# List of top-scoring protein chains for t2k-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.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 3cghA 516 4.39e-50 a.118.8.6 156618 3gzsA 515 1.30e-48 3ejnA 474 1.46e-45 a.118.8.6 158180 3ehmA 532 2.16e-42 3fdhA 499 2.42e-37 3i4gA 528 1.36e-32 3kezA 461 4.34e-32 3jq0A 493 6.77e-32 3jq1A 481 1.31e-31 3ihvA 535 2.75e-30 3iv0A 481 2.78e-29 3l22A 441 1.06e-27 3lewA 495 4.80e-27 3ckcA 527 1.09e-25 a.118.8.6 156736 3hdxA 478 1.97e-25 3jysA 499 3.68e-24 2wqhA 125 6.15e-03 1na3A 91 4.74e-02 k.38.1.1 85481 2avpA 70 1.32e+00 k.38.1.1 127382 3dmsA 427 1.43e+00 1jnyA 435 1.60e+00 b.43.3.1,b.44.1.1,c.37.1.8 66982,66983,66984 2fuvA 549 1.78e+00 3hurA 395 1.83e+00 3dmeA 369 1.86e+00 2dg5A 366 2.23e+00 d.153.1.6 131500 2e0cA 409 2.28e+00 2i3oA 516 2.48e+00 d.153.1.6 137027 1duvG 333 2.87e+00 1othA c.78.1.1,c.78.1.1 35228,35229 1jpnA 296 2.95e+00 a.24.13.1,c.37.1.10 67039,67040 2zwsA 646 3.04e+00 3m6wA 464 3.16e+00 2rbdA 171 3.45e+00 3edtB 283 3.67e+00 1izoA 417 3.98e+00 a.104.1.1 83851 2r3aA 300 4.00e+00 2cfuA 658 4.24e+00 d.106.1.3,d.157.1.13 146386,146387 1ls1A 295 4.35e+00 a.24.13.1,c.37.1.10 78170,78171 2zxcA 646 4.45e+00 1dbfA 127 4.57e+00 2chsA d.79.1.2 39761 1ng1 294 4.74e+00 1ng1 1eu1A 780 5.49e+00 1dmr b.52.2.2,c.81.1.1 26903,35311 1e96B 203 5.67e+00 1e96B a.118.8.1 19211 1pb1A 416 6.38e+00 c.77.1.1 88014 3c3yA 237 7.10e+00 1wteA 272 7.63e+00 c.52.1.29 114876 1hh8A 213 7.67e+00 1e96B a.118.8.1 61042 1gcyA 527 7.81e+00 1jdc b.71.1.1,c.1.8.1 27788,28775 3kl4A 433 7.84e+00 1f4pA 147 7.95e+00 5nul c.23.5.1 59651 3hfxA 504 8.02e+00 1wyuB 474 8.08e+00 c.67.1.7 121453 2vh4A 381 8.09e+00 1wkuA 254 8.14e+00 1wovA 250 8.49e+00 a.132.1.1 121124 2f5uA 447 8.62e+00 1wm5A 208 8.75e+00 a.118.8.1 121028 2pefA 373 8.89e+00 2fymA 431 9.03e+00 c.1.11.1,d.54.1.1 134379,134380 1ru3A 732 9.37e+00 e.26.1.3 97835 1rj9A 304 9.70e+00 a.24.13.1,c.37.1.10 97553,97554 2bpqA 373 9.70e+00 1jdc 429 9.86e+00 1jdc 1jdcA 429 9.86e+00 b.71.1.1,c.1.8.1 27789,28776 2zygA 480 1.03e+01 1ncx 162 1.04e+01 1ncx 1k7hA 476 1.06e+01 c.76.1.1 72101 2f4qA 346 1.07e+01 3fyfA 176 1.07e+01 1j3nA 408 1.12e+01 c.95.1.1,c.95.1.1 84074,84075 3b46A 447 1.15e+01 1topA 162 1.17e+01 a.39.1.5 17223 1vrmA 325 1.18e+01 d.96.2.1 120472 1gtrA 553 1.18e+01 1gtrA b.53.1.2,c.26.1.1 