# List of top-scoring protein chains for T0384.t04-w0.5 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 1evjA 352 2.71e-34 1ofgA c.2.1.3,d.81.1.5 30070,39985 1ofgA 381 4.53e-34 1ofgA c.2.1.3,d.81.1.5 30064,39979 1rydA 387 4.63e-34 1h6dA 433 5.01e-34 c.2.1.3,d.81.1.5 65656,65657 1zh8A 340 2.11e-33 1ydwA 362 1.05e-30 1tltA 319 5.63e-24 c.2.1.3,d.81.1.5 107135,107136 1xeaA 323 2.58e-22 c.2.1.3,d.81.1.5 109572,109573 1gcuA 295 8.46e-16 1gcuA c.2.1.3,d.81.1.4 30063,39978 1lc0A 294 8.98e-16 c.2.1.3,d.81.1.4 73823,73824 2h63A 292 1.26e-15 1ff9A 450 4.06e-10 1ff9A c.2.1.3,d.81.1.2 30039,39954 1cf2O 337 3.82e-08 1b7gO c.2.1.3,d.81.1.1 29994,39909 2czcA 334 4.38e-08 1b7gO 340 3.53e-07 1b7gO c.2.1.3,d.81.1.1 29992,39907 2ahrA 259 6.57e-05 1nptO 334 9.57e-05 c.2.1.3,d.81.1.1 85987,85988 1nvmB 312 9.80e-05 c.2.1.3,d.81.1.1 86251,86252 1nqoA 334 1.07e-04 c.2.1.3,d.81.1.1 86044,86045 1gd1O 334 1.19e-04 1dssG c.2.1.3,d.81.1.1 29962,39877 1ys4A 354 1.52e-04 3dbvO 334 1.88e-04 1dssG c.2.1.3,d.81.1.1 29982,39897 2dbvO 334 2.58e-04 1dssG c.2.1.3,d.81.1.1 29970,39885 1vpdA 299 5.35e-04 1q7gA 359 1.59e-03 c.2.1.3,d.81.1.2 96038,96039 1ebfA 358 1.62e-03 1ebuA c.2.1.3,d.81.1.2 30033,39948 2gf2A 296 2.43e-03 2cvoA 366 3.55e-03 1s7cA 331 5.01e-03 c.2.1.3,d.81.1.1 105346,105347 1gadO 330 5.56e-03 1dssG c.2.1.3,d.81.1.1 29950,39865 1hdgO 332 5.62e-03 1dssG c.2.1.3,d.81.1.1 29990,39905 1gaeO 330 5.93e-03 1dssG c.2.1.3,d.81.1.1 29954,39869 1drw 273 6.00e-03 1drw c.2.1.3,d.81.1.3 30057,39972 1y81A 138 7.08e-03 1oi7A 288 7.33e-03 c.2.1.8,c.23.4.1 87049,87050 1gpjA 404 7.80e-03 a.151.1.1,c.2.1.7,d.58.39.1 65451,65452,65453 1vc2A 331 8.01e-03 c.2.1.3,d.81.1.1 100555,100556 2g17A 337 1.07e-02 1f06A 320 1.49e-02 1dapA c.2.1.3,d.81.1.3 59556,59557 1cerA 331 2.23e-02 2f1kA 279 2.77e-02 1vknA 351 3.45e-02 c.2.1.3,d.81.1.1 108676,108677 1ywgO 337 4.04e-02 1yqgA 263 4.27e-02 1xygA 359 4.34e-02 2b4rO 345 4.80e-02 1obfO 335 6.02e-02 c.2.1.3,d.81.1.1 86768,86769 1ldnA 316 7.23e-02 1hyhA c.2.1.5,d.162.1.1 30166,42133 1ldbA 317 7.26e-02 1jayA 212 1.16e-01 c.2.1.6 66478 1p9lA 245 1.51e-01 c.2.1.3,d.81.1.3 94393,94394 1yrlA 491 2.13e-01 2c82A 413 2.25e-01 1a5z 319 2.32e-01 1ceqA c.2.1.5,d.162.1.1 30181,42148 1zcjA 463 2.51e-01 1vm6A 228 3.54e-01 c.2.1.3,d.81.1.3 108876,108877 1i32A 360 3.58e-01 c.2.1.3,d.81.1.1 65993,65994 1gypA 358 3.59e-01 1dssG c.2.1.3,d.81.1.1 30004,39919 1np3A 338 3.82e-01 a.100.1.2,c.2.1.6 85946,85947 1y6jA 318 4.04e-01 1yl5A 247 4.14e-01 1k3tA 359 4.47e-01 c.2.1.3,d.81.1.1 