# 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 1ihoA 283 7.01e-57 1ihoA c.26.1.4 62390 1cozA 129 1.52e-02 1cozA c.26.1.2 31598 1cpy 421 1.40e-01 1ivyA c.69.1.5 34651 1ysc 421 1.45e-01 1ivyA c.69.1.5 34652 1jhdA 396 5.39e-01 b.58.1.2 66712 c.26.1.5 66713 2mllA 241 8.35e-01 1mrj d.165.1.1 42195 1tmf1 276 8.90e-01 2mev1 1tme1 274 1.64e+00 2mev1 1dmuA 299 1.81e+00 1dmuA c.52.1.4 33294 2bidA 197 2.22e+00 2bidA f.1.4.1 43398 1b5fA 239 2.28e+00 1smrA b.50.1.2 26836 1b6tA 159 2.76e+00 1b6tA c.26.1.3 31600 1tyaE 319 2.78e+00 2ts1 c.26.1.1 31570 1qjcA 158 2.82e+00 1b6tA c.26.1.3 63328 1ce7A 241 2.88e+00 1mrj d.165.1.1 42194 4ts1A 319 3.58e+00 2ts1 c.26.1.1 31565 1jv2A 957 3.60e+00 b.1.15.1 67334 b.1.15.1 67335 b.1.15.1 67336 b.69.8.1 67337 1tyc 319 4.20e+00 2ts1 c.26.1.1 31568 1php 394 4.34e+00 16pk c.86.1.1 35452 2ts1 419 4.53e+00 2ts1 c.26.1.1 31564 1tydE 319 4.75e+00 2ts1 c.26.1.1 31567 1dppA 507 4.76e+00 1dpe c.94.1.1 35800 1dpe 507 4.89e+00 1dpe c.94.1.1 35799 1egeA 396 5.13e+00 3mdeA a.29.3.1 16604 e.6.1.1 42865 1tybE 319 5.19e+00 2ts1 c.26.1.1 31569 1lla 628 5.28e+00 1lla a.85.1.1 18485 a.86.1.1 18496 b.1.1.5 21861 1oxy 628 5.28e+00 1lla a.85.1.1 18486 a.86.1.1 18497 b.1.1.5 21862 1egdA 396 5.95e+00 3mdeA a.29.3.1 16596 e.6.1.1 42857 1ll1 590 6.38e+00 1lla a.85.1.1 18488 a.86.1.1 18499 b.1.1.5 21864 3hdhA 302 6.39e+00 2hdhA a.100.1.3 18805 c.2.1.6 30209 1fr9A 194 6.56e+00 1fr9A c.68.1.8 34579 1e5kA 201 6.64e+00 1fr9A c.68.1.8 34578 1f9aA 168 7.63e+00 1f9aA c.26.1.3 31602 1f66D 126 7.81e+00 1aoiD a.22.1.1 16450 1fehA 574 9.20e+00 1fehA c.96.1.1 36015 d.15.4.2 37690 d.58.1.5 38998 1indH 226 9.42e+00 1igtB b.1.1.1 19839 b.1.1.2 20943 1vcbB 112 9.52e+00 1vcbB d.42.1.1 38633 1vr1H 261 9.97e+00 5ptp 3mdeA 385 1.02e+01 3mdeA a.29.3.1 16594 e.6.1.1 42855 3mddA 385 1.02e+01 3mdeA a.29.3.1 16592 e.6.1.1 42853 1yprA 125 1.03e+01 3nul d.110.1.1 40888 1thpB 259 1.09e+01 5ptp 1b7xB 259 1.09e+01 1ucyE 1gcoA 261 1.10e+01 1ybvA c.2.1.2 29884 2thfB 259 1.16e+01 1ucyE 1ea6B 364 1.19e+01 d.14.1.3 64873 d.122.1.2 64874 1h7uA 365 1.19e+01 d.14.1.3 65709 d.122.1.2 65710 1ghxH 257 1.20e+01 1eb1H 257 1.20e+01 1jztA 246 1.23e+01 c.104.1.1 63319 1bplA 189 1.23e+01 1bli c.1.8.1 28703 1aoiD 99 1.24e+01 1aoiD a.22.1.1 16452 1unkA 87 1.26e+01 1cei a.28.2.1 16935 1h7sA 365 1.27e+01 d.14.1.3 65705 d.122.1.2 65706 1d6wA 287 1.29e+01 1ucyE b.47.1.2 