# 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 1e3pA 757 3.57e-11 1e3hA a.4.9.1 16258 b.40.4.5 25328 d.14.1.4 37574 d.14.1.4 37575 d.52.3.1 38811 d.101.1.1 40697 d.101.1.1 40698 1e3hA 757 3.94e-11 1e3hA a.4.9.1 16257 d.14.1.4 37572 d.14.1.4 37573 d.52.3.1 38810 d.101.1.1 40695 d.101.1.1 40696 3mefA 69 9.73e-10 1mjc b.40.4.5 25320 1mjc 69 1.02e-09 1mjc b.40.4.5 25319 1sro 76 1.31e-09 1sro b.40.4.5 25327 1h95A 79 1.76e-08 b.40.4.5 65742 1g6pA 66 2.85e-08 b.40.4.5 65168 1nmf 67 1.46e-07 1mjc b.40.4.5 25323 1csp 67 1.47e-07 1mjc b.40.4.5 25321 1i5fA 66 3.84e-07 b.40.4.5 66034 1hzcA 66 4.23e-07 b.40.4.5 65967 1c9oA 66 4.96e-07 1mjc b.40.4.5 25325 1hzbA 66 5.00e-07 b.40.4.5 65965 1hz9A 66 5.41e-07 b.40.4.5 65961 1hzaA 67 5.64e-07 b.40.4.5 65963 1go3E 187 1.40e-06 b.40.4.5 65406 1kl9A 182 1.79e-03 1bkf 107 1.95e-01 1fkj d.26.1.1 38382 1fkl 107 2.79e-01 1fkj d.26.1.1 38423 1fkf 107 3.13e-01 1fkj d.26.1.1 38386 1fkj 107 3.13e-01 1fkj d.26.1.1 38384 1fkd 107 3.13e-01 1fkj d.26.1.1 38383 1tcoC 107 3.16e-01 1fkj d.26.1.1 38426 1eymA 107 3.49e-01 1fkj d.26.1.1 38403 1bl4A 107 3.93e-01 1fkj d.26.1.1 38393 1fl2A 310 1.48e+00 1hyuA c.3.1.5 59869 c.3.1.5 59870 1g19A 350 2.11e+00 2reb c.37.1.11 32284 d.48.1.1 38770 1srdA 154 4.14e+00 1mfmA b.1.8.1 22275 1a62 130 4.25e+00 1a62 a.140.3.1 64708 b.40.4.5 64709 1db9A 200 4.64e+00 a.4.5.4 64782 b.82.3.2 64783 1c9hA 107 4.66e+00 1fkj d.26.1.1 38425 1db7A 200 4.71e+00 a.4.5.4 64778 b.82.3.2 64779 1hyuA 521 5.01e+00 1hyuA c.3.1.5 30547 c.3.1.5 30548 c.47.1.2 32779 c.47.1.2 32780 1a63 130 5.01e+00 1a62 a.140.3.1 64710 b.40.4.5 64711 1kefA 93 5.39e+00 2gsaA 432 6.04e+00 2gsaA c.67.1.4 34446 1cgpA 205 6.05e+00 a.4.5.4 16096 b.82.3.2 28135 2a8vA 118 6.08e+00 1a62 a.140.3.1 64752 b.40.4.5 64753 1a8vA 121 6.09e+00 1a62 a.140.3.1 64712 b.40.4.5 64713 1ruoB 209 6.11e+00 2cgpA a.4.5.4 16106 b.82.3.2 28145 1runA 209 6.17e+00 2cgpA a.4.5.4 16103 b.82.3.2 28142 1fo1A 271 6.37e+00 1fo1A c.10.2.3 30869 d.58.7.2 39213 1ft8E 271 6.37e+00 1ft8E d.58.7.2 39216 1jvwA 167 6.39e+00 4kbpA 432 6.41e+00 4kbpA b.1.12.1 22345 d.159.1.1 42064 1kbpA 432 6.41e+00 4kbpA b.1.12.1 22349 d.159.1.1 42068 1kooC 277 6.67e+00 c.10.2.3 68729 d.58.7.2 68730 2cgpA 210 6.69e+00 2cgpA a.4.5.4 16102 b.82.3.2 28141 1hw5A 210 6.71e+00 2cgpA a.4.5.4 16098 b.82.3.2 28137 1kohC 277 6.72e+00 c.10.2.3 68722 d.58.7.2 68723 1tfr 305 7.09e+00 1tfr a.60.7.1 18081 c.53.1.2 33351 1ffyA 