# List of top-scoring protein chains for t2k-w0.5 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 1.38e-23 1mspA 126 6.91e-23 1mspA b.1.11.2 22333 2mspA 126 2.14e-22 1mspA b.1.11.2 22335 1g0hA 252 5.73e-01 1dk4A e.7.1.1 60171 1dk4A 252 5.73e-01 1dk4A e.7.1.1 42970 1gjiA 275 6.93e-01 1g291 372 7.95e-01 1g291 1etzB 228 1.28e+00 1igtB b.1.1.1 20481 b.1.1.2 21445 1avgI 142 1.96e+00 1avgI b.60.1.3 27229 1hfoA 113 2.49e+00 d.80.1.3 61006 1hi6B 213 2.73e+00 1igtB b.1.1.1 20337 b.1.1.2 21329 1dun 134 2.85e+00 1dun b.85.4.1 28371 1ggbH 215 2.94e+00 1igtB b.1.1.1 19875 b.1.1.2 20971 1ggiH 222 3.07e+00 1igtB b.1.1.1 19877 b.1.1.2 20973 1cr9H 217 3.81e+00 8fabA b.1.1.1 20431 b.1.1.2 21401 1ehlH 219 3.84e+00 1igtB b.1.1.1 20503 b.1.1.2 21459 1forH 219 4.28e+00 1igtB b.1.1.1 19989 b.1.1.2 21045 1fptH 220 4.42e+00 1mfa b.1.1.1 20031 b.1.1.2 21085 1kb5H 219 4.46e+00 1igtB b.1.1.1 20229 b.1.1.2 21241 1j5oH 220 4.47e+00 1e4wH 213 4.61e+00 1igtB b.1.1.1 59232 b.1.1.2 59233 1ncbH 221 4.66e+00 1igtB b.1.1.1 19981 b.1.1.2 21037 1e4xH 217 4.71e+00 1igtB b.1.1.1 59236 b.1.1.2 59237 1mpaH 225 4.75e+00 1mfa b.1.1.1 20135 b.1.1.2 21165 4fabH 216 4.88e+00 1igtB b.1.1.1 19907 b.1.1.2 21001 1flrH 219 4.92e+00 1igtB b.1.1.1 19905 b.1.1.2 20999 1plgH 215 5.04e+00 1igtB b.1.1.1 20081 b.1.1.2 21113 1ncaH 221 5.11e+00 1igtB b.1.1.1 19983 b.1.1.2 21039 1yejH 222 5.30e+00 1mfa b.1.1.1 20141 b.1.1.2 21171 1iaiH 219 5.35e+00 1igtB b.1.1.1 20073 b.1.1.2 21105 1blj 114 5.82e+00 1lckA d.93.1.1 40524 1e4xI 217 5.85e+00 b.1.1.1 59238 b.1.1.2 59239 1a5r 103 5.94e+00 1a5r d.15.1.1 37597 1fjgD 209 6.01e+00 1c05A d.66.1.2 39553 1dqqB 210 6.06e+00 1igtB b.1.1.1 20421 b.1.1.2 21391 1egjH 220 6.13e+00 1igtB b.1.1.1 20501 b.1.1.2 21457 1igjB 218 6.17e+00 1igtB b.1.1.1 19819 b.1.1.2 20929 1j5eD 208 6.17e+00 1iblD 209 6.19e+00 1c05A i.1.1.1 62188 1ejoH 220 6.57e+00 1igtB b.1.1.1 20429 b.1.1.2 21399 1bbdH 218 6.78e+00 1igtB b.1.1.1 19783 b.1.1.2 20893 1jnrB 150 6.97e+00 d.58.1.5 66969 2a8vA 118 7.15e+00 1a62 a.140.3.1 64752 b.40.4.5 64753 1ia0K 394 7.19e+00 1yeeH 222 7.25e+00 1igtB