# List of top-scoring protein chains for t06-100-30-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 7.03e-03 2dbbA 151 7.17e-02 1fcyA 236 2.86e-01 2lbd a.123.1.1 19282 1qo0D 196 3.03e-01 1qo0D c.23.1.3 31125 2f5gA 133 6.38e-01 1s96A 219 7.07e-01 c.37.1.1 98740 2an9A 207 1.38e+00 1t0fA 276 1.57e+00 1vjeA 166 1.93e+00 d.185.1.2 100807 1zu4A 320 2.23e+00 1bqk 124 2.73e+00 1bqk b.6.1.1 22889 2cpgA 45 2.97e+00 2cpgA a.43.1.3 17455 1r5lA 262 3.02e+00 a.5.3.1,c.13.1.1 97099,97100 1u7lA 392 3.12e+00 1kicA 339 3.19e+00 c.70.1.1 72510 2faoA 309 3.34e+00 1e9rA 437 3.35e+00 c.37.1.11 64827 2eifA 136 3.69e+00 1bkb b.34.5.2,b.40.4.5 24607,25339 1qysA 106 3.96e+00 k.41.1.1 96603 1tfr 305 3.98e+00 1tfr a.60.7.1,c.120.1.2 18081,33351 1ysrA 150 4.00e+00 2fu0A 160 4.03e+00 1jmtA 104 4.55e+00 d.58.7.3 63180 2ffuA 501 4.63e+00 1ursA 402 4.65e+00 c.94.1.1 99833 1vkhA 273 5.75e+00 c.69.1.32 108662 1wdtA 665 5.94e+00 1m1hA 248 6.08e+00 b.114.1.1,d.58.42.1 78415,78416 1r3sA 367 6.09e+00 c.1.22.1 96963 1odkA 235 6.31e+00 c.56.2.1 86863 1xahA 354 6.52e+00 1qwdA 177 6.52e+00 b.60.1.1 96471 1o7nA 449 6.75e+00 b.33.1.2,d.129.3.3 81162,81163 1ko6A 187 7.03e+00 b.119.1.1 77471 1xnzA 264 7.04e+00 1rwzA 245 7.10e+00 d.131.1.2,d.131.1.2 98005,98006 1xubA 298 7.12e+00 1kt6A 183 7.41e+00 b.60.1.1 84466 1pzxA 289 7.43e+00 c.119.1.1 95484 2g2dA 193 7.45e+00 1qb5D 99 8.10e+00 b.40.2.1 88357 1i9gA 280 8.12e+00 c.66.1.13 62090 1ftrA 296 8.43e+00 1ftrA d.58.33.1,d.58.33.1 39485,39486 2a5dA 175 8.70e+00 1o60A 292 8.89e+00 c.1.10.4 92532 1u8sA 192 9.07e+00 d.58.18.5,d.58.18.5 107737,107738 1b8oA 284 9.40e+00 1b8oA c.56.2.1 33762 1qy1A 174 9.45e+00 b.60.1.1 96568 1uirA 314 9.58e+00 c.66.1.17 99429 1zndA 174 9.92e+00 1r5tA 142 1.01e+01 c.97.1.1 104812 1nu4A 97 1.03e+01 d.58.7.1 80731 1fi4A 416 1.04e+01 1fi4A d.14.1.5,d.58.26.2 59847,59848 1wn5A 130 1.05e+01 2cxcA 144 1.05e+01 2b4aA 138 1.10e+01 1f2tB 148 1.14e+01 1f2tB 1mzbA 136 1.14e+01 a.4.5.42 91497 1e12A 253 1.15e+01 1c3wA f.13.1.1 43428 1xtmA 175 1.22e+01 1ec7A 446 1.23e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1yw5A 177 1.23e+01 1r9cA 139 1.24e+01 d.32.1.2 97255 1z6nA 167 1.25e+01 1bykA 255 1.28e+01 1bykA c.93.1.1 35706 2al2A 436 1.29e+01 1cg5A 141 1.31e+01 1abwA a.1.1.2 15406 2bo4A 397 1.32e+01 1oc2A 348 1.35e+01 c.2.1.2 92765 1gtvA 214 1.36e+01 c.37.1.1 70537 1bazA 53 1.36e+01 1bazA a.43.1.1 17421 2al1A 436 1.38e+01 1qjcA 158 1.40e+01 1b6tA c.26.1.3 63328 1pot 325 1.40e+01 1pot c.94.1.1 35807 2cw5A 255 