# 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 1grwA 126 8.13e-25 1mspA 126 1.03e-23 1mspA b.1.11.2 22333 1qppA 218 1.20e-02 1qpxA b.1.11.1 22320 b.7.2.1 23202 1avgI 142 1.76e-02 1avgI b.60.1.3 27229 1qpxA 218 2.86e-02 1qpxA b.1.11.1 22318 b.7.2.1 23200 1itbB 315 2.29e-01 1itbB b.1.1.4 21720 b.1.1.4 21721 b.1.1.4 21722 1exmA 405 4.09e-01 1efcA b.43.3.1 25696 b.44.1.1 25736 c.37.1.8 32131 1cyx 205 4.81e-01 1cyx b.6.1.2 23023 1l4iA 206 5.21e-01 1g0dA 695 5.56e-01 1f13A b.1.1.5 60166 b.1.5.1 60167 b.1.5.1 60168 d.3.1.4 60169 1bebA 162 5.90e-01 1bebA b.60.1.1 27115 1fjgQ 105 5.98e-01 1fjfQ b.40.4.5 25352 2afgA 140 6.25e-01 1bfg b.42.1.1 25514 1bdfA 235 6.93e-01 1bdfA d.74.3.1 39727 d.181.1.1 42602 1a2yB 116 7.75e-01 1gc1H b.1.1.1 19927 1ha3A 405 7.95e-01 1efcA b.43.3.1 60869 b.44.1.1 60870 c.37.1.8 60871 1vfaB 116 8.47e-01 1gc1H b.1.1.1 19929 1dlfH 124 9.32e-01 1igtB b.1.1.1 20383 1e42A 258 9.35e-01 1e42A b.1.10.1 22316 d.105.1.1 40792 1aipE 405 1.05e+00 1efcA b.43.3.1 25699 b.44.1.1 25739 c.37.1.8 32134 1tf4A 605 1.10e+00 1tf4A a.102.1.2 18827 b.2.2.2 22393 1ibyA 112 1.13e+00 1ibzA b.6.1.4 62233 1ibzA 112 1.14e+00 1ibzA b.6.1.4 62237 1jt7A 146 1.23e+00 b.42.1.1 67255 1yer 228 1.65e+00 1yer d.122.1.1 41101 1bbpA 173 1.68e+00 1bbpA b.60.1.1 27147 1ktbA 405 1.75e+00 1ep2B 261 2.18e+00 1ep2B b.43.4.2 25666 c.25.1.3 31556 1ikoP 178 2.26e+00 8fabB 224 2.43e+00 1igtB b.1.1.1 19773 b.1.1.2 20883 1ivyA 452 2.62e+00 1ivyA c.69.1.5 34654 1btl 263 2.80e+00 1btl e.3.1.1 42691 1ermA 263 2.82e+00 1btl e.3.1.1 42690 1ddt 535 2.90e+00 1ddt b.2.1.1 22379 d.166.1.1 42241 f.1.2.1 43384 1kgyA 181 3.09e+00 1kqrA 179 3.10e+00 1hzoA 271 3.19e+00 1qrkA 731 3.20e+00 1f13A b.1.1.5 21889 b.1.5.1 22187 b.1.5.1 22188 d.3.1.4 37119 1ew3A 159 3.51e+00 1mup b.60.1.1 27114 1gguA 731 3.57e+00 1f13A b.1.1.5 21885 b.1.5.1 22179 b.1.5.1 22180 d.3.1.4 37115 1f89A 291 3.58e+00 d.160.1.1 64988 1l7uA 263 3.62e+00 1m40A 263 3.62e+00 1fqgA 263 3.62e+00 1btl e.3.1.1 42699 2bpa2 175 3.67e+00 2bpa2 3rp2A 224 3.73e+00 1a7s b.47.1.2 26298 1epfA 191 4.09e+00 2ncm b.1.1.4 