# List of top-scoring protein chains for t04-100-30-dssp-ehl2-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 1.33e-30 1dtdA 303 8.82e-30 1aye c.56.5.1 33823 1z5rA 306 6.56e-29 1kwmA 402 1.81e-28 c.56.5.1,d.58.3.1 73079,73080 1h8lA 380 1.04e-27 b.3.2.1,c.56.5.1 65737,65738 1m4lA 307 4.27e-27 c.56.5.1 78604 2ctc 307 8.98e-27 1aye c.56.5.1 33802 2c1cA 312 4.39e-26 1jqgA 433 1.42e-23 c.56.5.1,d.58.3.1 71791,71792 1yw4A 341 3.53e-22 1obr 326 9.53e-22 1aye c.56.5.2 33828 2bcoA 350 4.82e-19 1vjzA 341 1.15e-02 c.1.8.3 100838 1m22A 503 2.53e-02 c.117.1.1 78464 1bn7A 294 5.47e-02 1bn6A c.69.1.8 34677 1jwqA 179 1.07e-01 c.56.5.6 90921 1ycdA 243 1.43e-01 1tvnA 293 1.83e-01 1ur4A 399 2.41e-01 1qfeA 252 2.68e-01 1qfeA c.1.10.1 29167 1ysjA 404 2.72e-01 1xwyA 264 2.76e-01 2bv9A 290 3.00e-01 2citA 282 3.16e-01 1yloA 348 3.37e-01 1h49A 512 3.52e-01 c.1.8.4 83477 1j1iA 296 3.77e-01 c.69.1.10 83977 1gqnA 252 3.88e-01 c.1.10.1 90514 1e55A 512 3.92e-01 1e70M c.1.8.4 28934 1h4pA 408 4.05e-01 c.1.8.3 90617 1t71A 281 5.24e-01 1wnaA 131 5.82e-01 1v02A 565 6.66e-01 c.1.8.4 108194 1zynA 202 7.11e-01 1eqcA 394 7.19e-01 1cz1A c.1.8.3 28811 1fjgE 162 7.75e-01 1pkp d.14.1.1,d.50.1.2 37553,38789 1y0yA 353 8.93e-01 1t5bA 201 9.30e-01 c.23.5.3 106433 1eceA 358 9.43e-01 1eceA c.1.8.3 28813 1pe1A 267 1.03e+00 c.1.10.4 94591 1b8oA 284 1.04e+00 1b8oA c.56.2.1 33762 1jcxA 267 1.11e+00 c.1.10.4 66510 1rxxA 421 1.16e+00 d.126.1.4 98061 1t8xA 267 1.18e+00 1h1nA 305 1.21e+00 c.1.8.3 70855 1xfoA 357 1.28e+00 1fxqA 267 1.31e+00 1d9eA c.1.10.4 60108 1vknA 351 1.31e+00 c.2.1.3,d.81.1.1 108676,108677 1xm3A 264 1.32e+00 1j1uA 306 1.34e+00 c.26.1.1 83980 1wlsA 328 1.45e+00 1q0rA 298 1.52e+00 c.69.1.28 95508 1vcoA 550 1.54e+00 c.23.16.1,c.37.1.10 108508,108509 1j7lA 264 1.54e+00 d.144.1.6 62697 1fwsA 267 1.65e+00 1d9eA c.1.10.4 60063 1tikA 213 1.82e+00 c.23.5.3 107003 1tqyB 415 1.83e+00 c.95.1.1,c.95.1.1 107247,107248 1zr6A 503 1.99e+00 1wnfA 328 2.00e+00 1zhaA 267 2.01e+00 1sbyA 254 2.04e+00 1yh1A 359 2.04e+00 1ynpA 317 2.07e+00 1ceo 343 2.14e+00 1ceo c.1.8.3 28808 1b16A 254 2.14e+00 1b16A c.2.1.2 29875 1gowA 489 2.14e+00 1qvbA c.1.8.4 28981 1xsjA 778 2.39e+00 1ea5A 537 2.51e+00 2bce c.69.1.1 34592 1wkyA 464 2.58e+00 1b65A 375 2.59e+00 1b65A d.154.1.1 42020 1iirA 415 2.65e+00 1iirA c.87.1.5 62453 1ohvA 472 2.71e+00 c.67.1.4 93031 1yr2A 741 2.72e+00 1brt 277 2.74e+00 1brt c.69.1.12 34699 1broA 277 2.77e+00 1brt c.69.1.12 