# 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 1.24e-26 1dtdA 303 8.16e-26 1aye c.56.5.1 33823 1kwmA 402 4.47e-24 c.56.5.1,d.58.3.1 73079,73080 1z5rA 306 5.74e-24 1m4lA 307 1.05e-23 c.56.5.1 78604 2ctc 307 1.17e-23 1aye c.56.5.1 33802 1h8lA 380 5.50e-23 b.3.2.1,c.56.5.1 65737,65738 2c1cA 312 1.59e-21 1obr 326 1.23e-20 1aye c.56.5.2 33828 1jqgA 433 4.87e-20 c.56.5.1,d.58.3.1 71791,71792 1yw4A 341 1.84e-18 2bcoA 350 7.16e-16 1i7dA 659 1.66e-01 1d6mA e.10.1.1 61886 1h7eA 245 6.69e-01 c.68.1.13 60717 1pe1A 267 7.59e-01 c.1.10.4 94591 1fwsA 267 8.09e-01 1d9eA c.1.10.4 60063 1t8xA 267 8.18e-01 1zhaA 267 9.05e-01 1fxqA 267 9.24e-01 1d9eA c.1.10.4 60108 1jcxA 267 1.08e+00 c.1.10.4 66510 1h1nA 305 1.34e+00 c.1.8.3 70855 2bznA 351 1.35e+00 1jwqA 179 1.41e+00 c.56.5.6 90921 1m22A 503 1.50e+00 c.117.1.1 78464 1hc7A 477 1.72e+00 1hc7A c.51.1.1,d.104.1.1,d.68.5.1 60938,60939,60940 2c6qA 351 1.79e+00 1j2rA 199 1.84e+00 c.33.1.3 90788 2ac2A 309 2.73e+00 1eceA 358 2.75e+00 1eceA c.1.8.3 28813 1dozA 309 3.01e+00 1ak1 c.92.1.1 35592 1eqcA 394 3.50e+00 1cz1A c.1.8.3 28811 1o60A 292 4.05e+00 c.1.10.4 92532 1ycdA 243 4.67e+00 1xovA 326 4.72e+00 2b30A 301 4.79e+00 1bn7A 294 5.55e+00 1bn6A c.69.1.8 34677 1edg 380 6.06e+00 1edg c.1.8.3 28807 2chnA 716 6.56e+00 2gl5A 410 7.08e+00 1rqbA 539 7.15e+00 a.5.7.2,c.1.10.5 105057,105058 1vjzA 341 8.21e+00 c.1.8.3 100838 1vkcA 158 8.23e+00 1rwzA 245 8.42e+00 d.131.1.2,d.131.1.2 98005,98006 1ceo 343 8.64e+00 1ceo c.1.8.3 28808 2bleA 367 8.94e+00 1xhcA 367 9.36e+00 1wqaA 455 9.75e+00 1n82A 331 9.80e+00 c.1.8.3 91703 1ja9A 274 1.01e+01 c.2.1.2 62817 1gqiA 708 1.03e+01 c.1.8.10,d.92.2.2 76279,76280 2citA 282 1.08e+01 1vmaA 306 1.16e+01 a.24.13.1,c.37.1.10 108887,108888 1qbgA 272 1.18e+01 1d4aA c.23.5.3 31227 1gen 218 1.21e+01 1gen b.66.1.1 27536 1wkyA 464 1.25e+01 1ldjA 760 1.26e+01 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 1t64A 377 1.27e+01 c.42.1.2 106543 1l2lA 457 1.29e+01 c.72.1.3 77656 1ur4A 399 1.29e+01 1gm5A 780 1.31e+01 a.24.21.1,b.40.4.9,c.37.1.19,c.37.1.19 65298,65299,65300,65301 1lehA 364 1.32e+01 1bw9A c.2.1.7,c.58.1.1 30268,33916 1ad4A 266 1.35e+01 1aj2 c.1.21.1 29670 1b5qA 472 1.37e+01 1b37B c.3.1.2,d.16.1.5 30404,37968 1p5dX 463 1.43e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 94138,94139,94140,94141 2bv9A 290 1.46e+01 1ab4 477 1.49e+01 1ab4 e.11.1.1 43251 1w0mA 226 1.49e+01 c.1.1.1 109027 1vkyA 347 1.50e+01 e.53.1.1 108696 2afwA 329 