72022,72023 2ez3A 302 4.76e-01 2g5cA 281 4.79e-01 2h78A 302 5.17e-01 1bg6 359 5.58e-01 1bg6 a.100.1.5,c.2.1.6 18810,30214 1u8fO 335 6.67e-01 1znqO 338 7.09e-01 1yl7A 245 7.40e-01 1hyhA 309 8.18e-01 1hyhA c.2.1.5,d.162.1.1 30150,42117 1lsuA 147 9.22e-01 c.2.1.9 74250 1ygyA 529 9.51e-01 1onoA 398 1.00e+00 a.69.3.1,c.2.1.3,d.81.1.3 87159,87160,87161 1q0qA 406 1.00e+00 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1j0xO 332 1.17e+00 c.2.1.3,d.81.1.1 90750,90751 2d5cA 263 1.21e+00 1tvzA 388 1.26e+00 c.95.1.2,c.95.1.2 107367,107368 1t1rA 398 1.37e+00 a.69.3.1,c.2.1.3,c.2.1.3,d.81.1.3 106262,106263,106264,106265 1jvsA 400 1.38e+00 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1rm5A 337 1.51e+00 c.2.1.3,d.81.1.1 105006,105007 1pgjA 478 1.58e+00 2pgd a.100.1.1,c.2.1.6 18783,30195 1rm4A 337 1.58e+00 c.2.1.3,d.81.1.1 105000,105001 1rm3A 337 1.59e+00 c.2.1.3,d.81.1.1 104994,104995 1qydA 313 1.61e+00 c.2.1.2 96583 1ggaA 358 1.69e+00 1dssG c.2.1.3,d.81.1.1 30002,39917 1h2hA 241 1.73e+00 d.81.1.3,c.2.1.3 70861,83058 1fmtA 314 1.80e+00 1fmtA b.46.1.1,c.65.1.1 25758,34174 1cydA 244 2.00e+00 1cydA c.2.1.2 29825 2avyB 240 2.00e+00 1z82A 335 2.09e+00 1ortA 335 2.09e+00 1othA c.78.1.1,c.78.1.1 35204,35205 1j5pA 253 2.18e+00 d.81.1.3,c.2.1.3 71577,83092 1k2wA 256 2.23e+00 c.2.1.2 90927 1xpkC 388 2.42e+00 1dxhA 335 2.66e+00 1othA c.78.1.1,c.78.1.1 35202,35203 1xpkA 388 2.77e+00 1gr0A 367 2.85e+00 c.2.1.3,d.81.1.3 70379,70380 1jn0A 335 2.93e+00 c.2.1.3,d.81.1.1 66915,66916 1xpmA 396 3.00e+00 1pzgA 331 3.35e+00 c.2.1.5,d.162.1.1 95425,95426 1gsoA 431 3.94e+00 1gsoA b.84.2.1,c.30.1.1,d.142.1.2 28240,31647,41492 1p77A 272 4.27e+00 c.2.1.7,c.58.1.5 94214,94215 2ajtA 500 4.58e+00 1zejA 293 4.82e+00 1i36A 264 5.11e+00 a.100.1.8,c.2.1.6 71108,71109 1vl8A 267 5.14e+00 c.2.1.2 108733 1qycA 308 5.16e+00 c.2.1.2 96581 1ez4A 318 5.58e+00 c.2.1.5,d.162.1.1 64917,64918 1b74A 254 7.69e+00 1b74A c.78.2.1,c.78.2.1 35264,35265 2bllA 345 7.84e+00 1hey 128 8.64e+00 3chy c.23.1.1 31061 1x7dA 350 8.87e+00 1xwwA 157 8.89e+00 1treA 255 1.07e+01 1amk c.1.1.1 28505 1zowA 313 1.10e+01 1nvtA 287 1.11e+01 c.2.1.7,c.58.1.5 86270,86271 1z73A 358 1.13e+01 4uagA 437 1.13e+01 4uagA c.5.1.1,c.59.1.1,c.72.2.1 30651,33952,34955 1o7jA 327 1.18e+01 c.88.1.1 81140 1uufA 369 1.19e+01 b.35.1.2,c.2.1.1 100006,100007 1yb4A 295 1.25e+01 2apr 325 1.30e+01 2er7E b.50.1.2 26819 1xdwA 331 1.31e+01 1oc2A 348 1.32e+01 c.2.1.2 92765 1rwtA 232 1.34e+01 f.43.1.1 97992 1zitA 121 1.40e+01 1y1pA 342 1.43e+01 