# 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.soe.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 2drhA 361 1.94e-68 1b65A 375 6.68e-62 1b65A d.154.1.1 42020 1vz6A 393 2.27e-03 d.154.1.2 108949 3it4B 205 5.24e-03 2v4iB 213 1.13e-01 1augA 215 1.98e-01 1a2zA c.56.4.1 33798 2dh2A 424 5.19e-01 2j01E 206 7.36e-01 b.43.3.2 145566 1o2dA 371 7.55e-01 e.22.1.2 86591 1y7pA 223 7.74e-01 c.23.1.7,d.58.18.12 122708,122709 3km3A 206 9.84e-01 2hlzA 312 1.04e+00 2cy7A 396 1.50e+00 d.3.1.22 146431 3di4A 286 1.52e+00 1o9yA 84 1.63e+00 b.139.1.1 92692 2o1xA 629 1.70e+00 1t3tA 1303 1.87e+00 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 2d2eA 250 2.26e+00 1nox 205 2.44e+00 1nox 1noxA 205 2.44e+00 d.90.1.1 40242 2cg7A 90 2.48e+00 g.27.1.1,g.27.1.1 130423,130424 1sgwA 214 2.76e+00 c.37.1.12 105541 1uwvA 433 3.05e+00 b.40.4.12,c.66.1.40 100128,100129 2oryA 346 3.28e+00 2hqqA 298 3.42e+00 1go2A 304 3.66e+00 b.43.4.2,c.25.1.1 76243,76244 1in4A 334 3.80e+00 1hqcA a.4.5.11,c.37.1.20 62597,62598 3lqyA 190 4.08e+00 2q3xA 171 4.11e+00 2iz6A 176 4.29e+00 3cgiA 124 4.34e+00 2d59A 144 4.54e+00 c.2.1.8 131266 2bmwA 304 4.65e+00 b.43.4.2,c.25.1.1 128815,128816 2eq6A 464 4.76e+00 1mt6A 280 4.79e+00 b.76.2.1,b.85.7.1 79446,79447 1zjkA 403 4.81e+00 b.47.1.2,g.18.1.1,g.18.1.1 125149,125150,125151 2qezA 455 4.95e+00 1cjcA 460 4.99e+00 1cjcA c.3.1.1,c.4.1.1 30319,30604 1mwmA 320 5.84e+00 c.55.1.1,c.55.1.1 79580,79581 1pqzA 238 6.40e+00 b.1.1.2,d.19.1.1 104297,104298 2f7vA 369 6.63e+00 3e6aA 336 6.77e+00 2ztsA 251 6.81e+00 3hblA 1150 6.83e+00 1mq7A 154 6.88e+00 b.85.4.1 79404 2zdrA 349 7.13e+00 b.85.1.1,c.1.10.6 154398,154399 2we5A 310 7.22e+00 2wqpA 349 7.35e+00 1znwA 207 7.37e+00 c.37.1.1 125412 1hdhA 536 7.60e+00 c.76.1.2 65805 3luyA 329 8.17e+00 1qz9A 416 8.25e+00 c.67.1.3 96621 1e4eA 343 8.37e+00 1iow c.30.1.2,d.142.1.1 59221,59222 2px7A 236 8.51e+00 1t70A 255 8.52e+00 d.159.1.9 112275 1ny6A 267 8.84e+00 c.37.1.20 92321 3ho8A 1150 8.93e+00 1ogiA 303 8.93e+00 b.43.4.2,c.25.1.1 92914,92915 2qvsB 310 9.07e+00 1z8fA 228 9.52e+00 1wc1A 226 9.56e+00 d.58.29.1 114492 1s4qA 228 9.85e+00 c.37.1.1 98507 3bdvA 191 1.00e+01 1wc3A 219 1.01e+01 d.58.29.1 114495 1fzrA 138 1.02e+01 1fzrA c.52.1.17 33336 1m0dA 138 1.05e+01 c.52.1.17 74354 1w34A 304 1.05e+01 b.43.4.2,c.25.1.1 120620,120621 1nhsA 447 1.05e+01 c.3.1.5,c.3.1.5,d.87.1.1 