# List of top-scoring protein chains for t04-100-30-str2-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 1wqaA 455 3.89e-01 1vp4A 425 5.57e-01 1f2tB 148 1.20e+00 1f2tB 1d8wA 426 1.56e+00 1de5A c.1.15.2 29394 1e9rA 437 1.72e+00 c.37.1.11 64827 2dbbA 151 2.11e+00 1b8oA 284 2.17e+00 1b8oA c.56.2.1 33762 1xahA 354 2.27e+00 1bqk 124 2.45e+00 1bqk b.6.1.1 22889 1eceA 358 2.47e+00 1eceA c.1.8.3 28813 2ffuA 501 2.66e+00 1tcvA 287 2.72e+00 1aszB 490 3.10e+00 1b8aA b.40.4.1,d.104.1.1 25241,40762 1yj7A 171 3.59e+00 1amy 403 3.62e+00 1jdc b.71.1.1,c.1.8.1 27799,28786 1lc5A 364 3.71e+00 c.67.1.1 73827 1qo0D 196 3.91e+00 1qo0D c.23.1.3 31125 1w1wA 430 4.06e+00 1wtaA 275 4.33e+00 1yb0A 159 4.35e+00 4enl 436 4.82e+00 4enl c.1.11.1,d.54.1.1 29202,38846 1innA 166 5.00e+00 1j98A d.185.1.2 62608 1cb0A 283 5.18e+00 1cb0A c.56.2.1 33790 1avaA 403 5.26e+00 1jdc b.71.1.1,c.1.8.1 27797,28784 1jztA 246 5.32e+00 c.104.1.1 63319 2f5gA 133 5.32e+00 1vjeA 166 5.88e+00 d.185.1.2 100807 1b7gO 340 5.90e+00 1b7gO c.2.1.3,d.81.1.1 29992,39907 1s2dA 167 6.23e+00 c.23.14.1 98377 1q2lA 939 6.44e+00 2al2A 436 6.45e+00 1wstA 417 6.55e+00 1u7lA 392 6.59e+00 1oneA 436 6.82e+00 4enl c.1.11.1,d.54.1.1 29200,38844 2al1A 436 6.95e+00 1uirA 314 6.96e+00 c.66.1.17 99429 2c1cA 312 6.99e+00 1r5lA 262 7.39e+00 a.5.3.1,c.13.1.1 97099,97100 2fqxA 318 7.65e+00 2av4A 162 8.20e+00 2b4aA 138 8.34e+00 1b5pA 385 8.48e+00 c.67.1.1 90403 1cl1A 395 8.63e+00 1cl2A c.67.1.3 34395 1gegA 256 9.08e+00 1ybvA c.2.1.2 29888 1tfr 305 9.15e+00 1tfr a.60.7.1,c.120.1.2 18081,33351 1i50K 120 9.22e+00 d.74.3.2 61765 2fuvA 549 9.28e+00 2cviA 83 9.40e+00 2g40A 224 9.51e+00 1fcyA 236 9.63e+00 2lbd a.123.1.1 19282 1r7aA 504 9.79e+00 b.71.1.1,c.1.8.1 97192,97193 2b7kA 200 9.93e+00 1wduA 245 1.02e+01 d.151.1.1 109286 1xwyA 264 1.05e+01 1k2fA 190 1.06e+01 b.8.1.2 68054 1zd9A 188 1.11e+01 1bo1A 416 1.12e+01 1bo1A d.143.1.2 41591 1bjwA 382 1.13e+01 1bjwA c.67.1.1 34349 1twfK 120 1.13e+01 2aebA 322 1.14e+01 1te6A 439 1.14e+01 c.1.11.1,d.54.1.1 106797,106798 1ydnA 295 1.16e+01 1w77A 228 1.18e+01 2akzA 439 1.19e+01 1g63A 181 1.23e+01 1g5qA c.34.1.1 60299 1t64A 377 1.23e+01 c.42.1.2 106543 1g0cA 364 1.25e+01 7a3hA c.1.8.3 60165 1a05A 358 1.39e+01 1cnzA c.77.1.1 35059 1bdfA 235 1.42e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 1t7lA 766 1.42e+01 1z5oA 242 1.43e+01 1nrjB 218 1.44e+01 c.37.1.8 86125 1j9yA 385 1.44e+01 1j9yA c.1.8.3 62791 1xewY 172 