# List of top-scoring protein chains for t06-100-30-alpha-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 1.04e-02 1fcyA 236 2.72e-01 2lbd a.123.1.1 19282 2gj8A 172 3.05e-01 2cviA 83 7.68e-01 1xc3A 302 1.10e+00 1ymqA 261 1.12e+00 2dbbA 151 1.12e+00 1e9rA 437 1.49e+00 c.37.1.11 64827 2ffuA 501 1.57e+00 1odkA 235 1.68e+00 c.56.2.1 86863 1wdtA 665 1.75e+00 2fckA 181 1.85e+00 1s96A 219 1.96e+00 c.37.1.1 98740 2faoA 309 2.10e+00 1gegA 256 2.29e+00 1ybvA c.2.1.2 29888 1u04A 771 2.32e+00 b.34.14.1,c.55.3.10 107539,107540 2al2A 436 2.37e+00 1jysA 242 2.38e+00 c.56.2.1 77216 1oneA 436 2.59e+00 4enl c.1.11.1,d.54.1.1 29200,38844 1q6zA 528 2.70e+00 2akzA 439 2.71e+00 1vggA 161 3.32e+00 2al1A 436 3.41e+00 2an9A 207 3.57e+00 1qysA 106 3.75e+00 k.41.1.1 96603 1r9cA 139 4.07e+00 d.32.1.2 97255 1qo0D 196 4.07e+00 1qo0D c.23.1.3 31125 2fuvA 549 4.31e+00 1b3aA 67 4.33e+00 1b3aA d.9.1.1 37410 1zu4A 320 4.47e+00 2f5gA 133 4.49e+00 1oz9A 150 4.84e+00 d.92.1.15 93808 1wi1A 126 4.90e+00 1ftrA 296 4.94e+00 1ftrA d.58.33.1,d.58.33.1 39485,39486 1tfr 305 5.00e+00 1tfr a.60.7.1,c.120.1.2 18081,33351 1pvvA 315 5.34e+00 c.78.1.1,c.78.1.1 95190,95191 2bsxA 253 5.56e+00 2azeA 155 5.89e+00 1jmtA 104 5.99e+00 d.58.7.3 63180 1r5tA 142 6.14e+00 c.97.1.1 104812 2b0jA 358 6.19e+00 2g5cA 281 6.48e+00 1yovA 537 6.58e+00 2c0nA 203 6.79e+00 1ursA 402 6.85e+00 c.94.1.1 99833 1kicA 339 6.98e+00 c.70.1.1 72510 1wvfA 520 7.07e+00 2cw5A 255 7.27e+00 1d3yA 301 7.61e+00 1d3yA e.12.1.1 43252 1vjeA 166 8.00e+00 d.185.1.2 100807 1rwzA 245 8.28e+00 d.131.1.2,d.131.1.2 98005,98006 2cxcA 144 8.70e+00 1ht6A 405 8.72e+00 b.71.1.1,c.1.8.1 83629,83630 2dcnA 311 8.73e+00 1u8sA 192 8.81e+00 d.58.18.5,d.58.18.5 107737,107738 1u7lA 392 8.89e+00 2bwvA 440 9.09e+00 1nu4A 97 9.61e+00 d.58.7.1 80731 1zpvA 91 1.02e+01 1vecA 206 1.05e+01 c.37.1.19 100575 1pu6A 218 1.05e+01 a.96.1.5 95123 1mzbA 136 1.05e+01 a.4.5.42 91497 1j0dA 341 1.05e+01 c.79.1.1 83902 1zejA 293 1.07e+01 2eifA 136 1.10e+01 1bkb b.34.5.2,b.40.4.5 24607,25339 1rq2A 382 1.11e+01 c.32.1.1,d.79.2.1 105048,105049 1vjqA 79 1.11e+01 k.43.1.1 100830 2f4nA 273 1.19e+01 2ajrA 331 1.21e+01 1s3zA 165 1.21e+01 