34700 2bleA 367 2.80e+00 1e5dA 402 2.96e+00 1e5dA c.23.5.1,d.157.1.3 31208,42061 1rzmA 338 2.96e+00 c.1.10.4 105137 1ldjA 760 3.07e+00 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 2a9gA 418 3.11e+00 1tcvA 287 3.15e+00 1i74A 309 3.16e+00 1i74A c.107.1.1 61867 1fobA 334 3.16e+00 c.1.8.3 83255 1zedA 484 3.31e+00 1fnoA 417 3.35e+00 d.58.19.1,c.56.5.4 70145,75841 1i1qA 520 3.41e+00 1qdlA d.161.1.1 61543 1zemA 262 3.45e+00 1vgyA 393 3.60e+00 c.56.5.4,d.58.19.1 100620,100621 1l8nA 679 3.65e+00 c.1.8.10,d.92.2.2 84564,84565 2pvaA 345 3.68e+00 3pvaA d.153.1.3 41850 1uwsA 489 3.69e+00 c.1.8.4 108073 1gox 370 3.73e+00 1gox c.1.4.1 28607 1wv2A 265 3.76e+00 1gqiA 708 3.77e+00 c.1.8.10,d.92.2.2 76279,76280 1m2rA 327 3.79e+00 d.144.1.7 84760 1i7dA 659 3.84e+00 1d6mA e.10.1.1 61886 2f2hA 773 3.92e+00 1p3wA 404 4.03e+00 c.67.1.3 87752 1sfjA 238 4.14e+00 1vjnA 220 4.25e+00 d.157.1.4 100825 1om1A 332 4.27e+00 d.144.1.7 93347 1gq6A 313 4.28e+00 c.42.1.1 70341 1pcxA 810 4.30e+00 a.71.2.1,b.2.8.1,c.62.1.2,d.109.2.1,g.41.10.1 94497,94498,94499,94500,94501 1qvbA 481 4.33e+00 1qvbA c.1.8.4 28983 1kbpA 432 4.65e+00 4kbpA b.1.12.1,d.159.1.1 22349,42068 2freA 200 4.68e+00 1e5mA 416 4.74e+00 1dd8A c.95.1.1,c.95.1.1 58973,58974 2gshA 414 4.76e+00 1g0cA 364 4.95e+00 7a3hA c.1.8.3 60165 1dp4A 435 5.10e+00 1dp4A c.93.1.1 35710 1zq4A 693 5.16e+00 1bxkA 355 5.51e+00 1bxkA c.2.1.2 29803 2ebn 289 5.68e+00 2ebn c.1.8.5 28990 1dozA 309 5.72e+00 1ak1 c.92.1.1 35592 2ac2A 309 5.94e+00 1ew2A 513 5.95e+00 1b8jA c.76.1.1 59525 3pvaA 335 6.13e+00 3pvaA d.153.1.3 41854 2b0jA 358 6.14e+00 1hp5A 512 6.15e+00 1hp4A c.1.8.6,d.92.2.1 61113,61114 1t6cA 315 6.21e+00 c.55.1.8,c.55.1.8 106558,106559 1jakA 512 6.25e+00 c.1.8.6,d.92.2.1 66472,66473 1sflA 238 6.26e+00 1wloA 136 6.27e+00 1ad2 228 6.28e+00 1ad2 e.24.1.1 43353 1lfwA 470 6.41e+00 c.56.5.4,d.58.19.1 77942,77943 1mldA 314 6.44e+00 2cmd c.2.1.5,d.162.1.1 30122,42089 1edg 380 6.53e+00 1edg c.1.8.3 28807 1qmeA 702 6.63e+00 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1jbkA 195 6.63e+00 c.37.1.20 71631 1vmaA 306 6.82e+00 a.24.13.1,c.37.1.10 108887,108888 1twfB 1224 6.93e+00 1odkA 235 6.96e+00 c.56.2.1 86863 1s3eA 520 6.98e+00 c.3.1.2,d.16.1.5 98426,98427 1t0iA 191 7.17e+00 c.23.5.4 106209 1u4gA 301 7.17e+00 d.92.1.2 107670 1w8sA 263 7.22e+00 1pmmA 466 7.25e+00 c.67.1.6 94901 2bkkA 264 7.25e+00 1uwkA 557 7.29e+00 e.51.1.1 108065 1e0cA 271 7.30e+00 1e0cA c.46.1.2,c.46.1.2 