1.47e+01 1pvvA 315 1.47e+01 c.78.1.1,c.78.1.1 95190,95191 1hfc 169 1.50e+01 1hfc d.92.1.11 40335 1ltoA 245 1.53e+01 b.47.1.2 84707 1ht6A 405 1.55e+01 b.71.1.1,c.1.8.1 83629,83630 1fxlA 167 1.56e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1okgA 373 1.59e+01 c.46.1.2,c.46.1.2,d.26.1.3 93250,93251,93252 1zpvA 91 1.63e+01 1m7yA 435 1.64e+01 c.67.1.4 78761 2cw5A 255 1.66e+01 1nrfA 262 1.66e+01 e.3.1.1 92086 1ri7A 171 1.68e+01 a.4.5.32,d.58.4.2 97504,97505 2g5cA 281 1.69e+01 2b4gA 317 1.70e+01 1xrtA 467 1.75e+01 1kicA 339 1.78e+01 c.70.1.1 72510 1ut8A 291 1.78e+01 a.60.7.1,c.120.1.2 99908,99909 1ng4A 390 1.80e+01 c.3.1.2,d.16.1.3 85666,85667 1jysA 242 1.83e+01 c.56.2.1 77216 1tqjA 230 1.86e+01 c.1.2.2 107228 2bznA 351 1.87e+01 2f9nA 245 1.87e+01 1sviA 195 1.89e+01 c.37.1.8 106048 1b4bA 71 1.90e+01 1b4aA d.74.2.1 39718 2d0oA 610 1.93e+01 1vheA 373 1.95e+01 b.49.3.1,c.56.5.4 100669,100670 2fiqA 420 2.00e+01 1o1xA 155 2.02e+01 c.121.1.1 86553 1xo1A 291 2.06e+01 1exnA a.60.7.1,c.120.1.2 18086,33356 1dssG 333 2.06e+01 1dssG c.2.1.3,d.81.1.1 30022,39937 1r5tA 142 2.14e+01 c.97.1.1 104812 1ryiA 382 2.16e+01 1vl6A 388 2.20e+01 c.2.1.7,c.58.1.3 108724,108725 1u1hA 765 2.31e+01 c.1.22.2,c.1.22.2 107580,107581 5abp 306 2.33e+01 8abp c.93.1.1 35651 1hqz1 141 2.33e+01 1uvqB 198 2.34e+01 b.1.1.2,d.19.1.1 100064,100065 2glfA 450 2.37e+01 1odkA 235 2.37e+01 c.56.2.1 86863 1uozA 315 2.40e+01 2gcfA 73 2.43e+01 2bhwA 232 2.43e+01 1xdpA 687 2.54e+01 1geqA 248 2.56e+01 2tysA c.1.2.4 28589 2fmr 65 2.57e+01 2fmr d.51.1.1 38808 1wjuA 100 2.59e+01 1slqA 278 2.60e+01 f.47.1.1 105719 1oiaA 95 2.60e+01 d.58.7.1 87051 2ao9A 155 2.71e+01 2fckA 181 2.72e+01 1rwtA 232 2.74e+01 f.43.1.1 97992 2a5dA 175 2.74e+01 1o0uA 429 2.75e+01 c.118.1.1 80743 2bleA 367 2.77e+01 2cxcA 144 2.81e+01 1ur1A 378 2.82e+01 c.1.8.3 99804 1qe5A 266 2.83e+01 1b8oA c.56.2.1 33784 1f08A 148 2.85e+01 1f08A d.89.1.2 59564 1y9aA 360 2.89e+01 1o58A 303 2.94e+01 c.79.1.1 92491 1nf2A 268 2.94e+01 c.108.1.10 91849 1ws0A 156 2.95e+01 1z5nA 242 2.96e+01 2choA 716 2.99e+01 1zbsA 291 3.01e+01 2b4rO 345 3.02e+01 2ffmA 91 3.07e+01 1ru3A 732 3.07e+01 e.26.1.3 97835 1ghsA 306 3.07e+01 1aq0A c.1.8.3 28840 1iu8A 206 3.09e+01 c.56.4.1 71436 1b8gA 429 3.10e+01 1b8gA c.67.1.4 34499 1w6uA 302 3.12e+01 2chnA 716 3.12e+01 1wi1A 126 3.14e+01 8abp 306 3.14e+01 8abp c.93.1.1 35647 1bouB 302 3.17e+01 1bouB c.56.6.1 33859 1g66A 207 3.18e+01 1bs9 c.69.1.30 