# 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 1y8qA 346 1.05e-02 1a99A 344 1.34e-01 1pot c.94.1.1 35812 2cybA 323 1.44e-01 1zu0A 529 2.53e-01 1wm3A 72 4.36e-01 2d5cA 263 5.35e-01 1t0hB 224 6.48e-01 c.37.1.1 106208 1brwA 433 7.09e-01 1brwA a.46.2.1,c.27.1.1,d.41.3.1 17764,31628,38626 1gefA 123 7.19e-01 1gefA c.52.1.18 60465 1o0xA 262 8.15e-01 d.127.1.1 80755 2mhr 118 8.82e-01 2mhr a.24.4.1 16581 1e5dA 402 9.70e-01 1e5dA c.23.5.1,d.157.1.3 31208,42061 1xgsA 295 1.10e+00 1bn5 a.4.5.25,d.127.1.1 16216,41153 1j34B 123 1.15e+00 d.169.1.1 84049 2cy0A 263 1.20e+00 1jg5A 83 1.24e+00 d.205.1.1 66666 1d0cA 444 1.25e+00 d.174.1.1 64769 1y9kA 157 1.28e+00 1d1vA 444 1.28e+00 1nseA d.174.1.1 59101 2czrA 226 1.37e+00 1r3eA 309 1.42e+00 b.122.1.1,d.265.1.2 96907,96908 1nrfA 262 1.46e+00 e.3.1.1 92086 1vmiA 355 1.54e+00 1sgvA 316 1.57e+00 b.122.1.1,d.265.1.2 98858,98859 1j3mA 129 1.68e+00 d.129.7.1 103836 1wxdA 263 1.68e+00 2fb0A 94 1.69e+00 1w41A 101 1.77e+00 1yqfA 203 1.80e+00 2faoA 309 1.91e+00 1h7mA 102 1.98e+00 d.79.3.1 83485 1v8gA 329 2.03e+00 a.46.2.1,c.27.1.1 100505,100506 1xnzA 264 2.07e+00 1ldjA 760 2.19e+00 a.4.5.34,a.118.17.1,e.40.1.1 73847,73848,73849 1n3lA 372 2.31e+00 c.26.1.1 79966 2fi0A 81 2.38e+00 1r1dA 247 2.48e+00 c.69.1.29 96813 1qo7A 394 2.64e+00 1qo7A c.69.1.11 34697 1fukA 165 2.65e+00 1fukA c.37.1.19 32409 2a9fA 398 2.66e+00 1n9lA 109 2.72e+00 d.110.3.6 85468 1jzuA 157 2.73e+00 b.60.1.1 84271 1j1uA 306 2.76e+00 c.26.1.1 83980 1t3lA 337 2.78e+00 b.34.2.1,c.37.1.1 106358,106359 2gtqA 867 2.82e+00 1obbA 480 2.95e+00 c.2.1.5,d.162.1.2 86760,86761 1c24A 263 2.95e+00 1c24A d.127.1.1 41148 1tqhA 247 2.95e+00 c.69.1.29 107225 1ed5A 444 2.96e+00 1nseA d.174.1.1 42530 2cvlA 124 3.05e+00 1w6uA 302 3.09e+00 3il8 72 3.21e+00 1tvxA d.9.1.1 37356 1u7iA 136 3.31e+00 d.32.1.7 107724 1iukA 140 3.37e+00 c.2.1.8 83712 1u46A 291 3.39e+00 d.144.1.7 107656 1vp8A 201 3.43e+00 1f2aA 215 3.70e+00 1cs8A d.3.1.1 37040 1gmlA 178 3.74e+00 c.8.5.2 70273 2aqjA 538 3.75e+00 1j97A 211 3.81e+00 1f5sA c.108.1.4 62753 1l7mA 211 3.94e+00 c.108.1.4 73664 2ggcA 263 3.94e+00 1mjhA 162 4.06e+00 1mjhA c.26.2.4 31639 2ew8A 249 4.25e+00 1hh1A 143 4.28e+00 1gefA c.52.1.18 61036 1vd4A 62 4.62e+00 1w6tA 444 4.73e+00 1wurA 220 4.89e+00 1k2eA 156 5.11e+00 d.113.1.1 72010 1yemA 179 5.24e+00 1m2oA 768 5.26e+00 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 1xocA 520 5.35e+00 1ctqA 166 