30555,30556,40199 1ybxA 143 1.07e+01 1sixA 174 1.09e+01 b.85.4.1 98892 1te5A 257 1.11e+01 d.153.1.1 106795 3ehwA 164 1.11e+01 b.85.4.1 158154 1pfkA 320 1.12e+01 3pfk c.89.1.1 35575 1vraB 215 1.12e+01 1gtmA 419 1.13e+01 1hwyA c.2.1.7,c.58.1.1 30223,33871 1sjnA 170 1.18e+01 b.85.4.1 98896 3e5rA 337 1.23e+01 2et1A 201 1.27e+01 b.82.1.2 132351 1fi2A 201 1.27e+01 1fi2A b.82.1.2 59845 2b5oA 402 1.32e+01 3lmbA 165 1.32e+01 3cswA 285 1.34e+01 2zuvA 759 1.35e+01 2qgnA 322 1.41e+01 1g9oA 91 1.43e+01 1pdr b.36.1.1 60400 1svvA 359 1.47e+01 c.67.1.1 106054 1jjiA 311 1.49e+01 c.69.1.2 66766 1in6A 334 1.54e+01 1hqcA a.4.5.11,c.37.1.20 62601,62602 1hq0A 295 1.58e+01 1hzgA d.194.1.1 61122 1p3dA 475 1.59e+01 c.5.1.1,c.59.1.1,c.72.2.1 87728,87729,87730 1xuuA 349 1.62e+01 b.85.1.1,c.1.10.6 116067,116068 1qf5A 431 1.65e+01 1adeA c.37.1.10 32212 2w0mA 235 1.67e+01 2z1nA 260 1.70e+01 2nr7A 195 1.70e+01 d.2.1.9 148359 1q5xA 161 1.71e+01 c.8.7.1 95947 2bsaA 303 1.73e+01 b.43.4.2,c.25.1.1 129078,129079 3hzaA 174 1.75e+01 2nx2A 181 1.79e+01 c.129.1.2 148498 2h0uA 217 1.81e+01 1vqoC 246 1.81e+01 c.22.1.1 120364 1nhp 447 1.82e+01 1nhp 1nhpA 447 1.82e+01 c.3.1.5,c.3.1.5,d.87.1.1 30549,30550,40196 3i3vA 405 1.89e+01 2zvcA 295 1.92e+01 2hq1A 247 1.94e+01 3godA 328 1.98e+01 2ja2A 498 2.00e+01 1z2mA 155 2.02e+01 d.15.1.1,d.15.1.1 124387,124388 2fcjA 119 2.04e+01 c.136.1.1 133269 3dmoA 138 2.07e+01 2oplA 187 2.07e+01 d.227.1.1 148966 2gc7D 147 2.08e+01 a.3.1.1 134957 1ledA 243 2.12e+01 b.29.1.1 24039 1led 243 2.12e+01 1led 3jtyA 402 2.13e+01 3fmeA 290 2.14e+01 2gz4A 207 2.17e+01 a.211.1.1 147196 2pfyA 301 2.18e+01 2gjlA 328 2.21e+01 1n0uA 842 2.22e+01 b.43.3.1,c.37.1.8,d.14.1.1,d.58.11.1,d.58.11.1 79757,79758,79759,79760,79761 1euzA 419 2.24e+01 1k89 c.2.1.7,c.58.1.1 59513,59514 2pfkA 320 2.29e+01 3pfk c.89.1.1 35577 3a8yA 392 2.30e+01 1zgwA 139 2.41e+01 3hb9A 1150 2.46e+01 1xfkA 336 2.47e+01 c.42.1.1 115264 1qx4A 274 2.48e+01 b.43.4.2,c.25.1.1 104624,104625 3iauA 366 2.48e+01 2f48A 555 2.50e+01 c.89.1.1 132915 1lm6A 215 2.54e+01 d.167.1.1 84628 1jbwA 428 2.54e+01 c.59.1.2,c.72.2.2 62860,62861 1vljA 407 2.54e+01 e.22.1.2 108832 2nxcA 254 2.56e+01 c.66.1.39 138739 2fexA 188 2.56e+01 c.23.16.2 133354 2q7xA 326 2.58e+01 2fvhA 120 2.67e+01 3eazA 106 2.67e+01 1gc0A 398 2.70e+01 c.67.1.3 70168 2pcnA 161 2.71e+01 1thqA 170 2.71e+01 f.4.1.2 