# 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 4.45e-28 c.1.10.1 66501 1jcjA 260 1.72e-27 c.1.10.1 66499 2dorA 311 9.97e-02 2dorA c.1.4.1 28593 1dorA 311 9.97e-02 2dorA c.1.4.1 28595 1kv8A 216 4.26e-01 1al7 359 1.09e+00 1gox c.1.4.1 28609 1gox 369 1.10e+00 1gox c.1.4.1 28607 1gylA 369 1.12e+00 1gox c.1.4.1 28610 1ea0A 1479 1.28e+00 b.80.4.1 64854 c.1.4.1 64855 d.153.1.1 64856 1gpwC 253 1.47e+00 c.1.2.1 65462 1thfD 253 1.51e+00 1thfD c.1.2.1 28535 1d3hA 367 1.52e+00 1d3gA c.1.4.1 28601 1d3gA 367 1.52e+00 1d3gA c.1.4.1 28600 1hg3A 225 1.53e+00 1hg3A c.1.1.1 61025 1zfjA 491 1.61e+00 1ak5 c.1.5.1 28638 d.37.1.1 38540 d.37.1.1 38541 1jceA 344 1.64e+00 c.55.1.1 62876 c.55.1.1 62877 1ft2A 315 1.74e+00 1ft1A a.118.6.1 19190 1a53 247 1.75e+00 1a53 c.1.2.4 28564 1igs 248 1.75e+00 1a53 c.1.2.4 28565 1juk 248 1.75e+00 1a53 c.1.2.4 28567 1jcfA 344 1.88e+00 c.55.1.1 62878 c.55.1.1 62879 1d8dA 377 1.89e+00 1ft1A a.118.6.1 19185 1jcrA 377 1.89e+00 a.118.6.1 66506 1ft1A 377 1.89e+00 1ft1A a.118.6.1 19186 1lk5A 229 2.60e+00 1jxkA 491 3.53e+00 b.71.1.1 63316 c.1.8.1 63317 1smd 496 3.54e+00 1smd b.71.1.1 27768 c.1.8.1 28755 1jxjA 496 3.55e+00 b.71.1.1 63314 c.1.8.1 63315 1kbjA 412 4.10e+00 1qcwA 410 4.19e+00 1gox c.1.4.1 28622 1ltdA 506 4.50e+00 1gox c.1.4.1 28618 d.120.1.1 41086 1fcbA 511 4.51e+00 1gox c.1.4.1 28620 d.120.1.1 41087 1lcoA 511 4.52e+00 1gox c.1.4.1 28624 d.120.1.1 41088 1a6aB 187 4.87e+00 1iakB b.1.1.2 21616 d.19.1.1 38190 1qbqA 333 5.18e+00 1ft1A a.118.6.1 19187 1d5xB 192 5.62e+00 1iakB b.1.1.2 21624 d.19.1.1 38198 1kn9C 249 5.91e+00 b.87.1.2 68701 1b12A 248 5.91e+00 1b12A b.87.1.2 28388 1d5mB 192 6.30e+00 1iakB b.1.1.2 21618 d.19.1.1 38192 1j4bA 457 7.01e+00 c.37.1.10 66374 1exqA 154 7.64e+00 1b9dA c.55.3.2 33646 1i60A 278 7.93e+00 1dlhB 188 7.99e+00 1iakB b.1.1.2 21598 d.19.1.1 38172 1aqdK 198 8.11e+00 1iakB b.1.1.2 21592 d.19.1.1 38166 1sebB 192 8.16e+00 1iakB b.1.1.2 21602 d.19.1.1 38176 1hxyB 190 8.19e+00 1iakB b.1.1.2 61388 d.19.1.1 61389 1ydvA 248 8.22e+00 1amk c.1.1.1 28501 1qu9A 128 8.35e+00 1qu9A d.79.1.1 39755 1qu9C 128 8.35e+00 1qu9A d.79.1.1 39757 1qo2A 241 9.80e+00 1qo2A c.1.2.1 28533 1jcqA 382 1.02e+01 a.118.6.1 66504 1ak5 503 1.10e+01 1ak5 c.1.5.1 28639 1dliA 402 1.13e+01 1dliA a.100.1.4 18809 c.2.1.6 30213 c.26.3.1 31622 1dljA 402 1.14e+01 1dliA a.100.1.4 18808 c.2.1.6 30212 c.26.3.1 31621 1jmqA 46 1.15e+01 b.72.1.1 66888 1qm4A 396 1.23e+01 1mxb d.130.1.1 41350 d.130.1.1 41351 d.130.1.1 41352 1ex4A 239 1.25e+01 1b9dA b.34.7.1 24627 c.55.3.2 33670 1h5yA 253 1.28e+01 c.1.2.1 65638 1fv1E 190 1.36e+01 1iakB