# 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 1xv2A 237 3.80e-05 2al3A 90 1.13e-01 1wm3A 72 2.90e-01 1c1yB 77 3.05e-01 1c1yB d.15.1.5 37618 1kv0A 66 5.21e-01 g.3.7.1 91040 1wrvA 308 5.58e-01 2ffyA 358 1.04e+00 2gnxA 365 1.12e+00 1ys7A 233 1.14e+00 1p5fA 189 1.55e+00 c.23.16.2 94142 1z9lA 128 1.56e+00 2bh8A 101 2.04e+00 1dmhA 311 2.22e+00 1dmhA b.3.6.1 22633 2cvjA 180 2.42e+00 1z4rA 168 2.47e+00 1iyeA 309 2.77e+00 e.17.1.1 83786 1euvB 86 3.40e+00 1a5r d.15.1.1 37598 1kgsA 225 3.62e+00 a.4.6.1,c.23.1.1 68596,68597 1xsoA 150 4.17e+00 1mfmA b.1.8.1 22273 1omyA 65 4.23e+00 g.3.7.1 93354 1ydyA 356 4.50e+00 1ig8A 486 4.55e+00 2yhx c.55.1.3,c.55.1.3 64746,64747 1upiA 225 4.88e+00 b.82.1.1 99757 1zjjA 263 4.93e+00 2f1rA 171 4.96e+00 1oa2A 218 5.05e+00 b.29.1.11 86721 1vmjA 151 5.19e+00 2axwA 134 5.53e+00 1fukA 165 5.66e+00 1fukA c.37.1.19 32409 1idk 359 6.34e+00 1qcxA b.80.1.2 28025 1vr6A 350 6.92e+00 1sn4A 64 7.06e+00 1aho g.3.7.1 44136 2f91A 237 7.24e+00 1t3qA 168 7.25e+00 a.56.1.1,d.15.4.2 106367,106368 1vphA 149 7.53e+00 1vmfA 145 7.78e+00 1pm4A 119 7.93e+00 b.135.1.1 94891 1gskA 513 8.24e+00 b.6.1.3,b.6.1.3,b.6.1.3 83314,83315,83316 2yhx 457 8.48e+00 2yhx i.12.1.1 46024 2c6cA 707 8.52e+00 1pvmA 184 8.85e+00 d.37.1.1,d.37.1.1,g.41.13.1 95171,95172,95173 2eifA 136 8.90e+00 1bkb b.34.5.2,b.40.4.5 24607,25339 1vjoA 393 9.22e+00 c.67.1.3 100827 1dceA 567 9.25e+00 1dceA a.118.6.1,b.7.4.1,c.10.2.2 19191,23218,30867 1vpbA 451 9.33e+00 2cpgA 45 9.53e+00 2cpgA a.43.1.3 17455 1rkuA 206 9.77e+00 c.108.1.11 97627 1nbcA 155 1.00e+01 1nbcA b.2.2.2 22390 2f96A 224 1.03e+01 1ysrA 150 1.03e+01 1rkd 309 1.04e+01 1rkd c.72.1.1 34928 1c3mA 147 1.11e+01 1jotA b.77.3.1 27983 1ezwA 349 1.18e+01 1ezwA c.1.16.3 29558 1qkkA 155 1.25e+01 1dbwA c.23.1.1 31104 1wn2A 121 1.26e+01 1bkb 136 1.28e+01 1bkb b.34.5.2,b.40.4.5 24609,25341 2fp7B 172 1.28e+01 1w41A 101 1.30e+01 1aym3 238 1.31e+01 1aym3 1xxlA 239 1.32e+01 1siqA 392 1.33e+01 a.29.3.1,e.6.1.1 105585,105586 1vizA 240 1.33e+01 c.1.4.1 100784 1g0oA 283 1.36e+01 1ybvA c.2.1.2 60181 1wcdJ 441 1.39e+01 1y8qA 346 1.40e+01 