26098 1eojA 289 1.29e+01 1ucyE b.47.1.2 26105 1ej2A 181 1.30e+01 1f9aA c.26.1.3 59414 1gj4H 258 1.32e+01 1gj5H 258 1.32e+01 1cei 94 1.33e+01 1cei a.28.2.1 16939 1d9iA 288 1.40e+01 1ucyE b.47.1.2 26159 1i5sA 367 1.42e+01 1bg2 c.37.1.9 61822 1id3H 130 1.42e+01 a.22.1.1 66119 1i6iA 366 1.42e+01 1bg2 c.37.1.9 61844 1c5lH 259 1.44e+01 5ptp 1ahtH 259 1.44e+01 5ptp 8kme2 259 1.44e+01 1ucyE 1cv8 174 1.46e+01 1cv8 d.3.1.1 37089 1ia0K 394 1.47e+01 1jouB 259 1.47e+01 1ucyE 1bthH 259 1.47e+01 5ptp 1dm4B 260 1.48e+01 1ucyE 1dx5M 259 1.49e+01 1ucyE 1f17A 310 1.51e+01 2hdhA a.100.1.3 18797 c.2.1.6 30201 1il0A 302 1.52e+01 a.100.1.3 66189 c.2.1.6 66190 1f0yA 302 1.53e+01 2hdhA a.100.1.3 18793 c.2.1.6 30197 3hadA 308 1.53e+01 2hdhA a.100.1.3 18799 c.2.1.6 30203 1hagE 295 1.54e+01 1ucyE b.47.1.2 26135 1qdmA 478 1.59e+01 1smrA a.64.1.2 18141 b.50.1.2 26838 1go3E 187 1.69e+01 b.40.4.5 65406 1fgs 428 1.70e+01 1fgs c.59.1.2 33959 c.72.2.2 34962 1b48A 221 1.70e+01 1pgtA a.45.1.1 17703 c.47.1.5 32997 1gukA 222 1.70e+01 1pgtA a.45.1.1 17705 c.47.1.5 32999 1ggvA 232 1.78e+01 1din c.69.1.9 34683 4ubpC 570 1.79e+01 1ubpC b.92.1.1 28431 c.1.9.2 29053 1ubpC 570 1.79e+01 1ubpC b.92.1.1 28432 c.1.9.2 29054 1ie7C 570 1.79e+01 1ubpC b.92.1.1 62315 c.1.9.2 62316 1jbwA 428 1.81e+01 c.59.1.2 62860 c.72.2.2 62861 1gmvA 143 1.82e+01 b.107.1.1 65343 d.58.38.1 65344 1l7vA 326 1.87e+01 1qpkA 418 1.92e+01 1jdc b.71.1.1 27793 c.1.8.1 28780 1qreA 247 1.94e+01 1qreA b.81.1.5 28066 1bfd 528 1.96e+01 1bfd c.31.1.3 31745 c.36.1.1 31801 c.36.1.1 31802 1bev3 242 1.97e+01 1aym3 1vdc 333 1.99e+01 1trb c.3.1.5 30545 c.3.1.5 30546 1jwtA 305 2.00e+01 b.47.1.2 67398 1dyqA 234 2.06e+01 3seb b.40.2.2 59140 d.15.6.1 59141 1thjA 214 2.17e+01 1qreA b.81.1.5 28072 1h72C 296 2.18e+01 d.14.1.5 60712 d.58.26.1 60713 1fwkA 296 2.18e+01 1fwkA d.14.1.5 37576 d.58.26.1 39398 1augA 215 2.18e+01 1a2zA c.56.4.1 33798 1it2A 146 2.22e+01 a.1.1.2 66365 1vid 221 2.23e+01 1vid c.66.1.1 34178 1esfA 233 2.27e+01 3seb b.40.2.2 25146 d.15.6.1 37735 1i4gB 233 2.27e+01 3seb b.40.2.2 25149 d.15.6.1 37738 1sftA 388 2.30e+01 1bd0A b.49.2.1 26482 c.1.6.1 28644 1bd0A 388 2.30e+01 1bd0A b.49.2.1 26480 c.1.6.1 28642 1hilA 217 2.33e+01 8fabA b.1.1.1 19786 b.1.1.2 20896 1ifhL 218 2.34e+01 8fabA b.1.1.1 19790 b.1.1.2 20900 1sav 320 2.35e+01 1avc a.65.1.1 18158 1ibbA 151 2.39e+01 1yaiA b.1.8.1 62156 1hvg 