1t9hA 307 1.45e+01 1jdeA 873 1.46e+01 c.1.12.2,c.8.1.1,d.142.1.5 66546,66547,66548 1z7bA 358 1.53e+01 1ojuA 294 1.53e+01 c.2.1.5,d.162.1.1 103990,103991 1i19A 561 1.54e+01 1i19A d.58.32.3,d.145.1.1 61522,61523 1z74A 358 1.56e+01 1z75A 358 1.57e+01 1gudA 288 1.61e+01 c.93.1.1 83326 2dikA 873 1.64e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29306,30704,41574 1u9jA 358 1.64e+01 1llc 325 1.67e+01 1hyhA c.2.1.5,d.162.1.1 30176,42143 1dliA 402 1.70e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18809,30213,31622 1yqdA 366 1.73e+01 1dljA 402 1.73e+01 1dliA a.100.1.4,c.2.1.6,c.26.3.1 18808,30212,31621 3gpdG 334 1.80e+01 1dssG c.2.1.3,d.81.1.1 30029,39944 1a8q 274 1.80e+01 1brt c.69.1.12 34702 1uh9A 325 1.81e+01 b.50.1.2 107844 1dik 874 1.84e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29304,30702,41572 1lldA 319 1.84e+01 3ldh c.2.1.5,d.162.1.1 30177,42144 1x18X 292 1.86e+01 1vjpA 394 1.94e+01 c.2.1.3,d.81.1.3 100828,100829 2g1uA 155 1.97e+01 1qv9A 283 1.98e+01 c.127.1.1 96356 1kblA 873 2.01e+01 c.1.12.2,c.8.1.1,d.142.1.5 68384,68385,68386 1ggoA 873 2.01e+01 1dik c.1.12.2,c.8.1.1,d.142.1.5 29305,30703,41573 1p0vA 455 2.04e+01 a.104.1.1 93876 1qpcA 279 2.07e+01 1fgkA d.144.1.7 41685 1bu7A 455 2.12e+01 1bu7A a.104.1.1 18937 1ipeA 259 2.13e+01 c.2.1.2 83700 1pov0 341 2.13e+01 2ae2A 260 2.16e+01 1bdb c.2.1.2 29945 1jmeA 455 2.19e+01 a.104.1.1 66885 1p0xA 455 2.20e+01 a.104.1.1 93880 2dldA 337 2.20e+01 1dxy c.2.1.4,c.23.12.1 30099,31359 1yqpA 455 2.21e+01 1obbA 480 2.23e+01 c.2.1.5,d.162.1.2 86760,86761 1p0wA 455 2.23e+01 a.104.1.1 93878 1yqoA 455 2.27e+01 1nffA 260 2.31e+01 c.2.1.2 80457 1egaA 301 2.39e+01 1egaA c.37.1.8,d.52.3.1 32150,38836 2bnh 457 2.41e+01 1a4yA c.10.1.1 30850 1bvyA 458 2.41e+01 1bu7A a.104.1.1 18943 1dcnA 433 2.50e+01 1auwA a.127.1.1 19420 2bhwA 232 2.50e+01 1korA 400 2.53e+01 c.26.2.1,d.210.1.1 72824,72825 1xcbA 211 2.55e+01 a.4.5.38,c.2.1.12 109552,109553 1ub7A 322 2.56e+01 c.95.1.2,c.95.1.2 88402,88403 1sjiA 350 2.61e+01 1lssA 140 2.68e+01 c.2.1.9 74246 1dxiA 388 2.71e+01 4xis c.1.15.3 29407 1ffkB 337 2.75e+01 1ffkB b.43.3.2 25719 2cmd 312 2.76e+01 2cmd c.2.1.5,d.162.1.1 30135,42102 1crwG 333 2.80e+01 1dssG c.2.1.3,d.81.1.1 30026,39941 1shqA 478 2.84e+01 c.76.1.1 105560 1sqiA 393 2.86e+01 d.32.1.3,d.32.1.3 105914,105915 1skxA 313 2.89e+01 1nrlA 316 2.99e+01 a.123.1.1 92091 1vcrA 232 3.05e+01 i.5.1.1 100560 1pr9A 244 3.10e+01 c.2.1.2 95060 1dcnD 445 3.11e+01 1auwA a.127.1.1 19423 1dcnC 447 3.15e+01 1auwA a.127.1.1 