# 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 1g4yR 148 1.69e-02 1cll a.39.1.5 60252 1exrA 148 3.46e-02 1cll a.39.1.5 17299 1osa 148 3.88e-02 1cll a.39.1.5 17300 3cln 148 4.22e-02 1cll a.39.1.5 17286 1floA 422 4.46e-02 1floA a.60.9.1 18106 d.163.1.1 42166 1cll 148 7.36e-02 1cll a.39.1.5 17263 1uok 558 8.16e-02 1uok b.71.1.1 27801 c.1.8.1 28788 1hruA 188 1.56e-01 1hruA d.115.1.1 40926 1f37A 110 1.64e-01 1f37A c.47.1.11 33088 1a6q 382 1.83e-01 1a6q d.158.1.1 42063 1ggzA 148 2.01e-01 1hyeA 313 2.91e-01 2cmd c.2.1.5 61400 d.162.1.1 61401 1fua 215 2.98e-01 2fua c.74.1.1 34973 2fua 215 3.21e-01 2fua c.74.1.1 34977 1qhoA 686 5.28e-01 1cxlA b.1.1.5 21844 b.3.1.1 22513 b.71.1.1 27751 c.1.8.1 28738 1g5aA 628 6.04e-01 b.71.1.1 65152 c.1.8.1 65153 1sfe 180 8.12e-01 1sfe a.4.2.1 16073 c.55.7.1 33748 1e4cP 215 8.49e-01 2fua c.74.1.1 34969 1bmqB 88 8.70e-01 1pauB 1qbjA 81 1.09e+00 1qbjA a.4.5.19 16155 1hqsA 423 1.09e+00 1iso c.77.1.1 61154 1qgpA 77 1.10e+00 1qbjA a.4.5.19 16158 1c4xA 285 1.12e+00 1c4xA c.69.1.10 34684 1fjgC 239 1.13e+00 1fjfC d.52.3.1 38831 d.53.1.1 38839 1fjgI 128 1.24e+00 1fjfI d.14.1.1 37559 1cex 214 1.24e+00 1cex c.23.9.1 31285 1wdcC 156 1.34e+00 1wdcC a.39.1.5 17317 1ibcB 88 1.36e+00 1pauB 1edqA 540 1.38e+00 1ctn b.1.1.5 21873 c.1.8.5 29002 d.26.3.1 38436 1dtdB 61 1.39e+00 1dtvA g.30.1.1 44962 1yacA 208 1.48e+00 1yacA c.33.1.2 31757 1kkcA 221 1.51e+00 a.2.11.1 68660 d.44.1.1 68661 1cus 200 1.65e+00 1cex c.23.9.1 31287 1dtvA 67 1.66e+00 1dtvA g.30.1.1 44963 1ehyA 294 1.67e+00 1ehyA c.69.1.11 34693 1nbaA 264 1.72e+00 1nbaA c.33.1.1 31753 1e2xA 243 1.72e+00 1e2xA a.4.5.6 16113 a.78.1.1 18443 1bno 87 1.79e+00 1bpyA a.60.6.1 18079 1k4jA 230 1.82e+00 1hw1A 239 1.83e+00 1e2xA a.4.5.6 16111 a.78.1.1 18441 1dr9A 201 1.84e+00 1dr9A b.1.1.1 19762 b.1.1.3 21684 1qnnA 191 1.91e+00 1avmA a.2.11.1 15792 d.44.1.1 38755 1ctn 540 2.07e+00 1ctn b.1.1.5 21876 c.1.8.5 29005 d.26.3.1 38439 1tux 301 2.34e+00 1taxA c.1.8.3 28907 1korA 400 2.40e+00 1j5eC 239 2.59e+00 1h8cA 82 2.74e+00 1h8cA d.15.1.2 37608 2act 220 2.89e+00 1cs8A d.3.1.1 37002 1ggwA 140 2.92e+00 1ggwA a.39.1.5 60490 2masA 314 3.10e+00 2masA c.70.1.1 34810 1hdhA 536 3.47e+00 c.76.1.2 65805 1gkkA 297 4.84e+00 c.69.1.2 65248 1gklA 297 4.98e+00 c.69.1.2 65250 1faoA 126 5.17e+00 1faoA b.55.1.1 26974 1h6oA 204 5.22e+00 a.146.1.1 60689 1hqkA 154 6.20e+00 c.16.1.1 65902 1hnuA 280 6.23e+00 1hnoA c.14.1.3 61096 1ipd 345 6.24e+00 1cnzA c.77.1.1 35038 1akr 147 6.47e+00 1rcf c.23.5.1 31152 1i60A 278 6.71e+00 1jkeA 145 6.76e+00 c.110.1.1 66791 1bkpA 278 7.07e+00 1bkpA d.117.1.1 41029 1nal3 297 7.14e+00 1nal3 1fzqA 181 7.16e+00 1hurA c.37.1.8 32060 1eg9A 449 7.16e+00 1ndoA b.33.1.2 24443 d.129.3.3 41322 1dqsA 