# List of top-scoring protein chains for t2k-100-30-str2-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 2gvkA 317 7.51e-38 1fj2A 232 1.62e+00 1auoA c.69.1.14 34720 2bl9A 238 1.67e+00 2blcA 238 2.23e+00 1iq4A 179 2.55e+00 1iq4A d.77.1.1 62641 1omzA 293 2.64e+00 c.68.1.15 87093 1ri7A 171 2.70e+00 a.4.5.32,d.58.4.2 97504,97505 1k1gA 131 3.06e+00 d.51.1.1 68015 1r8gA 372 3.14e+00 d.128.1.3 104845 2chnA 716 3.28e+00 1ni4B 341 3.38e+00 c.36.1.7,c.48.1.2 85729,85730 1zkcA 197 3.82e+00 2a6aA 218 3.84e+00 1vimA 200 3.91e+00 c.80.1.3 100758 1nriA 306 4.16e+00 c.80.1.3 86123 1asx 159 4.58e+00 1a6dA c.8.5.2 30821 1e08A 371 4.64e+00 i.4.1.1 45914 1e2kA 331 4.85e+00 1qhiA c.37.1.1 31854 2bklA 695 4.85e+00 1nh9A 87 4.87e+00 d.68.6.1 91878 3vtk 343 5.04e+00 1qhiA c.37.1.1 31884 2cb2A 318 5.45e+00 1jq3A 296 5.61e+00 c.66.1.17 67079 1f06A 320 6.42e+00 1dapA c.2.1.3,d.81.1.3 59556,59557 2bgiA 272 6.58e+00 1umdB 324 6.84e+00 c.36.1.7,c.48.1.2 99600,99601 1j27A 102 6.86e+00 d.58.50.1 90778 3dapA 320 6.91e+00 1dapA c.2.1.3,d.81.1.3 30051,39966 1fmaE 150 7.67e+00 1fmaE d.41.5.1 38630 1j5uA 136 7.77e+00 d.208.1.1 71584 1v4sA 455 7.83e+00 c.55.1.3,c.55.1.3 100309,100310 1fm0E 150 7.94e+00 1fmaE d.41.5.1 38629 1dtwB 342 7.95e+00 1qs0B c.36.1.7,c.48.1.2 31828,33102 1qwrA 319 8.04e+00 b.82.1.3 96491 1inlA 296 8.05e+00 c.66.1.17 66220 2bfdB 345 8.27e+00 2bkyX 89 8.28e+00 1l3kA 196 8.81e+00 d.58.7.1,d.58.7.1 73539,73540 1udvA 89 9.00e+00 d.68.6.1 99224 1dapA 320 9.13e+00 1dapA c.2.1.3,d.81.1.3 30053,39968 1yagG 125 9.18e+00 1d0nA d.109.1.1 40846 1rlmA 271 9.19e+00 1nm1G 125 9.22e+00 d.109.1.1 80653 1b4bA 71 9.33e+00 1b4aA d.74.2.1 39718 1t0tV 248 9.37e+00 d.58.4.10 106229 1x7yB 342 9.42e+00 1d4xG 126 9.57e+00 1d0nA d.109.1.1 59109 1rlmB 271 9.75e+00 1xkpC 143 1.00e+01 1e1oA 504 1.00e+01 1lylA b.40.4.1,d.104.1.1 25258,40714 1ipaA 274 1.02e+01 c.116.1.1,d.79.3.3 71254,71255 1psdA 409 1.03e+01 1psdA c.2.1.4,c.23.12.1,d.58.18.1 30097,31357,39354 1o97D 320 1.04e+01 c.26.2.3,c.31.1.2 81233,81234 2b20A 403 1.04e+01 1nw3A 416 1.04e+01 c.66.1.31 86288 2bx6A 350 1.06e+01 1qhiA 366 1.09e+01 1qhiA c.37.1.1 31860 1i1qA 520 1.09e+01 1qdlA d.161.1.1 61543 1gkkA 297 1.09e+01 c.69.1.2 65248 1kimA 366 1.11e+01 1qhiA c.37.1.1 31864 2ki5A 366 1.12e+01 1qhiA c.37.1.1 31862 1v1rB 342 1.13e+01 c.36.1.7,c.48.1.2 108273,108274 1gklA 297 1.15e+01 c.69.1.2 65250 2gnpA 266 1.19e+01 1kinA 366 1.19e+01 1o12A 376 1.23e+01 