21694 b.1.1.4 21695 1lckA 175 4.19e+00 1lckA b.34.2.1 24552 d.93.1.1 40421 1bfg 146 4.28e+00 1bfg b.42.1.1 25485 1a5r 103 4.36e+00 1a5r d.15.1.1 37597 1jguH 217 4.68e+00 b.1.1.1 66688 b.1.1.2 66689 4ubpB 126 4.83e+00 1ubpB b.85.3.1 28345 1nbcA 155 4.85e+00 1nbcA b.2.2.2 22390 1je5A 206 5.05e+00 1je5A b.40.4.7 62909 1thjA 214 5.16e+00 1qreA b.81.1.5 28072 1cf1A 404 5.20e+00 1cf1A b.1.1.5 21907 b.1.1.5 21908 1ubpB 122 5.35e+00 1ubpB b.85.3.1 28346 1i8kB 124 5.77e+00 1qreA 247 6.12e+00 1qreA b.81.1.5 28066 1quqA 129 6.54e+00 1quqA b.40.4.3 25303 1fbaA 361 6.61e+00 1fbaA c.1.10.1 29120 3mddA 385 6.65e+00 3mdeA a.29.3.1 16592 e.6.1.1 42853 1azeA 56 6.69e+00 b.34.2.1 24536 1iraX 152 6.71e+00 1irp b.42.1.2 25556 1lvk 762 7.15e+00 1lvk b.34.3.1 24576 c.37.1.9 32173 1byqA 228 7.23e+00 1yer d.122.1.1 41100 2fnbA 95 7.48e+00 2fnbA b.1.2.1 21979 1dc1A 323 7.61e+00 1dc1A c.52.1.11 33321 1g4mA 393 7.67e+00 b.1.1.5 65143 b.1.1.5 65144 1a8p 258 7.69e+00 1fdr b.43.4.2 25654 c.25.1.1 31544 1gh7A 419 7.71e+00 b.1.2.1 65194 b.1.2.1 65195 b.1.2.1 65196 b.1.2.1 65197 1nukA 183 7.83e+00 1nukA b.18.1.4 23721 4blmA 265 8.14e+00 1btl e.3.1.1 42721 1igtB 444 8.24e+00 1igtB b.1.1.1 19765 b.1.1.2 20867 b.1.1.2 20868 b.1.1.2 20869 1efcA 393 8.29e+00 1efcA b.43.3.1 25680 b.44.1.1 25720 c.37.1.8 32113 1kiuB 279 8.35e+00 1noa 113 8.36e+00 2mcm b.1.7.1 22208 1ep3B 262 8.48e+00 1ep2B b.43.4.2 25664 c.25.1.3 31554 1vcaA 202 8.64e+00 1vcaA b.1.1.3 21649 b.1.1.4 21685 1ejrB 101 8.73e+00 1ubpB b.85.3.1 28320 1fwcB 106 8.74e+00 1ubpB b.85.3.1 28324 2kauB 106 8.74e+00 1ubpB b.85.3.1 28328 1f13A 731 8.74e+00 1f13A b.1.1.5 21877 b.1.5.1 22163 b.1.5.1 22164 d.3.1.4 37107 1qexA 288 8.92e+00 1qexA b.32.1.1 24425 1as4B 37 9.12e+00 1as4B 4rhv3 236 9.24e+00 1aym3 1kcvH 217 9.24e+00 1eudA 311 9.43e+00 2scuA c.2.1.8 30312 c.23.4.1 31140 1rhi3 236 9.56e+00 1aym3 1by3A 714 9.64e+00 1by5A f.4.3.3 43801 1kv7A 488 9.90e+00 b.6.1.3 68873 b.6.1.3 68874 b.6.1.3 68875 1bza 262 1.05e+01 1btl e.3.1.1 42701 1qunB 279 1.06e+01 b.2.3.2 22411 b.2.3.2 22412 1eybA 471 1.11e+01 1ey2A b.82.1.4 