31329 1dar 691 3.22e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1o4sA 389 3.23e+01 c.67.1.1 86620 1rm4A 337 3.24e+01 c.2.1.3,d.81.1.1 105000,105001 1pyoA 167 3.26e+01 c.17.1.1 95370 2c6qA 351 3.33e+01 1q45A 391 3.42e+01 c.1.4.1 95780 2gu2A 312 3.43e+01 1em8A 147 3.45e+01 c.128.1.1 90457 1svy 114 3.46e+01 1svy d.109.1.1 40831 1e5eA 404 3.46e+01 1ibjA c.67.1.3 59265 1i76A 163 3.47e+01 1hfc d.92.1.11 61877 1wlsA 328 3.47e+01 1d3yA 301 3.48e+01 1d3yA e.12.1.1 43252 1cl8A 276 3.48e+01 1ckqA c.52.1.1 33230 1oaa 259 3.51e+01 1oaa c.2.1.2 29829 1fcdA 401 3.56e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1zzoA 136 3.56e+01 1qwgA 251 3.57e+01 c.1.27.1 96473 1jftA 340 3.59e+01 a.35.1.5,c.93.1.1 66652,66653 1v60A 123 3.60e+01 1aqb 183 3.63e+01 1aqb b.60.1.1 27084 2d00A 109 3.63e+01 1lssA 140 3.63e+01 c.2.1.9 74246 1j27A 102 3.65e+01 d.58.50.1 90778 1d3vA 323 3.66e+01 1d3vA c.42.1.1 32559 1di0A 158 3.66e+01 1di0A c.16.1.1 30957 1szqA 483 3.72e+01 e.44.1.1 99045 1ojxA 263 3.76e+01 c.1.10.1 93164 1uroA 367 3.78e+01 1uroA c.1.22.1 29675 1eg9A 449 3.79e+01 1ndoA b.33.1.2,d.129.3.3 24443,41322 1o7nA 449 3.79e+01 b.33.1.2,d.129.3.3 81162,81163 2bfwA 200 3.81e+01 1ko6A 187 3.82e+01 b.119.1.1 77471 1vknA 351 3.83e+01 c.2.1.3,d.81.1.1 108676,108677 1r3sA 367 3.84e+01 c.1.22.1 96963 2gkeA 274 3.88e+01 1vkhA 273 3.89e+01 c.69.1.32 108662 1ja9A 274 3.94e+01 c.2.1.2 62817 2f51A 118 3.95e+01 1iupA 282 3.97e+01 c.69.1.10 76815 1st9A 143 3.97e+01 c.47.1.10 98987 1v8hA 107 4.00e+01 1hzdA 272 4.02e+01 c.14.1.3 65969 1f2dA 341 4.04e+01 1f2dA c.79.1.1 35298 1ynuA 473 4.05e+01 1a0i 348 4.05e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1c3yA 108 4.06e+01 1c3yA a.39.2.1 17387 1urnA 97 4.06e+01 1urnA d.58.7.1 39153 1rkqA 282 4.16e+01 c.108.1.10 97621 1r6xA 395 4.21e+01 b.122.1.3,c.26.1.5 97167,97168 2bcoA 350 4.23e+01 1mup 166 4.26e+01 1mup b.60.1.1 27133 1e8cA 498 4.26e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1efpB 252 4.29e+01 1efvB c.26.2.3 31636 1oqvA 192 4.33e+01 d.24.1.2 87320 1guzA 310 4.34e+01 c.2.1.5,d.162.1.1 65586,65587 1obwA 175 4.37e+01 2prd b.40.5.1 25416 1yr0A 175 4.38e+01 2bycA 137 4.38e+01 1w8sA 263 4.39e+01 1itxA 419 4.40e+01 c.1.8.5,d.26.3.1 71425,71426 2ax3A 502 4.42e+01 1yizA 429 4.42e+01 1yc5A 246 4.46e+01 1sg4A 260 4.46e+01 1in0A 163 4.50e+01 d.58.49.1,d.58.49.1 83694,83695 1rpxA 230 4.51e+01 1rpxA c.1.2.2 28536 1lbu 213 4.52e+01 1lbu a.20.1.1,d.65.1.1 