1.46e+01 1xwyA 264 1.47e+01 1x7oA 287 1.48e+01 1sviA 195 1.50e+01 c.37.1.8 106048 2evaA 307 1.51e+01 1id1A 153 1.52e+01 1id1A c.2.1.9 62286 2av4A 162 1.55e+01 1k8rB 110 1.55e+01 d.15.1.5 72180 1pvvA 315 1.57e+01 c.78.1.1,c.78.1.1 95190,95191 1zd9A 188 1.60e+01 1oneA 436 1.69e+01 4enl c.1.11.1,d.54.1.1 29200,38844 1lmiA 131 1.72e+01 b.1.19.1 78098 1vheA 373 1.72e+01 b.49.3.1,c.56.5.4 100669,100670 1aba 87 1.76e+01 1aba c.47.1.1 32760 1r8sA 164 1.77e+01 c.37.1.8 97247 1h1nA 305 1.83e+01 c.1.8.3 70855 1dekA 241 1.86e+01 1dekA c.37.1.1 31842 1t71A 281 1.86e+01 1g3qA 237 1.87e+01 1hyqA c.37.1.10 60237 1iu8A 206 1.89e+01 c.56.4.1 71436 1jmsA 381 1.89e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 2fckA 181 1.89e+01 1d3yA 301 1.91e+01 1d3yA e.12.1.1 43252 2glfA 450 1.93e+01 2b99A 156 1.98e+01 1jh6A 189 1.99e+01 d.61.1.1 66707 1ob8A 135 2.04e+01 2gukA 120 2.07e+01 1q6zA 528 2.09e+01 1mwmA 320 2.09e+01 c.55.1.1,c.55.1.1 79580,79581 2akzA 439 2.14e+01 1jndA 420 2.15e+01 c.1.8.5,d.26.3.1 71757,71758 1geqA 248 2.16e+01 2tysA c.1.2.4 28589 1oxxK 353 2.19e+01 b.40.6.3,c.37.1.12 93715,93716 1pu6A 218 2.23e+01 a.96.1.5 95123 1irdA 141 2.24e+01 a.1.1.2 66286 1wr8A 231 2.25e+01 2fiqA 420 2.25e+01 1xc3A 302 2.27e+01 2cxxA 190 2.28e+01 1zx4A 192 2.28e+01 1xg8A 111 2.35e+01 1twfK 120 2.38e+01 2a7mA 250 2.39e+01 1c0pA 363 2.44e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 2cyeA 133 2.46e+01 2gcuA 245 2.48e+01 1auiB 169 2.50e+01 1auiB a.39.1.5 17325 1e8gA 560 2.50e+01 1qltA d.58.32.1,d.145.1.1 39455,41718 1wa3A 205 2.53e+01 1ymqA 261 2.53e+01 1zpvA 91 2.53e+01 1czfA 362 2.54e+01 1czfA b.80.1.3 28031 1q3iA 214 2.55e+01 d.220.1.1 104524 1e6uA 321 2.55e+01 1bsvA c.2.1.2 29805 2aeeA 211 2.56e+01 1bj7 156 2.62e+01 1bj7 b.60.1.1 27113 1yemA 179 2.64e+01 1jljA 189 2.67e+01 c.57.1.1 63169 1ryiA 382 2.68e+01 1zboA 210 2.70e+01 1o3yA 166 2.70e+01 c.37.1.8 86618 1r6uA 437 2.72e+01 c.26.1.1 97163 1kyhA 276 2.77e+01 c.72.1.4 73222 2ew8A 249 2.78e+01 1z7xW 461 2.79e+01 1j0dA 341 2.81e+01 c.79.1.1 83902 1s4iA 175 2.83e+01 1e8cA 498 2.90e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1vbkA 307 2.91e+01 1vehA 92 2.92e+01 1e6yC 247 2.92e+01 1mroC d.58.31.1 39441 1fo8A 343 2.97e+01 1foaA c.68.1.10 59927 1yzvA 204 2.99e+01 2bsxA 253 3.00e+01 1n67A 359 3.03e+01 b.2.3.4,b.2.3.4 85354,85355 1dv1A 449 3.14e+01 1bncA b.84.2.1,c.30.1.1,d.142.1.2 28234,31641,41486 1qqfA 277 3.26e+01 1c3d a.102.4.4 18875 1ve3A 227 3.26e+01 1w6uA 302 3.27e+01 2gnoA 305 3.28e+01 1omzA 