917 7.70e+00 1qu2A a.27.1.1 16926 b.51.1.1 26891 c.26.1.1 31593 1qu2A 917 7.70e+00 1qu2A a.27.1.1 16925 b.51.1.1 26890 c.26.1.1 31592 1l1lA 739 7.86e+00 1whi 122 8.18e+00 1whi b.39.1.1 24810 2trcP 217 9.34e+00 1b9yC c.47.1.6 33051 1bmdA 327 9.79e+00 1bmdA c.2.1.5 30139 d.162.1.1 42106 1c3yA 108 9.86e+00 1c3yA a.39.2.1 17387 1bdmB 327 9.90e+00 1bmdA c.2.1.5 30138 d.162.1.1 42105 1bdmA 327 9.90e+00 1bmdA c.2.1.5 30137 d.162.1.1 42104 1ixxA 129 9.93e+00 1ixxB d.169.1.1 42335 1fx4A 231 1.05e+01 1fx2A d.58.29.1 39431 1qsrA 162 1.14e+01 1yghA d.108.1.1 40805 5gcnA 166 1.15e+01 1yghA d.108.1.1 40807 1fokA 568 1.17e+01 2fokA a.4.5.12 16137 a.4.5.12 16138 a.4.5.12 16139 c.52.1.12 33325 1k5vA 146 1.23e+01 b.42.1.1 68210 2fokA 579 1.28e+01 2fokA a.4.5.12 16131 a.4.5.12 16132 a.4.5.12 16133 c.52.1.12 33323 1qgiA 259 1.33e+01 1qgiA d.2.1.7 37001 3cms 323 1.36e+01 1smrA b.50.1.2 26865 1b9yC 246 1.37e+01 1b9yC c.47.1.6 33052 4cms 323 1.38e+01 1smrA b.50.1.2 26866 1b9xC 246 1.41e+01 1b9yC c.47.1.6 33053 1dqbA 83 1.46e+01 1dqbA g.3.11.1 44318 g.3.11.1 44319 2mssA 75 1.53e+01 1ha1 d.58.7.1 39190 1f3z 161 1.59e+01 1gpr b.84.3.1 28273 1f3jB 187 1.66e+01 1iakB b.1.1.2 21646 d.19.1.1 38220 1f2hA 169 1.71e+01 1f3vA d.58.22.1 59612 1glaF 168 1.73e+01 1gpr b.84.3.1 28274 1fgnH 214 1.75e+01 1igtB b.1.1.1 20217 b.1.1.2 21229 1iv6A 70 1.76e+01 1ityA 69 1.79e+01 1f3vA 179 1.81e+01 1f3vA d.58.22.1 39382 1b74A 254 1.88e+01 1b74A c.78.2.1 35264 c.78.2.1 35265 1b73A 254 1.88e+01 1b74A c.78.2.1 35266 c.78.2.1 35267 1bg6 359 1.90e+01 1bg6 a.100.1.5 18810 c.2.1.6 30214 1dsfH 119 1.97e+01 1igtB b.1.1.1 20247 1ptoH 198 2.02e+01 1bcpB b.40.2.1 25126 d.169.1.2 42435 1bcpB 199 2.02e+01 1bcpB b.40.2.1 25120 d.169.1.2 42429 1prtB 196 2.04e+01 1bcpB b.40.2.1 25116 d.169.1.2 42425 1zprA 264 2.07e+01 1bkpA d.117.1.1 40978 1ba5 53 2.11e+01 1ba5 a.4.1.4 16045 1i6cA 39 2.11e+01 1i6cA b.72.1.1 61828 1fmmS 132 2.20e+01 1bfg b.42.1.1 59883 1k6qH 216 2.21e+01 1fs0G 230 2.23e+01 1fs0G c.49.2.1 59999 1nwpA 128 2.24e+01 1nwpA b.6.1.1 23011 1vie 62 2.28e+01 1vie b.34.4.1 24592 1vif 62 2.28e+01 1vie b.34.4.1 24593 1yat 113 2.29e+01 1fkj d.26.1.1 38427 1jj2A 239 2.30e+01 1rl2A b.34.5.3 63084 b.40.4.5 63085 5tnc 162 2.30e+01 1ncx a.39.1.5 17246 1dupA 152 2.32e+01 1dupA b.85.4.1 28351 1euwA 152 2.32e+01 1dupA b.85.4.1 28349 1flsA 165 2.37e+01 1hfc d.92.1.11 59875 1dx5I 118 2.37e+01 1dx5I g.3.11.1 44302 g.3.11.1 44303 g.3.11.1 