b.1.1.1 20157 b.1.1.2 21187 1a8vA 121 7.27e+00 1a62 a.140.3.1 64712 b.40.4.5 64713 1i6iA 366 7.80e+00 1bg2 c.37.1.9 61844 1bk5A 422 7.80e+00 1bk5A a.118.1.1 19130 1i5sA 367 7.83e+00 1bg2 c.37.1.9 61822 1pskH 209 7.84e+00 1igtB b.1.1.1 20139 b.1.1.2 21169 1jdiA 231 7.88e+00 c.74.1.1 66551 1a63 130 8.56e+00 1a62 a.140.3.1 64710 b.40.4.5 64711 1bk6A 422 8.81e+00 1bk5A a.118.1.1 19133 1a62 130 8.89e+00 1a62 a.140.3.1 64708 b.40.4.5 64709 1ee4A 423 9.07e+00 1ee4A a.118.1.1 19128 1ee5A 424 9.12e+00 1ee4A a.118.1.1 19132 1mamH 217 9.24e+00 1igtB b.1.1.1 19887 b.1.1.2 20983 1jf0A 195 9.30e+00 1ej3A a.39.1.5 62926 1gkpA 458 1.00e+01 1bwdA 348 1.02e+01 1jdw d.126.1.2 41140 1lt3A 240 1.05e+01 1lt3A d.166.1.1 42230 1a6tB 217 1.08e+01 1igtB b.1.1.1 20249 b.1.1.2 21259 1dlfH 124 1.11e+01 1igtB b.1.1.1 20383 1blnB 218 1.15e+01 1igtB b.1.1.1 20331 b.1.1.2 21323 1bmr 68 1.15e+01 1aho g.3.7.1 44144 1kzuA 53 1.31e+01 1kzuA f.3.1.1 43727 1fl3A 208 1.33e+01 1igtB b.1.1.1 20486 b.1.1.2 21450 3hck 107 1.44e+01 1lckA d.93.1.1 40495 3mefA 69 1.47e+01 1mjc b.40.4.5 25320 1mjc 69 1.47e+01 1mjc b.40.4.5 25319 1qkzH 219 1.54e+01 1igtB b.1.1.1 20137 b.1.1.2 21167 1dl7H 112 1.55e+01 1f3rB b.1.1.1 20499 1dgwA 178 1.57e+01 1dgwA b.82.1.2 28090 1dgrC 178 1.57e+01 1dgwA b.82.1.2 28100 1jgvH 218 1.57e+01 b.1.1.1 66692 b.1.1.2 66693 1jguH 217 1.57e+01 b.1.1.1 66688 b.1.1.2 66689 1cauA 181 1.58e+01 1dgwA b.82.1.2 28102 1cwdL 98 1.60e+01 1lckA d.93.1.1 40418 1faiH 221 1.62e+01 1mfa b.1.1.1 19845 b.1.1.2 20949 1bhhB 103 1.64e+01 1lckA d.93.1.1 40417 1lklA 104 1.65e+01 1qadA d.93.1.1 40413 1lkkA 105 1.67e+01 1lckA d.93.1.1 40412 1ucwA 317 1.68e+01 1onrA c.1.10.1 29171 1bhfA 108 1.70e+01 1qadA d.93.1.1 40415 1lcjA 109 1.71e+01 1qadA d.93.1.1 40414 1aj3 110 1.71e+01 1cunA a.7.1.1 16319 1axtH 218 1.74e+01 1igtB b.1.1.1 20305 b.1.1.2 21297 1xtcA 194 1.76e+01 1lt3A d.166.1.1 42259 1jrhH 219 1.76e+01 1igtB b.1.1.1 20223 b.1.1.2 21235 1c9hA 107 1.79e+01 1fkj d.26.1.1 38425 1fbzA 104 1.80e+01 1lckA d.93.1.1 40422 1ijrA 104 1.80e+01 1mreH 215 1.88e+01 1mfa b.1.1.1 20019 b.1.1.2 