# List of top-scoring protein chains for T0403.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.soe.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 2fgqX 332 1.79e-33 f.4.3.1 133439 2fgrA 332 3.05e-33 f.4.3.1 133440 1phoA 330 5.28e-29 f.4.3.1 43758 2j1nA 346 6.21e-29 1osmA 342 7.67e-29 2omf f.4.3.1 43769 2ixwA 343 1.08e-28 1hxuA 340 1.76e-28 2omf f.4.3.1 61384 2omfA 340 2.56e-28 f.4.3.1 43749 1hxxA 340 3.07e-28 2omf f.4.3.1 61385 1bt9A 340 3.10e-28 2omf f.4.3.1 43756 2ixxA 354 3.14e-28 1mpfA 340 3.37e-28 f.4.3.1 43752 1gfpA 340 6.90e-28 f.4.3.1 43750 1gfmA 340 7.15e-28 f.4.3.1 43755 1gfoA 340 7.26e-28 f.4.3.1 43753 1gfqA 340 1.23e-27 f.4.3.1 43751 1gfnA 334 1.53e-26 f.4.3.1 43754 1hxtA 340 4.99e-26 2omf f.4.3.1 61383 2porA 301 1.38e-06 f.4.3.1 43759 2prnA 289 4.33e-03 f.4.3.1 43763 3prnA 289 1.03e-02 f.4.3.1 43761 1prnA 289 1.13e-02 f.4.3.1 43762 1bh3A 289 1.16e-02 f.4.3.1 43766 5prnA 289 2.28e-02 f.4.3.1 43764 6prnA 289 3.43e-02 f.4.3.1 43765 7prnA 289 3.97e-02 f.4.3.1 43768 1h6s1 307 5.25e-02 8prnA 289 7.28e-02 f.4.3.1 43767 1f74A 293 2.16e-01 1nal3 c.1.10.1 29079 1i78A 297 4.97e-01 f.4.4.1 66046 2odjA 428 8.65e-01 1wcdJ 441 1.21e+00 b.121.4.9 120887 1p4tA 155 1.22e+00 f.4.1.1 87779 1wceA 441 1.25e+00 2gufA 594 1.36e+00 f.4.3.3 135736 2gskA 590 1.36e+00 f.4.3.3 135587 2gsyA 456 1.37e+00 b.121.4.9 135599 1nqfA 594 1.60e+00 f.4.3.3 86028 1qd6C 240 2.49e+00 1qd5A 1qd5A 275 2.85e+00 1qd5A f.4.2.1 43748 1ilzA 275 3.23e+00 f.4.2.1 66209 1fw3A 275 3.24e+00 1qd5A f.4.2.1 60054 1by5A 714 3.57e+00 1by5A f.4.3.3 43800 1wiwA 290 3.69e+00 c.80.1.1 114681 2fcpA 723 4.77e+00 1by5A f.4.3.3 43802 1fcpA 705 4.77e+00 1by5A f.4.3.3 43805 1mmaA 762 5.24e+00 b.34.3.1,c.37.1.9 24587,32184 1w9iA 770 5.50e+00 1w9kA 770 5.58e+00 1mmnA 762 5.65e+00 b.34.3.1,c.37.1.9 24582,32179 1d0yA 761 5.73e+00 1lvk b.34.3.1,c.37.1.9 24581,32178 1yv3A 762 5.78e+00 2df7A 458 5.99e+00 b.121.4.9 131449 1w9jA 770 6.10e+00 1w9lA 770 6.10e+00 1qfgA 725 6.18e+00 1by5A f.4.3.3 43803 1fi1A 707 6.18e+00 1by5A f.4.3.3 59844 1jx2A 776 6.36e+00 b.34.3.1,c.37.1.9 67402,67403 2akaA 776 6.37e+00 2f1cX 286 6.51e+00 1fmvA 761 6.58e+00 1lvk b.34.3.1,c.37.1.9 24580,32177 1yizA 429 6.60e+00 c.67.1.1 123375 1vomA 762 6.91e+00 b.34.3.1,c.37.1.9 24577,32174 1lvkA 762 7.86e+00 b.34.3.1,c.37.1.9 24576,32173 1g8xA 1010 8.43e+00 1lvk k.1.1.1 46378 2jqyA 280 8.87e+00 2iwvA 281 8.95e+00 2dj0A 137 1.07e+01 2z3oA 233 1.08e+01 2dpsA 254 1.09e+01 2gt4A 160 1.15e+01 1ryaA 160 1.22e+01 d.113.1.5 105122 2iciA 227 1.34e+01 1k8tA 510 1.38e+01 e.41.1.1 68316 1pk0A 507 1.40e+01 e.41.1.1 94795 1mmgA 