b.92.1.5,c.1.9.10 80758,80759 1wb4A 297 1.23e+01 2exrA 524 1.25e+01 1aurA 218 1.25e+01 1auoA c.69.1.14 34718 1chmA 401 1.32e+01 1chmA c.55.2.1,d.127.1.1 33545,41142 1zvdA 380 1.33e+01 1p1lA 102 1.37e+01 d.58.5.2 87695 1cxvA 164 1.43e+01 1ck7A d.92.1.11 40404 1sc6A 404 1.45e+01 1yb2A 275 1.46e+01 1nfjA 89 1.48e+01 d.68.6.1 91866 1toaA 313 1.49e+01 1toaA c.92.2.2 35598 1r1mA 164 1.50e+01 d.79.7.1 96820 1c8bA 371 1.50e+01 1c8bA c.56.1.2 59082 1atiB 505 1.51e+01 1atiA c.51.1.1,d.104.1.1 33197,40746 1nbwA 607 1.51e+01 c.8.6.1,c.55.1.6,c.55.1.6 80393,80394,80395 1olsB 342 1.53e+01 c.36.1.7,c.48.1.2 93332,93333 1xygD 359 1.57e+01 1umsA 174 1.58e+01 1hfc d.92.1.11 40368 1nnhA 294 1.61e+01 d.104.1.1 92005 1m5sA 297 1.65e+01 d.58.33.1,d.58.33.1 74511,74512 1jeoA 180 1.66e+01 c.80.1.3 66611 1auoA 218 1.69e+01 1auoA c.69.1.14 34716 1zy9A 564 1.70e+01 1tz0A 114 1.71e+01 d.58.4.5 107463 1pch 88 1.72e+01 1ptf d.94.1.1 40564 1rloA 271 1.77e+01 1sg6A 393 1.77e+01 e.22.1.1 105522 1zejA 293 1.79e+01 1df7A 159 1.83e+01 3dfr c.71.1.1 34885 2ad9A 119 1.84e+01 1je5A 206 1.85e+01 1je5A b.40.4.7 62909 2apoA 357 1.91e+01 1hy7A 173 2.00e+01 d.92.1.11 65957 1xviA 275 2.04e+01 1ha1 184 2.07e+01 1ha1 d.58.7.1,d.58.7.1 39147,39148 1b96A 244 2.10e+01 1rvaA c.52.1.2 33268 2ap1A 327 2.12e+01 1dqsA 393 2.14e+01 1dqsA e.22.1.1 43347 1xo7A 166 2.15e+01 1xfjA 261 2.15e+01 d.194.1.2 109585 2dri 271 2.16e+01 2dri c.93.1.1 35637 1nbaA 264 2.17e+01 1nbaA c.33.1.3 31753 2aobA 99 2.17e+01 1b8yA 167 2.18e+01 1hfc d.92.1.11 40377 1b4aA 149 2.18e+01 1b4aA a.4.5.3,d.74.2.1 16088,39721 1xdzA 240 2.20e+01 1b65A 375 2.24e+01 1b65A d.154.1.1 42020 1q4rA 112 2.26e+01 d.58.4.4 95823 1amp 291 2.29e+01 1amp c.56.5.4 33837 1ys4A 354 2.30e+01 1b97A 244 2.30e+01 1rvaA c.52.1.2 33252 1asyA 490 2.31e+01 1b8aA b.40.4.1,d.104.1.1 25242,40763 1z9bA 135 2.32e+01 1b94A 244 2.34e+01 1rvaA c.52.1.2 33250 2bb6A 414 2.53e+01 2faoA 309 2.54e+01 1kb9B 352 2.55e+01 d.185.1.1,d.185.1.1 77313,77314 1ycdA 243 2.55e+01 1zcjA 463 2.57e+01 1ggvA 232 2.58e+01 1din c.69.1.9 34683 1l9kA 305 2.59e+01 c.66.1.25 84569 1ezvB 352 2.60e+01 1ezvB d.185.1.1,d.185.1.1 59543,59544 1l6wA 220 2.65e+01 c.1.10.1 73632 1din 236 2.68e+01 1din c.69.1.9 34682 1lylA 504 2.71e+01 1lylA b.40.4.1,d.104.1.1 25261,40717 1rvaA 244 2.72e+01 1rvaA c.52.1.2 33240 1odd 118 2.74e+01 1opc a.4.6.1 16232 2ewcA 126 2.76e+01 1gy8A 397 2.76e+01 c.2.1.2 83376 2aalA 131 2.79e+01 1qw9A 