# List of top-scoring protein chains for t04-100-30-bys-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 1.71e-01 1qo0D 196 4.09e-01 1qo0D c.23.1.3 31125 1s96A 219 5.96e-01 c.37.1.1 98740 1fcyA 236 6.23e-01 2lbd a.123.1.1 19282 2dbbA 151 7.65e-01 1ri7A 171 8.69e-01 a.4.5.32,d.58.4.2 97504,97505 2an9A 207 1.34e+00 1aszB 490 1.53e+00 1b8aA b.40.4.1,d.104.1.1 25241,40762 1w1wA 430 1.57e+00 1wdtA 665 1.98e+00 2f5gA 133 1.99e+00 1kicA 339 2.10e+00 c.70.1.1 72510 2ffuA 501 2.27e+00 1u7lA 392 2.44e+00 1yghA 164 2.84e+00 1yghA d.108.1.1 40802 1yr0A 175 3.24e+00 1vl6A 388 3.45e+00 c.2.1.7,c.58.1.3 108724,108725 2fu0A 160 3.62e+00 1qysA 106 4.36e+00 k.41.1.1 96603 1fsz 372 4.65e+00 1fsz c.32.1.1,d.79.2.1 31750,39802 1ursA 402 4.72e+00 c.94.1.1 99833 1tfr 305 5.08e+00 1tfr a.60.7.1,c.120.1.2 18081,33351 1t0fA 276 5.10e+00 1wn5A 130 5.47e+00 2a7mA 250 5.57e+00 2faoA 309 5.77e+00 1e9rA 437 5.88e+00 c.37.1.11 64827 1bqk 124 6.11e+00 1bqk b.6.1.1 22889 1f1zA 273 6.41e+00 1f1zA a.4.5.27,c.52.1.16 16081,33334 1zu4A 320 6.42e+00 1o7nA 449 7.03e+00 b.33.1.2,d.129.3.3 81162,81163 1oz9A 150 7.15e+00 d.92.1.15 93808 1eg9A 449 7.22e+00 1ndoA b.33.1.2,d.129.3.3 24443,41322 1f2tB 148 7.37e+00 1f2tB 1jx2B 315 7.38e+00 c.37.1.8 67404 1xhbA 472 8.09e+00 2cpgA 45 8.27e+00 2cpgA a.43.1.3 17455 1r5tA 142 8.79e+00 c.97.1.1 104812 1lbu 213 9.17e+00 1lbu a.20.1.1,d.65.1.1 16416,39549 1wnlA 235 9.31e+00 1urnA 97 9.94e+00 1urnA d.58.7.1 39153 1qy1A 174 1.03e+01 b.60.1.1 96568 1zndA 174 1.04e+01 1id1A 153 1.05e+01 1id1A c.2.1.9 62286 1innA 166 1.05e+01 1j98A d.185.1.2 62608 4enl 436 1.05e+01 4enl c.1.11.1,d.54.1.1 29202,38846 1r5lA 262 1.06e+01 a.5.3.1,c.13.1.1 97099,97100 1vjeA 166 1.12e+01 d.185.1.2 100807 1ryiA 382 1.13e+01 1iu8A 206 1.19e+01 c.56.4.1 71436 1wzlA 585 1.20e+01 1ghsA 306 1.20e+01 1aq0A c.1.8.3 28840 1nx8A 273 1.22e+01 b.82.2.8 86374 1o60A 292 1.22e+01 c.1.10.4 92532 1nu4A 97 1.24e+01 d.58.7.1 80731 1fzyA 149 1.26e+01 d.20.1.1 65072 1q2lA 939 1.26e+01 1uroA 367 1.26e+01 1uroA c.1.22.1 29675 2al1A 436 1.27e+01 2al2A 436 1.33e+01 1r3sA 367 1.36e+01 c.1.22.1 96963 2b4aA 138 1.37e+01 1szqA 483 1.39e+01 e.44.1.1 99045 2h3bA 494 1.39e+01 2b7kA 200 1.40e+01 1avaA 403 1.42e+01 1jdc b.71.1.1,c.1.8.1 27797,28784 2g2dA 193 1.43e+01 1kt6A 183 1.43e+01 b.60.1.1 84466 1q6zA 528 1.45e+01 1dar 691 1.46e+01 1dar b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1 25707,32142,37547,39300 1te6A 439 1.47e+01 c.1.11.1,d.54.1.1 106797,106798 1jv4A 162 1.49e+01 b.60.1.1 67343 1ysrA 150 1.57e+01 1a0i 348 1.59e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1oneA 436 1.60e+01 4enl