293 3.31e+01 c.68.1.15 87093 1jfzA 154 3.31e+01 a.149.1.1 66655 1np7A 489 3.33e+01 a.99.1.1,c.28.1.1 80677,80678 1wqwA 235 3.35e+01 1s99A 200 3.36e+01 1yc5A 246 3.38e+01 1g55A 343 3.40e+01 1g55A c.66.1.26 34247 1k3rA 268 3.42e+01 b.40.4.10,c.116.1.2 72018,72019 1zljA 78 3.44e+01 1im3D 95 3.45e+01 1im3D b.1.18.5 62568 1wyzA 242 3.46e+01 1zud1 251 3.49e+01 3sdhA 146 3.50e+01 3sdhA a.1.1.2 14984 1t3tA 1303 3.51e+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 3tmkA 216 3.53e+01 3tmkA c.37.1.1 31920 1ng6A 148 3.56e+01 a.182.1.1 85670 1yovA 537 3.57e+01 2ca6A 386 3.59e+01 1k47A 337 3.60e+01 d.14.1.5,d.58.26.4 72040,72041 1szqA 483 3.67e+01 e.44.1.1 99045 1ne8A 117 3.68e+01 b.34.6.2 80424 1kjlA 146 3.69e+01 2cviA 83 3.69e+01 2fxaA 207 3.69e+01 1vl5A 260 3.72e+01 c.66.1.41 108720 2g2cA 167 3.80e+01 1mml 265 3.81e+01 1mml e.8.1.2 43015 1g66A 207 3.81e+01 1bs9 c.69.1.30 31329 1hnjA 317 3.84e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1uqtA 482 3.87e+01 c.87.1.6 99794 1y8aA 332 3.89e+01 1cvrA 435 3.91e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 1wdjA 187 3.92e+01 1h70A 255 3.94e+01 1h70A d.126.1.3 60711 1rl4A 188 3.96e+01 d.167.1.1 97636 1ly1A 181 3.96e+01 c.37.1.1 74334 1mr3F 181 3.97e+01 c.37.1.8 79422 1l5wA 796 4.00e+01 c.87.1.4 73605 1w8iA 156 4.01e+01 1qahA 136 4.04e+01 d.79.1.1 96338 1yhtA 367 4.06e+01 1q0uA 219 4.06e+01 c.37.1.19 95512 2arhA 203 4.09e+01 1oz9A 150 4.10e+01 d.92.1.15 93808 1oo0B 110 4.10e+01 d.58.7.1 87183 1yj7A 171 4.14e+01 1lbu 213 4.15e+01 1lbu a.20.1.1,d.65.1.1 16416,39549 1bkpA 278 4.20e+01 1bkpA d.117.1.1 41029 1qwgA 251 4.21e+01 c.1.27.1 96473 1eu8A 409 4.22e+01 1eu8A c.94.1.1 59502 1w77A 228 4.23e+01 1bdfA 235 4.24e+01 1bdfA d.74.3.1,d.181.1.1 39727,42602 2fv1A 377 4.28e+01 1buoA 121 4.28e+01 1buoA d.42.1.1 38631 1eo6A 117 4.30e+01 1eo6A d.15.1.3 37609 1yiyA 429 4.31e+01 1nq7A 244 4.32e+01 a.123.1.1 92047 1x6mA 196 4.34e+01 1em8A 147 4.34e+01 c.128.1.1 90457 1xo5A 183 4.35e+01 1erw 105 4.38e+01 1erv c.47.1.1 32745 1l8bA 190 4.45e+01 d.86.1.1 73683 1l2tA 235 4.46e+01 c.37.1.12 73514 1kdgA 546 4.47e+01 c.3.1.2,d.16.1.1 77337,77338 1qu9A 128 4.56e+01 1qu9A d.79.1.1 39755 1wvfA 520 4.58e+01 1u7gA 385 4.59e+01 f.44.1.1 107723 1ukuA 102 4.61e+01 d.58.5.2 99533 2hvm 273 4.61e+01 1cnv c.1.8.5 28985 1c1dA 355 4.61e+01 1bw9A c.2.1.7,c.58.1.1 30270,33918 1svy 114 4.66e+01 1svy d.109.1.1 40831 2b7kA 200 4.66e+01 1swvA 267 4.71e+01 1rq2A 382 4.71e+01 c.32.1.1,d.79.2.1 105048,105049 1tedA 393 4.74e+01 