502 2.79e+01 b.71.1.2,c.1.8.3 96466,96467 1zdzA 302 2.80e+01 1lay 256 2.83e+01 1lay b.57.1.1 27014 1tzeE 98 2.84e+01 1griA d.93.1.1 40468 1bmbA 123 2.87e+01 1griA d.93.1.1 40466 1x7dA 350 2.93e+01 1womA 271 2.93e+01 1jmkC 230 2.93e+01 c.69.1.22 71747 1ylvA 342 2.97e+01 1b4kA c.1.10.3 29180 1e8cA 498 3.00e+01 c.98.1.1,c.59.1.1,c.72.2.1 59377,59378,59379 1mp9A 198 3.01e+01 d.129.1.1,d.129.1.1 91385,91386 1qf5A 431 3.05e+01 1adeA c.37.1.10 32212 1wu7A 434 3.10e+01 1wpoA 256 3.10e+01 1lay b.57.1.1 27012 1z08A 170 3.14e+01 1jg1A 235 3.15e+01 c.66.1.7 66661 1gw5M 435 3.15e+01 b.2.7.1,d.110.4.2 70631,70632 1jyrA 96 3.18e+01 d.93.1.1 71969 1kezA 300 3.19e+01 c.69.1.22 68546 1ou0A 207 3.21e+01 c.23.17.1 93536 1bhjA 292 3.23e+01 1xvaA c.66.1.5 34189 1byb 495 3.24e+01 1byb c.1.8.1 28790 1pydA 556 3.30e+01 1zpdA c.31.1.3,c.36.1.5,c.36.1.9 31735,31773,31774 1lokA 291 3.31e+01 c.56.5.4 78122 1hskA 326 3.31e+01 2mbr d.145.1.2,d.146.1.1 61241,61242 1ohlA 342 3.35e+01 c.1.10.3 87035 1f5sA 211 3.36e+01 1f5sA c.108.1.4 59656 1kjnA 157 3.36e+01 c.115.1.1 72614 2c2aA 258 3.39e+01 1kmvA 186 3.40e+01 c.71.1.1 72757 1opc 110 3.42e+01 1opc a.4.6.1 16231 8dfr 189 3.50e+01 1aoeA c.71.1.1 34895 1h0xA 100 3.51e+01 d.68.6.1 76451 1qk8A 146 3.52e+01 1ewxA c.47.1.10 33061 1l7mA 211 3.52e+01 c.108.1.4 73664 1aw5 326 3.56e+01 1b4kA c.1.10.3 29181 1i1gA 141 3.56e+01 a.4.5.32,d.58.4.2 65982,65983 1wpoB 256 3.60e+01 1lay b.57.1.1 27013 1eonA 245 3.60e+01 1rvaA c.52.1.2 33238 1u0tA 307 3.61e+01 e.52.1.1 107567 1j97A 211 3.62e+01 1f5sA c.108.1.4 62753 1j5xA 342 3.67e+01 c.80.1.1 71591 3mddA 385 3.74e+01 3mdeA a.29.3.1,e.6.1.1 16592,42853 1ovlA 271 3.76e+01 a.123.1.1 87455 1i1hA 219 3.79e+01 1f2vA c.23.17.1 61530 1vcdA 126 3.80e+01 1atiA 505 3.86e+01 1atiA c.51.1.1,d.104.1.1 33196,40745 2b2nA 344 3.92e+01 1tx4B 178 3.93e+01 1ctqA c.37.1.8 32045 1t4hA 290 3.99e+01 d.144.1.7 106420 1rtqA 299 4.03e+01 c.56.5.4 97819 1zfpE 98 4.04e+01 1griA d.93.1.1 40465 1eokA 290 4.09e+01 1eokA c.1.8.5 28991 1hr6B 443 4.12e+01 1be3A d.185.1.1,d.185.1.1 61166,61167 1pysB 785 4.20e+01 1pysB a.6.1.1,a.6.1.1,b.40.4.4,d.58.13.1,d.104.1.1,d.138.1.1 16299,16300,25311,39310,40779,41455 1s0yA 76 4.20e+01 d.80.1.1 98314 1kmqA 184 4.22e+01 c.37.1.8 84412 1jroB 777 4.24e+01 d.41.1.1,d.133.1.1 67141,67142 3sxlA 184 4.27e+01 1b7fA d.58.7.1,d.58.7.1 39173,39174 1tr0A 108 4.32e+01 d.58.4.4 107261 1e8nA 710 4.37e+01 1qfmA b.69.7.1,c.69.1.4 