d.108.1.1 105250 1qwdA 177 1.23e+01 b.60.1.1 96471 1m6yA 301 1.24e+01 a.60.13.1,c.66.1.23 78716,78717 1xahA 354 1.24e+01 1yj7A 171 1.24e+01 1y81A 138 1.27e+01 1dekA 241 1.28e+01 1dekA c.37.1.1 31842 2h6dA 276 1.29e+01 1o7nA 449 1.30e+01 b.33.1.2,d.129.3.3 81162,81163 1o0iA 138 1.32e+01 d.38.1.5 86532 1qy1A 174 1.32e+01 b.60.1.1 96568 2bitX 165 1.32e+01 1y9aA 360 1.33e+01 1k47A 337 1.37e+01 d.14.1.5,d.58.26.4 72040,72041 1y8aA 332 1.37e+01 3pmgA 561 1.42e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 2fxaA 207 1.42e+01 1zsyA 357 1.42e+01 2a5dA 175 1.43e+01 1vd5A 377 1.43e+01 a.102.1.7 108518 2cpgA 45 1.49e+01 2cpgA a.43.1.3 17455 1zndA 174 1.51e+01 1w77A 228 1.52e+01 2fa8A 105 1.57e+01 1ko6A 187 1.62e+01 b.119.1.1 77471 1bykA 255 1.62e+01 1bykA c.93.1.1 35706 1wvqA 167 1.67e+01 1kkeA 210 1.67e+01 b.21.1.2,b.83.1.2 68669,68670 1mwmA 320 1.68e+01 c.55.1.1,c.55.1.1 79580,79581 3sdhA 146 1.71e+01 3sdhA a.1.1.2 14984 1uqtA 482 1.73e+01 c.87.1.6 99794 1b7yA 350 1.74e+01 1pysA d.104.1.1 40776 1xo0A 324 1.78e+01 1kt6A 183 1.79e+01 b.60.1.1 84466 1wdvA 152 1.80e+01 1guzA 310 1.82e+01 c.2.1.5,d.162.1.1 65586,65587 1fo8A 343 1.87e+01 1foaA c.68.1.10 59927 2fymA 431 1.92e+01 2b99A 156 1.93e+01 1hnjA 317 1.93e+01 1hn9A c.95.1.2,c.95.1.2 35969,35970 1qjcA 158 1.94e+01 1b6tA c.26.1.3 63328 2fiqA 420 1.95e+01 1m1hA 248 1.98e+01 b.114.1.1,d.58.42.1 78415,78416 2cyeA 133 2.00e+01 1yzvA 204 2.00e+01 1s2dA 167 2.03e+01 c.23.14.1 98377 1bazA 53 2.05e+01 1bazA a.43.1.1 17421 1ooeA 236 2.06e+01 c.2.1.2 87196 1id1A 153 2.10e+01 1id1A c.2.1.9 62286 1v7pC 200 2.13e+01 c.62.1.1 108408 1ka1A 357 2.15e+01 e.7.1.1 68369 1e6yC 247 2.17e+01 1mroC d.58.31.1 39441 1z08A 170 2.18e+01 1qb5D 99 2.19e+01 b.40.2.1 88357 1vdnA 162 2.20e+01 2arhA 203 2.20e+01 2bmoA 447 2.23e+01 2ivyA 101 2.24e+01 1xvaA 292 2.30e+01 1xvaA c.66.1.5 34183 1zowA 313 2.32e+01 1ec7A 446 2.32e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1vbkA 307 2.37e+01 2a5jA 191 2.38e+01 1ev7A 317 2.39e+01 1ev7B c.52.1.9 33315 2gzaA 361 2.41e+01 1cg5A 141 2.42e+01 1abwA a.1.1.2 15406 1aun 208 2.43e+01 1thv b.25.1.1 23900 1dzkA 157 2.46e+01 1obpA b.60.1.1 27096 1czfA 