# List of top-scoring protein chains for t2k-100-30-alpha 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 1k1xA 659 1.50e-01 a.8.3.2 84279 b.30.5.8 84280 c.6.2.2 84281 1em2A 229 1.74e-01 1em2A d.129.3.2 41321 1fc2C 58 2.22e-01 1fc2C a.8.1.1 16345 1vjnA 220 7.90e-01 unknown_sccs -11458 1crb 134 1.03e+00 1hmt b.60.1.2 27220 1ks2A 219 1.06e+00 unknown_sccs 72908 d.58.40.1 72909 1deeG 54 1.12e+00 1fc2C a.8.1.1 16343 155c 135 1.27e+00 1ycc a.3.1.1 15900 2btvA 901 1.30e+00 2btvA e.28.1.1 43376 1s0uA 408 1.44e+00 b.43.3.1 -4053 b.44.1.1 -4061 c.37.1.8 -7096 1d0hA 469 1.49e+00 1a8d b.29.1.6 24265 b.42.4.2 25610 1co6A 107 1.71e+00 1ycc a.3.1.1 15894 1mtpA 323 1.97e+00 e.1.1.1 85107 1eg7A 557 2.08e+00 1eg7A c.37.1.10 32241 1o8bA 219 2.13e+00 unknown_sccs 81180 d.58.40.1 81181 1a8d 452 2.34e+00 1a8d b.29.1.6 24262 b.42.4.2 25607 1h0cA 392 2.42e+00 c.67.1.3 83424 1lkzA 219 2.68e+00 unknown_sccs 73991 d.58.40.1 73992 1c0pA 363 3.10e+00 1an9A c.4.1.2 30647 d.16.1.3 37934 1dgnA 89 3.10e+00 1dgnA a.77.1.3 18436 1diwA 441 3.10e+00 1a8d b.29.1.6 24264 b.42.4.2 25609 1p94A 76 3.31e+00 unknown_sccs -916 1cot 129 3.78e+00 1ycc a.3.1.1 15899 1bdc 60 3.79e+00 1fc2C a.8.1.1 16350 1tsp 559 4.08e+00 1tyv b.80.1.6 28044 1qa1A 554 4.38e+00 1tyv b.80.1.6 28047 1tyv 542 4.45e+00 1tyv b.80.1.6 28038 2cpgA 45 4.64e+00 2cpgA unknown_sccs 17455 1qq1A 559 4.71e+00 1tyv b.80.1.6 28041 1tyu 543 4.86e+00 1tyv b.80.1.6 28037 1p9eA 331 4.99e+00 1s1dA 331 5.63e+00 unknown_sccs -4566 1qgiA 259 5.83e+00 1qgiA d.2.1.7 37001 1ffkL 115 6.02e+00 1ffkL c.12.1.1 30881 1o6yA 299 6.17e+00 d.144.1.7 81106 1l8aA 886 6.27e+00 c.36.1.6 73678 c.36.1.10 73677 c.48.1.1 73679 1tys 265 6.60e+00 1bkpA d.117.1.1 40937 1jvsA 400 6.62e+00 a.69.3.1 77187 c.2.1.3 77188 d.81.1.3 77189 1p5sA 203 6.92e+00 a.40.1.1 -900 1edoA 244 7.10e+00 1ybvA c.2.1.2 29896 1eca 136 7.81e+00 1flp a.1.1.2 15209 1eco 136 7.84e+00 1flp a.1.1.2 15208 1ecd 136 8.08e+00 1flp a.1.1.2 15211 1taq 832 8.31e+00 1taq a.60.7.1 18082 c.120.1.2 33352 c.55.3.5 33698 e.8.1.1 42991 1mr7A 209 8.53e+00 b.81.1.3 -4798 1nnwA 252 8.95e+00 d.159.1.5 80674 1ehkA 562 9.09e+00 1ehkA f.24.1.1 43624 1qqqA 264 9.24e+00 1bkpA d.117.1.1 40931 1ccr 112 9.37e+00 1ycc a.3.1.1 15877 1nlqA 108 9.72e+00 b.121.3.1 85853 1ycc 108 9.97e+00 1ycc a.3.1.1 15834 1mn8A 100 1.09e+01 a.61.1.6 79318 1irw 108 1.15e+01 1ycc a.3.1.1 15855 1ei9A 279 1.17e+01 