26939,31578 1bu5A 147 1.22e+01 5nul c.23.5.1 31155 1lfwA 470 1.27e+01 c.56.5.4,d.58.19.1 77942,77943 2b5dX 528 1.28e+01 a.8.3.3,c.6.2.4 127886,127887 1zthA 258 1.35e+01 1vhmA 195 1.36e+01 d.110.2.1 100691 3gcb 470 1.41e+01 3gcb 3gcbA 470 1.41e+01 d.3.1.1 37032 2axtB 510 1.43e+01 f.55.1.1 144927 3bz1B 510 1.48e+01 1upkA 341 1.51e+01 a.118.1.15 99758 2dtxA 264 1.52e+01 1qtqA 553 1.58e+01 1gtrA b.53.1.2,c.26.1.1 26940,31579 1j9eA 147 1.60e+01 c.23.5.1 62756 1rztA 331 1.61e+01 a.60.6.1,a.60.12.1,d.218.1.2 98224,98225,98226 2rg4A 216 1.71e+01 3khkA 544 1.74e+01 1gzsB 165 1.76e+01 a.168.1.1 76425 2obhA 143 1.79e+01 a.39.1.5 148716 3evzA 230 1.80e+01 2i1yA 301 1.80e+01 1d3yA 301 1.80e+01 1d3yA e.12.1.1 43252 3czgA 644 1.85e+01 1a5cA 368 1.85e+01 1fbaA c.1.10.1 29148 3hx0A 335 1.87e+01 1pea 385 1.94e+01 1pea 1peaA 385 1.94e+01 c.93.1.1 35662 1om2A 95 1.98e+01 1om2A a.23.4.1 16520 2hgsA 474 2.00e+01 2hgsA c.30.1.4,d.142.1.6 31722,75997 2b1mA 246 2.13e+01 2bcqA 335 2.14e+01 a.60.6.1,a.60.12.1,d.218.1.2 128304,128305,128306 3ch3X 265 2.17e+01 2gn4A 344 2.22e+01 3gwjA 674 2.25e+01 1pxvA 183 2.30e+01 d.3.1.1 95301 1flcB 175 2.35e+01 1flcB h.3.1.1 45716 1uxtA 501 2.37e+01 c.82.1.1 108125 1mw7A 240 2.37e+01 e.39.1.1 79557 2v9tA 117 2.44e+01 2rijA 387 2.46e+01 2i7cA 283 2.46e+01 2g8lA 299 2.47e+01 e.50.1.1 134775 3fruA 269 2.47e+01 1agdA b.1.1.2,d.19.1.1 20657,38150 2bjkA 516 2.56e+01 3cvzA 273 2.56e+01 3adnA 294 2.63e+01 1d0nA 729 2.66e+01 1d0nA d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1,d.109.1.1 40834,40835,40836,40837,40838,40839 3c96A 415 2.67e+01 c.3.1.2,d.16.1.2 156122,156123 2cqsA 842 2.71e+01 1eps 427 2.72e+01 1eps 1gcb 454 2.80e+01 3gcb 3by5A 155 2.82e+01 c.151.1.1 155721 1rr7A 129 2.90e+01 a.4.1.14 105075 1q0qA 406 2.95e+01 a.69.3.1,c.2.1.3,d.81.1.3 104464,104465,104466 1r9lA 309 2.95e+01 c.94.1.1 97262 2wbfX 265 2.98e+01 1uzbA 516 3.01e+01 c.82.1.1 100220 3ek1A 504 3.05e+01 2e9yA 316 3.08e+01 2e01A 457 3.08e+01 1izlB 472 3.10e+01 i.5.1.1 76995 3cp2A 649 3.18e+01 3icfA 335 3.21e+01 3jz4A 481 3.28e+01 1a2xA 159 3.30e+01 1ncx a.39.1.5 17251 1h16A 759 3.38e+01 c.7.1.1 76462 1h80A 464 3.39e+01 b.80.1.8 65714 1dc1A 323 3.39e+01 1dc1A c.52.1.11 33321 3gjwA 350 3.39e+01 1ayx 492 3.41e+01 1ayx 3bjaA 139 3.43e+01 2zdsA 340 3.46e+01 2e7zA 727 3.48e+01 1h0hA 977 3.48e+01 