32717,32718 1ejdA 419 7.32e+00 1uae d.68.2.2 39576 1ezm 301 7.42e+00 1hyt d.92.1.2 58980 2afwA 329 7.43e+00 1l2lA 457 7.58e+00 c.72.1.3 77656 1nksA 194 7.65e+00 1nksA c.37.1.1 31886 1h16A 759 7.65e+00 c.7.1.1 76462 1khtA 192 7.70e+00 c.37.1.1 84401 1ea9C 583 7.71e+00 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 2bznA 351 7.81e+00 2ax4A 198 8.04e+00 2gl5A 410 8.05e+00 1cg2A 393 8.07e+00 1cg2A c.56.5.4,d.58.19.1 33844,39360 2cygA 312 8.21e+00 1pbv 195 8.37e+00 1pbv a.118.3.1 19179 1hrkA 359 8.38e+00 1hrkA c.92.1.1 61228 1o60A 292 8.43e+00 c.1.10.4 92532 1t64A 377 8.96e+00 c.42.1.2 106543 1dpe 507 9.00e+00 1dpe c.94.1.1 35799 1kfwA 435 9.06e+00 c.1.8.5,d.26.3.1 77376,77377 1gnxA 479 9.07e+00 c.1.8.4 76241 1eg7A 557 9.09e+00 1eg7A c.37.1.10 32241 1edqA 540 9.19e+00 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1ctn 540 9.29e+00 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1vefA 395 9.37e+00 1gu7A 364 9.40e+00 b.35.1.2,c.2.1.1 83321,83322 3pmgA 561 9.67e+00 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1fnsA 196 9.73e+00 1auq c.62.1.1 34136 1z5yE 149 9.85e+00 1rj9A 304 9.97e+00 a.24.13.1,c.37.1.10 97553,97554 1b1cA 181 1.01e+01 1amoA c.23.5.2 31212 1r6lA 239 1.01e+01 d.14.1.4,d.101.1.1 97153,97154 1yge 839 1.02e+01 1yge a.119.1.1,b.12.1.1 19234,23634 1rttA 193 1.04e+01 c.23.5.4 105098 1dqaA 467 1.04e+01 1dqaA d.58.20.1,d.179.1.1 39364,42585 2an3A 289 1.05e+01 1uk8A 282 1.05e+01 c.69.1.10 107907 1j2rA 199 1.05e+01 c.33.1.3 90788 1itxA 419 1.07e+01 c.1.8.5,d.26.3.1 71425,71426 2basA 431 1.07e+01 2av4A 162 1.08e+01 1iupA 282 1.09e+01 c.69.1.10 76815 1zzmA 259 1.09e+01 1uyrA 737 1.10e+01 c.14.1.4,c.14.1.4 100188,100189 1hruA 188 1.11e+01 1hruA d.115.1.1 40926 1r6dA 337 1.12e+01 c.2.1.2 97148 1wcgA 464 1.12e+01 1ijbA 202 1.13e+01 c.62.1.1 71229 1rovA 857 1.17e+01 a.119.1.1,b.12.1.1 97674,97675 1tkjA 284 1.17e+01 1l5xA 280 1.20e+01 c.106.1.1 77718 1i50B 1224 1.21e+01 e.29.1.1 61755 1tf9A 284 1.23e+01 1dosA 358 1.23e+01 1dosA c.1.10.2 29175 1hkhA 279 1.25e+01 c.69.1.12 90628 2axtB 510 1.26e+01 2btoA 473 1.29e+01 1ojaA 520 1.31e+01 c.3.1.2,d.16.1.5 93096,93097 1zosA 230 1.31e+01 1r9jA 673 1.33e+01 1cm5A 759 1.34e+01 1cm5A c.7.1.1 30671 1srqA 341 1.35e+01 e.55.1.1 105967 1bl3A 160 1.37e+01 1b9dA c.55.3.2 33655 4kbpA 432 1.41e+01 4kbpA b.1.12.1,d.159.1.1 22345,42064 2cybA 323 1.46e+01 2c6qA 351 1.48e+01 1qq9A 284 1.48e+01 1xjo c.56.5.4 33841 1gqeA 365 1.53e+01 