762 1.55e+01 b.34.3.1,c.37.1.9 24579,32176 1zl5A 420 1.58e+01 1vb3A 428 1.68e+01 c.79.1.1 119942 1uxvA 501 1.73e+01 c.82.1.1 108127 1vhwA 253 1.75e+01 c.56.2.1 100706 2c58A 537 1.82e+01 c.69.1.1 129891 1uxtA 501 1.87e+01 c.82.1.1 108125 2de0X 526 1.95e+01 1t3aA 421 1.97e+01 d.92.1.7 106339 1eeaA 534 1.97e+01 2bce c.69.1.1 34609 2cekA 535 1.97e+01 c.69.1.1 130347 1ut6A 537 1.98e+01 c.69.1.1 119698 1ea5A 537 1.98e+01 2bce c.69.1.1 34592 2dfpA 534 1.98e+01 2bce c.69.1.1 34597 1w6rA 543 1.98e+01 c.69.1.1 114283 1gqrA 532 1.98e+01 c.69.1.1 70374 1zkwA 420 2.00e+01 2cxaA 256 2.01e+01 d.108.1.6 130993 1t3cA 421 2.06e+01 d.92.1.7 106343 1gc1H 229 2.10e+01 1gc1H b.1.1.1,b.1.1.2 20265,21265 1g9mH 229 2.22e+01 1gc1H b.1.1.1,b.1.1.2 20263,21263 2aciA 418 2.34e+01 d.126.1.4 126551 1txkA 498 2.42e+01 b.1.18.2,b.30.5.9 107425,107426 1zkxA 420 2.60e+01 1pvgA 418 2.62e+01 d.14.1.3,d.122.1.2 95161,95162 2dpyA 438 2.70e+01 1qfxA 460 2.72e+01 1qfxA c.60.1.2 33994 1u8fO 335 3.10e+01 c.2.1.3,d.81.1.1 119626,119627 1znqO 338 3.15e+01 c.2.1.3,d.81.1.1 125401,125402 1qy3A 229 3.15e+01 d.22.1.1 96570 1qxtA 230 3.16e+01 d.22.1.1 96562 1mv8A 436 3.16e+01 a.100.1.4,c.2.1.6,c.26.3.1 85128,85129,85130 3gpdG 334 3.17e+01 1dssG c.2.1.3,d.81.1.1 30029,39944 1zl6A 420 3.34e+01 2abrA 418 3.34e+01 d.126.1.4 126530 2a9gA 418 3.39e+01 d.126.1.4 126435 1rxxA 421 3.39e+01 d.126.1.4 98061 2aafA 418 3.43e+01 d.126.1.4 126471 2ny1D 229 3.47e+01 b.1.1.1,b.1.1.2 138768,138769 1rz8B 228 3.47e+01 b.1.1.1,b.1.1.2 98139,98140 1j36A 607 3.49e+01 d.92.1.5 84054 1qz2A 336 3.52e+01 a.118.8.1,d.26.1.1 104663,104664 1xfuA 747 3.56e+01 1zn3A 420 3.71e+01 1j0xO 332 3.76e+01 c.2.1.3,d.81.1.1 90750,90751 1po0A 751 3.85e+01 f.4.3.3 94960 2issA 313 3.95e+01 1kmoA 774 4.01e+01 f.4.3.3 72753 2v94A 107 4.16e+01 1xfxA 777 4.20e+01 1dbiA 280 4.20e+01 1gci c.41.1.1 32543 2o4vA 411 4.46e+01 1lciA 550 4.46e+01 e.23.1.1 43349 2rdpA 150 4.54e+01 2uu7A 381 4.54e+01 2novA 496 4.62e+01 2onhA 543 5.12e+01 1h4jA 599 5.29e+01 4aahA b.70.1.1 60590 1ky8A 501 5.34e+01 c.82.1.1 77628 1n6uA 212 5.41e+01 b.1.2.1,b.1.2.1 85363,85364 2hfcA 239 5.53e+01 1jetA 517 5.79e+01 1jevA c.94.1.1 35718 1cshA 435 6.17e+01 a.103.1.1 18880 1al6A 437 6.18e+01 a.103.1.1 18885 1yhiA 239 6.31e+01 2h79A 269 6.46e+01 1w6sA 599 6.57e+01 b.70.1.1 114284 2atmA 331 6.57e+01 2i8tA 167 6.78e+01 1tiyA 164 7.00e+01 c.97.1.2 107012 1navA 263 7.11e+01 a.123.1.1 85500 2agkA 260 7.22e+01 2ojwA 384 7.58e+01 1wkqA 164 7.58e+01 c.97.1.2 109393 1h4iA 599 7.90e+01 4aahA b.70.1.1 60586 2qjuA 511 7.91e+01 2awjA 230 7.93e+01 1qyfA 228 7.97e+01 d.22.1.1 96588