# 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 2bo9A 308 8.14e-28 1dtdA 303 2.63e-27 1aye c.56.5.1 33823 1z5rA 306 1.04e-26 1kwmA 402 1.09e-25 c.56.5.1,d.58.3.1 73079,73080 2ctc 307 1.44e-24 1aye c.56.5.1 33802 1m4lA 307 2.33e-24 c.56.5.1 78604 2c1cA 312 6.69e-24 1h8lA 380 2.92e-23 b.3.2.1,c.56.5.1 65737,65738 1jqgA 433 9.95e-21 c.56.5.1,d.58.3.1 71791,71792 1obr 326 6.36e-20 1aye c.56.5.2 33828 1yw4A 341 2.95e-18 2bcoA 350 1.09e-16 1jwqA 179 1.39e-02 c.56.5.6 90921 1ycdA 243 6.85e-02 1i7dA 659 1.11e-01 1d6mA e.10.1.1 61886 1eceA 358 3.75e-01 1eceA c.1.8.3 28813 1m22A 503 4.11e-01 c.117.1.1 78464 1zuwA 272 7.16e-01 2fiqA 420 7.69e-01 1vjzA 341 7.99e-01 c.1.8.3 100838 1tvnA 293 1.03e+00 1hc7A 477 1.09e+00 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 2b61A 377 1.19e+00 1j1iA 296 1.34e+00 c.69.1.10 83977 1ohvA 472 1.78e+00 c.67.1.4 93031 1j2rA 199 2.03e+00 c.33.1.3 90788 1t8xA 267 2.24e+00 1h1nA 305 2.35e+00 c.1.8.3 70855 1xovA 326 2.49e+00 1lwjA 441 2.50e+00 b.71.1.1,c.1.8.1 74303,74304 1rqbA 539 2.97e+00 a.5.7.2,c.1.10.5 105057,105058 1eqcA 394 3.09e+00 1cz1A c.1.8.3 28811 1pmmA 466 3.30e+00 c.67.1.6 94901 1e5dA 402 3.32e+00 1e5dA c.23.5.1,d.157.1.3 31208,42061 1wkyA 464 3.42e+00 2citA 282 3.57e+00 1dkuA 317 3.77e+00 1dkuA c.61.1.2,c.61.1.2 34118,34119 1xyzA 347 4.17e+00 1taxA c.1.8.3 28804 1pe1A 267 4.27e+00 c.1.10.4 94591 1li5B 461 4.30e+00 a.27.1.1,c.26.1.1 73914,73915 1ceo 343 4.33e+00 1ceo c.1.8.3 28808 1pbv 195 4.42e+00 1pbv a.118.3.1 19179 1zhaA 267 4.45e+00 1fobA 334 4.82e+00 c.1.8.3 83255 2bv9A 290 4.97e+00 1xhcA 367 5.00e+00 1gzgA 337 5.13e+00 c.1.10.3 70805 1u0mA 382 5.49e+00 c.95.1.2,c.95.1.2 107557,107558 1qfeA 252 5.62e+00 1qfeA c.1.10.1 29167 1dorA 311 5.79e+00 2dorA c.1.4.1 28595 1lehA 364 5.81e+00 1bw9A c.2.1.7,c.58.1.1 30268,33916 2gl5A 410 6.12e+00 1ja9A 274 6.14e+00 c.2.1.2 62817 1li5A 461 6.26e+00 a.27.1.1,c.26.1.1 73912,73913 1a76 326 6.39e+00 1a76 a.60.7.1,c.120.1.2 18091,33361 1t6cA 315 6.41e+00 c.55.1.8,c.55.1.8 106558,106559 1fwsA 267 6.45e+00 1d9eA c.1.10.4 60063 1edg 380 6.58e+00 1edg c.1.8.3 28807 2bznA 351 6.65e+00 1jubA 311 6.69e+00 c.1.4.1 90908 1d7uA 433 6.69e+00 2dkb c.67.1.4 34439 1gqnA 252 6.76e+00 c.1.10.1 90514 1r8sE 203 7.16e+00 a.118.3.1 97248 1jcxA 267 7.48e+00 c.1.10.4 66510 1eny 268 7.59e+00 1eny c.2.1.2 29910 1u9yA 284 7.61e+00 1k32A 1045 7.69e+00 b.36.1.3,b.68.7.1,b.69.9.1,c.14.1.2 68068,68069,68070,68071 1vhmA 195 7.83e+00 d.110.2.1 100691 2dorA 311 8.07e+00 