% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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. % --------------------------------------------------------------------- % w0.5foo.1.YDR525W.t2k-w0.5.mod Host: cc34 Sat Dec 7 04:30:07 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDR5/YDR525W % --------------------------------------------------------------------- % Inserted Files: YDR525W.t2k-w0.5.mod % Database Files: /projects/compbio/experiments/protein-predict/SAM_T02/data/pdbaa % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Single Track Model: YDR525W.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 14196 sequences, 3167404 residues, 110 nodes, 111.00 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 (0.00) % E-value on N (=7316) sequences: % N / (1 + exp(-(lambda(=3.5229) * Reverse)^tau(=0.6961))) % Calculated when Simple < simple_threshold (0.00) % 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 1ggiH 222 -28.71 -8.90 1.22e-01 1ggbH 215 -28.67 -8.90 1.22e-01 2occC 261 -28.10 -8.13 2.38e-01 1ocrC 261 -28.10 -8.13 2.38e-01 1fhxB 129 -23.85 -5.97 1.76e+00 1fhwB 129 -23.80 -5.92 1.85e+00 1fgyA 127 -23.63 -5.82 2.03e+00 1l6jA 425 -26.51 -5.60 2.53e+00 1f28A 297 -25.21 -5.30 3.39e+00 1iruL 204 -24.49 -5.21 3.72e+00 1eb4A 509 -25.97 -5.14 4.00e+00 1gk2A 509 -25.97 -5.14 4.01e+00 1gkjA 509 -25.97 -5.13 4.03e+00 1gkmA 509 -25.97 -5.13 4.03e+00 1b8fA 509 -25.97 -5.13 4.03e+00 1j5oH 220 -24.41 -5.12 4.07e+00 1gk3A 509 -25.74 -4.91 5.09e+00 1bwvS 138 -22.90 -4.78 5.77e+00 1iu4A 331 -24.91 -4.65 6.68e+00 3pbgA 468 -24.90 -4.53 7.51e+00 1pbgA 468 -24.90 -4.53 7.51e+00 2pbg 468 -24.90 -4.53 7.53e+00 4pbgA 468 -24.90 -4.53 7.56e+00 1j6yA 139 -22.62 -4.51 7.71e+00 1d6vH 221 -23.77 -4.50 7.78e+00 1etzB 228 -25.37 -4.50 7.80e+00 1lucB 324 -24.29 -4.47 8.04e+00 1brlB 324 -24.29 -4.47 8.04e+00 1jrhH 219 -24.05 -4.41 8.55e+00 1emtH 213 -23.61 -4.37 8.97e+00 1cy9A 264 -23.69 -4.36 9.01e+00 1i3gH 121 -22.47 -4.26 1.00e+01 1en2A 91 -21.97 -4.19 1.08e+01 1jhlH 116 -22.07 -4.12 1.17e+01 1hxmA 229 -23.28 -4.10 1.20e+01 1mi2A 73 -20.08 -4.04 1.28e+01 1b4jH 220 -22.93 -4.03 1.29e+01 1cxwA 60 -20.73 -4.00 1.33e+01 1b2wH 220 -22.98 -3.98 1.36e+01 1fj7A 101 -21.36 -3.88 1.52e+01 1d5bB 221 -23.59 -3.82 1.63e+01 3hflH 215 -23.13 -3.78 1.70e+01 1a88A 275 -23.22 -3.77 1.71e+01 1axsB 221 -23.59 -3.77 1.71e+01 1rvfH 119 -22.33 -3.75 1.77e+01 1fskC 220 -23.27 -3.73 1.80e+01 1cy7A 599 -24.53 -3.69 1.87e+01 1afvH 220 -23.07 -3.68 1.91e+01 1fjeB 175 -21.95 -3.65 1.97e+01 1ecl 597 -24.53 -3.64 1.98e+01 1cf7B 95 -20.83 -3.64 1.98e+01 1lnrE 185 -21.91 -3.62 2.03e+01 1iawA 317 -23.56 -3.60 2.08e+01 1ev7A 317 -23.56 -3.60 2.08e+01 1ev7B 317 -23.56 -3.60 2.08e+01 1a7qH 116 -20.98 -3.57 2.16e+01 5csmA 256 -22.74 -3.57 2.16e+01 3csmA 256 -22.74 -3.53 2.26e+01 1qfwH 117 -21.16 -3.51 2.30e+01 1csmA 256 -22.74 -3.50 2.32e+01 1dqdH 222 -22.97 -3.50 2.32e+01 1eb7A 323 -23.17 -3.50 2.34e+01 1eg9A 449 -24.01 -3.48 2.39e+01 1ndoA 449 -24.01 -3.48 2.39e+01 1gnxA 479 -23.92 -3.46 2.43e+01 1mlcB 218 -22.80 -3.46 2.44e+01 4csmA 256 -22.74 -3.41 2.59e+01 1cicB 217 -23.63 -3.28 3.00e+01 1vng 609 -25.44 -3.26 3.08e+01 1gff2 177 -21.55 -3.24 3.13e+01 1e9eA 215 -21.93 -3.24 3.14e+01 1e9cA 215 -21.93 -3.24 3.14e+01 1lmkA 238 -22.60 -3.22 3.22e+01 1bgaA 447 -23.58 -3.19 3.31e+01 1bggA 448 -23.58 -3.19 3.32e+01 1gyxA 76 -19.04 -3.18 3.39e+01 1qnmA 198 -22.36 -3.17 3.41e+01 2occB 227 -23.42 -3.17 3.42e+01 1tr1A 447 -23.58 -3.17 3.42e+01 1e4iA 447 -23.58 -3.17 3.42e+01 1k4cA 219 -22.59 -3.17 3.43e+01 1qnkA 69 -19.46 -3.15 3.47e+01 1qcnA 421 -23.90 -3.15 3.49e+01 1h3fA 432 -23.42 -3.14 3.52e+01 1vne 609 -25.44 -3.13 3.56e+01 1vns 609 -25.44 -3.13 3.57e+01 1vnc 609 -25.44 -3.13 3.57e+01 1iduA 609 -25.44 -3.13 3.57e+01 1vnh 609 -25.44 -3.13 3.59e+01 1em1A 198 -22.31 -3.12 3.61e+01 1hxvA 113 -20.87 -3.11 3.67e+01 1jjiA 311 -22.96 -3.10 3.71e+01 1i49A 224 -22.11 -3.05 3.94e+01 1i4dA 224 -22.11 -3.05 3.94e+01 1i4lA 224 -22.11 -3.05 3.94e+01 1i4tB 224 -22.11 -3.05 3.94e+01