# 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 1jclA 260 3.06e-31 c.1.10.1 66501 1jcjA 260 1.41e-30 c.1.10.1 66499 2dorA 311 9.35e-02 2dorA c.1.4.1 28593 1dorA 311 9.35e-02 2dorA c.1.4.1 28595 1kv8A 216 2.50e-01 1ea0A 1479 8.28e-01 b.80.4.1 64854 c.1.4.1 64855 d.153.1.1 64856 1c7nA 399 8.99e-01 1d2fA c.67.1.3 34413 1lk5A 229 9.15e-01 1hg3A 225 9.22e-01 1hg3A c.1.1.1 61025 1gpwC 253 1.02e+00 c.1.2.1 65462 1thfD 253 1.04e+00 1thfD c.1.2.1 28535 1a6aB 187 1.42e+00 1iakB b.1.1.2 21616 d.19.1.1 38190 1d3hA 367 1.71e+00 1d3gA c.1.4.1 28601 1d3gA 367 1.71e+00 1d3gA c.1.4.1 28600 1d5xB 192 1.72e+00 1iakB b.1.1.2 21624 d.19.1.1 38198 1al7 359 1.83e+00 1gox c.1.4.1 28609 1gox 369 1.85e+00 1gox c.1.4.1 28607 1gylA 369 1.87e+00 1gox c.1.4.1 28610 1d5mB 192 1.88e+00 1iakB b.1.1.2 21618 d.19.1.1 38192 1dlhB 188 2.35e+00 1iakB b.1.1.2 21598 d.19.1.1 38172 1sebB 192 2.39e+00 1iakB b.1.1.2 21602 d.19.1.1 38176 1hxyB 190 2.39e+00 1iakB b.1.1.2 61388 d.19.1.1 61389 1aqdK 198 2.40e+00 1iakB b.1.1.2 21592 d.19.1.1 38166 1ft2A 315 2.66e+00 1ft1A a.118.6.1 19190 1zfjA 491 2.88e+00 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1d8dA 377 3.10e+00 1ft1A a.118.6.1 19185 1jcrA 377 3.10e+00 a.118.6.1 66506 1ft1A 377 3.10e+00 1ft1A a.118.6.1 19186 1iebB 227 3.39e+00 1iakB b.1.1.2 21636 d.19.1.1 38210 1fneB 224 3.61e+00 1iakB b.1.1.2 59898 d.19.1.1 59899 1fngB 224 3.62e+00 1iakB b.1.1.2 59906 d.19.1.1 59907 1ktdB 215 3.80e+00 1i3rD 228 3.85e+00 b.1.1.2 61626 d.19.1.1 61627 1j4bA 457 3.91e+00 c.37.1.10 66374 1fv1E 190 3.93e+00 1iakB b.1.1.2 21608 d.19.1.1 38182 1ehaA 558 4.12e+00 1ehaA b.1.1.5 21859 b.71.1.1 27786 c.1.8.1 28773 1a53 247 4.18e+00 1a53 c.1.2.4 28564 1igs 248 4.18e+00 1a53 c.1.2.4 28565 1juk 248 4.18e+00 1a53 c.1.2.4 28567 1kt2B 213 4.23e+00 1eh9A 558 4.40e+00 1ehaA b.1.1.5 21858 b.71.1.1 27785 c.1.8.1 28772 1qcwA 410 4.94e+00 1gox c.1.4.1 28622 1kbjA 412 5.13e+00 1czfA 362 5.19e+00 1czfA b.80.1.3 28031 1ltdA 506 5.71e+00 1gox c.1.4.1 28618 d.120.1.1 41086 1fcbA 511 5.74e+00 1gox c.1.4.1 28620 d.120.1.1 41087 1lcoA 511 5.75e+00 1gox c.1.4.1 28624 d.120.1.1 41088 1bx2B 191 6.39e+00 1iakB b.1.1.2 21610 d.19.1.1 38184 1kn9C 249 6.68e+00 b.87.1.2 68701 1b12A 248 6.69e+00 1b12A b.87.1.2 28388 1exqA 154 7.15e+00 1b9dA c.55.3.2 33646 1qbqA 333 7.49e+00 1ft1A a.118.6.1 19187 1gumA 222 7.70e+00 1pgtA a.45.1.1 17683 c.47.1.5 32977 1i60A 278 8.08e+00 1jg1A 235 8.67e+00 c.66.1.7 66661 1h5yA 253 9.18e+00 c.1.2.1 65638 1dljA 402 9.54e+00 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1qm4A 396 