1nzaA 103 1.42e+01 d.58.5.2 86444 1ec7A 446 1.44e+01 1bqg c.1.11.2,d.54.1.1 29218,38862 1ds1A 324 1.52e+01 1drtA b.82.2.2 28127 1usgA 346 1.56e+01 c.93.1.1 99864 1ny4A 82 1.57e+01 b.40.4.5 92316 1zo2A 129 1.58e+01 1jmcA 246 1.58e+01 1jmcA b.40.4.3,b.40.4.3 25300,25301 1x89A 178 1.59e+01 1gheA 177 1.60e+01 d.108.1.1 76222 1pt6A 213 1.61e+01 c.62.1.1 95091 1rgyA 360 1.61e+01 e.3.1.1 97456 1ylxA 103 1.63e+01 1wfyA 104 1.68e+01 1u8sA 192 1.70e+01 d.58.18.5,d.58.18.5 107737,107738 1zud1 251 1.76e+01 1vcoA 550 1.77e+01 c.23.16.1,c.37.1.10 108508,108509 1sdsA 117 1.78e+01 d.79.3.1 105439 1gox 370 1.78e+01 1gox c.1.4.1 28607 1d4xG 126 1.80e+01 1d0nA d.109.1.1 59109 1vjkA 98 1.81e+01 d.15.3.1 108631 1m1hA 248 1.83e+01 b.114.1.1,d.58.42.1 78415,78416 1vl5A 260 1.86e+01 c.66.1.41 108720 1vp4A 425 1.86e+01 1rfs 139 1.88e+01 1rfs b.33.1.1 24434 1xbiA 120 1.93e+01 3daaA 277 1.94e+01 1daaA e.17.1.1 43272 2b99A 156 1.95e+01 1xeuA 263 1.97e+01 1ogwA 76 1.98e+01 d.15.1.1 87001 1gwmA 153 2.02e+01 b.18.1.19 83348 1vl4A 447 2.02e+01 d.283.1.1 108718 1xrtA 467 2.12e+01 1uv7A 110 2.12e+01 d.67.4.1 100040 1nrwA 288 2.17e+01 c.108.1.10 86128 1wl4A 397 2.18e+01 1q7sA 117 2.20e+01 c.131.1.1 96055 2bklA 695 2.25e+01 1h12A 405 2.27e+01 a.102.1.2 83447 1sffA 426 2.33e+01 c.67.1.4 105482 2be1A 339 2.35e+01 1cs1A 386 2.37e+01 1ibjA c.67.1.3 34399 2ca6A 386 2.37e+01 1y9wA 140 2.37e+01 1w2wB 191 2.43e+01 2c78A 405 2.56e+01 2b0vA 153 2.58e+01 1ji1A 637 2.64e+01 b.1.18.2,b.71.1.1,c.1.8.1 71666,71667,71668 1pg4A 652 2.65e+01 e.23.1.1 88067 2aukA 190 2.67e+01 1din 236 2.69e+01 1din c.69.1.9 34682 1umgA 362 2.69e+01 d.280.1.1 107956 1n7kA 234 2.69e+01 c.1.10.1 85374 2gfaA 119 2.83e+01 1y2qA 143 2.84e+01 1epxA 370 2.84e+01 1fbaA c.1.10.1 29150 1t3tA 1303 2.89e+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 1vloA 381 2.91e+01 b.44.2.1,d.250.1.1 108838,108839 1uh4A 637 2.92e+01 b.1.18.2,b.71.1.1,c.1.8.1 99391,99392,99393 1zkjA 359 3.05e+01 1vjqA 79 3.07e+01 k.43.1.1 100830 1bolA 222 3.10e+01 1bolA d.124.1.1 41120 1wruA 379 3.10e+01 1xubA 298 3.11e+01 1q33A 292 3.13e+01 