1ei9A c.69.1.13 34713 1k5hA 398 1.25e+01 a.69.3.1 68192 c.2.1.3 68193 d.81.1.3 68194 1jj2N 115 1.25e+01 1ffkL c.12.1.1 63099 1ireB 228 1.25e+01 b.34.4.4 76770 1ugpB 226 1.26e+01 1kewA 361 1.27e+01 c.2.1.2 68544 1s72O 116 1.27e+01 1n3kA 130 1.28e+01 a.77.1.4 79965 1iy8A 267 1.29e+01 c.2.1.2 83774 1gw5S 142 1.30e+01 d.110.4.2 70633 1a4yA 460 1.36e+01 1a4yA c.10.1.1 30852 1h0oA 390 1.36e+01 a.25.1.2 70845 3rabA 169 1.37e+01 1ctqA c.37.1.8 32018 2dynA 122 1.38e+01 1dynA b.55.1.1 26957 1j6rA 214 1.39e+01 d.173.1.2 71598 3ygsP 97 1.39e+01 3ygsP a.77.1.3 18435 1na3A 91 1.43e+01 k.38.1.1 85481 1jjyA 636 1.44e+01 1jjyA 1nt2B 258 1.50e+01 a.183.1.1 86150 1tahB 318 1.51e+01 1cvl c.69.1.18 34774 1cvl 319 1.53e+01 1cvl c.69.1.18 34786 1vk3A 615 1.58e+01 d.79.4.1 -10416 d.79.4.1 -10417 d.139.1.1 -11154 d.139.1.1 -11155 1tahA 318 1.58e+01 1cvl c.69.1.18 34775 1mcpL 220 1.59e+01 8fabA b.1.1.1 19858 b.1.1.2 20958 2frvB 536 1.59e+01 1h2rL e.18.1.1 43291 1gq8A 319 1.59e+01 b.80.1.5 70350 1dypA 271 1.60e+01 1dypA b.29.1.2 24185 1jogA 146 1.60e+01 a.24.16.2 77142 2tscA 264 1.61e+01 1bkpA d.117.1.1 40952 1evfA 264 1.63e+01 1bkpA d.117.1.1 40932 1uc2A 481 1.63e+01 unknown_sccs -11725 1c28A 135 1.64e+01 1c28A b.22.1.1 23857 1kqwA 134 1.65e+01 b.60.1.2 72887 1dynA 125 1.69e+01 1dynA b.55.1.1 26955 1su8A 636 1.70e+01 e.26.1.2 -12015 1frvB 536 1.72e+01 1h2rL e.18.1.1 43296 1um8A 376 1.75e+01 c.37.1.20 -7251 1xsm 390 1.81e+01 1xsm a.25.1.2 16804 2bnh 457 1.82e+01 1a4yA c.10.1.1 30850 1lb2B 84 1.84e+01 a.60.3.1 77871 1sy6A 204 1.87e+01 1rylA 167 1.89e+01 1jmxB 349 1.89e+01 b.69.2.2 66906 1q16C 225 1.91e+01 unknown_sccs -12324 1dpuA 99 1.93e+01 1dpuA a.4.5.16 16150 1ytc 112 1.93e+01 1ycc a.3.1.1 15835 1r48A 35 1.95e+01 unknown_sccs -13006 1ib8A 164 1.97e+01 b.38.2.1 71168 d.52.4.1 71169 1qbqA 333 1.97e+01 1ft1A a.118.6.1 19187 1ev7B 317 1.97e+01 1ev7B c.52.1.9 33316 1lshB 319 1.98e+01 f.7.1.1 74245 1jcrA 377 2.01e+01 a.118.6.1 66506 1m6iA 493 2.02e+01 c.3.1.5 74533 c.3.1.5 74534 d.87.1.1 74535 1iawA 317 2.04e+01 c.52.1.9 62126 1kn0A 212 2.04e+01 d.50.1.3 77444 2nllB 103 2.05e+01 2nllB g.39.1.2 45115 1b37A 472 2.10e+01 1b37B c.3.1.2 30389 d.16.1.5 37953 1kk6A 209 2.11e+01 b.81.1.3 68657 1a65A 504 2.17e+01 1a65A b.6.1.3 23148 b.6.1.3 23149 b.6.1.3 23150 1caxB 184 2.22e+01 1caxB b.82.1.2 28105 1sczA 233 2.22e+01 c.43.1.1 -7326 1e2o 233 2.24e+01 1eaf c.43.1.1 