9.54e+00 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1jmqA 46 9.58e+00 b.72.1.1 66888 1f81A 88 1.01e+01 1f81A g.53.1.1 45383 1ld8A 382 1.02e+01 1jcqA 382 1.02e+01 a.118.6.1 66504 1dliA 402 1.06e+01 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1jxkA 491 1.11e+01 b.71.1.1 63316 c.1.8.1 63317 1ak5 503 1.12e+01 1ak5 c.1.5.1 28639 1smd 496 1.13e+01 1smd b.71.1.1 27768 c.1.8.1 28755 1jxjA 496 1.13e+01 b.71.1.1 63314 c.1.8.1 63315 1tlk 154 1.14e+01 1tlk b.1.1.4 21707 1tr1A 447 1.23e+01 1e70M c.1.8.4 28957 2rusB 490 1.23e+01 1burA c.1.14.1 29385 d.58.9.1 39291 1rusA 490 1.23e+01 1burA c.1.14.1 29388 d.58.9.1 39294 5rubA 490 1.23e+01 1burA c.1.14.1 29382 d.58.9.1 39288 1bgaA 447 1.25e+01 1e70M c.1.8.4 28961 1e4iA 447 1.25e+01 1e70M c.1.8.4 59225 1bggA 448 1.25e+01 1e70M c.1.8.4 28953 1ex4A 239 1.27e+01 1b9dA b.34.7.1 24627 c.55.3.2 33670 1jceA 344 1.28e+01 c.55.1.1 62876 c.55.1.1 62877 1k9qA 40 1.31e+01 b.72.1.1 68357 1gjiA 275 1.36e+01 1l6sA 323 1.37e+01 1e9mA 106 1.38e+01 1ayfA d.15.4.1 59397 1i8jA 323 1.41e+01 1b4kA c.1.10.3 61968 1h2rS 267 1.41e+01 2frvA e.19.1.1 43310 1rbaB 466 1.44e+01 1burA c.1.14.1 29391 d.58.9.1 39297 9rubA 466 1.47e+01 1burA c.1.14.1 29386 d.58.9.1 39292 1dv2A 452 1.52e+01 1bncA b.84.2.1 28238 c.30.1.1 31645 d.142.1.2 41490 1gv0A 310 1.60e+01 c.2.1.5 65594 d.162.1.1 65595 6xia 387 1.61e+01 4xis c.1.15.3 29406 1jcfA 344 1.62e+01 c.55.1.1 62878 c.55.1.1 62879 1h2aS 317 1.69e+01 2frvA e.19.1.1 43311 1b0fA 218 1.71e+01 1a7s b.47.1.2 26237 1b4eA 323 1.72e+01 1b4kA c.1.10.3 29186 1bncA 449 1.75e+01 1bncA b.84.2.1 28236 c.30.1.1 31643 d.142.1.2 41488 1dv1A 449 1.75e+01 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1bncB 449 1.75e+01 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 1c8m4 77 1.89e+01 1qo2A 241 1.95e+01 1qo2A c.1.2.1 28533 2prd 174 1.98e+01 2prd b.40.5.1 25435 1mhdA 132 2.01e+01 1mhdA d.164.1.1 42175 1qu9A 128 2.05e+01 1qu9A d.79.1.1 39755 1qu9C 128 2.05e+01 1qu9A d.79.1.1 39757 1kyqA 274 2.07e+01 1jidA 128 2.07e+01 d.201.1.1 66735 1ydvA 248 2.10e+01 1amk c.1.1.1 28501 1fi8A 228 2.11e+01 5ptp b.47.1.2 26374 1ejbA 168 2.13e+01 1rvv1 c.16.1.1 59417 1ikpA 613 2.15e+01 b.29.1.7 66182 d.166.1.1 66183 f.1.5.1 66184 1volA 204 2.16e+01 1tfb a.74.1.2 18370 a.74.1.2 18371 1eepB 404 2.17e+01 1ak5 c.1.5.1 28637 1ikqA 613 2.18e+01 b.29.1.7 66185 d.166.1.1 66186 f.1.5.1 66187 1cmf 73 2.20e+01 1cll a.39.1.5 17283 1b43A 340 2.25e+01 1a76 a.60.7.1 18092 c.53.1.2 33362 1fhgA 154 2.26e+01 1tlk b.1.1.4 21706 1repC 251 2.27e+01 1repC a.4.5.10 16125 a.4.5.10 