21073 1cvsA 132 1.89e+01 1bfg b.42.1.1 25498 2cgrH 214 1.93e+01 1igtB b.1.1.1 19919 b.1.1.2 21013 1oakH 223 2.00e+01 1igtB b.1.1.1 20291 b.1.1.2 21283 1bfg 146 2.01e+01 1bfg b.42.1.1 25485 1bfc 147 2.02e+01 1bfg b.42.1.1 25492 1fn4B 218 2.03e+01 b.1.1.1 59886 b.1.1.2 59887 1bas 154 2.05e+01 1bfg b.42.1.1 25488 1iilA 155 2.05e+01 1bfg b.42.1.1 62433 1bla 155 2.05e+01 1bfg b.42.1.1 25502 1fj1B 213 2.07e+01 1igtB b.1.1.1 20119 b.1.1.2 21149 1hre 67 2.08e+01 1xdtR g.3.11.1 44300 1ltsA 185 2.10e+01 1lt3A d.166.1.1 42229 1l2nA 101 2.11e+01 1ltaA 188 2.11e+01 1lt3A d.166.1.1 42232 1ltgA 191 2.14e+01 1lt3A d.166.1.1 42235 1ltiA 192 2.14e+01 1lt3A d.166.1.1 42233 1fvcB 120 2.16e+01 1igtB b.1.1.1 19863 1fnsH 225 2.16e+01 1igtB b.1.1.1 20289 b.1.1.2 21281 1cf8H 218 2.21e+01 1igtB b.1.1.1 20379 b.1.1.2 21371 1b35B 255 2.24e+01 1b35B b.10.1.3 23334 1shsA 147 2.35e+01 1shsA b.15.1.1 23675 1bqk 124 2.35e+01 1bqk b.6.1.1 22889 2cavA 445 2.36e+01 1dgwA b.82.1.2 28094 b.82.1.2 28095 1eapB 216 2.37e+01 1mfa b.1.1.1 20015 b.1.1.2 21069 1lo0Y 220 2.39e+01 1dovA 181 2.40e+01 1dovA a.24.9.1 16627 1ibgH 217 2.40e+01 1igtB b.1.1.1 20049 b.1.1.2 21091 1fl5B 219 2.41e+01 b.1.1.1 65017 b.1.1.2 65018 1idm 343 2.49e+01 1cnzA c.77.1.1 35035 1lt4A 247 2.50e+01 1lt3A d.166.1.1 42231 1acc 735 2.50e+01 1acc f.11.1.1 43828 1i94Q 104 2.51e+01 1fjfQ b.40.4.5 62008 1euvB 86 2.56e+01 1a5r d.15.1.1 37598 1cyx 205 2.58e+01 1cyx b.6.1.2 23023 1cyw 205 2.58e+01 1cyx b.6.1.2 23024 1gigH 221 2.61e+01 1igtB b.1.1.1 19911 b.1.1.2 21005 8fabB 224 2.74e+01 1igtB b.1.1.1 19773 b.1.1.2 20883 1jt5A 146 2.77e+01 b.42.1.1 67245 1rypC 244 2.80e+01 1rypC d.153.1.4 41934 1fntC 245 2.82e+01 1ad5A 438 2.86e+01 1fmk b.34.2.1 24505 d.93.1.1 40491 d.144.1.2 41681 2gfbB 219 2.87e+01 b.1.1.1 19993 b.1.1.2 21047 1djsB 135 2.88e+01 1bfg b.42.1.1 25518 1g38A 393 2.89e+01 2admA c.66.1.10 60235 1dvfD 120 2.90e+01 1mfa b.1.1.1 20107 1e4xL 214 2.94e+01 32c2A b.1.1.1 59240 b.1.1.2 59241 1d5tA 433 2.95e+01 1gnd c.3.1.3 30422 d.16.1.6 37986 1fd9A 213 2.98e+01 1fd9A d.26.1.1 59771 1bfoB 216 2.99e+01 1igtB