% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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-T2K, 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, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % w0.5foo.1.YGR013W.t2k-w0.5.mod Host: farm09.cse.ucsc.edu Sun Mar 19 20:22:55 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR013W % --------------------------------------------------------------------- % Inserted Files: YGR013W.t2k-w0.5.mod % Database Files: /projects/compbio/data/pdb/dunbrack-pdbaa % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Single Track Model: YGR013W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 23081 sequences, 5302281 residues, 621 nodes, 1354.34 seconds % % Sequence scores selected if better than: % E-value (Emax 4.0e+01) (select_score=4) % % Simple: NLL-NULL using FIM probabilities % Reverse: NLL-NULL for the reverse sequence NULL model % Calculated when Simple < simple_threshold (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=2.3024) * Reverse)^tau(=0.7215))) % Calculated when Simple < simple_threshold (10000.00) % Rescale E-values or use -dbsize for multiple scoring runs. % Scores sorted by E-value, best first % % Sequence ID Length Simple Reverse E-value X count 1v4hA 299 -19.25 -7.10 6.01e+00 :299 XRAY 2.80 0.219 0.275 octoprenyl-diphosphate s 1uf2K 506 -18.33 -7.06 6.22e+00 :506 XRAY 3.50 0.303 0.306 Structural protein P7 [ESCHERICHIA 1nxmA 197 -15.81 -5.14 2.86e+01 :197 XRAY 1.30 0.145 0.174 dTDP-6-deoxy-D-xylo-4-he 1hnnA 282 -15.51 -5.11 2.94e+01 :282 XRAY 2.40 0.232 0.273 PHENYLETHANOLAMINE N-MET 1xw8A 252 -15.48 -5.11 2.94e+01 :252 XRAY 2.00 0.241 0.265 UPF0271 protein ybgL