e.38.1.1 70351 1j0hA 588 1.54e+01 b.1.18.2,b.71.1.1,c.1.8.1 77027,77028,77029 1yt8A 539 1.54e+01 1u3dA 509 1.56e+01 a.99.1.1,c.28.1.1 107638,107639 1r3sA 367 1.58e+01 c.1.22.1 96963 1yrgA 385 1.58e+01 1yrgA c.10.1.2 30854 1z2lA 423 1.58e+01 1vhmA 195 1.60e+01 d.110.2.1 100691 1ug6A 431 1.60e+01 c.1.8.4 88490 1auk 489 1.61e+01 1auk c.76.1.2 35030 1hyvA 166 1.62e+01 1b9dA c.55.3.2 61424 1lf6A 684 1.62e+01 a.102.1.5,b.30.5.5 77918,77919 1ynuA 473 1.63e+01 1h7eA 245 1.64e+01 c.68.1.13 60717 1vmfA 145 1.64e+01 1rljA 139 1.66e+01 c.23.5.7 104983 1d8wA 426 1.66e+01 1de5A c.1.15.2 29394 1xyzA 347 1.66e+01 1taxA c.1.8.3 28804 1ki9A 192 1.68e+01 c.37.1.1 84404 1te6A 439 1.69e+01 c.1.11.1,d.54.1.1 106797,106798 1zrn 232 1.71e+01 1qq5A c.108.1.1 43323 1xjo 284 1.71e+01 1xjo c.56.5.4 33843 1vk3A 615 1.73e+01 d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 100846,100847,100848,100849 1umdA 367 1.73e+01 c.36.1.11 99599 1of8A 370 1.74e+01 c.1.10.4 92819 1ccwB 483 1.75e+01 1cb7B c.1.19.2 29646 1ua4A 455 1.75e+01 c.72.1.3 99128 1ve6A 582 1.76e+01 2bhuA 602 1.80e+01 2d0iA 333 1.80e+01 2akzA 439 1.82e+01 1esc 306 1.83e+01 1esc c.23.10.1 31334 1v77A 212 1.84e+01 c.6.3.2 108402 2fnaA 357 1.85e+01 2gdzA 267 1.86e+01 1uroA 367 1.88e+01 1uroA c.1.22.1 29675 1jqbA 351 1.89e+01 b.35.1.2,c.2.1.1 77151,77152 1xfkA 336 1.90e+01 2c71A 216 1.95e+01 1xd3A 230 1.96e+01 1vhvA 268 1.96e+01 c.90.1.1 100704 1mjhA 162 1.97e+01 1mjhA c.26.2.4 31639 1uch 230 1.98e+01 1uch d.3.1.6 37129 2dorA 311 1.99e+01 2dorA c.1.4.1 28593 1nofA 383 2.01e+01 b.71.1.2,c.1.8.3 92020,92021 1yixA 265 2.01e+01 1f52A 468 2.04e+01 1lgr d.15.9.1,d.128.1.1 37839,41169 3cox 507 2.05e+01 1b8sA c.3.1.2,d.16.1.1 30332,37863 1l5jA 865 2.08e+01 a.118.15.1,c.8.2.1,c.83.1.1 73592,73593,73594 1pqnA 127 2.09e+01 c.47.1.8 95025 2fo3A 125 2.09e+01 1wzlA 585 2.10e+01 1c4xA 285 2.12e+01 1c4xA c.69.1.10 34684 1h1yA 228 2.12e+01 c.1.2.2 76506 1vhoA 346 2.12e+01 b.49.3.1,c.56.5.4 100694,100695 1fecA 490 2.13e+01 3grs c.3.1.5,c.3.1.5,d.87.1.1 30489,30490,40176 1vm6A 228 2.15e+01 c.2.1.3,d.81.1.3 108876,108877 1ls1A 295 2.16e+01 a.24.13.1,c.37.1.10 78170,78171 1rvgA 305 2.16e+01 c.1.10.2 97920 1orvA 728 2.17e+01 b.70.3.1,c.69.1.24 87354,87355 1c3pA 375 2.17e+01 1c3pA c.42.1.2 32606 1o6dA 163 2.17e+01 c.116.1.3 92567 1z41A 338 2.26e+01 1gzgA 337 2.31e+01 c.1.10.3 70805 1x9dA 538 2.31e+01 1je0A 236 2.32e+01 c.56.2.1 66581 1pjr 724 2.36e+01 1pjr