# List of top-scoring protein chains for t2k-100-30-dssp-ebghstl 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 1dq3A 454 1.45e-02 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1mpgA 282 7.48e-02 1mpgA a.96.1.3 18747 d.129.1.2 41296 1agdA 276 9.28e-02 1agdA b.1.1.2 20741 d.19.1.1 38260 1kl9A 182 1.28e-01 1a7cA 379 1.81e-01 1sek e.1.1.1 42660 1cfzA 162 1.91e-01 1cfzA c.56.1.1 33754 1lj5A 379 3.25e-01 1eypA 222 3.79e-01 1eypA d.36.1.1 38536 1cuk 203 3.91e-01 1hjp a.5.1.1 16273 a.60.2.1 17946 b.40.4.2 25265 1swuA 127 4.48e-01 1swuA b.61.1.1 27230 1jx4A 352 5.39e-01 e.8.1.5 67405 1jr3E 334 6.81e-01 a.80.1.1 63253 c.37.1.13 63254 1jepA 222 7.57e-01 d.36.1.1 66612 1blxA 326 7.83e-01 1hcl d.144.1.1 41596 1eyqA 222 8.75e-01 1eypA d.36.1.1 38534 1pcfA 66 8.86e-01 1pcfA d.18.1.1 38142 1jl3A 139 9.48e-01 c.44.1.1 66826 1cz4A 185 1.09e+00 1cz4A b.52.2.3 26934 d.31.1.1 38468 2pfkA 320 1.10e+00 3pfk c.89.1.1 35577 1fgyA 127 1.15e+00 1faoA b.55.1.1 26976 1ez1A 392 1.25e+00 1ez1A b.84.2.1 28248 c.30.1.1 31655 d.142.1.2 41500 1erjA 393 1.25e+00 1erjA b.69.4.1 27660 1io1A 398 1.26e+00 1io1A e.32.1.1 62611 1eyzA 392 1.34e+00 1ez1A b.84.2.1 28246 c.30.1.1 31653 d.142.1.2 41498 1im4A 221 1.62e+00 e.8.1.5 62581 1pfkA 320 1.71e+00 3pfk c.89.1.1 35575 1pszA 303 1.88e+00 1toaA c.92.2.2 35600 2izhB 123 1.92e+00 1swuA b.61.1.1 27234 1a5t 334 1.96e+00 1a5t a.80.1.1 18450 c.37.1.13 32423 1qhlA 227 1.99e+00 1qhlA c.37.1.12 32382 1f35A 162 2.10e+00 1f35A b.94.1.1 59628 1kid 203 2.13e+00 1derA c.8.5.1 30771 2izgB 123 2.38e+00 1swuA b.61.1.1 27236 1hfoA 113 2.54e+00 d.80.1.3 61006 1fo0A 116 2.67e+00 1tvdA b.1.1.1 20610 6prcH 258 2.79e+00 6prcH b.41.1.1 25457 f.2.1.2 43436 3lynA 136 2.81e+00 1lis a.19.1.1 16413 1dxrH 258 2.83e+00 6prcH b.41.1.1 25456 f.2.1.2 43433 1j7nB 776 2.91e+00 d.92.1.14 66412 d.92.1.14 66413 d.166.1.1 66414 1hsbA 270 2.95e+00 1agdA b.1.1.2 20736 d.19.1.1 38257 1bgc 174 3.01e+00 1bgc a.26.1.1 16822 1ckmA 330 3.05e+00 1ckmA b.40.4.6 25358 d.142.2.3 41585 1gx5A 536 3.16e+00 1bio 228 3.24e+00 5ptp b.47.1.2 26314 1j8mF 297 3.25e+00 1ng1 a.24.13.1 62742 c.37.1.10 62743 1dcs 311 3.35e+00 1dcs b.82.2.1 28124 3dapA 320 3.40e+00 1dapA c.2.1.3 30051 d.81.1.3 39966 1tdj 514 3.45e+00 1tdj c.79.1.1 35297 d.58.18.2 39356 d.58.18.2 39357 1auvA 311 3.52e+00 1auvA c.30.1.5 31723 d.142.1.3 41558 1hi0P 664 3.54e+00 1hi0P e.8.1.6 61051 1f15B 218 3.54e+00 1f15B b.10.1.2 23321 1ezvB 352 3.59e+00 1ezvB d.185.1.1 59543 d.185.1.1 59544 1f06A 320 3.67e+00 1dapA