# List of top-scoring protein chains for t2k-100-30-str 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 1grwA 126 1.12e-19 1mspA 126 7.29e-19 1mspA b.1.11.2 22333 1qpxA 218 7.48e-03 1qpxA b.1.11.1 22318 b.7.2.1 23200 1qppA 218 1.02e-02 1qpxA b.1.11.1 22320 b.7.2.1 23202 1itbB 315 2.51e-02 1itbB b.1.1.4 21720 b.1.1.4 21721 b.1.1.4 21722 1exmA 405 9.21e-02 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1ha3A 405 1.31e-01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1g0dA 695 2.46e-01 1f13A b.1.1.5 60166 b.1.5.1 60167 b.1.5.1 60168 d.3.1.4 60169 1aipE 405 2.80e-01 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1l4iA 206 3.63e-01 1a2yB 116 5.06e-01 1gc1H b.1.1.1 19927 1avgI 142 5.79e-01 1avgI b.60.1.3 27229 1kgyA 181 6.44e-01 1vfaB 116 6.67e-01 1gc1H b.1.1.1 19929 1efcA 393 7.03e-01 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 2afgA 140 7.76e-01 1bfg b.42.1.1 25514 1d2eA 397 9.55e-01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1jt7A 146 1.03e+00 b.42.1.1 67255 1ibyA 112 1.03e+00 1ibzA b.6.1.4 62233 1bebA 162 1.15e+00 1bebA b.60.1.1 27115 1ibzA 112 1.23e+00 1ibzA b.6.1.4 62237 1yer 228 1.27e+00 1yer d.122.1.1 41101 1dlfH 124 1.27e+00 1igtB b.1.1.1 20383 8fabB 224 1.35e+00 1igtB b.1.1.1 19773 b.1.1.2 20883 3rp2A 224 1.42e+00 1a7s b.47.1.2 26298 1nukA 183 1.53e+00 1nukA b.18.1.4 23721 1kshB 152 1.54e+00 1bdfA 235 1.60e+00 1bdfA d.74.3.1 39727 d.181.1.1 42602 1f89A 291 2.12e+00 d.160.1.1 64988 1hw7A 255 2.27e+00 1i7fA d.193.1.1 61297 1dq3A 454 2.37e+00 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1fjgQ 105 2.44e+00 1fjfQ b.40.4.5 25352 1fdlH 218 2.49e+00 1igtB b.1.1.1 19961 b.1.1.2 21021 1am2 199 3.09e+00 1am2 b.86.1.2 28381 1i7fA 292 3.43e+00 1i7fA d.193.1.1 61888 4blmA 265 3.73e+00 1btl e.3.1.1 42721 1bbpA 173 4.14e+00 1bbpA b.60.1.1 27147 1dqqB 210 4.37e+00 1igtB b.1.1.1 20421 b.1.1.2 21391 1jguH 217 4.53e+00 b.1.1.1 66688 b.1.1.2 66689 1kcvH 217 4.67e+00 1ijaA 148 4.72e+00 1ijaA b.100.1.1 62484 1i8kB 124 4.95e+00 1axiB 236 4.96e+00 1axiB b.1.2.1 21997 b.1.2.1 21998 1epfA 191 4.99e+00 2ncm b.1.1.4 21694 b.1.1.4 21695 1f3rB 257 4.99e+00 1f3rB b.1.1.1 20416 b.1.1.1 20417 1ah6 220 5.37e+00 1yer d.122.1.1 41094 1ddt 535 5.40e+00 1ddt