1.61e+01 1jpzA 473 1.61e+01 a.104.1.1 67069 1h4pA 408 1.66e+01 c.1.8.3 90617 1pbgA 468 1.67e+01 1e70M c.1.8.4 28946 1ej5A 107 1.67e+01 1ej5A a.68.1.1 18268 2gsq 202 1.68e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1v02A 565 1.71e+01 c.1.8.4 108194 1e58A 249 1.76e+01 1qhfA c.60.1.1 59262 1d4aA 273 1.82e+01 1d4aA c.23.5.3 31219 1pv9A 348 1.83e+01 c.55.2.1,d.127.1.1 95157,95158 1iybA 208 1.85e+01 d.124.1.1 90720 2ch9A 131 1.89e+01 1s9uA 207 1.90e+01 a.184.1.1 105390 1j1iA 296 1.93e+01 c.69.1.10 83977 1rqpA 299 1.93e+01 b.141.1.1,c.132.1.1 97754,97755 1qo7A 394 1.96e+01 1qo7A c.69.1.11 34697 1wzlA 585 1.96e+01 1mroA 548 2.00e+01 1mroA a.89.1.1,d.58.31.2 18525,39443 2a67A 167 2.01e+01 1k2yX 463 2.03e+01 c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 68063,68064,68065,68066 1ysjA 404 2.03e+01 1hbnA 549 2.11e+01 1mroA a.89.1.1,d.58.31.2 60898,60899 1jae 471 2.17e+01 1smd b.71.1.1,c.1.8.1 27773,28760 2cunA 410 2.18e+01 1m7jA 484 2.24e+01 b.92.1.6,b.92.1.6,c.1.9.11 78732,78733,78734 1w24A 182 2.27e+01 1gskA 513 2.28e+01 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 2aqjA 538 2.28e+01 1dxy 333 2.30e+01 1dxy c.2.1.4,c.23.12.1 30094,31354 1dt9A 437 2.34e+01 1dt9A c.55.4.2,d.79.3.2,d.91.1.1 33738,39815,40257 1ak0 270 2.38e+01 1ak0 a.124.1.2 19345 1hx0A 496 2.42e+01 b.71.1.1,c.1.8.1 61346,61347 1s95A 333 2.44e+01 d.159.1.3 105375 1de4C 640 2.49e+01 1cx8B a.48.2.1,c.8.4.1,c.56.5.5 17779,30760,33848 1rk6A 496 2.53e+01 b.92.1.6,b.92.1.6,c.1.9.11 97599,97600,97601 2c5uA 375 2.64e+01 1wcgA 464 2.69e+01 1i4wA 353 2.71e+01 c.66.1.24 66028 1aqm 453 2.71e+01 1smd b.71.1.1,c.1.8.1 27717,28704 1tvnA 293 2.74e+01 1ki9A 192 2.79e+01 c.37.1.1 84404 1vhmA 195 2.80e+01 d.110.2.1 100691 1zbsA 291 2.83e+01 2ag5A 246 2.88e+01 1dixA 208 2.91e+01 1bk7A d.124.1.1 41122 1kqqA 139 2.97e+01 a.4.3.1 72885 1gpmA 525 3.04e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1w61A 414 3.15e+01 1ukvG 453 3.16e+01 c.3.1.3,c.3.1.3,d.16.1.6 107915,107916,107917 1vj7A 393 3.21e+01 a.211.1.1,d.218.1.8 100801,100802 2myr 501 3.21e+01 1thg 544 3.26e+01 1thg c.69.1.17 34763 1po5A 476 3.33e+01 a.104.1.1 94963 1ad1A 266 3.34e+01 1aj2 c.1.21.1 29668 1s3eA 520 3.35e+01 c.3.1.2,d.16.1.5 98426,98427 1khtA 192 3.40e+01 c.37.1.1 84401 1shwA 138 3.42e+01 b.6.1.5 105562 1hjsA 332 3.45e+01 c.1.8.3 83492 1u2xA 474 3.46e+01 c.72.1.3 107622 1qmeA 702 3.55e+01 1pmd d.11.1.1,d.11.1.1,d.175.1.1,e.3.1.1 37487,37488,42560,42769 1vf8A 377 