c.2.1.3 59556 d.81.1.3 59557 1at3A 247 3.73e+00 1at3A b.57.1.1 27021 6pfkA 319 3.73e+00 3pfk c.89.1.1 35583 1jmxA 494 3.74e+00 a.3.1.7 66901 a.3.1.7 66902 b.1.1.6 66903 b.1.1.6 66904 b.61.4.1 66905 1i1qA 520 3.76e+00 1qdlA d.161.1.1 61543 3aig 202 3.83e+00 1atlA d.92.1.9 40321 1hdmB 193 3.85e+00 1hdmB b.1.1.2 21584 d.19.1.1 38158 1vid 221 3.91e+00 1vid c.66.1.1 34178 1dapA 320 3.97e+00 1dapA c.2.1.3 30053 d.81.1.3 39968 1jobA 162 4.03e+00 1f35A b.94.1.1 63207 1at0 145 4.04e+00 1at0 b.86.1.1 28374 1bq3B 246 4.15e+00 1qhfA c.60.1.1 33979 1avqA 228 4.17e+00 1avqA c.52.1.13 33326 1hhsA 664 4.24e+00 1hi0P e.8.1.6 61045 2azaA 129 4.25e+00 1nwpA b.6.1.1 22901 1ja1A 622 4.30e+00 1amoA b.43.4.1 62803 c.23.5.2 62804 c.25.1.4 62805 1j97A 211 4.47e+00 1f5sA c.108.1.4 62753 1fjgI 128 4.58e+00 1fjfI d.14.1.1 37559 1c2pA 576 4.64e+00 1quvA e.8.1.4 43117 1b1cA 181 4.68e+00 1amoA c.23.5.2 31212 1f1zA 273 4.88e+00 1f1zA a.4.5.27 16081 c.52.1.16 33334 1iq4A 179 5.33e+00 1iq4A d.77.1.1 62641 1cknA 330 5.34e+00 1ckmA b.40.4.6 25360 d.142.2.3 41587 1kjqA 391 5.36e+00 1fzoA 274 5.39e+00 1agdA b.1.1.2 60155 d.19.1.1 60156 1cjcA 460 5.46e+00 1cjcA c.3.1.1 30319 c.4.1.1 30604 1hrhA 136 5.48e+00 1rthA c.55.3.1 33577 16pk 415 5.49e+00 16pk c.86.1.1 35454 1nwpA 128 5.58e+00 1nwpA b.6.1.1 23011 1qs1A 462 5.79e+00 1qs1A d.166.1.1 42260 d.166.1.1 42261 1f5sA 211 5.83e+00 1f5sA c.108.1.4 59656 1jnyA 435 5.93e+00 b.43.3.1 66982 b.44.1.1 66983 c.37.1.8 66984 1fp6A 289 5.96e+00 1cp2A c.37.1.10 32243 1g7tA 594 6.00e+00 1g7rA b.43.3.1 25714 b.43.3.1 25715 c.20.1.1 31033 c.37.1.8 32148 1avaA 403 6.05e+00 1jdc b.71.1.1 27797 c.1.8.1 28784 1g7pA 274 6.10e+00 1g7rA 594 6.11e+00 1g7rA b.43.3.1 25716 b.43.3.1 25717 c.20.1.1 31034 c.37.1.8 32149 1ftrA 296 6.13e+00 1ftrA d.58.33.1 39485 d.58.33.1 39486 1j6wA 175 6.50e+00 1j98A d.185.1.2 62663 1fbaA 361 6.52e+00 1fbaA c.1.10.1 29120 1g5pA 289 6.56e+00 1cp2A c.37.1.10 32253 2hrvA 142 6.62e+00 2hrvA b.47.1.4 26429 1hgxA 183 6.65e+00 1tc1A c.61.1.1 34027 1fvaA 217 6.85e+00 1fvaA d.58.28.1 39409 1aizA 129 6.92e+00 1nwpA b.6.1.1 22903 1dzkA 157 7.10e+00 1obpA b.60.1.1 27096 1csjA 531 7.13e+00 1quvA e.8.1.4 43120 1a7tA 232 7.19e+00 1a7tA d.157.1.1 42041 1l7mA 211 7.27e+00 1g7sA 594 7.28e+00 1g7rA b.43.3.1 25712 b.43.3.1 25713 c.20.1.1 31032 c.37.1.8 32147 1adoA 363 7.31e+00 1fbaA c.1.10.1 29124 1eq9A 222 7.51e+00 5ptp b.47.1.2 26068 1a0p 290 7.58e+00 1a0p a.60.9.1 18105 d.163.1.1 42165 1mtyD 512 7.59e+00 1mhyD a.25.1.2 16742 1fjgQ 105 