b.52.2.2,c.81.1.1 76435,76436 1zbpA 273 3.49e+01 e.61.1.1 124861 1oacA 727 3.53e+01 1oacA b.30.2.1,d.17.2.1,d.17.2.1,d.82.1.1 24390,38007,38008,40003 2hd5A 359 3.56e+01 d.3.1.9 145293 2q01A 497 3.59e+01 1wdkC 390 3.61e+01 c.95.1.1,c.95.1.1 109258,109259 2bjuA 453 3.63e+01 b.50.1.2 128633 2hldG 278 3.73e+01 3kvoA 346 3.74e+01 1hqsA 423 3.76e+01 1iso c.77.1.1 61154 3ga4A 178 3.76e+01 1yn9A 169 3.77e+01 2k3oA 129 3.78e+01 3gzdA 440 3.80e+01 1ezfA 340 3.86e+01 1ezfA a.128.1.2 19440 2pjmA 226 3.92e+01 1ortA 335 3.93e+01 1othA c.78.1.1,c.78.1.1 35204,35205 3cesA 651 3.93e+01 1tkkA 366 3.95e+01 c.1.11.2,d.54.1.1 107089,107090 3e1sA 574 3.95e+01 1dysA 348 4.05e+01 1bvwA c.6.1.1 30669 1cm5A 759 4.11e+01 1cm5A c.7.1.1 30671 1f3lA 321 4.13e+01 1g6q2 c.66.1.6 59630 1jvsA 400 4.13e+01 a.69.3.1,c.2.1.3,d.81.1.3 77187,77188,77189 1g6sA 427 4.18e+01 1eps d.68.2.2 39584 2c7yA 404 4.32e+01 3kkbA 130 4.36e+01 1mi4A 427 4.37e+01 d.68.2.2 79141 2fbaA 492 4.38e+01 a.102.1.1 133239 3igfA 374 4.38e+01 3kznA 359 4.39e+01 1zq6A 359 4.39e+01 3a9sA 595 4.40e+01 2ywdA 191 4.40e+01 3c0qA 301 4.48e+01 1rypH 205 4.71e+01 d.153.1.4 41876 3ixqA 226 4.73e+01 2ismA 352 4.74e+01 1jhfA 202 4.74e+01 a.4.5.2,b.87.1.1 63057,63058 3gn3A 182 4.74e+01 1iu4A 331 4.75e+01 d.3.1.8 71430 1xpnA 170 4.79e+01 b.3.7.1 115767 3ffrA 362 4.82e+01 1r4vA 171 4.83e+01 a.22.1.4 97049 2nygA 273 4.83e+01 c.140.1.2 148514 1t5oA 351 4.87e+01 c.124.1.5 106459 3ipkA 497 4.97e+01 1hmcA 148 5.02e+01 1hmcB a.26.1.2 16867 3l04A 359 5.02e+01 2ph7A 246 5.07e+01 1b0nA 111 5.09e+01 1b0nA a.34.1.1,a.35.1.3 17001,17064 1ujwB 135 5.09e+01 h.4.9.1 99472 3c8tA 451 5.11e+01 1a6zA 275 5.14e+01 1agdA b.1.1.2,d.19.1.1 20781,38280 1hx0A 496 5.19e+01 b.71.1.1,c.1.8.1 61346,61347 2v84A 343 5.20e+01 2e4uA 555 5.24e+01 1c0pA 363 5.25e+01 1an9A c.4.1.2,d.16.1.3 30647,37934 2aajA 130 5.38e+01 d.80.1.6 126481 2d2mB 142 5.38e+01 2gupA 292 5.53e+01 c.55.1.10,c.55.1.10 135744,135745 1sxjA 511 5.55e+01 a.80.1.1,c.37.1.20 106081,106082 3bujA 397 5.61e+01 2wwwA 349 5.61e+01 1qrdA 273 5.64e+01 1d4aA c.23.5.3 31217 1obbA 480 5.66e+01 c.2.1.5,d.162.1.2 86760,86761 3l05A 359 5.69e+01 2dlaA 222 5.75e+01 1qfcA 306 5.75e+01 1uteA d.159.1.1 42077 2dy3A 361 5.80e+01 1cnzA 363 5.85e+01 1cnzA c.77.1.1 35061 1b78A 193 5.89e+01 1b78A c.51.4.1 33221 2wyhA 923 5.93e+01 