2dorA c.1.4.1 28593 2c6qA 351 8.10e+00 1vkcA 158 8.50e+00 2bleA 367 8.77e+00 1gqiA 708 8.81e+00 c.1.8.10,d.92.2.2 76279,76280 2liv 344 8.88e+00 2liv c.93.1.1 35708 1h4pA 408 9.07e+00 c.1.8.3 90617 1j24A 143 9.20e+00 c.52.1.20 84008 1b4kA 337 9.50e+00 1b4kA c.1.10.3 29184 1fxqA 267 9.71e+00 1d9eA c.1.10.4 60108 1s9uA 207 9.99e+00 a.184.1.1 105390 1wnaA 131 1.04e+01 2aqjA 538 1.05e+01 1bn7A 294 1.06e+01 1bn6A c.69.1.8 34677 1thg 544 1.15e+01 1thg c.69.1.17 34763 7a3hA 303 1.16e+01 7a3hA c.1.8.3 28817 1fts 295 1.17e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1pcxA 810 1.19e+01 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 1t64A 377 1.21e+01 c.42.1.2 106543 1r8mE 203 1.26e+01 a.118.3.1 97242 1wloA 136 1.27e+01 1dozA 309 1.27e+01 1ak1 c.92.1.1 35592 2ac2A 309 1.28e+01 1yloA 348 1.34e+01 1ak0 270 1.37e+01 1ak0 a.124.1.2 19345 1ag9A 175 1.39e+01 1rcf c.23.5.1 31178 1vjnA 220 1.41e+01 d.157.1.4 100825 1v77A 212 1.42e+01 c.6.3.2 108402 1mkzA 172 1.42e+01 c.57.1.1 84998 1zedA 484 1.42e+01 1sflA 238 1.42e+01 2dkb 433 1.43e+01 2dkb c.67.1.4 34438 1fs7A 485 1.43e+01 1qdbA a.138.1.3 19691 1ynuA 473 1.44e+01 1nfvA 179 1.45e+01 a.25.1.1 85642 1z15A 344 1.46e+01 1qbgA 272 1.47e+01 1d4aA c.23.5.3 31227 1xvaA 292 1.49e+01 1xvaA c.66.1.5 34183 1gvnB 287 1.49e+01 c.37.1.21 76354 1ad4A 266 1.50e+01 1aj2 c.1.21.1 29670 1hl2A 297 1.50e+01 c.1.10.1 83581 1fsz 372 1.52e+01 1fsz c.32.1.1,d.79.2.1 31750,39802 1gen 218 1.57e+01 1gen b.66.1.1 27536 1lc5A 364 1.59e+01 c.67.1.1 73827 1vplA 256 1.60e+01 1gg1A 350 1.62e+01 1qr7A c.1.10.4 29187 1wyuB 474 1.64e+01 1p3wA 404 1.64e+01 c.67.1.3 87752 1ox6A 555 1.67e+01 c.1.2.1,c.23.16.1 87505,87506 1khtA 192 1.72e+01 c.37.1.1 84401 1r6dA 337 1.77e+01 c.2.1.2 97148 2ag5A 246 1.80e+01 1vj0A 380 1.82e+01 b.35.1.2,c.2.1.1 100786,100787 1cjaA 342 1.84e+01 1cjaA d.144.1.3 41708 1vefA 395 1.84e+01 1wg8A 285 1.86e+01 1ynpA 317 1.88e+01 1kolA 398 1.89e+01 b.35.1.2,c.2.1.1 77474,77475 1sfjA 238 1.94e+01 1jvbA 347 1.95e+01 b.35.1.2,c.2.1.1 77181,77182 1a8y 367 1.97e+01 1a8y c.47.1.3,c.47.1.3,c.47.1.3 32781,32782,32783 1g8kA 825 1.99e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1zbqA 327 2.00e+01 1ur4A 399 2.02e+01 1rwzA 245 2.03e+01 d.131.1.2,d.131.1.2 98005,98006 1d4aA 273 2.09e+01 1d4aA c.23.5.3 31219 1txvA 452 2.11e+01 2gsq 202 2.15e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1n8fA 350 2.17e+01 c.1.10.4 85397 1y5eA 169 2.19e+01 1nv8A 284 2.21e+01 c.66.1.30 86224 1jvnA 555 2.24e+01 