b.2.1.1 22379 d.166.1.1 42241 f.1.2.1 43384 4ubpB 126 5.79e+00 1ubpB b.85.3.1 28345 1bfg 146 5.92e+00 1bfg b.42.1.1 25485 1lvk 762 5.93e+00 1lvk b.34.3.1 24576 c.37.1.9 32173 1l7uA 263 5.98e+00 1m40A 263 5.98e+00 1byqA 228 6.02e+00 1yer d.122.1.1 41100 1e42A 258 6.05e+00 1e42A b.1.10.1 22316 d.105.1.1 40792 1btl 263 6.06e+00 1btl e.3.1.1 42691 1ermA 263 6.06e+00 1btl e.3.1.1 42690 1ejrB 101 6.12e+00 1ubpB b.85.3.1 28320 1fwcB 106 6.12e+00 1ubpB b.85.3.1 28324 2kauB 106 6.12e+00 1ubpB b.85.3.1 28328 2ncm 99 6.17e+00 2ncm b.1.1.4 21703 1fqgA 263 6.17e+00 1btl e.3.1.1 42699 1dun 134 6.19e+00 1dun b.85.4.1 28371 1noa 113 6.26e+00 2mcm b.1.7.1 22208 1hzoA 271 6.28e+00 1ubpB 122 6.31e+00 1ubpB b.85.3.1 28346 1a5r 103 6.42e+00 1a5r d.15.1.1 37597 1a8p 258 6.88e+00 1fdr b.43.4.2 25654 c.25.1.1 31544 3hhrB 203 6.89e+00 1axiB b.1.2.1 22005 b.1.2.1 22006 1gpr 162 6.96e+00 1gpr b.84.3.1 28267 1tvdA 116 7.08e+00 1tvdA b.1.1.1 20650 1jmxA 494 8.28e+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 1cdcB 99 8.29e+00 1cdcA b.1.1.1 19747 1g291 372 8.33e+00 1g291 1as4B 37 8.74e+00 1as4B 1dupA 152 9.27e+00 1dupA b.85.4.1 28351 1euwA 152 9.27e+00 1dupA b.85.4.1 28349 1igtB 444 9.30e+00 1igtB b.1.1.1 19765 b.1.1.2 20867 b.1.1.2 20868 b.1.1.2 20869 1igtD 444 9.37e+00 1igtB b.1.1.1 19767 b.1.1.2 20871 b.1.1.2 20872 b.1.1.2 20873 1ew3A 159 9.53e+00 1mup b.60.1.1 27114 2phlA 397 1.00e+01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1a64A 97 1.02e+01 1cdcA b.1.1.1 19750 1i2sA 282 1.06e+01 1ikoP 178 1.09e+01 1msaA 109 1.10e+01 1b2pA b.78.1.1 27987 1vcaA 202 1.14e+01 1vcaA b.1.1.3 21649 b.1.1.4 21685 1qunB 279 1.15e+01 b.2.3.2 22411 b.2.3.2 22412 1cdcA 99 1.16e+01 1cdcA b.1.1.1 19746 1xnb 185 1.17e+01 1axkA b.29.1.11 24308 1a6wH 120 1.17e+01 1mfa b.1.1.1 20253 1h4uA 265 1.18e+01 1h4uA d.22.1.2 60622 g.3.11.5 60623 1qrkA 731 1.18e+01 1f13A b.1.1.5 21889 b.1.5.1 22187 b.1.5.1 22188 d.3.1.4 37119 1qhuA 460 1.23e+01 1qhuA b.66.1.1 27530 b.66.1.1 27531 1g7jB 116 1.26e+01 1f3rB b.1.1.1 19933 1azeA 56 1.27e+01 b.34.2.1 24536 1gguA 731 1.28e+01 1f13A b.1.1.5 21885 b.1.5.1 22179 b.1.5.1 22180 d.3.1.4 37115 1ovaA 386 1.31e+01 1ovaA e.1.1.1 42619 1bsg 266 1.35e+01 1btl e.3.1.1 42729 1hae 63 1.40e+01 1xdtR