106920 3io1A 445 2.73e+01 2z4sA 440 2.73e+01 3d2lA 243 2.74e+01 2f7fA 494 2.78e+01 c.1.17.1,d.41.2.1 133088,133089 3g5bA 405 2.86e+01 1wmdA 434 2.86e+01 b.18.1.20,c.41.1.1 109408,109409 3gh5A 525 2.91e+01 2bhvA 246 2.98e+01 1ofuX 119 3.04e+01 c.37.1.22 86976 2j66A 428 3.04e+01 3ifrA 508 3.05e+01 1x12A 208 3.07e+01 2bmbA 545 3.16e+01 2ywjA 186 3.17e+01 1u58A 253 3.18e+01 b.1.1.2,d.19.1.1 144387,144388 1rmg 422 3.19e+01 1rmg 1rmgA 422 3.19e+01 b.80.1.3 28029 3grzA 205 3.21e+01 1mzbA 136 3.24e+01 a.4.5.42 91497 2cjpA 328 3.25e+01 1f7dA 136 3.26e+01 1dun b.85.4.1 28353 2gtlN 220 3.28e+01 b.61.7.1,g.12.1.1,h.1.32.1 135670,135671,135672 3kupA 65 3.33e+01 2qt1A 207 3.33e+01 3b82A 842 3.34e+01 1ieaB 228 3.35e+01 1iakB b.1.1.2,d.19.1.1 21632,38206 2je8A 848 3.36e+01 b.1.4.1,b.1.4.1,b.1.4.1,b.18.1.5,c.1.8.3 147998,147999,148000,148001,148002 2z0dA 357 3.37e+01 d.3.1.22 145769 3e0kA 150 3.40e+01 2o7cA 398 3.44e+01 c.67.1.3 148663 2douA 376 3.54e+01 1bbhA 131 3.56e+01 1bbhA a.24.3.2 16546 1wapA 75 3.56e+01 1wapA b.82.5.1 28153 2c0dA 221 3.61e+01 2ksvA 185 3.63e+01 2c5sA 413 3.65e+01 c.26.2.6,d.308.1.1 129950,129951 2qj8A 332 3.65e+01 1u8bA 133 3.68e+01 1b0uA 262 3.69e+01 1b0uA c.37.1.12 32370 2zgyA 320 3.71e+01 c.55.1.1,c.55.1.1 154425,154426 3cetA 334 3.71e+01 2gyqA 175 3.76e+01 a.25.1.4 135863 1nqkA 381 3.78e+01 c.1.16.4 92050 3dktA 265 3.80e+01 1oqeK 31 3.82e+01 g.24.1.2 87296 2j6bA 109 3.84e+01 d.321.1.1 138078 1nbaA 264 3.95e+01 1nbaA c.33.1.3 31753 2j7vA 298 3.96e+01 2hdvA 111 4.01e+01 1al3 324 4.01e+01 1al3 1al3A 324 4.01e+01 c.94.1.1 35835 3bruA 222 4.11e+01 1iazA 179 4.11e+01 1iazA b.97.1.1 62131 3lxrA 185 4.12e+01 3kdrA 310 4.20e+01 1ou0A 207 4.23e+01 c.23.17.1 93536 1w9zA 283 4.30e+01 2bnmA 198 4.32e+01 a.35.1.3,b.82.1.10 128835,128836 1uzbA 516 4.33e+01 c.82.1.1 100220 1zkpA 268 4.35e+01 d.157.1.9 125205 1q5hA 147 4.36e+01 b.85.4.1 95893 3bpuA 88 4.46e+01 2anrA 178 4.48e+01 2qsjA 154 4.50e+01 1v7zA 260 4.53e+01 c.125.1.1 100488 3a6fA 260 4.54e+01 2gjgA 248 4.55e+01 2vsyA 568 4.55e+01 1vjrA 271 4.58e+01 c.108.1.14 100832 2iyeA 263 4.62e+01 3kb5A 193 4.66e+01 3k9cA 289 4.67e+01 1bv1 159 4.77e+01 1bv1 1kjqA 391 4.83e+01 b.84.2.1,c.30.1.1,d.142.1.2 72616,72617,72618 2oy0A 262 4.92e+01 1otjA 283 4.92e+01 b.82.2.5 93517 1hf2A 210 4.96e+01 1hf2A b.80.3.1,c.102.1.1 60992,60993 2ajrA 331 4.97e+01 c.72.1.1 126892 