c.1.2.1,c.23.16.1 67355,67356 1lw7A 365 2.25e+01 c.26.1.3,c.37.1.1 74295,74296 1vyrA 364 2.29e+01 c.1.4.1 108906 1w4vA 119 2.31e+01 1vypX 364 2.31e+01 c.1.4.1 108905 1c4xA 285 2.33e+01 1c4xA c.69.1.10 34684 1h61A 364 2.36e+01 1oyc c.1.4.1 60657 2c07A 285 2.37e+01 1vf1A 229 2.37e+01 1wzlA 585 2.42e+01 2cbiA 594 2.43e+01 1ew2A 513 2.47e+01 1b8jA c.76.1.1 59525 1pqnA 127 2.49e+01 c.47.1.8 95025 1ewqA 765 2.51e+01 1ewqA a.113.1.1,c.37.1.12,c.55.6.1,d.75.2.1 19069,32383,33740,39743 1kevA 351 2.54e+01 1pedA b.35.1.2,c.2.1.1 24749,29765 1jqbA 351 2.59e+01 b.35.1.2,c.2.1.1 77151,77152 1ea9C 583 2.66e+01 b.1.18.2,b.71.1.1,c.1.8.1 70087,70088,70089 1rzmA 338 2.71e+01 c.1.10.4 105137 1x9iA 302 2.73e+01 1nni1 174 2.76e+01 1tzbA 302 2.77e+01 c.80.1.1 107470 1yixA 265 2.81e+01 1uvzA 119 2.83e+01 1h2bA 359 2.84e+01 b.35.1.2,c.2.1.1 90543,90544 1s58A 554 2.84e+01 b.121.5.2 105262 5reqA 727 2.87e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1nmoA 247 2.87e+01 c.135.1.1 91980 1hd7A 318 2.90e+01 1bix d.151.1.1 41780 1h1yA 228 2.93e+01 c.1.2.2 76506 1xqwA 293 2.93e+01 1o60A 292 2.94e+01 c.1.10.4 92532 1f3aA 222 2.95e+01 1pgtA a.45.1.1,c.47.1.5 17701,32995 1ad1A 266 2.99e+01 1aj2 c.1.21.1 29668 1dbxA 158 3.01e+01 1dbuA d.116.1.1 40928 1l8aA 886 3.02e+01 c.36.1.10,c.36.1.6,c.48.1.1 73677,73678,73679 1vhcA 224 3.03e+01 c.1.10.1 100661 1lhpA 312 3.06e+01 c.72.1.5 77960 1h7eA 245 3.10e+01 c.68.1.13 60717 2abbA 364 3.16e+01 1gz6A 319 3.23e+01 c.2.1.2 76410 1u5uA 374 3.23e+01 1w5nA 337 3.26e+01 2bpqA 373 3.27e+01 2c5uA 375 3.28e+01 1jae 471 3.37e+01 1smd b.71.1.1,c.1.8.1 27773,28760 1d8wA 426 3.40e+01 1de5A c.1.15.2 29394 1nal1 297 3.44e+01 1nal3 1h65A 270 3.44e+01 c.37.1.8 65640 1c7gA 456 3.51e+01 c.67.1.2 90415 1gvoA 364 3.53e+01 c.1.4.1 76357 1mx3A 347 3.54e+01 c.2.1.4,c.23.12.1 79638,79639 1ad2 228 3.56e+01 1ad2 e.24.1.1 43353 1xqoA 256 3.58e+01 1ls1A 295 3.59e+01 a.24.13.1,c.37.1.10 78170,78171 1v02A 565 3.65e+01 c.1.8.4 108194 2ng1 293 3.67e+01 1ng1 a.24.13.1,c.37.1.10 16962,32273 1yt8A 539 3.68e+01 2cvdA 198 3.71e+01 1wqaA 455 3.71e+01 1zavA 180 3.71e+01 1t0iA 191 3.75e+01 c.23.5.4 106209 1q1aA 289 3.78e+01 c.31.1.5 95561 1zj6A 187 3.78e+01 1upvA 257 3.86e+01 1xg7A 250 3.89e+01 1mlwA 301 3.93e+01 d.178.1.1 79289 1reqA 727 3.94e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1xm3A 264 3.95e+01 1s7hA 200 4.00e+01 d.58.48.2 105349 1mtzA 293 4.03e+01 c.69.1.7 79467 1b16A 254 4.03e+01 1b16A c.2.1.2 29875 1zbmA 280 4.05e+01 1fds 327 