362 2.46e+01 1czfA b.80.1.3 28031 1cvrA 435 2.53e+01 1cvrA b.1.18.12,c.17.1.2 21949,31006 2cfxA 144 2.55e+01 1vehA 92 2.57e+01 1eo6A 117 2.60e+01 1eo6A d.15.1.3 37609 1tcvA 287 2.61e+01 1iz6A 138 2.62e+01 b.34.5.2,b.40.4.5 76976,76977 1e3dA 266 2.62e+01 2frvA e.19.1.1 59188 1pzxA 289 2.67e+01 c.119.1.1 95484 1iow 306 2.68e+01 1iow c.30.1.2,d.142.1.1 31713,41481 2dchX 216 2.69e+01 1ub3A 220 2.70e+01 c.1.10.1 88395 2dlbA 80 2.72e+01 2ghpA 292 2.74e+01 1q3iA 214 2.78e+01 d.220.1.1 104524 1f4pA 147 2.78e+01 5nul c.23.5.1 59651 1b77A 228 2.81e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 2f1fA 164 2.85e+01 1ukuA 102 2.89e+01 d.58.5.2 99533 1g66A 207 2.90e+01 1bs9 c.69.1.30 31329 1lmiA 131 2.90e+01 b.1.19.1 78098 1kyhA 276 2.91e+01 c.72.1.4 73222 1xi3A 215 2.91e+01 c.1.3.1 109601 1yb0A 159 2.93e+01 1bj7 156 3.00e+01 1bj7 b.60.1.1 27113 1g63A 181 3.07e+01 1g5qA c.34.1.1 60299 1pcfA 66 3.07e+01 1pcfA d.18.1.1 38142 1utiA 58 3.09e+01 b.34.2.1 99962 1ryp1 222 3.09e+01 1ryp1 2bj7A 138 3.09e+01 2b61A 377 3.09e+01 1x6mA 196 3.12e+01 1zbsA 291 3.13e+01 2ew8A 249 3.14e+01 2bo4A 397 3.17e+01 1jb7B 260 3.18e+01 1otcB b.40.4.3 62839 1v95A 130 3.19e+01 c.51.1.1 108435 1twfK 120 3.22e+01 2gm3A 175 3.23e+01 2cxxA 190 3.28e+01 1wn5A 130 3.30e+01 1dywA 173 3.42e+01 2cpl b.62.1.1 27505 1hfc 169 3.42e+01 1hfc d.92.1.11 40335 1n5nA 180 3.43e+01 d.167.1.1 85336 1it2A 146 3.46e+01 a.1.1.2 66365 1mqiA 263 3.48e+01 c.94.1.1 91398 1pa7A 130 3.51e+01 a.40.1.1 94410 1aba 87 3.59e+01 1aba c.47.1.1 32760 1yvoA 172 3.59e+01 1ubkS 267 3.66e+01 e.19.1.1 88423 1n4qB 377 3.69e+01 a.102.4.3 91636 1b8oA 284 3.69e+01 1b8oA c.56.2.1 33762 1em8A 147 3.69e+01 c.128.1.1 90457 1wuiS 267 3.70e+01 2fv1A 377 3.73e+01 1vp4A 425 3.75e+01 1pot 325 3.77e+01 1pot c.94.1.1 35807 1uirA 314 3.78e+01 c.66.1.17 99429 2b8nA 429 3.81e+01 1x7oA 287 3.81e+01 1kjlA 146 3.85e+01 1pxfA 111 3.85e+01 b.40.4.4 88341 1us5A 314 3.87e+01 c.94.1.1 99856 1fvgA 199 3.88e+01 1fvaA d.58.28.1 39408 1sh8A 154 3.90e+01 d.38.1.5 105549 1tr8A 102 3.91e+01 1om1A 332 3.98e+01 d.144.1.7 93347 2fu0A 160 4.02e+01 1tuaA 191 4.02e+01 d.51.1.1,d.51.1.1 107321,107322 1jmsA 381 4.03e+01 