c.95.1.2 106807 2d1sA 548 4.75e+01 1yizA 429 4.82e+01 1t2dA 322 4.84e+01 c.2.1.5,d.162.1.1 99084,99085 2au3A 407 4.85e+01 2g5cA 281 4.87e+01 1tadA 324 4.89e+01 1cipA a.66.1.1,c.37.1.8 18194,32077 1n4qB 377 4.92e+01 a.102.4.3 91636 1p1mA 406 4.93e+01 b.92.1.4,c.1.9.9 87696,87697 1cipA 353 4.93e+01 1cipA a.66.1.1,c.37.1.8 18210,32093 1v74B 87 4.96e+01 a.24.20.1 100443 1us5A 314 5.00e+01 c.94.1.1 99856 1ufwA 95 5.00e+01 d.58.7.1 99358 1ylxA 103 5.00e+01 1rfyA 102 5.13e+01 1bd3A 243 5.14e+01 1bd3A c.61.1.1 34098 2h1tA 188 5.14e+01 1eu1A 780 5.14e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 1wi1A 126 5.14e+01 1f35A 162 5.19e+01 1f35A b.94.1.1 59628 2f94F 350 5.22e+01 1wruA 379 5.24e+01 1ws0A 156 5.25e+01 1wzlA 585 5.27e+01 2bgkA 278 5.29e+01 1s6cA 183 5.33e+01 a.39.1.5 98594 1vd5A 377 5.33e+01 a.102.1.7 108518 1gegA 256 5.40e+01 1ybvA c.2.1.2 29888 2b61A 377 5.40e+01 1gt1A 159 5.41e+01 b.60.1.1 90515 1tuaA 191 5.49e+01 d.51.1.1,d.51.1.1 107321,107322 1vhxA 150 5.51e+01 c.55.3.8 100712 1nrzA 164 5.53e+01 c.38.1.1 86131 2gsq 202 5.56e+01 1pd21 a.45.1.1,c.47.1.5 17715,33009 1jysA 242 5.65e+01 c.56.2.1 77216 2f6kA 307 5.66e+01 1fn9A 365 5.67e+01 1fn9A d.196.1.1 59894 1lfpA 249 5.69e+01 e.39.1.1 73885 1svsA 353 5.69e+01 c.37.1.8 106051 1v8hA 107 5.73e+01 1ui0A 205 5.73e+01 c.18.1.2 99411 1reqB 637 5.76e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1yseA 141 5.76e+01 1vmeA 410 5.77e+01 c.23.5.1,d.157.1.3 108893,108894 1i4wA 353 5.79e+01 c.66.1.24 66028 1h5rA 293 5.85e+01 c.68.1.6 65623 2mprA 421 5.86e+01 2mprA f.4.3.2 43788 2cxkA 95 5.88e+01 2cx5A 158 5.96e+01 1hfc 169 5.96e+01 1hfc d.92.1.11 40335 1xt8A 292 5.99e+01 1ooeA 236 6.09e+01 c.2.1.2 87196 1b3aA 67 6.12e+01 1b3aA d.9.1.1 37410 1r7mA 235 6.17e+01 1ve0A 134 6.18e+01 2f9sA 151 6.20e+01 2c0nA 203 6.22e+01 2ggcA 263 6.22e+01 1u2wA 122 6.31e+01 1eluA 390 6.36e+01 1elqA c.67.1.3 34434 2ap1A 327 6.40e+01 1jb7B 260 6.41e+01 1otcB b.40.4.3 62839 1kjnA 157 6.44e+01 c.115.1.1 72614 1jmkC 230 6.44e+01 c.69.1.22 71747 2aa1A 144 6.47e+01 1fvgA 199 6.49e+01 1fvaA d.58.28.1 39408 1zosA 230 6.49e+01 1zejA 293 6.54e+01 2chnA 716 6.55e+01 1tr8A 102 6.58e+01 2fbwD 103 6.64e+01 1ekeA 230 6.65e+01 1ekeA c.55.3.1 33572 1qusA 322 6.67e+01 1ltm d.2.1.6 36991 1mrj 247 6.70e+01 1mrj d.165.1.1 42177 1l6rA 227 6.72e+01 c.108.1.10 77768 1f5vA 240 6.76e+01 1bkjA d.90.1.1 40255 2d0oA 610 6.79e+01 1vecA 206 6.81e+01 c.37.1.19 100575 2ez6A 221 6.81e+01 1t8tA 271 6.82e+01 c.37.1.5 106685 1aun 208 