16416,39549 1gd1O 334 4.53e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 2a7mA 250 4.53e+01 1uouA 474 4.53e+01 a.46.2.1,c.27.1.1,d.41.3.1 99706,99707,99708 1h6hA 143 4.54e+01 d.189.1.1 65681 1kt6A 183 4.61e+01 b.60.1.1 84466 1jndA 420 4.62e+01 c.1.8.5,d.26.3.1 71757,71758 2bsxA 253 4.63e+01 2bj7A 138 4.63e+01 1xg4A 295 4.65e+01 2ab5A 269 4.66e+01 1qysA 106 4.66e+01 k.41.1.1 96603 1l2tA 235 4.68e+01 c.37.1.12 73514 2g2cA 167 4.68e+01 1hbq 183 4.70e+01 1aqb b.60.1.1 27078 1xtlA 175 4.74e+01 1p49A 562 4.78e+01 c.76.1.2 94089 1t4aA 84 4.79e+01 d.284.1.1 106404 1o26A 232 4.84e+01 d.207.1.1 86566 1mumA 295 4.85e+01 c.1.12.7 85108 1nt4A 391 4.87e+01 c.60.1.2 92102 1wnfA 328 4.88e+01 3mag 307 4.90e+01 3mag c.66.1.25 34205 2czcA 334 4.90e+01 1t3cA 421 4.96e+01 d.92.1.7 106343 1v6tA 255 5.01e+01 1xwsA 313 5.04e+01 2a5hA 416 5.05e+01 1jx6A 342 5.08e+01 c.93.1.1 67406 1id1A 153 5.08e+01 1id1A c.2.1.9 62286 1ks9A 291 5.13e+01 a.100.1.7,c.2.1.6 68857,68858 2di4A 238 5.14e+01 2f9sA 151 5.15e+01 1t13A 158 5.19e+01 2an9A 207 5.24e+01 1ypxA 375 5.27e+01 1zud1 251 5.28e+01 1elqA 390 5.29e+01 1elqA c.67.1.3 34436 1frpA 335 5.30e+01 1frpA e.7.1.1 42875 1em8B 112 5.31e+01 c.126.1.1 90458 1eluA 390 5.32e+01 1elqA c.67.1.3 34434 1f52A 468 5.35e+01 1lgr d.15.9.1,d.128.1.1 37839,41169 1twjA 84 5.35e+01 d.284.1.1 107407 1xesA 413 5.36e+01 1yrgA 385 5.36e+01 1yrgA c.10.1.2 30854 1zz1A 369 5.37e+01 1j0dA 341 5.37e+01 c.79.1.1 83902 1lci 550 5.38e+01 1lci e.23.1.1 43349 1tph1 247 5.38e+01 1amk 1f3lA 321 5.41e+01 1g6q2 c.66.1.6 59630 1fm0E 150 5.41e+01 1fmaE d.41.5.1 38629 1z47A 355 5.45e+01 1t0hB 224 5.47e+01 c.37.1.1 106208 1uk8A 282 5.48e+01 c.69.1.10 107907 2ajrA 331 5.48e+01 1xvaA 292 5.50e+01 1xvaA c.66.1.5 34183 1q0uA 219 5.51e+01 c.37.1.19 95512 2bitX 165 5.51e+01 1yzfA 195 5.52e+01 1wj9A 211 5.52e+01 1n4qB 377 5.55e+01 a.102.4.3 91636 1mg7A 417 5.57e+01 d.14.1.6,d.58.26.6 84954,84955 1m2oA 768 5.57e+01 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 2faoA 309 5.60e+01 1ii2A 524 5.60e+01 c.91.1.1,c.109.1.1 66146,66147 2fliA 220 5.63e+01 1wz8A 264 5.66e+01 1vqsA 116 5.66e+01 1i40A 175 5.67e+01 b.40.5.1 66024 2aamA 309 5.71e+01 1rkuA 206 5.71e+01 c.108.1.11 97627 2bikB 313 5.72e+01 1i60A 278 5.74e+01 c.1.15.4 71118 1z7dA 433 5.76e+01 1oo0B 110 5.79e+01 d.58.7.1 87183 2vhbA 146 5.84e+01 2vhbA a.1.1.2 15629 1wn5A 130 5.88e+01 1qh8B 519 5.90e+01 1qguB c.92.2.3 35634 1z41A 338 5.90e+01 