# List of top-scoring protein chains for t2k-100-30-near-backbone-11 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 1ucsA 64 3.07e-03 b.85.1.1 88466 1c89A 134 5.37e-03 1msi b.85.1.1 28314 b.85.1.1 28315 1msi 70 1.40e-02 1msi b.85.1.1 28281 1hg7A 66 1.64e-02 1msi b.85.1.1 28280 1ml9A 302 3.43e-01 b.85.7.1 79282 1fiuA 286 1.10e+00 1fiuA c.52.1.10 33317 1lizA 136 1.68e+00 1fcjA 322 1.88e+00 1oasA c.79.1.1 35289 1nzoA 363 2.04e+00 b.105.1.1 -2933 e.3.1.1 -11784 1ithA 141 2.38e+00 1ithA a.1.1.2 15623 1nj4A 363 2.50e+00 b.105.1.1 80545 e.3.1.1 80546 1bxiB 134 2.64e+00 1bxiB d.4.1.1 37136 1jr1A 514 3.58e+00 c.1.5.1 63241 d.37.1.1 63242 d.37.1.1 63243 1c3yA 108 5.52e+00 1c3yA a.39.2.1 17387 1hd8A 363 6.08e+00 b.105.1.1 65803 e.3.1.1 65804 1eriA 276 6.17e+00 1ckqA c.52.1.1 33231 1innA 166 7.82e+00 1j98A d.185.1.2 62608 1n3jA 119 8.36e+00 b.85.7.2 79963 1qpsA 261 8.55e+00 1ckqA c.52.1.1 33234 1qc9A 276 8.69e+00 1ckqA c.52.1.1 33235 1ckqA 276 8.73e+00 1ckqA c.52.1.1 33229 1emvB 134 9.05e+00 1bxiB d.4.1.1 37135 1ku2A 241 9.11e+00 a.4.13.1 83096 a.177.1.1 83097 1qbjA 81 9.47e+00 1qbjA a.4.5.19 16155 1vjeA 166 9.63e+00 d.185.1.2 -10261 1fp1D 372 9.92e+00 1fpqA a.4.5.29 59939 c.66.1.12 59940 1fr2B 134 1.00e+01 d.4.1.1 83257 1mgtA 174 1.02e+01 1mgtA a.4.2.1 16078 c.55.7.1 33753 1cl8A 276 1.02e+01 1ckqA c.52.1.1 33230 1gp1A 198 1.06e+01 1gp1A c.47.1.10 33059 1qgpA 77 1.14e+01 1qbjA a.4.5.19 16158 2sak 121 1.18e+01 2sak d.15.5.1 37711 1oasA 322 1.25e+01 1oasA c.79.1.1 35293 1c76A 136 1.25e+01 2sak d.15.5.1 37718 1mwwA 128 1.37e+01 unknown_sccs -10451 1ten 90 1.53e+01 1ten b.1.2.1 21990 1ov2A 99 1.72e+01 a.13.1.1 -457 1k0hA 117 1.73e+01 b.106.1.2 71975 1ryt 190 1.83e+01 1ryt a.25.1.1 16646 g.41.5.1 45245 1a8h 500 1.90e+01 1a8h a.27.1.1 16922 c.26.1.1 31589 1mldA 314 1.98e+01 2cmd c.2.1.5 30122 d.162.1.1 42089 1bt0A 76 1.98e+01 1ubi d.15.1.1 37607 1fpqA 372 2.07e+01 1fpqA a.4.5.29 59947 c.66.1.12 59948 1ag2 103 2.13e+01 1b10A d.6.1.1 37305 1amx 180 2.20e+01 1amx b.2.3.1 22410 1ogaD 215 2.20e+01 b.1.1.1 86990 b.1.1.2 86991 1lkoA 191 2.21e+01 a.25.1.1 78063 g.41.5.1 78064 1akhB 83 2.23e+01 1akhB a.4.1.1 15985 1b71A 191 2.33e+01 1ryt a.25.1.1 16647 g.41.5.1 45246 1umdA 367 2.42e+01 c.36.1.11 -6969 1yrnB 83 2.49e+01 1akhB a.4.1.1 15986 1p9qC 256 2.55e+01 1s5pA 235 2.70e+01 c.31.1.5 -6774 1t95A 240 2.70e+01 1ssn 136 2.74e+01 2sak d.15.5.1 37720 2sas 185 2.77e+01 2sas a.39.1.5 17258 1rl6A 177 2.85e+01 1rl6A d.141.1.1 41473 d.141.1.1 41474 1r53A 382 2.97e+01 unknown_sccs -11177 1q4rA 112 2.98e+01 d.58.4.4 -9943 2kauA 100 3.00e+01 1ubpA d.8.1.1 37335 1gzwA 134 3.07e+01 b.29.1.3 -3412 1brwA 433 3.16e+01 1brwA a.46.2.1 17764 c.27.1.1 31628 d.41.3.1 38626 1fwcA 100 3.31e+01 1ubpA d.8.1.1 37331 1ef8A 261 3.31e+01 1ef8A c.14.1.3 30921 1q53A 112 3.31e+01 d.58.4.4 -9944 1uurA 473 3.41e+01 a.47.1.1 -968 b.2.5.5 -2904 d.93.1.1 -10632 1ejxA 100 3.42e+01 d.8.1.1 83182 1m5sA 297 3.42e+01 d.58.33.1 74511 d.58.33.1 74512 1neq 74 3.58e+01 1neq a.35.1.2 17063