6.82e+01 1thv b.25.1.1 23900 1hb6A 86 6.83e+01 a.11.1.1 70959 1fxlA 167 6.85e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1p4xA 250 6.89e+01 a.4.5.28,a.4.5.28 87784,87785 1qstA 160 6.90e+01 1yghA d.108.1.1 40804 1ru3A 732 6.91e+01 e.26.1.3 97835 1qgdA 662 6.91e+01 c.36.1.6,c.36.1.10,c.48.1.1 88367,88368,88369 1xewY 172 6.92e+01 2av5A 120 6.97e+01 2dlbA 80 6.97e+01 2gw8A 114 6.98e+01 1ri5A 298 7.02e+01 c.66.1.34 97502 2choA 716 7.04e+01 1r1uA 106 7.05e+01 a.4.5.5 104771 1ltqA 301 7.06e+01 c.108.1.9,c.37.1.1 78208,78209 1k3bB 164 7.09e+01 d.3.1.1 72015 1gy8A 397 7.10e+01 c.2.1.2 83376 1epxA 370 7.11e+01 1fbaA c.1.10.1 29150 1lzlA 323 7.21e+01 c.69.1.2 78306 2cbiA 594 7.25e+01 7odcA 424 7.25e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1wwzA 159 7.25e+01 1aocA 175 7.25e+01 1aocA g.17.1.5 44817 1v25A 541 7.32e+01 e.23.1.1 108275 1wxxA 382 7.34e+01 1it2A 146 7.36e+01 a.1.1.2 66365 1xmxA 385 7.36e+01 1s14A 194 7.37e+01 d.122.1.2 98329 1nrjA 158 7.38e+01 d.110.4.4 86124 2as0A 396 7.42e+01 1oqvA 192 7.46e+01 d.24.1.2 87320 1vp4A 425 7.46e+01 1dl5A 317 7.58e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 1n83A 270 7.60e+01 a.123.1.1 80276 2b0jA 358 7.60e+01 1q7hA 153 7.60e+01 b.122.1.1,d.17.6.2 96042,96043 2a72A 146 7.72e+01 1w41A 101 7.73e+01 1q9uA 130 7.73e+01 d.129.7.1 96314 1ccwB 483 7.77e+01 1cb7B c.1.19.2 29646 2fa8A 105 7.80e+01 1tcvA 287 7.85e+01 1cnzA 363 7.89e+01 1cnzA c.77.1.1 35061 2b9wA 424 7.91e+01 1u11A 182 7.94e+01 c.23.8.1 107576 1x3lA 440 8.02e+01 1vqsA 116 8.07e+01 1st9A 143 8.10e+01 c.47.1.10 98987 1q2lA 939 8.11e+01 1xrtA 467 8.12e+01 1v60A 123 8.12e+01 1y1pA 342 8.16e+01 2aeuA 374 8.16e+01 1s3zA 165 8.17e+01 d.108.1.1 105250 1cby 259 8.23e+01 1cby d.103.1.1 40705 1xi3A 215 8.24e+01 c.1.3.1 109601 2agmA 167 8.30e+01 1q45A 391 8.31e+01 c.1.4.1 95780 1dqpA 230 8.31e+01 1dqnA c.61.1.1 34069 1odfA 290 8.35e+01 c.37.1.6 92782 1pu1A 94 8.38e+01 d.266.1.1 104307 1nf2A 268 8.44e+01 c.108.1.10 91849 1mqiA 263 8.46e+01 c.94.1.1 91398 1vggA 161 8.53e+01 1vr5A 547 8.53e+01 1g291 372 8.60e+01 1g291 2di4A 238 8.61e+01 1xteA 154 8.64e+01 1wvqA 167 8.66e+01 1m0dA 138 8.68e+01 c.52.1.17 74354 1sqsA 242 8.68e+01 c.23.5.5 98968 1zuwA 272 8.70e+01 1in0A 163 8.72e+01 d.58.49.1,d.58.49.1 83694,83695 2bj7A 138 8.79e+01 1hfoA 113 8.81e+01 d.80.1.3 61006 1zowA 313 8.82e+01 1mj5A 302 8.85e+01 c.69.1.8 91285 1w9pA 433 8.86e+01 1z4rA 168 8.87e+01 1iqqA 200 8.92e+01 d.124.1.1 66274 1p30A 952 8.96e+01 b.121.2.2,b.121.2.2 93964,93965