5.56e+00 1ctqA c.37.1.8 31965 1e0bA 68 5.58e+00 1e0bA b.34.13.2 37476 1qpcA 279 5.58e+00 1fgkA d.144.1.7 41685 1xuuA 349 5.60e+00 1va4A 279 5.64e+00 c.69.1.12 108458 1ww8A 439 5.80e+00 1om4A 422 5.91e+00 d.174.1.1 87067 1pfkA 320 6.05e+00 3pfk c.89.1.1 35575 1me4A 215 6.09e+00 d.3.1.1 79023 1wvfA 520 6.09e+00 1q5yA 85 6.19e+00 d.58.18.4 95950 2b0cA 206 6.25e+00 1qwgA 251 6.35e+00 c.1.27.1 96473 1np6A 174 6.48e+00 c.37.1.10 85954 1wosA 364 6.49e+00 b.44.2.1,d.250.1.1 109468,109469 2gcfA 73 6.56e+00 1vjeA 166 6.61e+00 d.185.1.2 100807 2d4pA 141 6.62e+00 1f52A 468 6.73e+00 1lgr d.15.9.1,d.128.1.1 37839,41169 1s68A 249 6.75e+00 d.142.2.4 98591 1ooeA 236 7.18e+00 c.2.1.2 87196 1nzjA 298 7.27e+00 c.26.1.1 92377 1o4vA 183 7.33e+00 c.23.8.1 86628 1f1xA 322 7.38e+00 d.32.1.3,d.32.1.3 83208,83209 1vquA 374 7.41e+00 1a9xA 1058 7.46e+00 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18550,31479,31657,31658,41502,41503 1tit 98 7.56e+00 1tit b.1.1.4 21716 1zlqA 502 7.58e+00 1sauA 115 7.61e+00 2fulA 178 7.64e+00 1tl0D 103 7.89e+00 1uiuA 502 7.98e+00 c.94.1.1 99434 1b24A 188 8.14e+00 1b24A d.95.2.1,d.95.2.1 40573,40574 1wu7A 434 8.17e+00 1tzbA 302 8.23e+00 c.80.1.1 107470 1g0oA 283 8.33e+00 1ybvA c.2.1.2 60181 1h75A 81 8.37e+00 1h75A c.47.1.1 60716 1jv4A 162 8.47e+00 b.60.1.1 67343 1x9iA 302 8.57e+00 2dtr 226 8.57e+00 1bi0 a.4.5.24,a.76.1.1,b.34.1.2 16193,18399,24450 1mmvB 419 8.67e+00 d.174.1.1 91318 1whi 122 8.69e+00 1whi b.39.1.1 24810 1nbwA 607 8.83e+00 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1ml4A 308 9.01e+00 c.78.1.1,c.78.1.1 79255,79256 1gy8A 397 9.06e+00 c.2.1.2 83376 1fe0A 68 9.06e+00 1cc8A d.58.17.1 39345 1lx7A 253 9.18e+00 c.56.2.1 74329 1ubi 76 9.21e+00 1ubi d.15.1.1 37584 1o22A 170 9.27e+00 d.238.1.1 86557 2fvhA 120 9.29e+00 1uohA 226 9.35e+00 d.211.1.1 99690 1tfe 145 9.36e+00 1tfe d.43.1.1 38680 1vqoU 66 9.45e+00 1jm1A 204 9.68e+00 b.33.1.1 71745 1f1uA 323 9.80e+00 d.32.1.3,d.32.1.3 83200,83201 2b8tA 223 9.89e+00 1g6oA 330 1.00e+01 1g6oA c.37.1.11 32430 1i05A 180 1.01e+01 1mup b.60.1.1 27130 1u8zA 168 1.01e+01 1rfzA 168 1.03e+01 a.195.1.1 97411 1rqlA 267 1.03e+01 c.108.1.3 97750 2fblA 153 1.04e+01 1ktbA 405 1.06e+01 b.71.1.1,c.1.8.1 72960,72961 1jg1A 235 1.07e+01 c.66.1.7 66661 1xqaA 113 1.09e+01 2fhzA 109 1.09e+01 1j8rA 196 1.10e+01 1j8rA b.2.3.3 62745 1rxyA 253 1.12e+01 c.56.2.1 98065 1innA 166 1.13e+01 1j98A d.185.1.2 62608 1omp 370 