a.60.6.1,a.60.12.1,d.218.1.2 66889,75862,75863 1wj9A 211 4.04e+01 1np7A 489 4.14e+01 a.99.1.1,c.28.1.1 80677,80678 1uc8A 280 4.15e+01 c.30.1.6,d.142.1.7 99165,99166 1vheA 373 4.16e+01 b.49.3.1,c.56.5.4 100669,100670 1lfpA 249 4.17e+01 e.39.1.1 73885 1lq9A 112 4.20e+01 d.58.4.3 78129 1c7qA 445 4.28e+01 2pgi c.80.1.2 35307 1oc2A 348 4.32e+01 c.2.1.2 92765 1nijA 318 4.35e+01 c.37.1.10,d.237.1.1 85741,85742 1fthA 122 4.36e+01 d.150.1.2 60028 1xg8A 111 4.37e+01 1ne8A 117 4.37e+01 b.34.6.2 80424 1sr9A 644 4.39e+01 a.5.7.1,c.1.10.5,d.270.1.1 105960,105961,105962 1gtvA 214 4.40e+01 c.37.1.1 70537 1x1oA 286 4.42e+01 1iq4A 179 4.45e+01 1iq4A d.77.1.1 62641 1q2lA 939 4.47e+01 1v8hA 107 4.52e+01 2f2eA 146 4.55e+01 1bn7A 294 4.61e+01 1bn6A c.69.1.8 34677 2erbA 125 4.61e+01 1zhhB 242 4.64e+01 1mo9A 523 4.65e+01 c.3.1.5,c.3.1.5,d.87.1.1 79341,79342,79343 1auiB 169 4.66e+01 1auiB a.39.1.5 17325 1avqA 228 4.67e+01 1avqA c.52.1.13 33326 1ztdA 133 4.68e+01 2esrA 177 4.69e+01 1zosA 230 4.74e+01 1ro5A 201 4.75e+01 d.108.1.3 105023 2pii 112 4.75e+01 2pii d.58.5.1 39071 1jfzA 154 4.85e+01 a.149.1.1 66655 1f02T 66 4.93e+01 1f02T j.67.1.1 46360 2ap1A 327 4.94e+01 1yxmA 303 4.99e+01 1q0vA 81 5.00e+01 j.105.1.1 95514 1g2rA 100 5.04e+01 1g2rA d.192.1.1 60231 1yemA 179 5.05e+01 1k3bB 164 5.06e+01 d.3.1.1 72015 1jljA 189 5.07e+01 c.57.1.1 63169 2cbiA 594 5.07e+01 2a7mA 250 5.07e+01 1ysrA 150 5.10e+01 1mh1 186 5.11e+01 1eesA c.37.1.8 32002 1oaoC 729 5.13e+01 e.26.1.3 86746 1ws0A 156 5.15e+01 1yiyA 429 5.16e+01 1q4rA 112 5.18e+01 d.58.4.4 95823 1ow1A 195 5.21e+01 b.131.1.3 93625 1huxA 270 5.24e+01 1huxA c.55.1.5 61278 1t0fA 276 5.27e+01 1t3tA 1303 5.28e+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 2gcfA 73 5.29e+01 1v4pA 157 5.37e+01 1m6sA 347 5.39e+01 c.67.1.1 78701 1kk1A 410 5.40e+01 b.43.3.1,b.44.1.1,c.37.1.8 72634,72635,72636 1hqz1 141 5.43e+01 2btiA 63 5.43e+01 1gd0A 122 5.44e+01 1dptA d.80.1.3 39834 1g3qA 237 5.46e+01 1hyqA c.37.1.10 60237 2cx5A 158 5.48e+01 1zud1 251 5.48e+01 1b4bA 71 5.51e+01 1b4aA d.74.2.1 39718 1oj8A 105 5.52e+01 d.5.1.1 103975 1qahA 136 5.57e+01 d.79.1.1 96338 2di4A 238 5.58e+01 7odcA 424 5.61e+01 