44304 830cA 168 2.42e+01 1ck7A d.92.1.11 40400 1es0B 221 2.45e+01 1iakB b.1.1.2 21644 d.19.1.1 38218 1l1sA 113 2.45e+01 1jv2A 957 2.50e+01 b.1.15.1 67334 b.1.15.1 67335 b.1.15.1 67336 b.69.8.1 67337 2plt 98 2.51e+01 1plc b.6.1.1 22862 1eubA 171 2.52e+01 1hfc d.92.1.11 59503 1bj3A 129 2.58e+01 1ixxB d.169.1.1 42341 1b37B 472 2.60e+01 1b37B c.3.1.2 30390 d.16.1.5 37954 1b5qA 472 2.60e+01 1b37B c.3.1.2 30404 d.16.1.5 37968 1g9fA 253 2.61e+01 1led b.29.1.1 60398 1tmo 829 2.69e+01 1dmr b.52.2.2 26919 c.81.1.1 35327 3gpdG 334 2.72e+01 1dssG c.2.1.3 30029 d.81.1.1 39944 4tnc 162 2.72e+01 1ncx a.39.1.5 17228 1qg3A 195 2.75e+01 1qg3A b.1.2.1 21993 b.1.2.1 21994 2iadB 205 2.90e+01 1iakB b.1.1.2 21640 d.19.1.1 38214 1tnw 162 2.92e+01 1ncx a.39.1.5 17235 1lcyA 325 2.93e+01 1mabA 510 2.97e+01 1skyB a.69.1.1 18311 b.49.1.1 26476 c.37.1.11 32356 1f3dH 217 2.99e+01 1igtB b.1.1.1 20462 b.1.1.2 21426 1fwxA 595 3.04e+01 b.6.1.4 60069 b.69.3.1 60070 1g85A 159 3.10e+01 1obpA 159 3.10e+01 1obpA b.60.1.1 27092 1euoA 180 3.11e+01 1np1A b.60.1.1 27163 1bxvA 91 3.13e+01 1aac b.6.1.1 22875 1iaoB 222 3.14e+01 1iakB b.1.1.2 21642 d.19.1.1 38216 1top 162 3.15e+01 1ncx a.39.1.5 17223 1ncx 162 3.15e+01 1ncx a.39.1.5 17222 1jigA 146 3.15e+01 1hh2P 344 3.25e+01 b.40.4.5 65835 d.52.3.1 65836 d.52.3.1 65837 d.202.1.1 65838 1efrC 510 3.26e+01 1skyB a.69.1.1 18301 b.49.1.1 26466 c.37.1.11 32346 1e79A 510 3.26e+01 1skyB a.69.1.1 18269 b.49.1.1 26434 c.37.1.11 32314 1bmfA 510 3.26e+01 1skyB a.69.1.1 18281 b.49.1.1 26446 c.37.1.11 32326 1h8eA 510 3.26e+01 1skyB a.69.1.1 60738 b.49.1.1 60739 c.37.1.11 60740 1ksaA 366 3.26e+01 4bcl b.75.1.1 27969 2a2uA 181 3.30e+01 1mup b.60.1.1 27135 1c9wA 315 3.40e+01 1frb c.1.7.1 28699 1adwA 123 3.49e+01 1bqk b.6.1.1 22893 1k0rA 366 3.56e+01 b.40.4.5 67961 d.52.3.1 67962 d.52.3.1 67963 d.202.1.1 67964 1eqjA 511 3.63e+01 1ejjA c.105.1.1 59495 c.76.1.3 59496 1ejjA 511 3.63e+01 1ejjA c.105.1.1 59422 c.76.1.3 59423 1cc5 83 3.67e+01 1cc5 a.3.1.1 15901 1iakB 185 3.69e+01 1iakB b.1.1.2 21626 d.19.1.1 38200 1aww 67 3.70e+01 1bbzA b.34.2.1 24529 1d9kD 188 3.73e+01 1iakB b.1.1.2 21628 d.19.1.1 38202 1be9A 119 3.74e+01 1pdr b.36.1.1 24774 1bfeA 119 3.74e+01 1pdr b.36.1.1 24775 1dykA 394 3.76e+01 1dykA b.29.1.4 24223 b.29.1.4 24224 1skyB 502 3.80e+01 1skyB a.69.1.1 18313 b.49.1.1 26478 c.37.1.11 32358 1f1cA 129 3.80e+01 1e29A a.3.1.1 59569 1pboA 159 3.90e+01 1obpA b.60.1.1 27094