1.14e+01 4mbp c.94.1.1 35778 1t6t1 118 1.16e+01 1dazC 99 1.16e+01 1hvc b.50.1.1 26501 2bzoB 79 1.17e+01 1vhzA 198 1.19e+01 d.113.1.1 100718 2avnA 260 1.19e+01 2bkqA 212 1.20e+01 2a14A 263 1.20e+01 1xmrA 243 1.20e+01 1ytvA 366 1.24e+01 1o4wA 147 1.25e+01 c.120.1.1 86629 1v7rA 186 1.26e+01 c.51.4.1 100482 1oahA 519 1.30e+01 a.138.1.3 86736 2gsfA 373 1.30e+01 2bkrA 212 1.31e+01 1nf2A 268 1.31e+01 c.108.1.10 91849 1j7nA 776 1.32e+01 d.92.1.14,d.92.1.14,d.166.1.1 66409,66410,66411 1aw7A 194 1.33e+01 1aw7A b.40.2.2,d.15.6.1 25164,37753 1fmb 104 1.34e+01 1fmb b.50.1.1 26777 1r89A 437 1.38e+01 a.160.1.3,d.218.1.7,d.58.16.2 97221,97222,97223 2f20A 240 1.39e+01 1oz9A 150 1.39e+01 d.92.1.15 93808 1mlwA 301 1.40e+01 d.178.1.1 79289 1jnrB 150 1.41e+01 d.58.1.5 66969 1heiA 451 1.41e+01 1heiA c.37.1.14,c.37.1.14 32463,32464 2eryA 172 1.41e+01 1q77A 138 1.45e+01 c.26.2.4 96023 2fwtA 125 1.49e+01 1vchA 175 1.52e+01 1xmpA 170 1.53e+01 1qysA 106 1.54e+01 k.41.1.1 96603 1mwyA 73 1.55e+01 d.58.17.1 79616 1reqB 637 1.55e+01 1reqB c.1.19.1,c.23.6.1 29621,31248 1kzkA 99 1.57e+01 b.50.1.1 73371 1ta0A 197 1.59e+01 c.108.1.16 106729 1ht6A 405 1.59e+01 b.71.1.1,c.1.8.1 83629,83630 1yzyA 413 1.59e+01 1t6aA 126 1.59e+01 d.129.8.1 106555 1jo0A 98 1.60e+01 d.68.4.1 77140 1difA 99 1.60e+01 1fmb b.50.1.1 26503 1jbeA 128 1.61e+01 3chy c.23.1.1 62845 2fexA 188 1.61e+01 2gi9A 56 1.62e+01 1y7tA 327 1.62e+01 1bmdA 327 1.63e+01 1bmdA c.2.1.5,d.162.1.1 30139,42106 1q9uA 130 1.63e+01 d.129.7.1 96314 1htrB 329 1.64e+01 1smrA 1nrwA 288 1.64e+01 c.108.1.10 86128 1p6oA 161 1.65e+01 c.97.1.2 94185 1j6zA 376 1.65e+01 1yagA c.55.1.1,c.55.1.1 62667,62668 1yzbA 182 1.66e+01 1nx8A 273 1.67e+01 b.82.2.8 86374 1k8wA 327 1.68e+01 b.122.1.1,d.265.1.2 83094,90388 1yqdA 366 1.69e+01 1qnrA 344 1.70e+01 1qnoA c.1.8.3 28834 1yspA 181 1.72e+01 1ogwA 76 1.73e+01 d.15.1.1 87001 1juvA 193 1.74e+01 c.71.1.1 90912 1a0i 348 1.76e+01 1a0i b.40.4.6,d.142.2.1 25363,41577 1vljA 407 1.76e+01 e.22.1.2 108832 1srb 21 1.80e+01 j.28.1.1 46201 2bgcA 238 1.80e+01 2c71A 216 1.84e+01 1n13B 113 1.84e+01 2d1pA 140 1.85e+01 1mkiA 330 1.89e+01 e.3.1.2 84994 3seb 238 1.89e+01 3seb b.40.2.2,d.15.6.1 25184,37773 1z5yE 149 1.90e+01 1t4hA 290 1.91e+01 d.144.1.7 106420 2ethA 154 1.94e+01 1xa1A 255 1.95e+01 e.3.1.1 109529 1nh0A 99 1.96e+01 b.50.1.1 91869 2d8sA 80 1.96e+01 1bdmA 327 1.99e+01 1bmdA c.2.1.5,d.162.1.1 30137,42104 1hywA 68 1.99e+01 1hywA