# List of top-scoring protein chains for t2k-100-30-stride-ebghtl 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 1tocR 120 3.41e-02 1tocR g.8.1.2 44558 g.8.1.2 44559 1ycsB 239 3.47e-01 1ycsB b.34.2.1 24553 d.211.1.1 19155 1vmoA 163 3.50e-01 1vmoA b.77.1.1 27974 1qe3A 489 4.43e-01 2bce c.69.1.1 34630 1abmA 198 9.36e-01 1avmA 1pl4A 198 9.45e-01 a.2.11.1 -132 d.44.1.1 -9733 1ap6A 198 9.95e-01 1avmA a.2.11.1 15746 d.44.1.1 38705 1n0nA 199 1.21e+00 a.2.11.1 79750 d.44.1.1 79751 1eucA 311 1.80e+00 2scuA c.2.1.8 30311 c.23.4.1 31139 1ohtA 215 2.36e+00 d.118.1.1 87036 1eudA 311 3.11e+00 2scuA c.2.1.8 30312 c.23.4.1 31140 1p0iA 529 3.81e+00 c.69.1.1 -8291 1vcbA 118 4.02e+00 1vcbA d.15.1.1 37603 1lm8B 118 4.35e+00 d.15.1.1 74033 1grj 158 5.35e+00 1grj a.2.1.1 15691 d.26.1.2 38433 2nllB 103 5.52e+00 2nllB g.39.1.2 45115 1qz8A 113 5.72e+00 unknown_sccs -4264 1qndA 123 5.73e+00 1qndA d.106.1.1 40794 1p80A 753 6.40e+00 c.23.16.3 -6547 e.5.1.1 -11840 1ne6A 283 6.90e+00 b.82.3.2 -4918 b.82.3.2 -4919 1d8bA 81 7.06e+00 1d8bA a.60.8.1 18094 1jwiB 125 8.58e+00 d.169.1.1 67384 1jj2I 145 8.72e+00 1ffkG c.21.1.1 63094 1cf9A 753 9.05e+00 1cf9A c.23.16.3 31441 e.5.1.1 42815 1i85A 110 9.47e+00 1i85A b.1.1.1 61946 1pwxA 254 1.03e+01 c.2.1.2 -5858 1ffkG 145 1.05e+01 1ffkG c.21.1.1 31035 1ndbA 596 1.10e+01 c.43.1.3 80411 c.43.1.3 80412 1dceA 567 1.11e+01 1dceA a.118.6.1 19191 b.7.4.1 23218 c.10.2.2 30867 2phlA 397 1.14e+01 1dgwA b.82.1.2 28082 b.82.1.2 28083 1cbh 36 1.25e+01 2cbh g.3.8.1 44182 2cbh 36 1.25e+01 2cbh g.3.8.1 44181 1kf6D 119 1.40e+01 f.21.2.2 72400 1snzA 344 1.42e+01 b.30.5.4 -3496 1q87A 221 1.52e+01 unknown_sccs -12028 1j0hA 588 1.63e+01 b.1.18.2 77027 b.71.1.1 77028 c.1.8.1 77029 1pmaA 233 1.73e+01 1pmaA d.153.1.4 41918 1gg1A 350 1.74e+01 1qr7A c.1.10.4 29187 1psdA 409 1.76e+01 1psdA c.2.1.4 30097 c.23.12.1 31357 d.58.18.1 39354 1ud0A 113 1.78e+01 unknown_sccs -450 1dkuA 317 1.81e+01 1dkuA c.61.1.2 34118 c.61.1.2 34119 1okiA 210 1.92e+01 b.11.1.1 -3030 b.11.1.1 -3031 7catA 506 1.99e+01 1cf9A e.5.1.1 42781 1otcB 260 2.03e+01 1otcB b.40.4.3 25310 1eit 37 2.05e+01 1eit g.3.6.2 44108 1qr7A 350 2.06e+01 1qr7A c.1.10.4 29191 1qcrH 60 2.11e+01 1qcrH f.28.1.1 43678 1josA 128 2.17e+01 d.52.7.1 84191 1v33A 366 2.43e+01 unknown_sccs -11384 1hqoA 258 2.61e+01 1hqoA a.45.1.1 17749 c.47.1.5 33043 1nm8A 616 2.67e+01 c.43.1.3 85872 c.43.1.3 85873 1rgs 288 2.67e+01 1rgs b.82.3.2 28146 b.82.3.2 28147 153l 185 2.71e+01 153l d.2.1.5 36984 1n8fA 350 2.76e+01 c.1.10.4 85397 1igqA 62 2.77e+01 b.34.1.3 66130 1mhnA 59 2.77e+01 b.34.9.1 84964 1k8tA 510 2.89e+01 e.41.1.1 68316 1dkrA 317 2.92e+01 1dkuA c.61.1.2 34114 c.61.1.2 34115 1b8aA 438 3.09e+01 1b8aA b.40.4.1 25244 d.104.1.1 40765 1c44A 123 3.22e+01 1qndA d.106.1.1 40795 1nb8A 353 3.25e+01 d.3.1.9 80385 1nlnA 204 3.32e+01 d.3.1.7 -8897 1rypD 241 3.33e+01 1rypD d.153.1.4 41935 1gnxA 479 3.41e+01 c.1.8.4 76241 1f3aA 222 3.43e+01 1pgtA a.45.1.1 17701 c.47.1.5 32995 1b06A 210 3.51e+01 1avmA a.2.11.1 15740 d.44.1.1 38737 1vypX 364 3.59e+01 1fntc 245 3.60e+01 1jv2A 957 3.67e+01 b.1.15.1 67334 b.1.15.1 67335 b.1.15.1 67336 b.69.8.1 67337 1ir3A 306 3.72e+01 1fmk d.144.1.7 41702 1bbzE 58 3.78e+01 1bbzA b.34.2.1 24479 1aboA 62 3.81e+01 1bbzA b.34.2.1 24474 2aaa 484 3.82e+01 7taa b.71.1.1 27777 c.1.8.1 28764 3pbgA 468 3.93e+01 1e70M c.1.8.4 28951 1bkjA 240 3.99e+01 1bkjA d.90.1.1 40243 1awo 62 4.00e+01 1bbzA b.34.2.1 24482