27675,34643 1l9gA 192 4.37e+01 c.18.1.2 84568 1m3sA 186 4.38e+01 c.80.1.3 78573 1wi1A 126 4.39e+01 2bbeA 108 4.43e+01 2kinB 100 4.46e+01 3kinB 1kskA 234 4.47e+01 d.66.1.5,d.265.1.3 72920,90389 1phk 298 4.49e+01 1cdkA d.144.1.7 41635 1yj7A 171 4.51e+01 1qfmA 710 4.52e+01 1qfmA b.69.7.1,c.69.1.4 27673,34641 1mo1A 87 4.52e+01 d.94.1.1 91363 1kmnD 424 4.53e+01 1adjA c.51.1.1,d.104.1.1 33185,40734 1h2wA 710 4.55e+01 b.69.7.1,c.69.1.4 76596,76597 1nekA 588 4.56e+01 a.7.3.1,c.3.1.4,d.168.1.1 80426,80427,80428 1f2vA 219 4.57e+01 1f2vA c.23.17.1 59627 1oboA 169 4.61e+01 c.23.5.1 86776 1rw7A 243 4.62e+01 c.23.16.2 97963 1quqB 121 4.63e+01 1quqB b.40.4.3 25305 1h2xA 710 4.67e+01 b.69.7.1,c.69.1.4 76598,76599 1zi8A 236 4.67e+01 3bamB 213 4.67e+01 1bam c.52.1.3 33289 1f45B 197 4.70e+01 1f45B a.26.1.1 59642 1fxlA 167 4.72e+01 1b7fA d.58.7.1,d.58.7.1 39183,39184 1egdA 396 4.72e+01 3mdeA a.29.3.1,e.6.1.1 16596,42857 1k3eA 156 4.75e+01 d.198.1.1 68103 1h7nA 342 4.76e+01 1b4kA c.1.10.3 60726 1vkfA 188 4.78e+01 c.1.29.1 108656 1tvlA 454 4.80e+01 c.1.16.4 107366 1n57A 291 4.80e+01 c.23.16.2 85328 3mdeA 385 4.83e+01 3mdeA a.29.3.1,e.6.1.1 16594,42855 1xvaA 292 4.88e+01 1xvaA c.66.1.5 34183 1sqiA 393 4.89e+01 d.32.1.3,d.32.1.3 105914,105915 1q8bA 105 4.91e+01 d.58.4.6 96201 2cg4A 152 5.00e+01 1ckv 141 5.00e+01 1ckv d.137.1.1 41452 2fb0A 94 5.05e+01 1x0pA 143 5.06e+01 1sb8A 352 5.07e+01 c.2.1.2 105410 1qvzA 237 5.11e+01 c.23.16.2 96453 1ualA 274 5.12e+01 c.116.1.4 88383 1souA 194 5.13e+01 c.124.1.6 105858 1ewxA 146 5.17e+01 1ewxA c.47.1.10 33062 1yirA 408 5.20e+01 1aoeA 192 5.24e+01 1aoeA c.71.1.1 34923 1vq3A 94 5.25e+01 1tfe 145 5.26e+01 1tfe d.43.1.1 38680 1pn0A 665 5.31e+01 c.3.1.2,c.47.1.10,d.16.1.2 94918,94919,94920 2as0A 396 5.35e+01 1k8wA 327 5.37e+01 b.122.1.1,d.265.1.2 83094,90388 1hkcA 917 5.42e+01 1qhaA c.55.1.3,c.55.1.3,c.55.1.3,c.55.1.3 33475,33476,33477,33478 1rm6B 324 5.42e+01 1o54A 277 5.43e+01 c.66.1.13 92482 1nt4A 391 5.52e+01 c.60.1.2 92102 1vp6A 138 5.57e+01 1ttwA 138 5.59e+01 d.198.1.1 107308 1adeA 431 5.59e+01 1adeA c.37.1.10 32213 1dyr 206 5.75e+01 1aoeA c.71.1.1 34916 1ftrA 296 5.80e+01 1ftrA d.58.33.1,d.58.33.1 39485,39486 1cliA 345 5.81e+01 1cliA d.79.4.1,d.139.1.1 39816,41459 1pg5A 299 5.81e+01 c.78.1.1,c.78.1.1 104146,104147 2hppP 79 5.84e+01 5hpgA g.14.1.1 44654 1c4kA 730 5.85e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31273,34502,41123 1vr7A 142 5.86e+01 