d.186.1.1 61425 1z08A 170 2.01e+01 1wv9A 94 2.01e+01 1cs0A 1073 2.04e+01 a.92.1.1,c.24.1.1,c.30.1.1,c.30.1.1,d.142.1.2,d.142.1.2 18558,31487,31673,31674,41518,41519 1u11A 182 2.04e+01 c.23.8.1 107576 4mbp 370 2.04e+01 4mbp c.94.1.1 35777 2ao0A 324 2.06e+01 1yzhA 214 2.07e+01 1mxiA 160 2.08e+01 c.116.1.1 79646 3tss 194 2.08e+01 1aw7A b.40.2.2,d.15.6.1 25160,37749 1k20A 310 2.08e+01 c.107.1.1 68027 2f1kA 279 2.09e+01 2f7fA 494 2.09e+01 1d1gA 168 2.11e+01 1d1gA c.71.1.1 34889 1wuaA 375 2.11e+01 1jj2T 66 2.14e+01 1ffkR g.39.1.6 63105 1s72U 66 2.14e+01 g.39.1.6 105340 2c1gA 431 2.15e+01 1wojA 214 2.19e+01 1d4xA 375 2.21e+01 1yagA c.55.1.1,c.55.1.1 59107,59108 1sgpI 51 2.25e+01 2ovo g.68.1.1 44678 2a7oA 112 2.27e+01 2c31A 568 2.27e+01 1v25A 541 2.28e+01 e.23.1.1 108275 1r0rI 51 2.29e+01 g.68.1.1 96736 1yj1A 76 2.29e+01 1xt9A 212 2.30e+01 1qo2A 241 2.33e+01 1qo2A c.1.2.1 28533 1dxrC 336 2.34e+01 6prcC a.138.1.2 19670 1aqm 453 2.34e+01 1smd b.71.1.1,c.1.8.1 27717,28704 1lt5D 103 2.35e+01 3chbD b.40.2.1 24875 2bkrB 77 2.36e+01 1oivA 191 2.38e+01 c.37.1.8 93076 1jmuB 666 2.39e+01 1ny1A 240 2.41e+01 c.6.2.3 86395 1nbfD 76 2.44e+01 d.15.1.1 80390 1wyuA 438 2.44e+01 1g94A 448 2.44e+01 b.71.1.1,c.1.8.1 65169,65170 1u5mA 73 2.45e+01 1htqA 477 2.46e+01 d.15.9.1,d.128.1.1 71035,71036 1yseA 141 2.52e+01 1dj7A 117 2.53e+01 1dj7A g.36.1.1 44997 1wj9A 211 2.53e+01 1iyxA 432 2.55e+01 c.1.11.1,d.54.1.1 83815,83816 1ji8A 111 2.55e+01 d.203.1.1 66733 1gnkA 112 2.56e+01 2pii d.58.5.1 39073 1wd7A 261 2.56e+01 2ctoA 93 2.59e+01 1wcwA 261 2.60e+01 1oixA 191 2.65e+01 1hq3D 103 2.66e+01 1aoiB a.22.1.1 16464 2an3A 289 2.66e+01 1qz5A 375 2.70e+01 c.55.1.1,c.55.1.1 96614,96615 2pfkA 320 2.71e+01 3pfk c.89.1.1 35577 1f20A 435 2.74e+01 b.43.4.1,c.25.1.4 64932,64933 1bkpA 278 2.77e+01 1bkpA d.117.1.1 41029 2f5gA 133 2.78e+01 1xreA 217 2.78e+01 1wod 233 2.79e+01 1wod c.94.1.1 35832 1mup 166 2.79e+01 1mup b.60.1.1 27133 1swvA 267 2.79e+01 1o1xA 155 2.80e+01 c.121.1.1 86553 1li4A 432 2.84e+01 c.2.1.4,c.23.12.3 84616,84617 1qczA 169 2.84e+01 1qczA c.23.8.1 31276 2b3yA 888 2.85e+01 1amf 233 2.87e+01 1wod c.94.1.1 35833 1z02A 446 2.88e+01 1opjA 293 2.89e+01 d.144.1.7 87230 2bswA 146 2.90e+01 1m6kA 251 2.91e+01 e.3.1.1 78695 1e25A 282 2.93e+01 1e25A e.3.1.1 42731 1dzkA 157 2.93e+01 1obpA b.60.1.1 27096 1zljA 78 2.93e+01 1xwfA 431 2.95e+01 1nv8A 284 2.96e+01 c.66.1.30 86224 1dq3A 454 2.97e+01 1dq3A