19422 1ib6A 312 3.15e+01 c.2.1.5,d.162.1.1 62146,62147 1r0kA 388 3.18e+01 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 1jfuA 186 3.35e+01 c.47.1.10 62940 1mzhA 225 3.40e+01 c.1.10.1 79698 1sovA 328 3.43e+01 1nytA 271 3.43e+01 c.2.1.7,c.58.1.5 86417,86418 2braA 484 3.48e+01 1ydnA 295 3.49e+01 1t8fA 164 3.50e+01 1zcfA 327 3.54e+01 1rvgA 305 3.58e+01 c.1.10.2 97920 2gjlA 328 3.62e+01 2g50A 530 3.65e+01 2gn4A 344 3.67e+01 1pbwA 216 3.67e+01 1pbwA a.116.1.1 19103 2ba0A 229 3.79e+01 1hy0A 466 3.79e+01 1auwA a.127.1.1 61392 1s3iA 310 3.83e+01 b.46.1.1,c.65.1.1 98435,98436 1k7hA 476 3.85e+01 c.76.1.1 72101 1pea 385 3.86e+01 1pea c.93.1.1 35662 1qnlA 385 3.87e+01 1pea c.93.1.1 35665 1e6jP 210 3.88e+01 1ak4C a.28.3.1,a.73.1.1 16956,18323 1eaxA 241 3.90e+01 b.47.1.2 64889 1qpdA 279 3.95e+01 1fmk d.144.1.7 41687 1itwA 741 4.01e+01 c.77.1.2 76793 2hpdA 471 4.01e+01 1bu7A a.104.1.1 18939 1dssG 333 4.05e+01 1dssG c.2.1.3,d.81.1.1 30022,39937 1smiA 471 4.06e+01 a.104.1.1 105758 1l5zA 155 4.07e+01 c.23.1.1 77722 2d1yA 256 4.10e+01 1rpxA 230 4.12e+01 1rpxA c.1.2.2 28536 1fahA 471 4.18e+01 1bu7A a.104.1.1 18945 1jpzA 473 4.18e+01 a.104.1.1 67069 2aw4C 273 4.21e+01 1p85A 272 4.22e+01 i.1.1.1 87870 1vajA 214 4.25e+01 2d4qA 257 4.26e+01 1vlwA 217 4.31e+01 c.1.10.1 108868 1wwkA 307 4.37e+01 1dcnB 446 4.39e+01 1auwA a.127.1.1 19421 1sp8A 418 4.40e+01 d.32.1.3,d.32.1.3 105868,105869 1gpdG 334 4.42e+01 1dssG c.2.1.3,d.81.1.1 30020,39935 1xgkA 352 4.52e+01 1oq1A 223 4.65e+01 b.29.1.17 93408 1a2oA 349 4.69e+01 1chd c.23.1.1,c.40.1.1 31120,32479 1yl3E 338 4.71e+01 1jj2B 337 4.72e+01 1ffkB b.43.3.2 63086 4gpd1 333 4.80e+01 1dssG 1xvpB 246 4.80e+01 1vqoB 338 4.86e+01 1tc5A 194 4.95e+01 c.110.1.1 106752 1m54A 363 4.97e+01 c.79.1.1 74463 2a0uA 383 4.98e+01 1mqbA 333 4.99e+01 d.144.1.7 91392 1qkkA 155 5.02e+01 1dbwA c.23.1.1 31104 1ihxA 333 5.03e+01 c.2.1.3,d.81.1.1 71211,71212 3lck 271 5.05e+01 1fmk d.144.1.7 41686 1eah2 271 5.11e+01 1aym2 3pgmA 244 5.14e+01 1ujnA 348 5.17e+01 e.22.1.1 99460 2gasA 307 5.17e+01 1m14A 333 5.22e+01 d.144.1.7 78367 2gs6A 330 5.30e+01 2bw0A 329 5.30e+01 2bmfA 451 5.31e+01 1qhoA 686 5.34e+01 1cxlA b.1.18.2,b.3.1.1,b.71.1.1,c.1.8.1 21844,22513,27751,28738 1fouA 309 5.39e+01 1fouA e.27.1.1 43364 2ew2A 316 5.46e+01 1brmA 367 5.46e+01 1brmA c.2.1.3,d.81.1.1 30030,39945 1duwA 292 5.65e+01 19hcA a.138.1.1 59138 1a7j 290 5.71e+01 1a7j c.37.1.6 31952 2gs7A 330 5.76e+01 1ybvA 283 5.83e+01 1ybvA c.2.1.2 29948 2b1eA 564 5.87e+01 1g0oA 283 6.05e+01 1ybvA