7.70e+00 1fjfQ b.40.4.5 25352 1h70A 255 7.75e+00 1h70A d.126.1.3 60711 1j9yA 385 7.82e+00 1j9yA c.1.8.3 62791 1dkgD 383 7.93e+00 1ba1 c.55.1.1 33427 c.55.1.1 33428 1mmoD 512 7.97e+00 1mhyD a.25.1.2 16770 1sriA 121 8.03e+00 1swuA b.61.1.1 27276 1fzkA 274 8.11e+00 1agdA b.1.1.2 60149 d.19.1.1 60150 2bc2A 227 8.14e+00 1a7tA d.157.1.1 42031 1jflA 228 8.26e+00 1fc3A 120 8.31e+00 1fc3A a.4.6.3 16237 1b93B 152 8.38e+00 1b93A c.24.1.2 31508 1jl2A 156 8.59e+00 c.55.3.1 66822 1ex2A 189 8.63e+00 1ex2A c.51.4.2 33225 4pfk 319 8.98e+00 3pfk c.89.1.1 35582 9rnt 104 9.14e+00 9rnt d.1.1.1 36055 2ebn 289 9.16e+00 2ebn c.1.8.5 28990 1kkhA 317 9.95e+00 1fvgA 199 1.00e+01 1fvaA d.58.28.1 39408 1tgoA 773 1.02e+01 1tgoA c.55.3.5 33721 e.8.1.1 43010 1t7pA 698 1.02e+01 1t7pA c.55.3.5 33712 e.8.1.1 43005 1i0vA 104 1.03e+01 9rnt d.1.1.1 36054 3pfk 319 1.04e+01 3pfk c.89.1.1 35581 2bc2B 227 1.05e+01 1a7tA d.157.1.1 42032 1euoA 180 1.07e+01 1np1A b.60.1.1 27163 1a3yA 149 1.09e+01 1obpA b.60.1.1 27110 1fcqA 350 1.11e+01 c.1.8.9 65006 1gca 309 1.15e+01 1gca c.93.1.1 35659 1vaoA 560 1.19e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1hjp 203 1.21e+01 1hjp a.5.1.1 16274 a.60.2.1 17947 b.40.4.2 25266 1etu 394 1.23e+01 1efcA c.37.1.8 64737 1lcyA 325 1.24e+01 1g4uS 383 1.26e+01 1g4uS a.24.11.1 16643 c.45.1.2 32691 1qs2A 401 1.27e+01 1qs1A d.166.1.1 42268 d.166.1.1 42269 1sxl 97 1.27e+01 1b7fA d.58.7.1 39180 1qhuA 460 1.27e+01 1qhuA b.66.1.1 27530 b.66.1.1 27531 1g5aA 628 1.28e+01 b.71.1.1 65152 c.1.8.1 65153 1k8wA 327 1.28e+01 d.58.35.2 68317 d.58.35.2 68318 1h99A 224 1.30e+01 a.142.1.1 60814 a.142.1.1 60815 1befA 181 1.30e+01 1befA b.47.1.3 26419 1b93A 152 1.32e+01 1b93A c.24.1.2 31507 1ecxA 384 1.34e+01 1ecxA c.67.1.3 34431 1mgtA 174 1.34e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1ceqA 316 1.35e+01 1ceqA c.2.1.5 30163 d.162.1.1 42130 1qltA 560 1.36e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 3rnt 104 1.37e+01 9rnt d.1.1.1 36069 2rmcA 182 1.37e+01 2cpl b.62.1.1 27491 1k0tA 80 1.39e+01 2lbp 346 1.39e+01 2liv c.93.1.1 35709 1jj2S 119 1.40e+01 1ffkQ b.34.5.1 63104 1bea 127 1.49e+01 1bea a.52.1.2 17826 1fliA 98 1.49e+01 1awcA a.4.5.21 16160 1jeoA 180 1.52e+01 c.80.1.3 66611 4aahA 571 1.56e+01 4aahA b.70.1.1 27678 1apa 266 1.56e+01 1qi7A d.165.1.1 42205 1ab9C 97 1.57e+01 5ptp 1b24A 188 1.57e+01 1b24A d.95.2.1 40573 d.95.2.1 40574 1bg4 302 1.58e+01 1taxA c.1.8.3 28806 1kgsA 225 1.60e+01 a.4.6.1 68596 c.23.1.1 68597 1j7nA 776 1.62e+01 