c.1.11.1,d.54.1.1 29200,38844 3tmkA 216 1.63e+01 3tmkA c.37.1.1 31920 1ukuA 102 1.64e+01 d.58.5.2 99533 2akzA 439 1.64e+01 2a5dA 175 1.65e+01 1phk 298 1.65e+01 1cdkA d.144.1.7 41635 1wqwA 235 1.66e+01 1jmsA 381 1.67e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1pzxA 289 1.68e+01 c.119.1.1 95484 1xg8A 111 1.68e+01 1i9gA 280 1.69e+01 c.66.1.13 62090 2c1cA 312 1.71e+01 1aqb 183 1.73e+01 1aqb b.60.1.1 27084 1bfd 528 1.74e+01 1bfd c.31.1.3,c.36.1.5,c.36.1.9 31745,31801,31802 1em8A 147 1.79e+01 c.128.1.1 90457 1amy 403 1.80e+01 1jdc b.71.1.1,c.1.8.1 27799,28786 2cxcA 144 1.81e+01 2fckA 181 1.87e+01 1hbq 183 1.89e+01 1aqb b.60.1.1 27078 1rq2A 382 1.89e+01 c.32.1.1,d.79.2.1 105048,105049 1pot 325 1.90e+01 1pot c.94.1.1 35807 1ng4A 390 1.94e+01 c.3.1.2,d.16.1.3 85666,85667 1ftkA 279 1.96e+01 1gr2A c.94.1.1 35819 1c0pA 363 1.96e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 1bykA 255 1.96e+01 1bykA c.93.1.1 35706 1fa0A 537 1.96e+01 1fa0B d.58.16.1,a.160.1.1,d.218.1.3 39335,75837,75838 1oc2A 348 2.03e+01 c.2.1.2 92765 1odkA 235 2.04e+01 c.56.2.1 86863 1kepA 348 2.05e+01 c.2.1.2 68536 1kk1A 410 2.09e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1c24A 263 2.12e+01 1c24A d.127.1.1 41148 1cg5A 141 2.12e+01 1abwA a.1.1.2 15406 1u6bA 98 2.12e+01 d.58.7.1 107703 2gsq 202 2.17e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1dzkA 157 2.17e+01 1obpA b.60.1.1 27096 1mup 166 2.18e+01 1mup b.60.1.1 27133 2bo4A 397 2.18e+01 1hjzA 192 2.18e+01 c.50.1.2 83520 1ec7A 446 2.21e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1cc1S 283 2.23e+01 2frvA e.19.1.1 43313 1mwmA 320 2.23e+01 c.55.1.1,c.55.1.1 79580,79581 1yj7A 171 2.26e+01 1h1nA 305 2.28e+01 c.1.8.3 70855 1fo8A 343 2.29e+01 1foaA c.68.1.10 59927 1k8rB 110 2.31e+01 d.15.1.5 72180 1jj2L 194 2.31e+01 1ffkI d.12.1.2 63097 1xnzA 264 2.33e+01 1zpvA 91 2.33e+01 1nq7A 244 2.35e+01 a.123.1.1 92047 1u8sA 192 2.36e+01 d.58.18.5,d.58.18.5 107737,107738 1qjcA 158 2.37e+01 1b6tA c.26.1.3 63328 1xahA 354 2.37e+01 1s0uA 408 2.38e+01 b.43.3.1,b.44.1.1,c.37.1.8 98302,98303,98304 2di4A 238 2.38e+01 1vhuA 211 2.41e+01 c.50.1.2 100703 2cxxA 190 2.41e+01 1ve3A 227 2.44e+01 1v3rA 116 2.45e+01 1n83A 270 2.47e+01 a.123.1.1 80276 1i06A 180 2.47e+01 1mup b.60.1.1 27131 2evaA 307 2.53e+01 1sviA 195 2.59e+01 c.37.1.8 106048 1z6nA 167 2.59e+01 2cxkA 95 2.61e+01 1tr8A 102 2.64e+01 1zd9A 188 2.65e+01 1ej1A 190 2.66e+01 1ejhA d.86.1.1 40144 1gtvA 214 2.67e+01 c.37.1.1 70537 1svy 114 2.71e+01 1svy d.109.1.1 40831 1r8sA 164 2.74e+01 c.37.1.8 97247 2eifA 136 2.75e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1i05A 180 2.78e+01 