b.1.1.1 20311 b.1.1.2 21303 1lckA 175 3.01e+01 1lckA b.34.2.1 24552 d.93.1.1 40421 1lo4H 220 3.03e+01 1frgH 220 3.03e+01 1igtB b.1.1.1 19925 b.1.1.2 21019 1g8mA 593 3.06e+01 1g8mA c.24.1.3 60371 c.97.2.1 60372 1jt4A 146 3.07e+01 b.42.1.1 67243 1aqjB 421 3.10e+01 2admA c.66.1.10 34243 2admA 421 3.11e+01 2admA c.66.1.10 34238 2drpA 66 3.11e+01 2drpA g.37.1.1 45026 g.37.1.1 45027 1i2nA 316 3.19e+01 1onrA c.1.10.1 61572 1gof 639 3.24e+01 1gof b.1.1.5 21807 b.18.1.1 23709 b.69.1.1 27631 1goh 639 3.24e+01 1gof b.1.1.5 21809 b.18.1.1 23711 b.69.1.1 27633 1i2pA 316 3.25e+01 1onrA c.1.10.1 61576 1k3iA 656 3.25e+01 b.1.1.5 68113 b.18.1.1 68114 b.69.1.1 68115 1ospH 218 3.26e+01 1igtB b.1.1.1 20117 b.1.1.2 21147 1a2yB 116 3.26e+01 1gc1H b.1.1.1 19927 1vfaB 116 3.26e+01 1gc1H b.1.1.1 19929 1g7jB 116 3.26e+01 1f3rB b.1.1.1 19933 1i2rA 316 3.26e+01 1onrA c.1.10.1 61580 1onrA 316 3.27e+01 1onrA c.1.10.1 29169 1i2oA 316 3.27e+01 1onrA c.1.10.1 61574 1k3bA 119 3.30e+01 1hzaA 67 3.30e+01 b.40.4.5 65963 1a7nH 116 3.31e+01 1gc1H b.1.1.1 19941 1cloH 222 3.36e+01 1igtB b.1.1.1 20123 b.1.1.2 21153 1kipB 116 3.37e+01 1gc1H b.1.1.1 19957 1kiqB 116 3.39e+01 1gc1H b.1.1.1 19939 1gc8A 345 3.40e+01 1cnzA c.77.1.1 35042 1f3rB 257 3.41e+01 1f3rB b.1.1.1 20416 b.1.1.1 20417 1mcpH 222 3.45e+01 1igtB b.1.1.1 19859 b.1.1.2 20959 1i2qA 316 3.52e+01 1onrA c.1.10.1 61578 1hzbA 66 3.53e+01 b.40.4.5 65965 1hae 63 3.54e+01 1xdtR g.3.11.1 44298 1dr8B 344 3.56e+01 1cnzA c.77.1.1 35052 1osjA 345 3.58e+01 1cnzA c.77.1.1 35039 1dpzA 349 3.59e+01 1cnzA c.77.1.1 35053 1dr0A 346 3.59e+01 1cnzA c.77.1.1 35045 1i5fA 66 3.63e+01 b.40.4.5 66034 1c9oA 66 3.72e+01 1mjc b.40.4.5 25325 1ey2A 471 3.73e+01 1ey2A b.82.1.4 28116 1eybA 471 3.73e+01 1ey2A b.82.1.4 28115 1fe8H 210 3.74e+01 1igtB b.1.1.1 59786 b.1.1.2 59787 1g2uA 345 3.74e+01 1cnzA c.77.1.1 35036 1skz 119 3.76e+01 1skz g.3.15.1 44366 g.3.15.1 44367 1nbcA 155 3.81e+01 1nbcA b.2.2.2 22390 1qcfA 454 3.83e+01 1fmk b.34.2.1 24498 d.93.1.1 40490 d.144.1.2 41680 1xaa 345 3.84e+01 1cnzA c.77.1.1 35033 1gc9A 345 3.91e+01 1cnzA c.77.1.1 35037