b.86.1.2,d.50.3.1,d.95.2.2,d.95.2.2 28380,38798,40585,40586 1yt8A 539 2.98e+01 1rypL 212 2.98e+01 d.153.1.4 41880 2g7jA 124 2.99e+01 1i1qB 192 3.00e+01 1qdlB c.23.16.1 61544 1vloA 381 3.00e+01 b.44.2.1,d.250.1.1 108838,108839 1jnyA 435 3.02e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1fviA 297 3.03e+01 1fviA b.40.4.6,d.142.2.1 25364,41578 1qd9A 124 3.03e+01 1qu9A d.79.1.1 39758 1d3bA 75 3.03e+01 1d3bA b.38.1.1 24798 2bolA 314 3.04e+01 1dd9A 338 3.06e+01 1dd9A e.13.1.1 43254 2glfA 450 3.08e+01 1vk8A 106 3.09e+01 d.58.48.1 108636 1j0pA 108 3.09e+01 a.138.1.1 90743 1zhvA 134 3.12e+01 1vf8A 377 3.17e+01 2ewcA 126 3.18e+01 2a9sA 171 3.20e+01 1bn7A 294 3.20e+01 1bn6A c.69.1.8 34677 1y60A 169 3.20e+01 1x74A 360 3.20e+01 1hr6B 443 3.23e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1xv5A 401 3.24e+01 2culA 232 3.27e+01 1jykA 254 3.30e+01 c.68.1.13 67458 1w85I 49 3.33e+01 1v6tA 255 3.35e+01 1otkA 249 3.36e+01 a.25.1.2 93521 1nddA 76 3.36e+01 1ubi d.15.1.1 37599 1xb4A 202 3.36e+01 2a9kA 187 3.38e+01 1xwyA 264 3.38e+01 1dl5A 317 3.38e+01 1dl5A c.66.1.7,d.197.1.1 64720,64721 3chbD 104 3.39e+01 3chbD b.40.2.1 24970 3chy 128 3.40e+01 3chy c.23.1.1 31038 2c1iA 431 3.44e+01 1njqA 39 3.44e+01 g.37.1.3 85822 1zhsA 113 3.51e+01 1othA 321 3.51e+01 1othA c.78.1.1,c.78.1.1 35260,35261 2frnA 278 3.52e+01 1i3dA 146 3.53e+01 a.1.1.2 61587 1m32A 366 3.53e+01 c.67.1.3 78508 1a05A 358 3.55e+01 1cnzA c.77.1.1 35059 1zmaA 118 3.55e+01 1y1xA 191 3.56e+01 1sr4B 261 3.57e+01 d.151.1.1 105949 1fuiA 591 3.61e+01 1fuiA b.43.2.1,c.85.1.1 25674,35444 1dgaA 375 3.63e+01 1yagA 1tzyD 103 3.63e+01 a.22.1.1 107533 1ihnA 113 3.67e+01 1ihnA c.103.1.1 62388 1wa3A 205 3.71e+01 1rf6A 427 3.75e+01 d.68.2.2 97366 1wh0A 134 3.76e+01 1t7sA 137 3.79e+01 a.7.7.1 106636 1tkeA 224 3.82e+01 1i8aA 189 3.86e+01 1i82A b.1.9.2 61951 1ksiA 642 3.93e+01 1ksiB b.30.2.1,d.17.2.1,d.17.2.1 24408,38043,38044 2ci9A 102 3.96e+01 1edn 21 3.98e+01 j.28.1.1 46197 1m36A 33 3.99e+01 g.37.1.2 91172 2gshA 414 4.01e+01 1p8kZ 254 4.03e+01 d.95.2.1,d.95.2.1 94361,94362 1oaoC 729 4.05e+01 e.26.1.3 86746 1k38A 254 4.07e+01 e.3.1.1 84303 1y9wA 140 4.08e+01 2agaA 190 4.08e+01 1bi6H 41 4.12e+01 1bi6H g.3.12.1 44340 1dumA 23 4.13e+01 j.4.1.1 59136 1fkqA 124 4.15e+01 3lzt d.2.1.2 36601 2btfA 375 4.16e+01 1yagA c.55.1.1,c.55.1.1 33429,33430 1hnnA 282 4.16e+01 c.66.1.15 65895 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