28115 1c5cH 215 1.13e+01 1igtB b.1.1.1 20475 b.1.1.2 21439 1mnd 762 1.14e+01 1lvk b.34.3.1 24591 c.37.1.9 32188 1evuA 731 1.14e+01 1f13A b.1.1.5 21883 b.1.5.1 22175 b.1.5.1 22176 d.3.1.4 37113 1i7fA 292 1.15e+01 1i7fA d.193.1.1 61888 2fgf 146 1.17e+01 1bfg b.42.1.1 25487 1yge 839 1.21e+01 1yge a.119.1.1 19234 b.12.1.1 23634 1d2eA 397 1.22e+01 1efcA b.43.3.1 25701 b.44.1.1 25741 c.37.1.8 32136 1bqk 124 1.24e+01 1bqk b.6.1.1 22889 1quqB 121 1.26e+01 1quqB b.40.4.3 25305 1f3rB 257 1.28e+01 1f3rB b.1.1.1 20416 b.1.1.1 20417 1wejH 223 1.28e+01 1igtB b.1.1.1 20361 b.1.1.2 21353 2rhe 114 1.29e+01 8fabA b.1.1.1 20523 1lkkA 105 1.30e+01 1lckA d.93.1.1 40412 3mdeA 385 1.33e+01 3mdeA a.29.3.1 16594 e.6.1.1 42855 2scuA 288 1.33e+01 2scuA c.2.1.8 30303 c.23.4.1 31131 1ah6 220 1.34e+01 1yer d.122.1.1 41094 1dupA 152 1.37e+01 1dupA b.85.4.1 28351 1euwA 152 1.37e+01 1dupA b.85.4.1 28349 1ktgA 138 1.38e+01 1klt 226 1.40e+01 5ptp b.47.1.2 26300 1lnh 857 1.43e+01 1yge a.119.1.1 19237 b.12.1.1 23637 1i78A 297 1.44e+01 f.4.4.1 66046 1igtD 444 1.45e+01 1igtB b.1.1.1 19767 b.1.1.2 20871 b.1.1.2 20872 b.1.1.2 20873 1fdlH 218 1.46e+01 1igtB b.1.1.1 19961 b.1.1.2 21021 1by5A 714 1.46e+01 1by5A f.4.3.3 43800 1ey2A 471 1.47e+01 1ey2A b.82.1.4 28116 1gefA 123 1.47e+01 1gefA c.52.1.18 60465 1f39A 101 1.49e+01 1umuA b.87.1.1 28386 1f0lA 535 1.57e+01 1ddt b.2.1.1 22377 d.166.1.1 42239 f.1.2.1 43382 1a6wH 120 1.58e+01 1mfa b.1.1.1 20253 1e32A 458 1.59e+01 1e32A b.52.2.3 59183 c.37.1.13 59184 d.31.1.1 59185 1dun 134 1.60e+01 1dun b.85.4.1 28371 1gcpA 70 1.64e+01 1gcpA b.34.2.1 60430 1ca1 370 1.66e+01 1ca1 a.124.1.1 19340 b.12.1.3 23648 1ggtB 731 1.67e+01 1f13A b.1.1.5 21882 b.1.5.1 22173 b.1.5.1 22174 d.3.1.4 37112 1egdA 396 1.68e+01 3mdeA a.29.3.1 16596 e.6.1.1 42857 1jc4A 148 1.69e+01 1jc4A d.32.1.4 62863 1gcqC 70 1.71e+01 1gcpA b.34.2.1 60436 1az3A 244 1.74e+01 1rvaA c.52.1.2 33276 1tvdA 116 1.78e+01 1tvdA b.1.1.1 20650 1ilr1 152 1.84e+01 1irp 1chrA 370 1.86e+01 1mucA c.1.11.2 29252 d.54.1.1 38896 1cdcA 99 1.87e+01 1cdcA b.1.1.1 19746 1bsg 266 1.89e+01 