7odcA b.49.2.3,c.1.6.1 26488,28650 1t2dA 322 5.61e+01 c.2.1.5,d.162.1.1 99084,99085 1g55A 343 5.62e+01 1g55A c.66.1.26 34247 1f35A 162 5.64e+01 1f35A b.94.1.1 59628 1wduA 245 5.67e+01 d.151.1.1 109286 1wa3A 205 5.68e+01 1clvI 32 5.74e+01 1qfdA g.3.2.1 44075 1ob8A 135 5.76e+01 1e8cA 498 5.76e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1vbwA 68 5.77e+01 1f15A 218 5.82e+01 1f15B b.121.4.5 23320 1i4wA 353 5.85e+01 c.66.1.24 66028 1ekeA 230 5.88e+01 1ekeA c.55.3.1 33572 2gdgA 114 5.89e+01 1woqA 267 5.90e+01 c.55.1.10,c.55.1.10 109462,109463 2fexA 188 6.02e+01 1wdjA 187 6.02e+01 1pt6A 213 6.04e+01 c.62.1.1 95091 1i12A 160 6.05e+01 1i21A d.108.1.1 61515 1t5hX 504 6.06e+01 e.23.1.1 106449 1w2fA 276 6.10e+01 d.143.1.3 109125 1dceB 331 6.11e+01 1dceB a.102.4.3 18872 1h5rA 293 6.15e+01 c.68.1.6 65623 1gvjA 146 6.19e+01 a.4.5.21 90525 1l4uA 176 6.19e+01 c.37.1.2 73568 2ffsA 157 6.22e+01 1r8sA 164 6.23e+01 c.37.1.8 97247 2cwzA 141 6.24e+01 2mprA 421 6.26e+01 2mprA f.4.3.2 43788 1mrzA 293 6.26e+01 b.43.5.1,c.26.1.3 91452,91453 1wz8A 264 6.29e+01 1k8rB 110 6.33e+01 d.15.1.5 72180 1eu1A 780 6.36e+01 1dmr b.52.2.2,c.81.1.1 26903,35311 2bgkA 278 6.38e+01 2be4A 272 6.39e+01 2agmA 167 6.42e+01 1xo5A 183 6.48e+01 2cvlA 124 6.50e+01 2ez6A 221 6.61e+01 2gcuA 245 6.62e+01 2gw8A 114 6.69e+01 1oo0B 110 6.69e+01 d.58.7.1 87183 1i9gA 280 6.84e+01 c.66.1.13 62090 1bqk 124 6.85e+01 1bqk b.6.1.1 22889 1ve0A 134 6.85e+01 1nrzA 164 6.85e+01 c.38.1.1 86131 1nwaA 203 6.90e+01 d.58.28.1 86295 1l6sA 323 6.94e+01 c.1.10.3 73627 1gd1O 334 6.96e+01 1dssG c.2.1.3,d.81.1.1 29962,39877 1oxxK 353 7.02e+01 b.40.6.3,c.37.1.12 93715,93716 1e6uA 321 7.05e+01 1bsvA c.2.1.2 29805 1o7zA 77 7.05e+01 d.9.1.1 86660 1l6rA 227 7.06e+01 c.108.1.10 77768 1cseI 71 7.07e+01 1egpA d.40.1.1 38559 1yp2A 451 7.09e+01 1avbA 226 7.12e+01 1led b.29.1.1 24158 1ejfA 125 7.15e+01 1ejfA b.15.1.2 23683 1k3rA 268 7.17e+01 b.40.4.10,c.116.1.2 72018,72019 1yizA 429 7.18e+01 2beiA 170 7.19e+01 1zd9A 188 7.21e+01 2dri 271 7.23e+01 2dri c.93.1.1 35637 8dfr 189 7.23e+01 1aoeA c.71.1.1 34895 1p0zA 131 7.23e+01 d.110.6.1 93882 1rm8A 169 7.23e+01 d.92.1.11 97660 1mjfA 281 