3f6nA 129 5.94e+01 3l6dA 306 5.97e+01 3cmqA 415 6.00e+01 2oegA 505 6.05e+01 5csmA 256 6.09e+01 5csmA a.130.1.2 19494 1qcrF 103 6.12e+01 1be3F f.27.1.1 43676 2kpqA 100 6.15e+01 2p58A 65 6.17e+01 1ru0A 105 6.23e+01 d.74.1.1 111937 1ta8A 332 6.26e+01 d.142.2.2 112375 1cs8A 316 6.32e+01 1cs8A d.3.1.1 37065 2icyA 469 6.33e+01 b.81.1.4,c.68.1.5 137257,137258 3d6nB 291 6.34e+01 2q9oA 559 6.35e+01 b.6.1.3,b.6.1.3,b.6.1.3 150149,150150,150151 3gzuC 397 6.37e+01 2z3qA 119 6.37e+01 a.26.1.2 154002 2fytA 340 6.39e+01 c.66.1.6 134391 3dkhA 559 6.44e+01 1dl2A 511 6.44e+01 1dl2A a.102.2.1 18844 2qiwA 255 6.47e+01 1o17A 345 6.47e+01 a.46.2.1,c.27.1.1 80765,80766 3dsbA 157 6.51e+01 3ie0A 431 6.52e+01 1ocxA 182 6.53e+01 b.81.1.3 86814 1wt4A 73 6.55e+01 2ih8A 559 6.64e+01 b.6.1.3,b.6.1.3,b.6.1.3 137407,137408,137409 1dbqA 289 6.67e+01 1qpzA c.93.1.1 35666 3ma5A 100 6.69e+01 2q00A 129 6.75e+01 3kz9A 206 6.82e+01 1r9jA 673 6.86e+01 c.36.1.6,c.36.1.10,c.48.1.1 111722,111723,111724 3l06A 359 6.92e+01 2afaA 425 6.94e+01 a.102.1.3 126668 1qhdA 398 7.00e+01 1qhdA a.115.1.2,b.19.1.1 63324,63325 2x1yA 761 7.02e+01 3gqjA 261 7.03e+01 2v36A 376 7.04e+01 3a11A 338 7.04e+01 3l02A 359 7.08e+01 1rwhA 757 7.13e+01 a.102.3.2,b.24.1.1,b.30.5.2 97984,97985,97986 2qxvA 361 7.14e+01 1jeyB 565 7.15e+01 1jeqB b.131.1.2,c.62.1.4 90372,90373 3d2uA 281 7.21e+01 2zs0B 142 7.23e+01 1b77A 228 7.25e+01 1b77A d.131.1.2,d.131.1.2 41362,41363 2zy5A 546 7.26e+01 2cvxA 888 7.30e+01 1g73C 121 7.33e+01 1g3fA g.52.1.1 45375 1o94A 729 7.44e+01 c.1.4.1,c.3.1.1,c.4.1.1 81200,81201,81202 2v1tA 73 7.45e+01 2fztA 79 7.45e+01 a.46.3.1 134476 1b5pA 385 7.46e+01 c.67.1.1 90403 1ivnA 190 7.47e+01 c.23.10.5 83719 2aalA 131 7.51e+01 d.80.1.6 126483 1aua 296 7.54e+01 1aua 1auaA 296 7.54e+01 a.5.3.1,c.13.1.1 16290,30882 2ffjA 300 7.54e+01 e.50.1.1 133387 3l55A 353 7.55e+01 3if2A 444 7.59e+01 3fjzA 427 7.59e+01 3duwA 223 7.60e+01 1vpwA 340 7.64e+01 1qpzA a.35.1.5,c.93.1.1 17087,35680 1inlA 296 7.68e+01 c.66.1.17 66220 3kz4C 397 7.68e+01 2hcfA 234 7.73e+01 c.108.1.6 136333 3k5bA 188 7.74e+01 3dp7A 363 7.74e+01 2b7oA 464 7.76e+01 c.1.10.8 128047 3fwnA 480 7.78e+01 1nxcA 478 7.80e+01 a.102.2.1 92293 2uy1A 493 7.86e+01 1jeqB 565 7.97e+01 1jeqB b.131.1.2,c.62.1.4 90368,90369 2b5uA 551 7.99e+01 b.101.1.1,b.110.1.1,h.4.9.1 127906,127907,127908