4.08e+01 1fds c.2.1.2 29838 1uwkA 557 4.08e+01 e.51.1.1 108065 1phk 298 4.13e+01 1cdkA d.144.1.7 41635 2absA 383 4.18e+01 1ktbA 405 4.22e+01 b.71.1.1,c.1.8.1 72960,72961 1kewA 361 4.22e+01 c.2.1.2 68544 1ki9A 192 4.28e+01 c.37.1.1 84404 1d2nA 272 4.35e+01 1d2nA c.37.1.20 32428 1zk4A 251 4.35e+01 1b1cA 181 4.40e+01 1amoA c.23.5.2 31212 1sbyA 254 4.43e+01 1ug7A 128 4.44e+01 a.24.24.1 107824 1s99A 200 4.45e+01 1wmjA 130 4.49e+01 1srqA 341 4.53e+01 e.55.1.1 105967 1ht6A 405 4.54e+01 b.71.1.1,c.1.8.1 83629,83630 1eljA 381 4.55e+01 4mbp c.94.1.1 35791 1n82A 331 4.57e+01 c.1.8.3 91703 1z41A 338 4.61e+01 1bf2 750 4.63e+01 1bf2 b.1.18.2,b.71.1.1,c.1.8.1 21860,27787,28774 1nszA 347 4.63e+01 b.30.5.4 80724 1zemA 262 4.70e+01 1s2dA 167 4.78e+01 c.23.14.1 98377 1wlsA 328 4.80e+01 1q5xA 161 4.81e+01 c.8.7.1 95947 1pbyB 337 4.85e+01 b.69.2.2 94422 2cy7A 396 4.89e+01 1k38A 254 4.94e+01 e.3.1.1 84303 1bxkA 355 5.03e+01 1bxkA c.2.1.2 29803 2fpmA 322 5.08e+01 1dp4A 435 5.08e+01 1dp4A c.93.1.1 35710 1nxqA 251 5.09e+01 c.2.1.2 86388 1b5qA 472 5.09e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1ysjA 404 5.12e+01 1odzA 386 5.14e+01 c.1.8.3 86889 1usgA 346 5.15e+01 c.93.1.1 99864 1v73A 342 5.16e+01 1wvfA 520 5.22e+01 1wu7A 434 5.28e+01 1cm5A 759 5.31e+01 1cm5A c.7.1.1 30671 1b5l 172 5.32e+01 1b5l a.26.1.3 16900 1b8gA 429 5.33e+01 1b8gA c.67.1.4 34499 1vpqA 273 5.36e+01 1jbkA 195 5.39e+01 c.37.1.20 71631 1jtvA 327 5.41e+01 c.2.1.2 84230 1wdtA 665 5.41e+01 1vcoA 550 5.44e+01 c.23.16.1,c.37.1.10 108508,108509 1wnfA 328 5.49e+01 1lnzA 342 5.50e+01 b.117.1.1,c.37.1.8 78112,78113 1h16A 759 5.51e+01 c.7.1.1 76462 1rovA 857 5.52e+01 a.119.1.1,b.12.1.1 97674,97675 1vp8A 201 5.52e+01 1wrjA 156 5.54e+01 1jmcA 246 5.62e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1kmdA 117 5.62e+01 d.189.1.1 72744 1z2lA 423 5.66e+01 1yzgA 179 5.75e+01 1ej5A 107 5.80e+01 1ej5A a.68.1.1 18268 1t71A 281 5.85e+01 1nvmA 345 5.88e+01 a.5.7.1,c.1.10.5 86249,86250 1r6lA 239 5.88e+01 d.14.1.4,d.101.1.1 97153,97154 1xwyA 264 6.03e+01 7aatA 401 6.05e+01 1ajsA c.67.1.1 34250 1vr6A 350 6.08e+01 1ihgA 370 6.10e+01 2cpl a.118.8.1,b.62.1.1 62380,62381 1rk6A 496 6.26e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 2av4A 162 6.26e+01 1frb 315 6.28e+01 1frb c.1.7.1 28665 1tqxA 227 6.30e+01 1nsf 273 6.32e+01 1d2nA c.37.1.20 32429 1e9rA 437 6.32e+01 c.37.1.11 64827 1m7yA 435 6.41e+01 c.67.1.4 78761 1ks8A 433 6.42e+01 a.102.1.2 77519 1yqdA 366 6.44e+01 1eudB 396 