1fa0A 537 5.91e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1fc4A 401 5.92e+01 1bs0A c.67.1.4 59760 1v7oA 165 5.97e+01 d.67.1.2 100480 1suwA 249 6.00e+01 e.52.1.1 106027 1sgwA 214 6.00e+01 c.37.1.12 105541 1uumA 372 6.03e+01 c.1.4.1 100010 1on0A 158 6.05e+01 d.108.1.1 87095 1np7A 489 6.06e+01 a.99.1.1,c.28.1.1 80677,80678 1zkdA 387 6.10e+01 1p8kZ 254 6.15e+01 d.95.2.1,d.95.2.1 94361,94362 1hfeL 421 6.15e+01 1fehA c.96.1.1,d.58.1.5 36018,39001 1yiyA 429 6.16e+01 2f4nA 273 6.17e+01 1xbsA 149 6.19e+01 1qgvA 142 6.27e+01 1qgvA c.47.1.8 33056 1jb7B 260 6.27e+01 1otcB b.40.4.3 62839 2ca6A 386 6.30e+01 1rfmA 344 6.31e+01 c.122.1.1 97385 1xhlA 297 6.32e+01 c.2.1.2 109591 1pdz 434 6.41e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1q0vA 81 6.42e+01 j.105.1.1 95514 1hyeA 313 6.44e+01 2cmd c.2.1.5,d.162.1.1 61400,61401 1k3rA 268 6.53e+01 b.40.4.10,c.116.1.2 72018,72019 1jv4A 162 6.56e+01 b.60.1.1 67343 1fg7A 356 6.58e+01 1gewA c.67.1.1 59819 1vj1A 363 6.61e+01 b.35.1.2,c.2.1.1 100794,100795 1vkpA 383 6.61e+01 d.126.1.6 108686 1psdA 409 6.65e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1bjt 793 6.65e+01 1bjt e.11.1.1 43249 1iyxA 432 6.67e+01 c.1.11.1,d.54.1.1 83815,83816 1p0iA 529 6.69e+01 c.69.1.1 93867 1jcfA 344 6.71e+01 c.55.1.1,c.55.1.1 62878,62879 1o7zA 77 6.73e+01 d.9.1.1 86660 1dbqA 289 6.74e+01 1qpzA c.93.1.1 35666 1zjjA 263 6.74e+01 1rl4A 188 6.77e+01 d.167.1.1 97636 1p77A 272 6.77e+01 c.2.1.7,c.58.1.5 94214,94215 1w36C 1122 6.79e+01 1kepA 348 6.81e+01 c.2.1.2 68536 1rh9A 373 6.83e+01 1ve5A 311 6.85e+01 1zuoA 186 6.92e+01 1u2wA 122 6.99e+01 2arhA 203 7.00e+01 1ppjB 439 7.02e+01 d.185.1.1,d.185.1.1 104254,104255 2cw6A 298 7.05e+01 1ftrA 296 7.05e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 2a8yA 270 7.06e+01 1rlmB 271 7.07e+01 1oc2A 348 7.07e+01 c.2.1.2 92765 1obfO 335 7.08e+01 c.2.1.3,d.81.1.1 86768,86769 1q9uA 130 7.12e+01 d.129.7.1 96314 1sw6A 327 7.14e+01 1sw6A d.211.1.1 19176 1lmeA 176 7.17e+01 d.167.1.1 84629 1oatA 439 7.22e+01 2dkb c.67.1.4 34461 1uwcA 261 7.22e+01 c.69.1.17 100101 1wa3A 205 7.27e+01 1i88A 389 7.27e+01 c.95.1.2,c.95.1.2 66070,66071 1fzrA 138 7.34e+01 1fzrA c.52.1.17 33336 1bi5A 389 7.37e+01 1bi5A c.95.1.2,c.95.1.2 35985,35986 1jk3A 158 7.39e+01 d.92.1.11 66790 1rlmA 271 7.42e+01 1i05A 180 7.44e+01 1mup b.60.1.1 27130 2ga9A 297 7.45e+01 1zndA 174 7.48e+01 1r8sA 164 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