1btl e.3.1.1 42729 1fna 93 1.90e+01 1fnf b.1.2.1 21971 1agqD 135 1.93e+01 1agqA g.17.1.2 44792 1al0G 175 2.00e+01 2bpa2 b.10.1.1 23275 1rypJ 204 2.02e+01 d.153.1.4 41878 1qfgA 725 2.04e+01 1by5A f.4.3.3 43803 1hw7A 255 2.07e+01 1i7fA d.193.1.1 61297 1scuA 288 2.09e+01 2scuA c.2.1.8 30307 c.23.4.1 31135 1cdcB 99 2.10e+01 1cdcA b.1.1.1 19747 1kay 381 2.11e+01 1ba1 c.55.1.1 33385 c.55.1.1 33386 1ba1 386 2.11e+01 1ba1 c.55.1.1 33387 c.55.1.1 33388 1dq3A 454 2.11e+01 1dq3A b.86.1.2 28380 d.50.3.1 38798 d.95.2.2 40585 d.95.2.2 40586 1bupA 386 2.14e+01 1ba1 c.55.1.1 33377 c.55.1.1 33378 1bhe 376 2.14e+01 1bhe b.80.1.3 28030 1vom 762 2.17e+01 1lvk b.34.3.1 24577 c.37.1.9 32174 1kshB 152 2.18e+01 1bquA 215 2.24e+01 1bquA b.1.2.1 22066 b.1.2.1 22067 1ah9 71 2.24e+01 1ah9 b.40.4.5 25330 1hae 63 2.24e+01 1xdtR g.3.11.1 44298 2fcpA 723 2.37e+01 1by5A f.4.3.3 43802 1io1A 398 2.40e+01 1io1A e.32.1.1 62611 1b35B 255 2.44e+01 1b35B b.10.1.3 23334 1hpwA 129 2.46e+01 1hpwA d.24.1.1 61118 1agqA 135 2.46e+01 1agqA g.17.1.2 44789 1jmxA 494 2.47e+01 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 1ndh 272 2.52e+01 1ndh b.43.4.2 25662 c.25.1.1 31552 1qhuA 460 2.57e+01 1qhuA b.66.1.1 27530 b.66.1.1 27531 1f6fB 210 2.61e+01 1axiB b.1.2.1 22033 b.1.2.1 22034 1rdzA 337 2.67e+01 1frpA e.7.1.1 42882 1jf8A 131 2.68e+01 c.44.1.1 66621 1i2sA 282 2.69e+01 1qk8A 146 2.69e+01 1ewxA c.47.1.10 33061 1nciA 110 2.70e+01 1edhA b.1.6.1 22191 1a64A 97 2.70e+01 1cdcA b.1.1.1 19750 1gteA 1025 2.76e+01 1atzB 189 2.77e+01 1atzA c.62.1.1 34133 1h7wA 1025 2.83e+01 1h7wA a.1.2.2 15683 c.1.4.1 28628 c.3.1.1 30324 c.4.1.1 30609 d.58.1.5 39007 1ncg 110 2.84e+01 1edhA b.1.6.1 22193 1gkkA 297 2.84e+01 c.69.1.2 65248 1jfvA 131 2.85e+01 c.44.1.1 66654 1a44 185 2.86e+01 1a44 b.17.1.1 23704 1kt9A 138 2.87e+01 1gthD 1025 2.89e+01 1gteD 1025 2.89e+01 2mcm 112 2.89e+01 2mcm b.1.7.1 22207 1onc 104 2.91e+01 1onc d.5.1.1 37278 1que 303 2.92e+01 1fnc b.43.4.2 25647 c.25.1.1 31537 1gthC 1025 2.92e+01 1h7wB 1025 2.94e+01 a.1.2.2 15684 c.1.4.1 28629 c.3.1.1 30325 c.4.1.1 30610 d.58.1.5 