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1jzgA 128 1.62e+01 b.6.1.1 67855 1fo8A 343 1.63e+01 1foaA c.68.1.10 59927 1i0dA 332 1.63e+01 1pscA c.1.9.3 61487 1hzyA 332 1.65e+01 1pscA c.1.9.3 61468 1ky9B 448 1.65e+01 1eywA 331 1.67e+01 1pscA c.1.9.3 29057 1gl4B 98 1.70e+01 b.1.1.4 65288 1epxA 370 1.73e+01 1fbaA c.1.10.1 29150 1g4wR 383 1.75e+01 1g4uS a.24.11.1 16644 c.45.1.2 32692 1regX 122 1.76e+01 1regX d.58.27.1 39406 1f5mB 180 1.76e+01 1f5mB d.110.2.1 40896 1pscA 365 1.77e+01 1pscA c.1.9.3 29058 1yagG 125 1.80e+01 1d0nA d.109.1.1 40846 1g72A 573 1.80e+01 4aahA b.70.1.1 27680 1mctA 223 1.84e+01 5ptp b.47.1.2 25961 1efuB 282 1.85e+01 1efuB a.5.2.2 58975 d.43.1.1 58976 d.43.1.1 38677 1kzyC 259 1.88e+01 1dymA 402 1.89e+01 1celA b.29.1.10 24304 1f5mA 180 1.89e+01 1f5mB d.110.2.1 40895 1cd9C 175 1.95e+01 1bgc a.26.1.1 16816 1e8gA 560 1.97e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1derA 547 1.98e+01 1derA a.129.1.1 19459 c.8.5.1 30788 d.56.1.1 38907 1mrg 263 2.00e+01 1mrj d.165.1.1 42183 1jb0E 75 2.00e+01 1pse b.34.4.2 62824 1g5cA 170 2.00e+01 1g5cA c.53.2.1 60264 1foaA 348 2.03e+01 1foaA c.68.1.10 59929 1bxoA 323 2.03e+01 2er7E b.50.1.2 26805 1air 353 2.04e+01 1air b.80.1.1 28018 1d8hA 311 2.08e+01 1d8iA d.63.1.1 39544 1bqv 110 2.14e+01 1bqv a.60.1.1 17932 1a05A 358 2.14e+01 1cnzA c.77.1.1 35059 1dd5A 185 2.15e+01 1dd5A d.67.3.1 39564 1i4fA 275 2.19e+01 1agdA b.1.1.2 61687 d.19.1.1 61688 1eudA 311 2.19e+01 2scuA c.2.1.8 30312 c.23.4.1 31140 1bv4A 118 2.19e+01 1rtm1 d.169.1.1 42380 1b8gA 429 2.21e+01 1b8gA c.67.1.4 34499 1fjgM 126 2.22e+01 1fjfM a.5.5.1 16293 1acf 125 2.24e+01 3nul d.110.1.1 40882 1ewjA 126 2.26e+01 1ecsA d.32.1.2 59526 7icd 416 2.37e+01 1iso c.77.1.1 35072 2frvB 536 2.40e+01 1h2rL e.18.1.1 43291 1e8xA 961 2.41e+01 1e8xA a.118.1.6 19148 b.7.1.1 23183 d.15.1.5 37631 d.144.1.4 41711 1bvsB 203 2.41e+01 1hjp a.5.1.1 16281 a.60.2.1 17956 b.40.4.2 25275 1gg6C 97 2.41e+01 5ptp 2pec 353 2.43e+01 1air b.80.1.1 28019 1fp3A 402 2.43e+01 1fp3A a.102.1.3 18842 1louA 101 2.43e+01 1ris d.58.14.1 39323 1crzA 403 2.46e+01 1crzA b.68.4.1 27629 c.51.2.1 33211 1h4wA 224 2.48e+01 b.47.1.2 65622 1amoA 615 2.49e+01 1amoA b.43.4.1 25669 c.23.5.2 31210 c.25.1.4 31557 1hyuA 521 2.51e+01 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1f6yA 262 2.54e+01 1f6yA c.1.21.2 29673 1ffk1 177 2.58e+01 1ffk1 1pytA 94 2.60e+01 1pytA d.58.3.1 39064 1dy9A 187 2.60e+01 1jxpA b.47.1.3 26400 1f7zA 233 2.64e+01 5ptp b.47.1.2 59681 1lk5A 229 2.66e+01 1mtnC 