393 7.29e+00 1dqsA e.22.1.1 43347 1dtdA 303 7.48e+00 1aye c.56.5.1 33823 1l92 164 7.56e+00 1l92 d.2.1.3 36629 1fdyA 297 7.69e+00 1nal3 c.1.10.1 29071 1ndh 272 7.85e+00 1ndh b.43.4.2 25662 c.25.1.1 31552 1g61A 228 7.90e+00 1g61A d.126.1.1 41126 1hnoA 280 8.00e+00 1hnoA c.14.1.3 61095 1k6aA 303 8.09e+00 1tfr 305 8.16e+00 1tfr a.60.7.1 18081 c.53.1.2 33351 1nal1 297 8.21e+00 1nal3 1l58 164 8.30e+00 1l92 d.2.1.3 36635 1hcrA 52 8.35e+00 1hcrA a.4.1.2 16020 1eqjA 511 8.40e+00 1ejjA c.105.1.1 59495 c.76.1.3 59496 1ejjA 511 8.42e+00 1ejjA c.105.1.1 59422 c.76.1.3 59423 1idm 343 9.09e+00 1cnzA c.77.1.1 35035 1bak 119 9.11e+00 1bak b.55.1.1 26973 1e8aA 91 9.19e+00 1b4cA a.39.1.2 17188 1a32 88 9.68e+00 1a32 a.16.1.2 16384 119l 164 9.76e+00 1l92 d.2.1.3 36622 1mai 131 9.99e+00 1mai b.55.1.1 26951 1qo2A 241 1.00e+01 1qo2A c.1.2.1 28533 1k8cA 322 1.01e+01 1avsA 90 1.02e+01 1cll a.39.1.5 17226 2cgpA 210 1.05e+01 2cgpA a.4.5.4 16102 b.82.3.2 28141 1g6oA 330 1.07e+01 1g6oA c.37.1.13 32430 1aye 401 1.08e+01 1aye c.56.5.1 33824 d.58.3.1 39065 1iqvA 218 1.12e+01 1rss a.75.1.1 62661 1ck9A 104 1.12e+01 1ck9A d.79.3.1 39806 1rvv1 154 1.12e+01 1rvv1 1rvvA 154 1.12e+01 1rvv1 c.16.1.1 30927 1hw5A 210 1.15e+01 2cgpA a.4.5.4 16098 b.82.3.2 28137 1itf 165 1.16e+01 1b5l a.26.1.3 16899 1f4pA 147 1.17e+01 5nul c.23.5.1 59651 1jmsA 381 1.18e+01 a.60.6.1 66889 e.9.1.1 66890 2tpsA 227 1.21e+01 2tpsA c.1.3.1 28591 1tns 76 1.21e+01 1qpmA a.4.5.26 16228 1ipaA 274 1.23e+01 1qjgA 125 1.24e+01 1opy d.17.4.3 38102 1cwoA 165 1.26e+01 2cpl b.62.1.1 27445 1c75A 71 1.29e+01 451c a.3.1.1 15796 1fepA 724 1.31e+01 1fepA f.4.3.3 43808 1qghA 156 1.32e+01 1qghA a.25.1.1 16728 1f0cA 305 1.38e+01 1c8oA e.1.1.1 42676 1fpzA 212 1.45e+01 1fpzA c.45.1.1 59976 1dr8B 344 1.45e+01 1cnzA c.77.1.1 35052 8cho 125 1.47e+01 1opy d.17.4.3 38108 1hqi 90 1.48e+01 1hqi d.137.1.1 41454 1awsA 164 1.49e+01 2cpl b.62.1.1 27431 1gq6A 313 1.49e+01 1ezwA 349 1.51e+01 1ezwA c.1.16.3 29558 2fx2 147 1.53e+01 1rcf c.23.5.1 31158 1dhr 241 1.57e+01 1dhr c.2.1.2 29832 1j9eA 147 1.59e+01 c.23.5.1 62756 1gajA 257 1.62e+01 1gajA c.37.1.12 60416 1qpaA 345 1.70e+01 1arv a.93.1.1 18585 1ncx 162 1.70e+01 1ncx a.39.1.5 17222 1c7nA 399 1.73e+01 1d2fA c.67.1.3 34413 2cpl 165 1.75e+01 2cpl b.62.1.1 27420 1bu5A 147 1.76e+01 5nul c.23.5.1 31155 1e68A 70 1.78e+01 1e68A a.64.2.1 18144 1ldjA 760 1.78e+01 1mngA 203 1.82e+01 1avmA a.2.11.1 15776 d.44.1.1 38701 1zac 90 1.90e+01 1ncx a.39.1.5 17236 1ndoA 449 1.91e+01 1ndoA b.33.1.2 24444 d.129.3.3 41323 1cyj 90 1.93e+01 1ctj a.3.1.1 15805 1clxA 347 1.94e+01 1taxA c.1.8.3 28899 1ery 39 1.96e+01 1ery a.10.1.1 16364 2sniI 83 2.01e+01 2sniI d.40.1.1 38573 1ib3A 349 2.02e+01 1ib2A a.118.1.8 62142 1ep2B 261 