6.44e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1zklA 353 6.47e+01 2lbp 346 6.48e+01 2liv c.93.1.1 35709 1atlA 202 6.49e+01 1atlA d.92.1.9 40322 1gcyA 527 6.59e+01 1jdc b.71.1.1,c.1.8.1 27788,28775 1fc4A 401 6.59e+01 1bs0A c.67.1.4 59760 1hjsA 332 6.61e+01 c.1.8.3 83492 1bag 425 6.63e+01 1bag b.71.1.1,c.1.8.1 27720,28707 1q6oA 216 6.69e+01 c.1.2.3 95986 1ykwA 435 6.72e+01 2bdwA 362 6.76e+01 1k07A 263 6.78e+01 d.157.1.1 77218 1d8dA 377 6.79e+01 1ft1A a.118.6.1 19185 1wzzA 334 6.79e+01 1w5qA 337 6.81e+01 1qhtA 775 6.88e+01 1tgoA c.55.3.5,e.8.1.1 33722,43011 1iyhA 198 6.89e+01 a.45.1.1,c.47.1.5 83790,83791 1ydmA 187 6.90e+01 2if1 126 6.92e+01 2if1 d.64.1.1 39547 1kv8A 216 6.92e+01 c.1.2.3 73054 2a67A 167 6.97e+01 2b30A 301 6.98e+01 1gc0A 398 6.99e+01 c.67.1.3 70168 1fhuA 320 6.99e+01 1fhuA c.1.11.2,d.54.1.1 29234,38878 1s3eA 520 7.09e+01 c.3.1.2,d.16.1.5 98426,98427 2d4rA 147 7.12e+01 1mtyD 512 7.19e+01 1mhyD a.25.1.2 16742 1dk8A 147 7.20e+01 1agrE a.91.1.1 18548 1wab 232 7.20e+01 1wab c.23.10.3 31341 1h09A 338 7.25e+01 b.109.1.1,c.1.8.8 83420,83421 1j9yA 385 7.29e+01 1j9yA c.1.8.3 62791 1heiA 451 7.33e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 2fk8A 318 7.35e+01 2hbg 147 7.38e+01 2hbg a.1.1.2 15014 1liiA 363 7.43e+01 c.72.1.1 73921 1g0cA 364 7.44e+01 7a3hA c.1.8.3 60165 2csbA 519 7.45e+01 1yqeA 282 7.60e+01 1n97A 389 7.62e+01 a.104.1.1 80335 1j8uA 325 7.66e+01 d.178.1.1 71611 2arkA 188 7.74e+01 1xp3A 307 7.83e+01 1u6zA 513 7.84e+01 2bc2A 227 7.85e+01 1a7tA d.157.1.1 42031 1zq4A 693 7.87e+01 1gklA 297 7.96e+01 c.69.1.2 65250 1uuqA 440 7.97e+01 c.1.8.3 100015 1qs1A 462 8.01e+01 1qs1A d.166.1.1,d.166.1.1 42260,42261 1uwsA 489 8.02e+01 c.1.8.4 108073 2czdA 208 8.04e+01 1oshA 232 8.08e+01 a.123.1.1 93496 1w0mA 226 8.08e+01 c.1.1.1 109027 1yarO 237 8.11e+01 1ojaA 520 8.14e+01 c.3.1.2,d.16.1.5 93096,93097 1es9A 232 8.20e+01 1wab c.23.10.3 31340 1ex2A 189 8.20e+01 1ex2A c.51.4.2 33225 1rt8A 513 8.32e+01 a.40.1.1 105095 1bt3A 345 8.39e+01 1bt3A a.86.1.2 18507 1wv2A 265 8.40e+01 1wkbA 810 8.40e+01 1yn9A 169 8.40e+01 1jjeA 222 8.44e+01 1a7tA d.157.1.1 63117 1vhvA 268 8.47e+01 c.90.1.1 100704 2gfsA 372 8.47e+01 1v6tA 255 8.57e+01 1m7jA 484 8.59e+01 b.92.1.6,b.92.1.6,c.1.9.11 78732,78733,78734 4pah 308 8.59e+01 4pah d.178.1.1 42576 2gjgA 248 8.72e+01 1h9dB 134 8.73e+01 2jhbA b.54.1.1 60822 1iybA 208 8.75e+01 d.124.1.1 90720 1f7uA 607 8.77e+01 1bs2A a.27.1.1,c.26.1.1,d.67.2.1 59673,59674,59675 3mag 307 8.93e+01 3mag c.66.1.25 34205