3.63e+01 1nv8A 284 3.64e+01 c.66.1.30 86224 1shxA 138 3.65e+01 1j1nA 492 3.74e+01 c.94.1.1 83978 1g94A 448 3.76e+01 b.71.1.1,c.1.8.1 65169,65170 1ojaA 520 3.78e+01 c.3.1.2,d.16.1.5 93096,93097 1npyA 271 3.80e+01 c.2.1.7,c.58.1.5 85995,85996 1gox 370 3.82e+01 1gox c.1.4.1 28607 2b8nA 429 3.86e+01 1rj9A 304 3.88e+01 a.24.13.1,c.37.1.10 97553,97554 1smd 496 3.93e+01 1smd b.71.1.1,c.1.8.1 27768,28755 1z2lA 423 3.93e+01 1txvA 452 3.93e+01 2bcgG 453 3.94e+01 1e4iA 447 3.96e+01 1e70M c.1.8.4 59225 1qhfA 240 3.97e+01 1qhfA c.60.1.1 33960 1i74A 309 4.06e+01 1i74A c.107.1.1 61867 2gfsA 372 4.11e+01 1o0uA 429 4.12e+01 c.118.1.1 80743 8abp 306 4.17e+01 8abp c.93.1.1 35647 2b7oA 464 4.18e+01 1u9yA 284 4.18e+01 1e9lA 377 4.23e+01 1e9lA c.1.8.5,d.26.3.1 59395,59396 1v73A 342 4.33e+01 1bu7A 455 4.37e+01 1bu7A a.104.1.1 18937 1y5eA 169 4.41e+01 1h09A 338 4.42e+01 b.109.1.1,c.1.8.8 83420,83421 1t71A 281 4.42e+01 1c4xA 285 4.45e+01 1c4xA c.69.1.10 34684 1pea 385 4.50e+01 1pea c.93.1.1 35662 2b61A 377 4.51e+01 1b79A 119 4.52e+01 1b79A a.81.1.1 18451 5abp 306 4.54e+01 8abp c.93.1.1 35651 1bxkA 355 4.62e+01 1bxkA c.2.1.2 29803 1vefA 395 4.66e+01 1zr6A 503 4.73e+01 2b34A 199 4.81e+01 1zedA 484 4.81e+01 1l8nA 679 4.88e+01 c.1.8.10,d.92.2.2 84564,84565 1lwjA 441 4.89e+01 b.71.1.1,c.1.8.1 74303,74304 1wloA 136 4.95e+01 1tzzA 392 4.98e+01 1g8kA 825 4.98e+01 1g8jA b.52.2.2,c.81.1.1 26920,35328 1yh1A 359 5.01e+01 1pqnA 127 5.02e+01 c.47.1.8 95025 1kfwA 435 5.05e+01 c.1.8.5,d.26.3.1 77376,77377 1ornA 226 5.10e+01 a.96.1.1 87342 1r3cA 366 5.12e+01 d.144.1.7 96906 1w66A 232 5.16e+01 1fobA 334 5.19e+01 c.1.8.3 83255 1tml 286 5.19e+01 1tml c.6.1.1 30656 1d3vA 323 5.21e+01 1d3vA c.42.1.1 32559 1ynuA 473 5.25e+01 1ydmA 187 5.26e+01 2g8lA 299 5.27e+01 1x0lA 333 5.28e+01 1ojrA 274 5.32e+01 c.74.1.1 93147 1qd1A 325 5.35e+01 1qd1A d.58.34.1,d.58.34.1 39493,39494 1vclA 432 5.36e+01 b.42.2.1,b.42.2.1,d.281.1.1 108498,108499,108500 1xm3A 264 5.43e+01 1pamA 686 5.46e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21846,22515,27753,28740 1a7j 290 5.65e+01 1a7j c.37.1.6 31952 1phk 298 5.72e+01 1cdkA d.144.1.7 41635 1owqA 361 5.73e+01 c.1.8.5,d.26.3.1 104041,104042 1pbyB 337 5.80e+01 b.69.2.2 94422 1rq2A 382 5.83e+01 c.32.1.1,d.79.2.1 105048,105049 1yobA 179 5.89e+01 1nt4A 391 5.94e+01 c.60.1.2 92102 1sbyA 254 5.96e+01 1li5B 461 5.99e+01 a.27.1.1,c.26.1.1 73914,73915 1vpbA 451 6.10e+01 1b16A 254 6.13e+01 1b16A c.2.1.2 29875 1v77A 212 