2.05e+01 1ep2B b.43.4.2 25666 c.25.1.3 31556 1ib2A 349 2.06e+01 1ib2A a.118.1.8 62141 1c0nA 406 2.07e+01 1c0nA c.67.1.3 34433 1bg4 302 2.10e+01 1taxA c.1.8.3 28806 1awqA 164 2.14e+01 2cpl b.62.1.1 27461 1dbhA 354 2.14e+01 1awe a.87.1.1 18514 b.55.1.1 26967 1cbf 285 2.18e+01 1cbf c.90.1.1 35587 1fj2A 232 2.18e+01 1auoA c.69.1.14 34720 8prkB 287 2.20e+01 1wgjA b.40.5.1 25396 1epuA 591 2.22e+01 1dn1A e.25.1.1 43358 7icd 416 2.23e+01 1iso c.77.1.1 35072 1knt 58 2.26e+01 1bpi g.8.1.1 44538 3aig 202 2.29e+01 1atlA d.92.1.9 40321 1jkoC 52 2.29e+01 a.4.1.2 66809 1cyi 90 2.31e+01 1ctj a.3.1.1 15804 1guqA 348 2.34e+01 1guqA d.13.1.2 37522 d.13.1.2 37523 8prkA 287 2.36e+01 1wgjA b.40.5.1 25395 1e9gB 286 2.37e+01 1wgjA b.40.5.1 59394 1gupA 348 2.41e+01 1guqA d.13.1.2 37534 d.13.1.2 37535 1jf9A 408 2.44e+01 1c0nA c.67.1.3 62931 1gnd 447 2.52e+01 1gnd c.3.1.3 30423 d.16.1.6 37987 1iso 416 2.52e+01 1iso c.77.1.1 35065 1psrA 100 2.59e+01 1psrA a.39.1.2 17180 1gw5S 142 2.61e+01 1eziA 228 2.63e+01 1eyrA c.68.1.3 34512 1dgrW 93 2.64e+01 1caxB 1azo 232 2.78e+01 1azo c.52.1.14 33329 1efpB 252 2.81e+01 1efvB c.29.1.1 31636 1e9gA 286 2.83e+01 1wgjA b.40.5.1 59393 1ybvA 283 2.84e+01 1ybvA c.2.1.2 29948 1sriA 121 2.84e+01 1swuA b.61.1.1 27276 1gk8I 140 2.87e+01 d.73.1.1 65242 1d5tA 433 2.94e+01 1gnd c.3.1.3 30422 d.16.1.6 37986 1cy5A 97 2.96e+01 1cy5A a.77.1.1 18430 1ep3B 262 2.98e+01 1ep2B b.43.4.2 25664 c.25.1.3 31554 1wgjA 286 3.01e+01 1wgjA b.40.5.1 25397 1jjiA 311 3.02e+01 c.69.1.2 66766 1a3c 181 3.04e+01 1a3c c.61.1.1 34095 1fds 327 3.04e+01 1fds c.2.1.2 29838 1dmmA 131 3.05e+01 1opy d.17.4.3 38114 1top 162 3.08e+01 1ncx a.39.1.5 17223 1qq2A 199 3.11e+01 1qq2A c.47.1.10 33064 1go3E 187 3.16e+01 b.40.4.5 65406 1dgrM 93 3.20e+01 1caxB b.82.1.2 28101 1hyqA 263 3.22e+01 1hyqA c.37.1.10 61412 2knt 58 3.23e+01 1bpi g.8.1.1 44537 1qbqA 333 3.23e+01 1ft1A a.118.6.1 19187 1aa7A 158 3.27e+01 1aa7A a.95.1.1 18741 1hdr 244 3.35e+01 1dhr c.2.1.2 29837 2acy 98 3.35e+01 2acy d.58.10.1 39298 2sns 149 3.40e+01 1snc b.40.1.1 24860 1awcB 153 3.41e+01 1bd8 a.118.2.1 19156 1din 236 3.42e+01 1din c.69.1.9 34682 1jruA 89 3.43e+01 1jruA d.15.1.2 63257 2prgC 88 3.47e+01 2prgC a.137.6.1 19644 1a27 289 3.48e+01 1fds c.2.1.2 29839 1j8wB 273 3.51e+01 c.68.1.2 66441 1swuA 127 3.58e+01 1swuA b.61.1.1 27230 1g0oA 283 3.66e+01 1ybvA c.2.1.2 60181 1qb2A 109 3.67e+01 1qb2A a.36.1.1 17125 1foaA 348 3.69e+01 1foaA c.68.1.10 59929 1jw2A 72 3.75e+01 a.23.5.1 67372 1i2tA 61 3.81e+01 1i2tA a.144.1.1 61582 1jnuA 104 3.85e+01 1il8A 72 3.86e+01 1tvxA d.9.1.1 37365 1gm6A 175 3.87e+01 1jksA 294 3.89e+01 1hleA 345 3.92e+01 1ovaA e.1.1.1 42618 1jcrA 377 3.93e+01 a.118.6.1 66506 1ft1A 377 3.98e+01 1ft1A a.118.6.1 19186