39008 1pszA 303 2.94e+01 1toaA c.92.2.2 35600 1atzA 189 2.95e+01 1atzA c.62.1.1 34132 1ewfA 456 2.96e+01 1bp1 d.83.1.1 40024 d.83.1.1 40025 1i5gA 144 2.98e+01 1ewxA c.47.1.10 61784 1gthA 1025 3.01e+01 1h7wD 1025 3.06e+01 a.1.2.2 15686 c.1.4.1 28631 c.3.1.1 30327 c.4.1.1 30612 d.58.1.5 39010 2phlA 397 3.14e+01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1jpaA 312 3.14e+01 d.144.1.2 67011 1ayaA 101 3.16e+01 1qadA d.93.1.1 40460 1gklA 297 3.18e+01 c.69.1.2 65250 1j7nB 776 3.21e+01 d.92.1.14 66412 d.92.1.14 66413 d.166.1.1 66414 1a41 234 3.21e+01 1a41 d.163.1.2 42174 1axiB 236 3.22e+01 1axiB b.1.2.1 21997 b.1.2.1 21998 1h7xD 1025 3.23e+01 a.1.2.2 15690 c.1.4.1 28635 c.3.1.1 30331 c.4.1.1 30616 d.58.1.5 39014 1fo0B 112 3.33e+01 1kb5B b.1.1.1 20631 1h7xA 1025 3.36e+01 1h7wA a.1.2.2 15687 c.1.4.1 28632 c.3.1.1 30328 c.4.1.1 30613 d.58.1.5 39011 1h7xB 1025 3.37e+01 a.1.2.2 15688 c.1.4.1 28633 c.3.1.1 30329 c.4.1.1 30614 d.58.1.5 39012 1h4uA 265 3.38e+01 1h4uA d.22.1.2 60622 g.3.11.5 60623 1h7xC 1025 3.39e+01 a.1.2.2 15689 c.1.4.1 28634 c.3.1.1 30330 c.4.1.1 30615 d.58.1.5 39013 1kb5B 117 3.40e+01 1kb5B b.1.1.1 20632 1avaC 181 3.41e+01 1avaC b.42.4.1 25604 1tit 98 3.44e+01 1tit b.1.1.4 21716 1j7nA 776 3.48e+01 d.92.1.14 66409 d.92.1.14 66410 d.166.1.1 66411 1dgwA 178 3.53e+01 1dgwA b.82.1.2 28090 1ihkA 174 3.56e+01 1bfg b.42.1.1 62384 1aozA 552 3.57e+01 1aozA b.6.1.3 23124 b.6.1.3 23125 b.6.1.3 23126 1f7dA 136 3.58e+01 1dun b.85.4.1 28353 1qc9A 276 3.58e+01 1ckqA c.52.1.1 33235 1jmuB 666 3.59e+01 1bp3B 211 3.62e+01 1axiB b.1.2.1 22031 b.1.2.1 22032 1rypC 244 3.66e+01 1rypC d.153.1.4 41934 1qlaB 239 3.66e+01 1qlaB a.1.2.1 15679 d.15.4.2 37707 1g291 372 3.70e+01 1g291 4fgf 146 3.72e+01 1bfg b.42.1.1 25486 1k6xA 352 3.74e+01 c.2.1.2 68238 1ffkN 95 3.81e+01 1ffkN b.34.5.1 24606 1f94A 63 3.82e+01 1f94A g.7.1.1 44435 1ewxA 146 3.85e+01 1ewxA c.47.1.10 33062 1bteA 97 3.86e+01 1bteA g.7.1.3 44463 1k6iA 352 3.88e+01 c.2.1.2 68223 2ncm 99 3.92e+01 2ncm b.1.1.4 21703 1eguA 731 3.97e+01 1eguA a.102.3.2 18850 b.24.1.1 23899 b.30.3.1 24423