d.113.1.1 95657 1rdg 53 3.14e+01 1rb9 g.41.5.1 45221 3pcgA 200 3.14e+01 3pchA b.3.6.1 22647 1naqA 112 3.21e+01 d.58.5.2 91761 1p90A 145 3.22e+01 c.55.5.2 94377 2d42A 249 3.24e+01 1k2eA 156 3.24e+01 d.113.1.1 72010 1zx2A 147 3.30e+01 1fjgE 162 3.30e+01 1pkp d.14.1.1,d.50.1.2 37553,38789 1w5rA 278 3.32e+01 1iz6A 138 3.33e+01 b.34.5.2,b.40.4.5 76976,76977 1ej0A 180 3.47e+01 1ej0A c.66.1.2 34179 1vljA 407 3.51e+01 e.22.1.2 108832 1zgzA 122 3.54e+01 1ktgA 138 3.55e+01 d.113.1.1 72972 1rdfA 267 3.57e+01 c.108.1.3 104884 2ex5A 207 3.58e+01 1i8fA 81 3.62e+01 1i8fA b.38.1.1 61959 1ohvA 472 3.68e+01 c.67.1.4 93031 1gwyA 175 3.70e+01 b.97.1.1 83356 1gx3A 284 3.74e+01 d.3.1.5 70678 1gvfA 286 3.83e+01 c.1.10.2 70599 1s3sG 127 3.85e+01 d.15.1.2 98457 1gutA 68 3.87e+01 b.40.6.1 65576 1uqrA 154 3.93e+01 c.23.13.1 99779 1ryiA 382 3.95e+01 1i60A 278 3.96e+01 c.1.15.4 71118 1pytA 94 3.96e+01 1pytA d.58.3.1 39064 1xebA 150 3.96e+01 1vr3A 191 3.98e+01 1zd3A 555 3.99e+01 1qzzA 374 4.00e+01 a.4.5.29,c.66.1.12 96719,96720 1rlmA 271 4.01e+01 1ydmA 187 4.04e+01 1r75A 141 4.04e+01 b.134.1.1 97189 1z15A 344 4.06e+01 1j31A 262 4.07e+01 d.160.1.2 90808 1moq 368 4.09e+01 1moq c.80.1.1 35302 1qhqA 140 4.10e+01 1qhqA b.6.1.1 63326 2f6uA 234 4.10e+01 1nn6A 228 4.18e+01 b.47.1.2 85893 1f89A 291 4.19e+01 d.160.1.1 64988 1egwA 77 4.20e+01 1mnmA d.88.1.1 40234 1s1qA 145 4.20e+01 d.20.1.2 98351 1k3iA 656 4.22e+01 b.1.18.2,b.18.1.1,b.69.1.1 68113,68114,68115 1edqA 540 4.25e+01 1ctn b.1.18.2,c.1.8.5,d.26.3.1 21873,29002,38436 2azpA 318 4.28e+01 2basA 431 4.29e+01 2fp8A 322 4.32e+01 1yllA 200 4.36e+01 2bb6A 414 4.39e+01 1wzaA 488 4.40e+01 1pmmA 466 4.47e+01 c.67.1.6 94901 1wmqA 147 4.58e+01 1d0cA 444 4.62e+01 d.174.1.1 64769 1wpuA 147 4.67e+01 1j05A 111 4.68e+01 b.1.1.1 90735 1w8sA 263 4.68e+01 1rdqE 350 4.70e+01 d.144.1.7 97314 1hl9A 449 4.71e+01 b.71.1.3,c.1.8.11 90650,90651 2a2cA 478 4.71e+01 1bupA 386 4.72e+01 1ba1 c.55.1.1,c.55.1.1 33377,33378 2cxhA 217 4.73e+01 1l5pA 93 4.79e+01 d.15.4.1 73598 2g3aA 152 4.84e+01 1gt1A 159 4.87e+01 b.60.1.1 90515 1z6mA 175 4.87e+01 1rz3A 201 4.90e+01 