e+01 1u24A 337 6.15e+01 1rxyA 253 6.16e+01 c.56.2.1 98065 1o7qA 289 6.17e+01 c.68.1.9 92626 1ve2A 235 6.22e+01 1ad1A 266 6.28e+01 1aj2 c.1.21.1 29668 1gu7A 364 6.29e+01 b.35.1.2,c.2.1.1 83321,83322 1yrtA 364 6.29e+01 2anuA 255 6.30e+01 1t7vA 278 6.30e+01 1gntA 553 6.33e+01 e.26.1.1 70290 1jztA 246 6.34e+01 c.104.1.1 63319 1zczA 464 6.34e+01 5nul 138 6.36e+01 5nul c.23.5.1 31191 1f8vA 355 6.40e+01 2bbvA b.121.4.4 23329 1wleA 501 6.41e+01 1ddgA 374 6.43e+01 1amoA b.43.4.1,c.25.1.4 25671,31559 1kngA 156 6.51e+01 c.47.1.10 72777 1wb4A 297 6.51e+01 1bvyF 191 6.52e+01 1bvyF c.23.5.1 31207 2g39A 497 6.58e+01 1p0yA 444 6.60e+01 a.166.1.1,b.85.7.3 87654,87655 1u4gA 301 6.60e+01 d.92.1.2 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8.99e+01 b.68.6.2 100240