2db3A 434 5.02e+01 2z61A 370 5.03e+01 1gu3A 149 5.04e+01 b.18.1.14 76350 2rghA 571 5.05e+01 1ci9A 392 5.06e+01 e.3.1.1 64767 2mtaC 147 5.12e+01 2mtaC a.3.1.1 15908 1q3kA 259 5.12e+01 c.125.1.1 95693 1gci 269 5.25e+01 1gci 1gciA 269 5.25e+01 c.41.1.1 32503 2qyxA 238 5.29e+01 3lqwA 163 5.29e+01 1u09A 476 5.31e+01 e.8.1.4 107545 3i44A 497 5.34e+01 3h4oA 191 5.36e+01 2aieP 203 5.39e+01 3a46A 289 5.41e+01 1mg2D 155 5.47e+01 a.3.1.1 79062 1lm4A 194 5.51e+01 d.167.1.1 84626 2ga9A 297 5.66e+01 c.66.1.25 134885 2gifA 1057 5.68e+01 2oztA 332 5.69e+01 2hayA 224 5.71e+01 2vriA 174 5.76e+01 1xadA 345 5.82e+01 c.77.1.1 35055 3a42A 295 5.83e+01 1vr9A 213 5.85e+01 d.37.1.1 144433 1sdjA 310 5.93e+01 d.21.1.2,d.21.1.2 98807,98808 2nzhA 113 6.01e+01 1qwrA 319 6.02e+01 b.82.1.3 96491 1n1tA 641 6.03e+01 b.29.1.15,b.68.1.1 79821,79822 3d2yA 261 6.18e+01 3md1A 83 6.20e+01 2airB 153 6.24e+01 d.58.2.1,g.41.7.1 126832,126833 1cliA 345 6.26e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 3devA 320 6.28e+01 1fgs 428 6.28e+01 1fgs 2wk7A 393 6.29e+01 1cex 214 6.34e+01 1cex 1cexA 214 6.34e+01 c.69.1.30 31285 2bjoA 136 6.50e+01 2q7tA 301 6.55e+01 2ksmA 131 6.58e+01 1p2zA 968 6.64e+01 b.121.2.2,b.121.2.2 93962,93963 1jhsA 188 6.69e+01 d.107.1.1 84172 2bgxA 261 6.73e+01 a.20.1.1,d.118.1.1 128504,128505 1oftA 161 6.74e+01 c.37.1.22 86968 3f42A 99 6.74e+01 1v93A 296 6.88e+01 c.1.23.1 100532 2cbzA 237 6.91e+01 3fhtA 412 6.97e+01 1t15A 214 7.03e+01 c.15.1.3,c.15.1.3 99067,99068 1s3aA 102 7.10e+01 c.47.1.22 118847 2o34A 250 7.10e+01 d.96.2.2 148565 3ijpA 288 7.12e+01 1iu8A 206 7.15e+01 c.56.4.1 71436 2efjA 384 7.15e+01 1x99A 145 7.17e+01 b.97.1.2 114978 2fssA 365 7.19e+01 3giuA 215 7.24e+01 1qyaA 307 7.25e+01 d.21.1.2,d.21.1.2 104653,104654 1uc2A 481 7.37e+01 d.261.1.1 99161 3b9tA 484 7.39e+01 1njgA 250 7.43e+01 c.37.1.20 85785 2rp4A 76 7.45e+01 3h7vA 330 7.49e+01 2dwcA 433 7.50e+01 3d7lA 202 7.56e+01 2hhcA 330 7.61e+01 1uz5A 402 7.62e+01 b.85.6.1,b.103.1.1,c.57.1.2 100217,100218,100219 2k3aA 155 7.66e+01 1bjt 793 7.70e+01 1bjt 1bjtA 793 7.70e+01 e.11.1.1 43249 2zl4A 196 7.73e+01 1gqoA 143 7.81e+01 c.23.13.1 76295 3dhxA 106 7.83e+01 d.58.18.13 157739 3cumA 302 7.83e+01 a.100.1.1,c.2.1.6 156995,156996 3idbB 161 7.87e+01 3d72A 149 7.92e+01 3kyfA 231 7.98e+01 5csmA 256 8.00e+01 5csmA a.130.1.2 19494 2w492 141 8.00e+01 3ip3A 337 8.00e+01