16126 1aym4 68 2.29e+01 1ffkW 73 2.30e+01 1ffkW g.41.8.1 45315 1qk5B 233 2.30e+01 1qk3A c.61.1.1 34036 1ex7A 186 2.31e+01 1gky c.37.1.1 59537 1c9bA 207 2.31e+01 1tfb a.74.1.2 18372 a.74.1.2 18373 1gky 187 2.32e+01 1gky c.37.1.1 31839 1tfb 208 2.33e+01 1tfb a.74.1.2 18382 a.74.1.2 18383 1fw4A 71 2.33e+01 1cll a.39.1.5 60056 1dbrA 231 2.35e+01 1qk3A c.61.1.1 34041 1fsgA 233 2.37e+01 1qk3A c.61.1.1 34029 1qk3A 233 2.37e+01 1qk3A c.61.1.1 34031 1qk4A 233 2.37e+01 1qk3A c.61.1.1 34037 1ad1A 266 2.44e+01 1aj2 c.1.21.1 29668 2oatA 439 2.48e+01 2dkb c.67.1.4 34452 1oatA 439 2.48e+01 2dkb c.67.1.4 34461 1gbnA 402 2.48e+01 2dkb c.67.1.4 34455 1qq8A 214 2.56e+01 1qq8A a.132.1.1 19508 1qnrA 344 2.56e+01 1qnoA c.1.8.3 28834 1qnoA 344 2.56e+01 1qnoA c.1.8.3 28838 7a3hA 303 2.57e+01 7a3hA c.1.8.3 28817 1h5vA 304 2.57e+01 1qi2A 305 2.57e+01 7a3hA c.1.8.3 28824 1a3h 300 2.58e+01 7a3hA c.1.8.3 28819 1pmy 123 2.61e+01 1bqk b.6.1.1 22888 1e8gA 560 2.62e+01 1qltA d.58.32.1 39455 d.145.1.1 41718 1f71A 67 2.68e+01 1wdcC a.39.1.5 17289 1k5rA 41 2.70e+01 b.72.1.1 68206 1gw9A 388 2.75e+01 2pkaA 80 2.91e+01 2pkaA b.47.1.2 26302 2kaiA 80 2.91e+01 2pkaA b.47.1.2 26306 1qflA 389 2.98e+01 1afwA c.95.1.1 35908 c.95.1.1 35909 4xis 387 3.02e+01 4xis c.1.15.3 29421 3xis 387 3.02e+01 4xis c.1.15.3 29423 2xis 387 3.02e+01 4xis c.1.15.3 29427 1mba 147 3.05e+01 2fal a.1.1.2 15149 2fal 147 3.05e+01 2fal a.1.1.2 15150 1ep3A 311 3.08e+01 2dorA c.1.4.1 28597 1indL 215 3.10e+01 1mfa b.1.1.1 19838 b.1.1.2 20942 1ff9A 450 3.11e+01 1ff9A c.2.1.3 30039 d.81.1.2 39954 1hy3A 294 3.26e+01 1dm1A 146 3.29e+01 2fal a.1.1.2 15153 4thiA 362 3.38e+01 2thiA c.94.1.1 35793 1hneE 218 3.40e+01 1a7s b.47.1.2 26235 1bxdA 161 3.41e+01 1bxdA d.122.1.3 41111 3thiA 371 3.42e+01 2thiA c.94.1.1 35792 2thiA 379 3.44e+01 2thiA c.94.1.1 35794 1a8p 258 3.58e+01 1fdr b.43.4.2 25654 c.25.1.1 31544 1eexG 173 3.62e+01 1dioG a.23.2.1 16490 1dioG 173 3.62e+01 1dioG a.23.2.1 16496 1vaoA 560 3.67e+01 1qltA d.58.32.1 39461 d.145.1.1 41724 1lc5A 364 3.73e+01 1lkcA 364 3.73e+01 2taaA 478 3.76e+01 7taa b.71.1.1 27780 c.1.8.1 28767 1b3oB 514 3.79e+01 1ak5 c.1.5.1 28641 d.37.1.1 38538 d.37.1.1 38539 1dfoA 417 3.79e+01 1bj4A c.67.1.4 34480 1ihp 438 3.81e+01 1ihp c.60.1.3 33993 1eqbB 417 3.82e+01 1bj4A c.67.1.4 34485 1lf1A 308 3.84e+01 1deg 142 3.85e+01 1cll a.39.1.5 17280 1qltA 560 3.88e+01 1qltA d.58.32.1 39457 d.145.1.1 41720 1ppfE 218 3.95e+01 1a7s b.47.1.2 26234 1ppgE 218 3.95e+01 1a7s b.47.1.2 26236 1xrb 383 3.99e+01 1mxb d.130.1.1 41335 d.130.1.1 41336 d.130.1.1 41337