1aipC 196 5.86e+01 1tfe a.5.2.2,d.43.1.1 58930,58931 1r0kA 388 5.87e+01 a.69.3.1,c.2.1.3,d.81.1.3 104723,104724,104725 1d2gA 292 5.94e+01 1xvaA c.66.1.5 34187 2f1rA 171 6.01e+01 2ez3A 302 6.02e+01 1uufA 369 6.06e+01 b.35.1.2,c.2.1.1 100006,100007 1lyxA 248 6.06e+01 c.1.1.1 78304 1cfr 285 6.13e+01 1cfr c.52.1.7 33312 1nz0A 118 6.17e+01 d.14.1.2 86433 1vddA 228 6.20e+01 e.49.1.1 108519 3kinB 117 6.21e+01 3kinB 1griA 217 6.25e+01 1griA b.34.2.1,b.34.2.1,d.93.1.1 24531,24532,40473 1jkvA 266 6.27e+01 a.25.1.3 71719 1ykfA 352 6.29e+01 1pedA b.35.1.2,c.2.1.1 24757,29773 2gtqA 867 6.29e+01 1reqA 727 6.32e+01 1reqA c.1.19.1,c.23.6.1 29620,31247 1yy7A 213 6.33e+01 1ohtA 215 6.34e+01 d.118.1.1 87036 1q6cA 495 6.39e+01 c.1.8.1 95970 1hp4A 512 6.43e+01 1hp4A c.1.8.6,d.92.2.1 61111,61112 1o9iA 266 6.45e+01 a.25.1.3 92671 1v64A 108 6.49e+01 a.21.1.1 108392 1o5xA 248 6.51e+01 c.1.1.1 92528 5reqA 727 6.52e+01 1reqA c.1.19.1,c.23.6.1 29632,31259 1thqA 170 6.58e+01 f.4.1.2 106920 1z3iX 644 6.61e+01 1qlmA 316 6.63e+01 1qlmA d.147.1.1 41765 1np6A 174 6.64e+01 c.37.1.10 85954 1esmA 316 6.68e+01 1esmA c.37.1.6 31953 1qayA 428 6.68e+01 1qaxA d.58.20.1,d.179.1.1 39378,42599 1fohA 664 6.69e+01 1fohA c.3.1.2,c.47.1.10,d.16.1.2 30381,33078,37900 2blnA 305 6.69e+01 1dqrA 557 6.70e+01 1dqrA c.80.1.2 35305 1k0fA 277 6.73e+01 c.92.2.2 71974 1sxgA 280 6.75e+01 1l5aA 436 6.79e+01 c.43.1.2,c.43.1.2 75923,75924 1u8sA 192 6.79e+01 d.58.18.5,d.58.18.5 107737,107738 1rcf 169 6.81e+01 1rcf c.23.5.1 31170 1jkeA 145 6.84e+01 c.110.1.1 66791 1b7fA 168 6.85e+01 1b7fA d.58.7.1,d.58.7.1 39169,39170 1pjqA 457 6.86e+01 c.2.1.11,c.90.1.1,e.37.1.1 94766,94767,94768 1wmaA 276 6.86e+01 1j3kA 280 6.87e+01 c.71.1.1 84070 1rk8A 165 6.89e+01 d.58.7.1 97603 1z06A 189 6.91e+01 1q53A 112 6.94e+01 d.58.4.4 95858 1k75A 434 6.94e+01 c.82.1.2 68253 1glv 303 6.94e+01 1gsa c.30.1.3,d.142.1.1 31721,41480 1qaxA 428 6.95e+01 1qaxA d.58.20.1,d.179.1.1 39376,42597 1ordA 730 7.00e+01 1ordA c.23.1.4,c.67.1.5,d.125.1.1 31274,34503,41124 1tygB 87 7.02e+01 d.15.3.2 107455 1jw3A 140 7.03e+01 d.208.1.1 67373 1ow1A 195 7.07e+01 b.131.1.3 93625 1pnj 86 7.10e+01 1ckaA b.34.2.1 24487 1hu4A 288 7.10e+01 1hu4A 1n5dA 288 7.10e+01 c.2.1.2 80030 2ftrA 108 7.14e+01 1uxy 340 7.21e+01 2mbr d.145.1.2,d.146.1.1 41748,41761 1yemA 179 7.42e+01 1ton 235 7.53e+01 5ptp b.47.1.2 26307 1kaeA 434 7.55e+01 c.82.1.2 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