g.3.11.1 44298 1kiuB 279 1.41e+01 1c5cH 215 1.48e+01 1igtB b.1.1.1 20475 b.1.1.2 21439 1g6q2 328 1.48e+01 1g6q2 1gcpA 70 1.51e+01 1gcpA b.34.2.1 60430 2fgf 146 1.54e+01 1bfg b.42.1.1 25487 1cauA 181 1.58e+01 1dgwA b.82.1.2 28102 1ky9B 448 1.61e+01 1mnd 762 1.64e+01 1lvk b.34.3.1 24591 c.37.1.9 32188 1jc4A 148 1.66e+01 1jc4A d.32.1.4 62863 2mcm 112 1.67e+01 2mcm b.1.7.1 22207 1cyx 205 1.67e+01 1cyx b.6.1.2 23023 1ej8A 140 1.73e+01 1qupA b.1.8.1 22300 1ospH 218 1.73e+01 1igtB b.1.1.1 20117 b.1.1.2 21147 1f0lA 535 1.76e+01 1ddt b.2.1.1 22377 d.166.1.1 42239 f.1.2.1 43382 1bza 262 1.79e+01 1btl e.3.1.1 42701 1wejH 223 1.84e+01 1igtB b.1.1.1 20361 b.1.1.2 21353 1qhlA 227 1.86e+01 1qhlA c.37.1.12 32382 1ivyA 452 1.89e+01 1ivyA c.69.1.5 34654 4fgf 146 1.93e+01 1bfg b.42.1.1 25486 1rdzA 337 1.96e+01 1frpA e.7.1.1 42882 1dc1A 323 2.06e+01 1dc1A c.52.1.11 33321 1mrg 263 2.07e+01 1mrj d.165.1.1 42183 1np1A 184 2.09e+01 1np1A b.60.1.1 27155 1lckA 175 2.10e+01 1lckA b.34.2.1 24552 d.93.1.1 40421 1acc 735 2.11e+01 1acc f.11.1.1 43828 1dgwA 178 2.13e+01 1dgwA b.82.1.2 28090 1fc1A 224 2.15e+01 1igtB b.1.1.2 21520 b.1.1.2 21521 1fc2D 224 2.17e+01 1igtB b.1.1.2 21516 b.1.1.2 21517 1d7cA 190 2.22e+01 1d7bA b.1.9.1 22309 1d7bA 186 2.24e+01 1d7bA b.1.9.1 22307 1ky9A 448 2.26e+01 1eq6A 189 2.27e+01 1eq6A d.107.1.1 40796 1b35B 255 2.29e+01 1b35B b.10.1.3 23334 1ifrA 121 2.35e+01 1lxtA 561 2.37e+01 3pmgA c.84.1.1 35432 c.84.1.1 35433 c.84.1.1 35434 d.129.2.1 41309 1a15A 67 2.40e+01 1a15A d.9.1.1 37451 1gcqC 70 2.40e+01 1gcpA b.34.2.1 60436 1ju3A 583 2.41e+01 b.18.1.13 67300 c.69.1.21 67301 1krs 120 2.51e+01 1krs b.40.4.1 25256 1kxvC 121 2.52e+01 3rabA 169 2.58e+01 1ctqA c.37.1.8 32018 1gh7A 419 2.58e+01 b.1.2.1 65194 b.1.2.1 65195 b.1.2.1 65196 b.1.2.1 65197 1qmeA 702 2.59e+01 1pmd d.11.1.1 37487 d.11.1.1 37488 d.175.1.1 42560 e.3.1.1 42769 1r092 262 2.64e+01 1aym2 1evuA 731 2.65e+01 1f13A b.1.1.5 21883 b.1.5.1 22175 b.1.5.1 22176 d.3.1.4 37113 1cf1A 404 2.67e+01 1cf1A b.1.1.5 21907 b.1.1.5 21908 2hrvA 142 2.68e+01 2hrvA b.47.1.4 26429 1agqD 135 2.71e+01 1agqA g.17.1.2 44792 1klt 226 2.73e+01 5ptp b.47.1.2 26300 1b25A 619 2.73e+01 1b25A a.110.1.1 19044 d.152.1.1 41796 1tf4A 605 2.77e+01 1tf4A a.102.1.2 