c.37.1.19,c.37.1.19 32391,32392 1snlA 103 2.36e+01 a.39.1.7 105820 2bklA 695 2.36e+01 1fsu 492 2.36e+01 1auk c.76.1.2 35032 2ng1 293 2.39e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 2aebA 322 2.39e+01 1zxiB 809 2.42e+01 2c30A 321 2.42e+01 1uouA 474 2.45e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1x8dA 104 2.49e+01 1hd7A 318 2.50e+01 1bix d.151.1.1 41780 2bvyA 475 2.50e+01 1gz6A 319 2.50e+01 c.2.1.2 76410 1ox6A 555 2.53e+01 c.1.2.1,c.23.16.1 87505,87506 2myr 501 2.53e+01 1uocA 289 2.53e+01 c.55.3.9 99686 1upvA 257 2.54e+01 1gklA 297 2.56e+01 c.69.1.2 65250 1r5lA 262 2.57e+01 a.5.3.1,c.13.1.1 97099,97100 1jubA 311 2.58e+01 c.1.4.1 90908 2d4rA 147 2.62e+01 1zuwA 272 2.62e+01 1dorA 311 2.62e+01 2dorA c.1.4.1 28595 1ur5A 309 2.64e+01 c.2.1.5,d.162.1.1 99807,99808 1ohtA 215 2.64e+01 d.118.1.1 87036 1h2wA 710 2.65e+01 b.69.7.1,c.69.1.4 76596,76597 1qfmA 710 2.65e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1xhcA 367 2.66e+01 1mj5A 302 2.69e+01 c.69.1.8 91285 1bdmA 327 2.71e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1x3zA 335 2.72e+01 1nc5A 373 2.79e+01 a.102.1.6 85548 1jvbA 347 2.79e+01 b.35.1.2,c.2.1.1 77181,77182 1qhoA 686 2.81e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 2anpA 291 2.81e+01 1qnrA 344 2.83e+01 1qnoA c.1.8.3 28834 2d1yA 256 2.83e+01 1r8mE 203 2.83e+01 a.118.3.1 97242 1a2zA 220 2.85e+01 1a2zA c.56.4.1 33794 1kewA 361 2.86e+01 c.2.1.2 68544 1wyuB 474 2.88e+01 1wqaA 455 2.88e+01 1lokA 291 2.90e+01 c.56.5.4 78122 1kevA 351 2.91e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1korA 400 2.93e+01 c.26.2.1,d.210.1.1 72824,72825 2fymA 431 2.93e+01 2acvA 463 2.99e+01 1zy7A 403 3.00e+01 1qs1A 462 3.07e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1u0kA 288 3.07e+01 d.21.1.2,d.21.1.2 107547,107548 1o7jA 327 3.07e+01 c.88.1.1 81140 1r3dA 264 3.09e+01 1gg1A 350 3.10e+01 1qr7A c.1.10.4 29187 2bjfA 329 3.10e+01 1f46A 140 3.11e+01 1f46A d.129.4.1 59643 1f0lA 535 3.14e+01 1ddt b.2.1.1,d.166.1.1,f.1.2.1 22377,42239,43382 1j5sA 463 3.15e+01 c.1.9.8 71580 1nd4A 264 3.19e+01 d.144.1.6 91815 1rtqA 299 3.20e+01 c.56.5.4 97819 1ivnA 190 3.20e+01 c.23.10.5 83719 1wb4A 297 3.20e+01 2bvcA 486 3.21e+01 1k3sA 113 3.24e+01 d.198.1.1 68120 1uwvA 433 3.25e+01 b.40.4.12,c.66.1.40 100128,100129 1u9yA 284 3.26e+01 1i9zA 347 3.29e+01 1i9yA d.151.1.2 62102 1d3vA 323 3.29e+01 1d3vA c.42.1.1 32559 1e6wA 260 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