97 2.66e+01 5ptp 2sniI 83 2.67e+01 2sniI d.40.1.1 38573 1edt 271 2.74e+01 2ebn c.1.8.5 28993 1h6oA 204 2.75e+01 a.146.1.1 60689 1qhtA 775 2.79e+01 1tgoA c.55.3.5 33722 e.8.1.1 43011 1d4xG 126 2.82e+01 1d0nA d.109.1.1 59109 1f20A 435 2.87e+01 b.43.4.1 64932 c.25.1.4 64933 1h6hA 143 2.91e+01 d.189.1.1 65681 1qpzA 340 2.92e+01 1qpzA a.35.1.5 17097 c.93.1.1 35673 1gdoA 240 2.96e+01 1gdoA d.153.1.1 41804 1qq4A 198 2.96e+01 1qq4A b.47.1.1 25768 1kamA 194 2.97e+01 1qhqA 140 2.99e+01 1qhqA b.6.1.1 63326 1jic 62 3.03e+01 1azpA d.9.2.1 37462 1eaxA 241 3.05e+01 b.47.1.2 64889 1ecsA 126 3.05e+01 1ecsA d.32.1.2 59407 1qftA 175 3.08e+01 1qftA b.60.1.1 27151 1cs6A 382 3.08e+01 1cs6A b.1.1.4 21760 b.1.1.4 21761 b.1.1.4 21762 b.1.1.4 21763 2pia 321 3.09e+01 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1bg7 176 3.12e+01 2fha a.25.1.1 16686 1ba1 386 3.14e+01 1ba1 c.55.1.1 33387 c.55.1.1 33388 1duzA 275 3.16e+01 1agdA b.1.1.2 20670 d.19.1.1 38224 1a44 185 3.16e+01 1a44 b.17.1.1 23704 1i45A 248 3.17e+01 1amk c.1.1.1 61665 1mspA 126 3.18e+01 1mspA b.1.11.2 22333 1kay 381 3.19e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1ecl 597 3.20e+01 1ecl e.10.1.1 43238 1ecrA 309 3.21e+01 1ecrA e.2.1.1 42678 1ljoA 77 3.22e+01 2rn2 155 3.23e+01 2rn2 c.55.3.1 33551 1f9fA 83 3.24e+01 1f9fA d.58.8.1 39224 1ffkQ 119 3.26e+01 1ffkQ b.34.5.1 24605 1vasA 137 3.28e+01 2end a.18.1.1 16404 1i1gA 141 3.28e+01 a.4.5.32 65982 d.58.37.1 65983 1behA 187 3.36e+01 1a44 b.17.1.1 23700 1skyB 502 3.42e+01 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1qhfA 240 3.45e+01 1qhfA c.60.1.1 33960 1kq3A 376 3.53e+01 e.22.1.2 68790 7catA 506 3.55e+01 1cf9A e.5.1.1 42781 1ky9A 448 3.58e+01 1g2rA 100 3.62e+01 1g2rA d.192.1.1 60231 1bj7 156 3.66e+01 1bj7 b.60.1.1 27113 1j98A 157 3.70e+01 1j98A d.185.1.2 62755 1g99A 408 3.71e+01 1g99A c.55.1.2 33457 c.55.1.2 33458 1ihrA 76 3.78e+01 1ihrA d.191.1.1 62392 1e9lA 377 3.83e+01 1e9lA c.1.8.5 59395 d.26.3.1 59396 7timA 247 3.83e+01 1amk c.1.1.1 28457 1dbqA 289 3.84e+01 1qpzA c.93.1.1 35666 1eg5A 384 3.90e+01 1ecxA c.67.1.3 34429 1fsgA 233 3.91e+01 1qk3A c.61.1.1 34029 1fts 295 3.91e+01 1ng1 a.24.13.1 16968 c.37.1.10 32279 1go3F 107 3.92e+01 a.60.8.2 65407 1as4A 341 3.94e+01 1sek e.1.1.1 42623 1lay 256 3.94e+01 1lay b.57.1.1 27014 1jb0D 138 3.94e+01 1jb0D d.187.1.1 62823 1clqA 903 3.95e+01 1clqA c.55.3.5 33717 e.8.1.1 43006 1sgpE 185 3.97e+01 1qq4A b.47.1.1 25816 1g0cA 364 3.97e+01 7a3hA c.1.8.3 60165 4xiaA 393 3.98e+01 4xis c.1.15.3 29439