c.37.1.6 98132 1d3bA 75 4.93e+01 1d3bA b.38.1.1 24798 2fvvA 194 4.95e+01 1dosA 358 4.98e+01 1dosA c.1.10.2 29175 1zpwX 90 5.02e+01 1u9aA 160 5.04e+01 1u9aA d.20.1.1 38333 1yx1A 264 5.04e+01 1nv8A 284 5.14e+01 c.66.1.30 86224 3prn 289 5.15e+01 3prn f.4.3.1 43761 1m4iA 181 5.20e+01 d.108.1.1 74457 2al6A 375 5.28e+01 1jbwA 428 5.29e+01 c.59.1.2,c.72.2.2 62860,62861 1tmxA 293 5.36e+01 1gxjA 186 5.39e+01 d.215.1.1 70707 1ve6A 582 5.41e+01 1o7iA 119 5.45e+01 b.40.4.3 86642 1h75A 81 5.45e+01 1h75A c.47.1.1 60716 1gbg 214 5.50e+01 1axkA b.29.1.2 24171 1zdnA 158 5.51e+01 1ei9A 279 5.51e+01 1ei9A c.69.1.13 34713 1ecmA 109 5.58e+01 1ecmA a.130.1.1 19492 1msc 129 5.66e+01 1msc d.85.1.1 40039 1uwmA 106 5.73e+01 2b8eA 273 5.78e+01 1jnyA 435 5.80e+01 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 1pcfA 66 5.80e+01 1pcfA d.18.1.1 38142 1e25A 282 5.90e+01 1e25A e.3.1.1 42731 1lk2A 274 5.90e+01 b.1.1.2,d.19.1.1 91056,91057 1wy2A 351 5.90e+01 1tuwA 109 5.98e+01 d.58.4.8 107346 1nszA 347 6.03e+01 b.30.5.4 80724 1pz7A 204 6.07e+01 b.29.1.4 95405 1gpmA 525 6.11e+01 1gpmA c.23.16.1,c.26.2.1,d.52.2.1 31405,31608,38826 1yh3A 256 6.11e+01 1xngA 268 6.14e+01 1ygtA 111 6.19e+01 1uwzA 136 6.22e+01 c.97.1.1 108081 1ub0A 258 6.24e+01 c.72.1.2 88394 1w66A 232 6.25e+01 1qzgA 187 6.30e+01 b.40.4.3 96643 1uzxA 169 6.31e+01 d.20.1.2 100238 1khdA 345 6.32e+01 a.46.2.1,c.27.1.1 77400,77401 1jmvA 141 6.36e+01 c.26.2.4 66897 1hqsA 423 6.42e+01 1iso c.77.1.1 61154 2ghsA 326 6.43e+01 1k66A 149 6.47e+01 c.23.1.1 90941 1uk8A 282 6.48e+01 c.69.1.10 107907 2a3nA 355 6.52e+01 1j3wA 163 6.53e+01 d.110.7.1 90833 1dciA 275 6.53e+01 1dciA c.14.1.3 30918 1v4sA 455 6.54e+01 c.55.1.3,c.55.1.3 100309,100310 1jg1A 235 6.54e+01 c.66.1.7 66661 1st9A 143 6.54e+01 c.47.1.10 98987 1m4tA 392 6.56e+01 c.95.1.1,c.95.1.1 78617,78618 1mvoA 136 6.59e+01 c.23.1.1 79513 1o5zA 442 6.65e+01 c.59.1.2,c.72.2.2 92530,92531 1l6rA 227 6.66e+01 c.108.1.10 77768 1p4kA 295 6.68e+01 d.153.1.5 87772 1ydwA 362 6.74e+01 1m3kA 392 6.75e+01 c.95.1.1,c.95.1.1 78565,78566 1ekqA 272 6.76e+01 1c3qA c.72.1.2 34941 1wn5A 