6.19e+01 c.6.3.2 108402 1wnfA 328 6.21e+01 2c1iA 431 6.23e+01 1bvoA 175 6.29e+01 1a3qA b.2.5.3 22457 1u7iA 136 6.32e+01 d.32.1.7 107724 1yarO 237 6.33e+01 2cbiA 594 6.60e+01 1ydnA 295 6.63e+01 1uwkA 557 6.63e+01 e.51.1.1 108065 1zzlA 351 6.78e+01 1z41A 338 6.81e+01 1wlsA 328 6.83e+01 1p4cA 380 6.90e+01 c.1.4.1 94100 2bpqA 373 6.97e+01 1wnaA 131 7.04e+01 1cruA 454 7.05e+01 1c9uA b.68.2.1 27617 1a6q 382 7.12e+01 1a6q a.159.1.1,d.219.1.1 75801,75802 1vd5A 377 7.12e+01 a.102.1.7 108518 1ypxA 375 7.13e+01 1lzlA 323 7.15e+01 c.69.1.2 78306 1vypX 364 7.17e+01 c.1.4.1 108905 1e4mM 501 7.24e+01 1e70M c.1.8.4 59226 1t0bA 252 7.28e+01 c.23.16.6 106199 1kb9D 246 7.29e+01 a.3.1.3,f.23.11.1 77317,77318 2czdA 208 7.32e+01 2a46A 238 7.35e+01 1xp3A 307 7.37e+01 1zn8A 180 7.40e+01 1eudB 396 7.40e+01 2scuB c.23.4.1,d.142.1.4 31150,41571 1o0wA 252 7.44e+01 a.149.1.1,d.50.1.1 80751,80752 1kz7A 353 7.44e+01 a.87.1.1,b.55.1.1 73333,73334 1wbsA 360 7.46e+01 2gwgA 350 7.49e+01 1pmmA 466 7.55e+01 c.67.1.6 94901 1pch 88 7.56e+01 1ptf d.94.1.1 40564 1p32A 209 7.58e+01 1p32A d.25.1.1 38379 1ka2A 499 7.61e+01 d.92.1.5 77305 1u5uA 374 7.62e+01 1tcvA 287 7.72e+01 1edqA 540 7.75e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 1fts 295 7.82e+01 1ng1 a.24.13.1,c.37.1.10 16968,32279 1mkfA 382 7.86e+01 b.116.1.1 79232 1n5dA 288 7.86e+01 c.2.1.2 80030 1ht6A 405 7.90e+01 b.71.1.1,c.1.8.1 83629,83630 1zckA 154 7.96e+01 1ezvD 245 7.96e+01 1be3D a.3.1.3,f.23.11.1 59546,59547 1sat 471 7.99e+01 1sat b.80.7.1,d.92.1.6 28014,40300 1heiA 451 8.07e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 1nmoA 247 8.12e+01 c.135.1.1 91980 1tw6A 133 8.17e+01 1dbxA 158 8.19e+01 1dbuA d.116.1.1 40928 1gc5A 467 8.24e+01 1gc5A c.72.1.3 60429 1nbaA 264 8.27e+01 1nbaA c.33.1.3 31753 1hu4A 288 8.31e+01 1hu4A 1rxdA 159 8.32e+01 1yacA 208 8.33e+01 1yacA c.33.1.3 31757 1twfF 155 8.35e+01 1pszA 303 8.40e+01 1toaA c.92.2.2 35600 2arkA 188 8.49e+01 1vyrA 364 8.53e+01 c.1.4.1 108906 1h3gA 601 8.56e+01 b.1.18.2,b.71.1.1,c.1.8.1 90594,90595,90596 1h61A 364 8.57e+01 1oyc c.1.4.1 60657 1wznA 252 8.60e+01 1vkpA 383 8.74e+01 d.126.1.6 108686 1bli 483 8.75e+01 1bli b.71.1.1,c.1.8.1 27715,28702 1xkpA 246 8.78e+01 1gqeA 365 8.79e+01 e.38.1.1 70351 1ny1A 240 8.79e+01 c.6.2.3 86395 1ctn 540 8.84e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21876,29005,38439 1ynpA 317 8.85e+01 1rtqA 299 8.95e+01 c.56.5.4 97819 1kepA 348 8.96e+01 c.2.1.2 68536 2c1gA 431 8.98e+01