1mup b.60.1.1 27130 1xtmA 175 2.86e+01 1lmiA 131 2.86e+01 b.1.19.1 78098 1x7oA 287 2.86e+01 1kqzA 273 2.88e+01 c.1.8.5 68844 1xwyA 264 2.95e+01 1l2tA 235 2.98e+01 c.37.1.12 73514 1k2fA 190 2.98e+01 b.8.1.2 68054 1qwdA 177 3.01e+01 b.60.1.1 96471 1tiiD 99 3.03e+01 1tiiD b.40.2.1 24965 1ml8A 134 3.06e+01 d.227.1.2 85013 1ob8A 135 3.06e+01 1zz1A 369 3.07e+01 2bkqA 212 3.07e+01 1nrfA 262 3.09e+01 e.3.1.1 92086 1m1hA 248 3.09e+01 b.114.1.1,d.58.42.1 78415,78416 1twfK 120 3.10e+01 1czfA 362 3.11e+01 1czfA b.80.1.3 28031 1bazA 53 3.15e+01 1bazA a.43.1.1 17421 1vkhA 273 3.17e+01 c.69.1.32 108662 2b61A 377 3.20e+01 2glfA 450 3.21e+01 2hvm 273 3.23e+01 1cnv c.1.8.5 28985 1zx4A 192 3.23e+01 1lmeA 176 3.23e+01 d.167.1.1 84629 1jndA 420 3.26e+01 c.1.8.5,d.26.3.1 71757,71758 1bj7 156 3.26e+01 1bj7 b.60.1.1 27113 1ws0A 156 3.27e+01 1wr8A 231 3.29e+01 1g3qA 237 3.35e+01 1hyqA c.37.1.10 60237 1t3cA 421 3.42e+01 d.92.1.7 106343 1mzbA 136 3.48e+01 a.4.5.42 91497 1wi1A 126 3.55e+01 1ftrA 296 3.57e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1mjfA 281 3.57e+01 c.66.1.17 79198 1jh6A 189 3.60e+01 d.61.1.1 66707 1t2dA 322 3.62e+01 c.2.1.5,d.162.1.1 99084,99085 1m4zA 238 3.63e+01 b.34.12.1 78630 1g55A 343 3.63e+01 1g55A c.66.1.26 34247 1mqiA 263 3.67e+01 c.94.1.1 91398 1vecA 206 3.67e+01 c.37.1.19 100575 2bexA 460 3.69e+01 1fcdA 401 3.70e+01 1fcdA c.3.1.5,c.3.1.5,d.87.1.1 30593,30594,40218 1fi4A 416 3.71e+01 1fi4A d.14.1.5,d.58.26.2 59847,59848 1n67A 359 3.75e+01 b.2.3.4,b.2.3.4 85354,85355 1jmtA 104 3.76e+01 d.58.7.3 63180 1irdA 141 3.76e+01 a.1.1.2 66286 1o26A 232 3.77e+01 d.207.1.1 86566 1pdz 434 3.78e+01 4enl c.1.11.1,d.54.1.1 29215,38859 1uirA 314 3.78e+01 c.66.1.17 99429 1e7rA 321 3.78e+01 1bsvA c.2.1.2 29808 2gcuA 245 3.85e+01 1mml 265 3.85e+01 1mml e.8.1.2 43015 2eueA 279 3.86e+01 2gcfA 73 3.88e+01 1s7hA 200 3.96e+01 d.58.48.2 105349 1pc6A 146 3.97e+01 d.262.1.1 94430 1fjgB 256 4.00e+01 1fjfB c.23.15.1 31400 1he7A 126 4.02e+01 1wwcA b.1.1.4 60970 1l8bA 190 4.04e+01 d.86.1.1 73683 1e6uA 321 4.07e+01 1bsvA c.2.1.2 29805 1dekA 241 4.08e+01 1dekA c.37.1.1 31842 1yemA 179 4.09e+01 1tph1 247 4.12e+01 1amk 1f8yA 157 4.12e+01 1f8xA c.23.14.1 31395 1e8cA 498 4.13e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1ihcA 188 4.21e+01 1di6A c.57.1.1 62379 1s99A 200 4.24e+01 3sdhA 146 4.28e+01 3sdhA a.1.1.2 14984 1q9uA 130 4.32e+01 d.129.7.1 96314 1ymqA 261 4.32e+01 1ve0A 134 4.33e+01 1h70A 255 4.34e+01 1h70A d.126.1.3 60711 2fxaA 207 4.35e+01 1kyhA 276 4.38e+01 c.72.1.4 73222 2a72A 146 4.39e+01 1vl7A 157 4.40e+01 b.45.1.1 108732 1eu8A 409 4.47e+01 1eu8A c.94.1.1 59502 1rwzA 