7.26e+01 c.66.1.17 79198 1zj6A 187 7.29e+01 1zc1A 208 7.30e+01 1xmxA 385 7.32e+01 1xt8A 292 7.35e+01 1yndA 165 7.35e+01 1xubA 298 7.35e+01 2bkrA 212 7.37e+01 2aa4A 289 7.37e+01 1vhwA 253 7.42e+01 c.56.2.1 100706 1sc6A 404 7.43e+01 2a1iA 146 7.43e+01 1s6cA 183 7.44e+01 a.39.1.5 98594 1zljA 78 7.50e+01 1w5rA 278 7.55e+01 1tkeA 224 7.56e+01 1vc3B 97 7.58e+01 1v54F 98 7.61e+01 g.41.5.3 100327 1opd 85 7.61e+01 1ptf d.94.1.1 40560 1hhnA 101 7.62e+01 1hhnA b.104.1.1 61043 1z6nA 167 7.65e+01 1bco 327 7.65e+01 1bco b.48.1.1,c.55.3.3 26431,33676 1uekA 275 7.71e+01 d.14.1.5,d.58.26.5 88483,88484 1i52A 236 7.73e+01 1i52A c.68.1.13 61767 2d1sA 548 7.79e+01 1ddwA 120 7.80e+01 1evhA b.55.1.4 27001 2d1pA 140 7.84e+01 1fzqA 181 7.86e+01 1hurA c.37.1.8 32060 1yhtA 367 7.86e+01 2g1uA 155 7.87e+01 1zmaA 118 7.88e+01 1zuwA 272 7.88e+01 1wn4A 28 7.92e+01 j.113.1.1 109426 8abp 306 7.93e+01 8abp c.93.1.1 35647 1xeoA 168 7.95e+01 1tedA 393 7.97e+01 c.95.1.2 106807 1fi4A 416 8.00e+01 1fi4A d.14.1.5,d.58.26.2 59847,59848 1ufwA 95 8.03e+01 d.58.7.1 99358 2au3A 407 8.04e+01 1nkqA 259 8.12e+01 d.177.1.1 103862 1q9uA 130 8.14e+01 d.129.7.1 96314 1lwdA 413 8.16e+01 c.77.1.1 78265 1eluA 390 8.19e+01 1elqA c.67.1.3 34434 1ta0A 197 8.25e+01 c.108.1.16 106729 1bwwA 109 8.27e+01 8fabA b.1.1.1 20518 1dyr 206 8.27e+01 1aoeA c.71.1.1 34916 1fwxA 595 8.29e+01 b.6.1.4,b.69.3.1 60069,60070 1i8kA 107 8.32e+01 b.1.1.1 71130 1wstA 417 8.36e+01 2ftrA 108 8.39e+01 1wzuA 300 8.39e+01 1zarA 282 8.41e+01 1rxyA 253 8.41e+01 c.56.2.1 98065 2evaA 307 8.43e+01 1efpB 252 8.48e+01 1efvB c.26.2.3 31636 1qwgA 251 8.48e+01 c.1.27.1 96473 1nq7A 244 8.49e+01 a.123.1.1 92047 2b4aA 138 8.49e+01 1mtpA 323 8.50e+01 e.1.1.1 85107 1sj1A 66 8.51e+01 d.58.1.4 105595 1zq6A 359 8.51e+01 1r29A 127 8.56e+01 d.42.1.1 96856 2gukA 120 8.62e+01 1vkhA 273 8.71e+01 c.69.1.32 108662 1q77A 138 8.77e+01 c.26.2.4 96023 1sbyA 254 8.77e+01 1ef8A 261 8.82e+01 1ef8A c.14.1.3 30921 1pc6A 146 8.82e+01 d.262.1.1 94430 1t4aA 84 8.83e+01 d.284.1.1 106404 1sviA 195 8.89e+01 c.37.1.8 106048 1lbu 213 8.95e+01 1lbu a.20.1.1,d.65.1.1 16416,39549 1aie 31 8.99e+01 1aie a.53.1.1 17829 1z5bA 469 9.00e+01