319 2.46e+01 1avc a.65.1.1 18166 1hplA 449 2.46e+01 1gpl b.12.1.2 23639 c.69.1.19 34787 1dupA 152 2.49e+01 1dupA b.85.4.1 28351 1euwA 152 2.49e+01 1dupA b.85.4.1 28349 1fsz 372 2.49e+01 1fsz c.32.1.1 31750 d.79.2.1 39802 1bzoA 151 2.51e+01 1yaiA b.1.8.1 22292 1djqA 729 2.51e+01 2tmdA c.1.4.1 28614 c.3.1.1 30315 c.4.1.1 30600 1djnA 729 2.52e+01 2tmdA c.1.4.1 28612 c.3.1.1 30313 c.4.1.1 30598 2tmdA 729 2.52e+01 2tmdA c.1.4.1 28616 c.3.1.1 30317 c.4.1.1 30602 1a0lA 244 2.53e+01 5ptp b.47.1.2 26286 1qhqA 140 2.63e+01 1qhqA b.6.1.1 63326 4matA 278 2.64e+01 1c24A d.127.1.1 41150 1jecA 510 2.65e+01 b.58.1.2 66595 c.26.1.5 66596 c.37.1.15 66597 2ctc 307 2.66e+01 1aye c.56.5.1 33802 2ctb 307 2.66e+01 1aye c.56.5.1 33803 2hdhA 293 2.67e+01 2hdhA a.100.1.3 18795 c.2.1.6 30199 1qrlA 214 2.67e+01 1qreA b.81.1.5 28070 1rds 105 2.70e+01 9rnt d.1.1.1 36236 1rms 105 2.70e+01 9rnt d.1.1.1 36235 1pytB 309 2.70e+01 1aye c.56.5.1 33820 1qrmA 213 2.70e+01 1qreA b.81.1.5 28071 1emvA 86 2.72e+01 1cei a.28.2.1 16944 1e0hA 86 2.72e+01 1cei a.28.2.1 16947 1bxiA 86 2.72e+01 1cei a.28.2.1 16945 1gkdA 163 2.73e+01 1f57A 307 2.75e+01 1aye c.56.5.1 33805 1e6dM 307 2.78e+01 6prcM f.2.1.2 43459 1l6fA 388 2.79e+01 1yme 309 2.80e+01 1aye c.56.5.1 33804 1g8fA 511 2.83e+01 1g8fA b.58.1.2 60348 c.26.1.5 60349 c.37.1.15 60350 1gkcA 163 2.84e+01 1f1fA 89 2.86e+01 1ctj a.3.1.1 59571 3matA 265 3.00e+01 1c24A d.127.1.1 41149 1yaiA 151 3.03e+01 1yaiA b.1.8.1 22289 1gnkB 112 3.03e+01 2pii d.58.5.1 39074 1c24A 263 3.06e+01 1c24A d.127.1.1 41148 2matA 264 3.07e+01 1c24A d.127.1.1 41146 1avhA 320 3.10e+01 1avc a.65.1.1 18159 1mat 264 3.10e+01 1c24A d.127.1.1 41152 1anxA 319 3.13e+01 1avc a.65.1.1 18161 1eexA 554 3.16e+01 1dioA c.1.19.3 29650 1dioA 554 3.16e+01 1dioA c.1.19.3 29656 1myo 118 3.28e+01 2myo a.118.2.1 19174 2myo 118 3.28e+01 2myo a.118.2.1 19175 1mpsM 307 3.38e+01 6prcM f.2.1.2 43468 1oakA 196 3.40e+01 1auq c.62.1.1 34138 1auq 208 3.45e+01 1auq c.62.1.1 34137 1hcy 657 3.45e+01 1lla a.85.1.1 18495 a.86.1.1 18506 b.1.1.5 21871 1kguA 496 3.50e+01 b.71.1.1 68598 c.1.8.1 68599 1f0kA 364 3.66e+01 1f0kA c.87.1.2 35465 1ibhA 151 3.69e+01 1yaiA b.1.8.1 62159 1e96B 203 3.71e+01 1e96B a.118.8.1 19211 1ksgB 152 3.76e+01 1kshB 152 3.79e+01 1jrmA 104 3.81e+01 d.206.1.1 67136 1ff9A 450 3.87e+01 1ff9A c.2.1.3 30039 d.81.1.2 39954 1iayA 428 3.88e+01 1b8gA c.67.1.4 62130