245 4.48e+01 d.131.1.2,d.131.1.2 98005,98006 1us5A 314 4.50e+01 c.94.1.1 99856 1jb7B 260 4.51e+01 1otcB b.40.4.3 62839 2bkrA 212 4.57e+01 1auiB 169 4.60e+01 1auiB a.39.1.5 17325 1ko6A 187 4.61e+01 b.119.1.1 77471 2f6kA 307 4.62e+01 1j0dA 341 4.63e+01 c.79.1.1 83902 1mh1 186 4.66e+01 1eesA c.37.1.8 32002 1qb5D 99 4.67e+01 b.40.2.1 88357 1q45A 391 4.70e+01 c.1.4.1 95780 1f5vA 240 4.71e+01 1bkjA d.90.1.1 40255 1d6jA 211 4.72e+01 1d6jA c.37.1.4 31940 1mp4A 292 4.73e+01 c.68.1.6 79376 1jljA 189 4.76e+01 c.57.1.1 63169 1uf2C 421 4.87e+01 a.115.1.3,b.19.1.1 99291,99292 1w77A 228 4.88e+01 1omzA 293 4.91e+01 c.68.1.15 87093 1bkpA 278 4.92e+01 1bkpA d.117.1.1 41029 2d00A 109 4.95e+01 2b99A 156 4.96e+01 2gukA 120 4.99e+01 1hqz1 141 5.08e+01 1wvqA 167 5.10e+01 1xt8A 292 5.11e+01 1byqA 228 5.11e+01 1yer d.122.1.1 41100 2cviA 83 5.15e+01 1q3iA 214 5.17e+01 d.220.1.1 104524 1l5wA 796 5.18e+01 c.87.1.4 73605 1oiaA 95 5.20e+01 d.58.7.1 87051 1y8aA 332 5.31e+01 1us6A 102 5.41e+01 a.2.13.1 107999 2aeeA 211 5.42e+01 1t8tA 271 5.44e+01 c.37.1.5 106685 1u6mA 199 5.45e+01 1r9cA 139 5.47e+01 d.32.1.2 97255 1vp4A 425 5.47e+01 1i50K 120 5.47e+01 d.74.3.2 61765 2d0oA 610 5.47e+01 1pzgA 331 5.52e+01 c.2.1.5,d.162.1.1 95425,95426 1wa3A 205 5.52e+01 1b43A 340 5.54e+01 1a76 a.60.7.1,c.120.1.2 18092,33362 1it2A 146 5.57e+01 a.1.1.2 66365 1w0dA 337 5.62e+01 1fvpA 231 5.65e+01 1nfp c.1.16.2 29556 1ldg 316 5.68e+01 1ceqA c.2.1.5,d.162.1.1 30165,42132 1hurA 180 5.71e+01 1hurA c.37.1.8 32052 1f2dA 341 5.71e+01 1f2dA c.79.1.1 35298 1tedA 393 5.79e+01 c.95.1.2 106807 1cnzA 363 5.82e+01 1cnzA c.77.1.1 35061 1zud1 251 5.90e+01 2fv1A 377 5.92e+01 1t5jA 313 5.92e+01 a.209.1.1 99125 1vbkA 307 5.98e+01 2fbwD 103 5.99e+01 1geqA 248 6.01e+01 2tysA c.1.2.4 28589 1vehA 92 6.02e+01 1bdfA 235 6.04e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 2fa8A 105 6.04e+01 2aeuA 374 6.16e+01 1yovA 537 6.22e+01 1rl4A 188 6.23e+01 d.167.1.1 97636 2g5cA 281 6.25e+01 1usgA 346 6.28e+01 c.93.1.1 99864 1qstA 160 6.29e+01 1yghA d.108.1.1 40804 1zsyA 357 6.33e+01 1yc5A 246 6.39e+01 1w8iA 156 6.41e+01 1w30A 201 6.44e+01 1ufwA 95 6.44e+01 d.58.7.1 99358 1ru3A 732 6.46e+01 e.26.1.3 97835 2av4A 162 6.47e+01 1ble 163 6.48e+01 1ble c.38.1.1 32475 1o3yA 166 6.52e+01 c.37.1.8 86618 1ng6A 148 6.69e+01 a.182.1.1 85670 1t3oA 95 6.70e+01 1x6mA 196 6.71e+01 1xqaA 113 6.71e+01 2f4nA 273 6.76e+01 1bco 327 6.81e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1fxlA 167 6.85e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1rfyA 102 6.87e+01 1j7yA 141 6.91e+01 a.1.1.2 66426 2chnA 716 6.92e+01 1fvgA 199 6.93e+01 1fvaA d.58.28.1 