b.1.1.2 21608 d.19.1.1 38182 1czfA 362 1.37e+01 1czfA b.80.1.3 28031 1lc5A 364 1.39e+01 2prd 174 1.45e+01 2prd b.40.5.1 25435 1dv2A 452 1.47e+01 1bncA b.84.2.1 28238 c.30.1.1 31645 d.142.1.2 41490 1f81A 88 1.48e+01 1f81A g.53.1.1 45383 1c8m4 77 1.55e+01 1iebB 227 1.58e+01 1iakB b.1.1.2 21636 d.19.1.1 38210 1gv0A 310 1.59e+01 c.2.1.5 65594 d.162.1.1 65595 1bncA 449 1.71e+01 1bncA b.84.2.1 28236 c.30.1.1 31643 d.142.1.2 41488 1dv1A 449 1.71e+01 1bncA b.84.2.1 28234 c.30.1.1 31641 d.142.1.2 41486 1bncB 449 1.71e+01 1bncA b.84.2.1 28237 c.30.1.1 31644 d.142.1.2 41489 1fneB 224 1.73e+01 1iakB b.1.1.2 59898 d.19.1.1 59899 1fngB 224 1.73e+01 1iakB b.1.1.2 59906 d.19.1.1 59907 1c7nA 399 1.77e+01 1d2fA c.67.1.3 34413 1ktdB 215 1.83e+01 1k9qA 40 1.84e+01 b.72.1.1 68357 1i3rD 228 1.87e+01 b.1.1.2 61626 d.19.1.1 61627 1aym4 68 1.87e+01 1tlk 154 1.89e+01 1tlk b.1.1.4 21707 1l6sA 323 1.91e+01 1i8jA 323 1.93e+01 1b4kA c.1.10.3 61968 1kt2B 213 1.99e+01 1a3h 300 2.11e+01 7a3hA c.1.8.3 28819 7a3hA 303 2.12e+01 7a3hA c.1.8.3 28817 1h5vA 304 2.12e+01 1qi2A 305 2.12e+01 7a3hA c.1.8.3 28824 1b0fA 218 2.20e+01 1a7s b.47.1.2 26237 1l8tA 263 2.22e+01 1kyqA 274 2.23e+01 1j7lA 264 2.23e+01 d.144.1.6 62697 1j7iA 264 2.23e+01 1j7iA d.144.1.6 62694 1e9mA 106 2.32e+01 1ayfA d.15.4.1 59397 1b4eA 323 2.33e+01 1b4kA c.1.10.3 29186 1ihp 438 2.34e+01 1ihp c.60.1.3 33993 1ad1A 266 2.42e+01 1aj2 c.1.21.1 29668 1gal 583 2.45e+01 1gpeA c.3.1.2 30386 d.16.1.4 37950 1bx2B 191 2.62e+01 1iakB b.1.1.2 21610 d.19.1.1 38184 4thiA 362 2.78e+01 2thiA c.94.1.1 35793 3thiA 371 2.80e+01 2thiA c.94.1.1 35792 2thiA 379 2.82e+01 2thiA c.94.1.1 35794 1dbiA 280 2.88e+01 1gci c.41.1.1 32543 1tr1A 447 2.93e+01 1e70M c.1.8.4 28957 1bgaA 447 2.99e+01 1e70M c.1.8.4 28961 1bggA 448 3.00e+01 1e70M c.1.8.4 28953 1e4iA 447 3.00e+01 1e70M c.1.8.4 59225 1j8rA 196 3.04e+01 1j8rA b.2.3.3 62745 1qlrB 232 3.11e+01 1igtB b.1.1.1 19835 b.1.1.2 20939 1pmy 123 3.17e+01 1bqk b.6.1.1 22888 1jgcA 161 3.19e+01 a.25.1.1 66673 6xia 387 3.25e+01 4xis c.1.15.3 29406 1c6vA 164 3.46e+01 1b9dA c.55.3.2 33672 1jhnA 424 3.48e+01 b.29.1.12 66720 b.29.1.12 66721 b.104.1.1 66722 1guyC 309 3.49e+01 c.2.1.5 65584 d.162.1.1 65585 1b3oB 514 3.51e+01 1ak5 c.1.5.1 28641 d.37.1.1 38538 d.37.1.1 38539 1eepB 404 3.55e+01 1ak5 c.1.5.1 28637 1dn0D 232 3.57e+01 1igtB b.1.1.1 19833 b.1.1.2 20937 1k5rA 41 3.62e+01 b.72.1.1 68206 1cr6B 554 3.64e+01 1cr6B c.108.1.2 43338 c.69.1.11 34688 1ek1A 554 3.64e+01 1cr6B c.108.1.2 43335 c.69.1.11 34685 1cqzA 554 3.64e+01 1cr6B c.108.1.2 43339 c.69.1.11 34689 1jmvA 141 3.81e+01 c.29.1.2 66897