18827 b.2.2.2 22393 1bqk 124 2.80e+01 1bqk b.6.1.1 22889 1bteA 97 2.82e+01 1bteA g.7.1.3 44463 1nbcA 155 2.84e+01 1nbcA b.2.2.2 22390 4rhv3 236 2.89e+01 1aym3 1f94A 63 2.89e+01 1f94A g.7.1.1 44435 2scuB 388 2.90e+01 2scuB c.23.4.1 31141 d.142.1.4 41562 35c8H 217 2.97e+01 8fabA b.1.1.1 20297 b.1.1.2 21289 1xypA 190 2.97e+01 1axkA b.29.1.11 24327 1nom 248 2.98e+01 1bpyA e.9.1.1 43220 1euu 605 3.01e+01 1eut b.1.1.5 21892 b.18.1.1 23713 b.68.1.1 27610 1hcv 117 3.01e+01 1igtB b.1.1.1 20514 1kskA 234 3.02e+01 1mrj 247 3.04e+01 1mrj d.165.1.1 42177 1quqA 129 3.05e+01 1quqA b.40.4.3 25303 1qupA 222 3.06e+01 1qupA b.1.8.1 22301 d.58.17.1 39352 1bf8 205 3.07e+01 1qpxA b.1.11.1 22332 b.7.2.1 23214 1e32A 458 3.07e+01 1e32A b.52.2.3 59183 c.37.1.13 59184 d.31.1.1 59185 2pia 321 3.08e+01 2pia b.43.4.2 25663 c.25.1.2 31553 d.15.4.2 37704 1fr7A 260 3.11e+01 2cba b.74.1.1 27828 1aozA 552 3.11e+01 1aozA b.6.1.3 23124 b.6.1.3 23125 b.6.1.3 23126 1f60B 94 3.18e+01 1b64 d.58.12.1 39307 1erxA 184 3.25e+01 1np1A b.60.1.1 27164 1fnhA 271 3.28e+01 1fnhA b.1.2.1 21976 b.1.2.1 21977 b.1.2.1 21978 1lkkA 105 3.32e+01 1lckA d.93.1.1 40412 1i9aA 182 3.35e+01 1i9aA d.113.1.2 62082 1hyxH 224 3.37e+01 1igtB b.1.1.1 20167 b.1.1.2 21191 1dm0A 287 3.38e+01 1dm0A d.165.1.2 42227 1dvfD 120 3.38e+01 1mfa b.1.1.1 20107 1qg7A 67 3.38e+01 1a15A d.9.1.1 37449 2mev2 256 3.39e+01 1aym2 1jjoC 261 3.42e+01 2fnbA 95 3.43e+01 2fnbA b.1.2.1 21979 1bpb 248 3.43e+01 1bpyA e.9.1.1 43215 1eut 605 3.44e+01 1eut b.1.1.5 21891 b.18.1.1 23712 b.68.1.1 27609 1ca1 370 3.47e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1je5A 206 3.53e+01 1je5A b.40.4.7 62909 1e1aA 314 3.54e+01 1e1aA b.68.6.1 59155 1hztA 190 3.56e+01 1i9aA d.113.1.2 61459 2rhe 114 3.60e+01 8fabA b.1.1.1 20523 1aqt 138 3.60e+01 1aqt a.2.10.1 15718 b.93.1.1 28435 1pvc2 271 3.63e+01 1aym2 1l6xA 207 3.64e+01 1ia9A 280 3.70e+01 1ia9A d.144.1.5 62113 1iam 185 3.73e+01 1zxq b.1.1.3 21653 b.1.1.4 21689 1koiA 184 3.77e+01 b.60.1.1 68725 1f7dA 136 3.77e+01 1dun b.85.4.1 28353 1qqp2 218 3.78e+01 1qqp2 1euvA 221 3.80e+01 1euvA d.3.1.7 37133 1f39A 101 3.80e+01 1umuA b.87.1.1 28386 1ihkA 174 3.82e+01 1bfg b.42.1.1 62384 1bxnA 485 3.87e+01 1burA c.1.14.1 29376 d.58.9.1 39282