39408 1vd5A 377 6.97e+01 a.102.1.7 108518 1zxzA 197 6.97e+01 1xo5A 183 6.98e+01 1lucB 324 6.98e+01 1lucA c.1.16.1 29548 1v8hA 107 7.02e+01 1z54A 132 7.05e+01 2bvfA 459 7.10e+01 1oo0B 110 7.13e+01 d.58.7.1 87183 1xdpA 687 7.16e+01 1el5A 389 7.19e+01 1b3mA c.3.1.2,d.16.1.3 30369,37937 2ew8A 249 7.24e+01 1d3yA 301 7.25e+01 1d3yA e.12.1.1 43252 1v74B 87 7.25e+01 a.24.20.1 100443 1hb6A 86 7.41e+01 a.11.1.1 70959 1vr9A 213 7.44e+01 2ar9A 278 7.45e+01 1eu1A 780 7.48e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1w6uA 302 7.51e+01 2bitX 165 7.53e+01 1r6uA 437 7.59e+01 c.26.1.1 97163 1cvrA 435 7.60e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1b8oA 284 7.63e+01 1b8oA c.56.2.1 33762 1u2cA 246 7.64e+01 b.1.6.2,d.272.1.1 107610,107611 1cipA 353 7.67e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 1rqlA 267 7.68e+01 c.108.1.3 97750 1vjuA 309 7.68e+01 d.248.1.1 100835 2cbiA 594 7.69e+01 1svsA 353 7.72e+01 c.37.1.8 106051 1o1xA 155 7.73e+01 c.121.1.1 86553 1zuwA 272 7.73e+01 2choA 716 7.79e+01 7odcA 424 7.80e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1i1rB 181 7.84e+01 1i1rB a.26.1.1 61548 1eo6A 117 7.86e+01 1eo6A d.15.1.3 37609 1ii2A 524 7.88e+01 c.91.1.1,c.109.1.1 66146,66147 1wdjA 187 7.91e+01 1e6yC 247 7.92e+01 1mroC d.58.31.1 39441 1mr3F 181 7.95e+01 c.37.1.8 79422 1hfeL 421 7.96e+01 1fehA c.96.1.1,d.58.1.5 36018,39001 1e8gA 560 7.98e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1sc6A 404 7.99e+01 1d8cA 723 8.00e+01 1d8cA c.1.13.1 29325 1t3tA 1303 8.02e+01 a.5.10.1,c.23.16.1,d.284.1.2,d.79.4.1,d.79.4.1,d.139.1.1,d.139.1.1 106381,106382,106383,106384,106385,106386,106387 1z4rA 168 8.03e+01 1s6cA 183 8.06e+01 a.39.1.5 98594 1zoqC 47 8.07e+01 1guzA 310 8.09e+01 c.2.1.5,d.162.1.1 65586,65587 1jfzA 154 8.16e+01 a.149.1.1 66655 1ws6A 171 8.18e+01 1wvfA 520 8.24e+01 1wduA 245 8.30e+01 d.151.1.1 109286 1fsiA 189 8.42e+01 1fsiA d.61.1.1 39536 2cyeA 133 8.43e+01 1odfA 290 8.45e+01 c.37.1.6 92782 1vkbA 161 8.56e+01 d.269.1.1 108643 1im3D 95 8.57e+01 1im3D b.1.18.5 62568 1nf2A 268 8.65e+01 c.108.1.10 91849 1pu6A 218 8.65e+01 a.96.1.5 95123 1zljA 78 8.67e+01 1dywA 173 8.67e+01 2cpl b.62.1.1 27505 1bbpA 173 8.67e+01 1bbpA b.60.1.1 27147 2f2eA 146 8.68e+01 1nonA 179 8.68e+01 c.61.1.1 103868 1zjjA 263 8.70e+01 2bb3A 221 8.75e+01 1yrgA 385 8.80e+01 1yrgA c.10.1.2 30854 1qu9A 128 8.82e+01 1qu9A d.79.1.1 39755 1i2mA 216 8.83e+01 1byuA c.37.1.8 61568 1vc3B 97 8.88e+01 1eluA 390 8.90e+01 1elqA c.67.1.3 34434 1ys7A 233 8.91e+01 1vkjA 285 8.95e+01 c.37.1.5 108666 1h5rA 293 8.95e+01 c.68.1.6 65623 1uc8A 280 9.00e+01 c.30.1.6,d.142.1.7 99165,99166