32631 1p2xA 159 2.31e+01 1opaA 135 2.31e+01 1hmt b.60.1.2 27214 1us7B 265 2.31e+01 unknown_sccs -1518 1d8dA 377 2.36e+01 1ft1A a.118.6.1 19185 1emvB 134 2.37e+01 1bxiB d.4.1.1 37135 1jcqA 382 2.37e+01 a.118.6.1 66504 1tia 279 2.38e+01 3tgl c.69.1.17 34737 1aihA 170 2.38e+01 1aihA d.163.1.1 42149 1b37B 472 2.41e+01 1b37B c.3.1.2 30390 d.16.1.5 37954 1pbtA 244 2.42e+01 unknown_sccs -6866 1bxiB 134 2.44e+01 1bxiB d.4.1.1 37136 1b5qA 472 2.49e+01 1b37B c.3.1.2 30404 d.16.1.5 37968 1opbA 135 2.50e+01 1hmt b.60.1.2 27216 1hl8A 449 2.51e+01 unknown_sccs -4690 unknown_sccs -5361 1np1A 184 2.54e+01 1np1A b.60.1.1 27155 1ft1A 377 2.61e+01 1ft1A a.118.6.1 19186 1dqnA 230 2.71e+01 1dqnA c.61.1.1 34067 1dqpA 230 2.79e+01 1dqnA c.61.1.1 34069 1jj2C 246 2.79e+01 1ffkC c.22.1.1 63087 1s72C 246 2.81e+01 1rypK 198 2.82e+01 d.153.1.4 41879 1nrjA 158 2.83e+01 d.110.4.4 86124 1g2cB 43 2.84e+01 1g2cB 1p2fA 220 2.86e+01 a.4.6.1 87720 c.23.1.1 87721 1enfA 212 2.86e+01 3seb b.40.2.2 25198 d.15.6.1 37787 1gjsA 65 2.87e+01 1gab a.8.1.2 60578 1bazA 53 2.93e+01 1bazA a.43.1.1 17421 1ld8A 382 2.93e+01 a.118.6.1 73838 1dxgA 36 2.97e+01 1dxgA g.41.5.2 45247 1fr2B 134 3.05e+01 d.4.1.1 83257 1fwxA 595 3.06e+01 b.6.1.4 60069 b.69.3.1 60070 1uekA 275 3.07e+01 d.14.1.5 88483 d.58.26.5 88484 1qdlA 422 3.16e+01 1qdlA d.161.1.1 42088 1forL 210 3.24e+01 8fabA b.1.1.1 19988 b.1.1.2 21044 1orc 71 3.26e+01 1orc a.35.1.2 17054 1mjfA 281 3.27e+01 c.66.1.17 79198 1is2A 661 3.31e+01 a.29.3.2 71382 a.29.3.2 71383 e.6.1.2 71384 1e8yA 966 3.35e+01 1e8xA a.118.1.6 19152 b.7.1.1 23187 d.15.1.5 37635 d.144.1.4 41715 1g2cL 43 3.37e+01 1g2cL 1mijA 152 3.47e+01 a.4.1.1 79150 1lk9A 448 3.54e+01 c.67.1.1 78057 1j1uA 306 3.57e+01 c.26.1.1 83980 1jksA 294 3.64e+01 d.144.1.7 71710 1nsf 273 3.64e+01 1d2nA c.37.1.20 32429 1c3oA 1073 3.65e+01 1c3oA a.92.1.1 18562 c.24.1.1 31491 c.30.1.1 31681 c.30.1.1 31682 d.142.1.2 41526 d.142.1.2 41527 1mxa 383 3.66e+01 1mxb d.130.1.1 41326 d.130.1.1 41327 d.130.1.1 41328 1a17 166 3.76e+01 1a17 a.118.8.1 19206 1nkd 65 3.78e+01 1nkd a.30.1.1 16974 1d2nA 272 3.79e+01 1d2nA c.37.1.20 32428 1ovaA 386 3.82e+01 1ovaA e.1.1.1 42619 1rpo 65 3.83e+01 1nkd a.30.1.1 16975 1ev0A 58 3.83e+01 1ev0A d.71.1.1 39594 1e5rA 290 3.84e+01 1e5rA b.82.2.4 59276 1squA 155 3.87e+01 unknown_sccs -10229 1ffkC 246 3.91e+01 1ffkC c.22.1.1 31037 1hcl 298 3.94e+01 1hcl d.144.1.7 41593