c.2.1.2 60181 1ltlA 279 6.09e+01 b.40.4.11 84701 2bryA 497 6.15e+01 1mv8A 436 6.19e+01 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 1guzA 310 6.21e+01 c.2.1.5,d.162.1.1 65586,65587 2b7mA 566 6.21e+01 1ur5A 309 6.21e+01 c.2.1.5,d.162.1.1 99807,99808 1omoA 322 6.27e+01 c.2.1.13 104017 1y4iA 398 6.33e+01 2d0iA 333 6.34e+01 1wyuB 474 6.37e+01 1k7wA 468 6.37e+01 a.127.1.1 72130 1xodA 118 6.38e+01 2c1xA 456 6.43e+01 1pkn 530 6.48e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27042,29271,33125 2fp4A 305 6.55e+01 1hy1A 468 6.60e+01 1auwA a.127.1.1 61394 1uxgA 309 6.60e+01 c.2.1.5,d.162.1.1 108100,108101 1o5iA 249 6.64e+01 c.2.1.2 92499 1liwA 528 6.76e+01 b.58.1.1,c.1.12.1,c.49.1.1 77982,77983,77984 1tj6A 118 6.82e+01 1a49A 530 6.86e+01 1a49A b.58.1.1,c.1.12.1,c.49.1.1 27026,29255,33109 1eudA 311 6.87e+01 2scuA c.2.1.8,c.23.4.1 30312,31140 1vhnA 318 6.88e+01 c.1.4.1 100693 1cpt 428 6.88e+01 1cpt a.104.1.1 18968 2cvzA 289 6.90e+01 1v4vA 376 6.91e+01 c.87.1.3 100313 1k4nA 192 7.01e+01 d.32.1.5 72059 1wa3A 205 7.06e+01 2bnuA 203 7.07e+01 1f3wA 530 7.10e+01 b.58.1.1,c.1.12.1,c.49.1.1 64934,64935,64936 2cfvA 316 7.14e+01 1z7aA 308 7.15e+01 1qp8A 303 7.16e+01 1qp8A c.2.1.4,c.23.12.1 30092,31352 1kvt 338 7.22e+01 1xel c.2.1.2 29798 1tjuA 474 7.23e+01 a.127.1.1 107050 2a0nA 265 7.24e+01 1auwA 468 7.28e+01 1auwA a.127.1.1 19416 1mhmA 288 7.30e+01 1vllA 334 7.48e+01 c.2.1.13 108834 1gveB 327 7.49e+01 c.1.7.1 70598 3pmgA 561 7.52e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 4thiA 362 7.52e+01 2thiA c.94.1.1 35793 1j49A 333 7.54e+01 c.2.1.4,c.23.12.1 71498,71499 1i16 130 7.54e+01 1i16 b.36.1.2 24787 1gveA 327 7.63e+01 c.1.7.1 70597 2c91A 338 7.66e+01 1uxkA 309 7.66e+01 c.2.1.5,d.162.1.1 108116,108117 1c3eA 209 7.78e+01 2gar c.65.1.1 34165 1tjvA 474 7.79e+01 a.127.1.1 107054 1h5wA 309 7.82e+01 e.27.1.1 65635 2gar 212 7.86e+01 2gar c.65.1.1 34161 1uxjA 309 7.95e+01 c.2.1.5,d.162.1.1 108112,108113 1jkxA 212 8.03e+01 c.65.1.1 66813 1gv1A 310 8.16e+01 c.2.1.5,d.162.1.1 65598,65599 1ev12 254 8.18e+01 1aym2 1kvr 338 8.27e+01 1xel c.2.1.2 29793 1ua7A 422 8.27e+01 b.71.1.1,c.1.8.1 107759,107760 1cjxA 357 8.28e+01 1cjxA d.32.1.3,d.32.1.3 38516,38517 1yuwA 554 8.35e+01 2bbzA 249 8.36e+01 2g0tA 350 8.40e+01 1gv0A 310 8.52e+01 c.2.1.5,d.162.1.1 65594,65595 1dg9A 157 8.64e+01 1dg9A c.44.1.1 32637 1kvq 338 8.67e+01 1xel c.2.1.2 29797 1f3xA 530 8.73e+01 b.58.1.1,c.1.12.1,c.49.1.1 64958,64959,64960 1bhy 482 8.86e+01 1lvl c.3.1.5,c.3.1.5,d.87.1.1 30583,30584,40213