130 6.79e+01 1f1gA 154 6.81e+01 b.1.8.1 76153 1nb8A 353 6.87e+01 d.3.1.9 80385 1gy6A 127 6.88e+01 d.17.4.2 70736 1zdrA 164 7.02e+01 1p1lA 102 7.04e+01 d.58.5.2 87695 1vcdA 126 7.11e+01 1utyA 187 7.11e+01 b.147.1.1 108036 1bu8A 452 7.12e+01 1gpl b.12.1.2,c.69.1.19 23647,34795 2f06A 144 7.14e+01 1o4wA 147 7.16e+01 c.120.1.1 86629 1wlsA 328 7.17e+01 2f9sA 151 7.21e+01 1gefA 123 7.27e+01 1gefA c.52.1.18 60465 1djtA 64 7.28e+01 1aho g.3.7.1 44132 1mzbA 136 7.29e+01 a.4.5.42 91497 1qstA 160 7.30e+01 1yghA d.108.1.1 40804 1vf8A 377 7.36e+01 2fsqA 243 7.38e+01 1e1oA 504 7.40e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1bazA 53 7.46e+01 1bazA a.43.1.1 17421 2ftbA 125 7.50e+01 1zfjA 491 7.63e+01 1ak5 c.1.5.1,d.37.1.1,d.37.1.1 28638,38540,38541 1z4vA 532 7.63e+01 3pmgA 561 7.65e+01 3pmgA c.84.1.1,c.84.1.1,c.84.1.1,d.129.2.1 35408,35409,35410,41301 1kzfA 230 7.70e+01 d.108.1.3 73354 2cxxA 190 7.70e+01 2aq5A 402 7.71e+01 2fqxA 318 7.74e+01 1zghA 260 7.83e+01 1uasA 362 7.89e+01 b.71.1.1,c.1.8.1 88388,88389 1a7w 69 7.92e+01 1a7w a.22.1.2 16477 1wddS 128 7.95e+01 1vgyA 393 7.95e+01 c.56.5.4,d.58.19.1 100620,100621 1o98A 511 7.95e+01 c.105.1.1,c.76.1.3 86684,86685 2bgcA 238 7.96e+01 1oewA 329 7.97e+01 b.50.1.2 86924 2fikA 287 8.01e+01 1x93A 55 8.04e+01 1i2uA 44 8.06e+01 g.3.7.4 65987 1wzuA 300 8.08e+01 1i12A 160 8.08e+01 1i21A d.108.1.1 61515 2gdnA 267 8.10e+01 1bif 469 8.12e+01 1bif c.37.1.7,c.60.1.4 31961,34003 1h7zA 194 8.12e+01 1qhvA b.21.1.1 60733 2dexX 671 8.20e+01 1pi1A 185 8.26e+01 a.29.7.1 94699 1oqqA 106 8.27e+01 d.15.4.1 93422 1c44A 123 8.28e+01 1qndA d.106.1.1 40795 1yvoA 172 8.32e+01 1m4lA 307 8.34e+01 c.56.5.1 78604 1gs5A 258 8.37e+01 c.73.1.2 70395 2cvhA 220 8.51e+01 1pv0A 46 8.52e+01 a.2.12.1 95141 1lbu 213 8.55e+01 1lbu a.20.1.1,d.65.1.1 16416,39549 1vjzA 341 8.55e+01 c.1.8.3 100838 1dozA 309 8.57e+01 1ak1 c.92.1.1 35592 1xg5A 279 8.61e+01 1nddA 76 8.82e+01 1ubi d.15.1.1 37599 1p77A 272 8.87e+01 c.2.1.7,c.58.1.5 94214,94215 1xjcA 169 8.93e+01 1a12A 413 8.93e+01 1a12A b.69.5.1 27663 1u0kA 288 8.98e+01 d.21.1.2,d.21.1.2 107547,107548