% 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.YGR235C.t2k-w0.5.mod Host: cc86 Tue Nov 12 18:39:16 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR235C % --------------------------------------------------------------------- % Inserted Files: YGR235C.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: YGR235C.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 234 nodes, 233.97 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(=2.2095) * Reverse)^tau(=0.7876))) % 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 1e9lA 377 -28.45 -7.17 1.09e+00 1f57A 307 -28.89 -7.16 1.11e+00 2ctc 307 -28.89 -7.15 1.11e+00 2ctb 307 -28.89 -7.15 1.11e+00 1yme 309 -28.89 -7.15 1.11e+00 1pytB 309 -28.89 -7.15 1.12e+00 1sig 339 -27.90 -6.84 1.50e+00 1lg1A 365 -27.78 -6.70 1.72e+00 1iq0A 592 -28.18 -6.27 2.64e+00 1kmdA 117 -25.28 -6.09 3.16e+00 2dhbB 146 -25.56 -6.07 3.21e+00 1hcnA 92 -24.13 -5.94 3.67e+00 1dz7A 92 -24.14 -5.94 3.67e+00 6cpa 307 -27.67 -5.93 3.71e+00 1cbx 307 -27.66 -5.93 3.72e+00 1bavA 309 -27.67 -5.93 3.72e+00 1qfwA 92 -24.12 -5.92 3.73e+00 1ass 159 -26.51 -5.89 3.85e+00 1asx 159 -26.51 -5.89 3.85e+00 1fcqA 350 -28.01 -5.84 4.05e+00 1g4mA 393 -27.02 -5.84 4.08e+00 1g13A 162 -24.89 -5.78 4.29e+00 1fliA 98 -24.28 -5.75 4.43e+00 1jsyA 418 -27.09 -5.57 5.32e+00 1wdb 104 -23.56 -5.53 5.59e+00 1dxqA 273 -26.88 -5.45 6.03e+00 1blu 82 -22.78 -5.36 6.60e+00 1jetA 517 -28.02 -5.36 6.64e+00 1jevA 517 -28.02 -5.36 6.64e+00 2olbA 517 -28.02 -5.36 6.64e+00 1do9A 94 -23.17 -5.30 7.08e+00 1ax8 146 -24.29 -5.13 8.38e+00 1d2kA 392 -26.95 -5.04 9.19e+00 2axx 94 -22.93 -5.03 9.29e+00 1aw3 94 -22.93 -5.03 9.32e+00 1aerB 195 -25.08 -5.01 9.49e+00 1i87A 98 -22.98 -5.00 9.66e+00 1bfx 99 -22.99 -4.99 9.74e+00 1ib7A 94 -23.01 -4.97 9.94e+00 1cyo 93 -22.70 -4.94 1.03e+01 1jxjA 496 -26.92 -4.91 1.06e+01 1smd 496 -26.91 -4.90 1.07e+01 1jxkA 491 -26.90 -4.87 1.10e+01 1qdeA 224 -25.02 -4.85 1.12e+01 1iwhB 146 -24.32 -4.83 1.15e+01 1k3vA 579 -26.60 -4.80 1.18e+01 1kb3A 496 -26.95 -4.75 1.25e+01 1lrzA 426 -26.83 -4.65 1.39e+01 1mhxA 65 -21.67 -4.63 1.42e+01 1bds 43 -20.82 -4.60 1.47e+01 2bds 43 -20.82 -4.60 1.47e+01 1nksA 194 -24.26 -4.59 1.48e+01 1kbkA 496 -26.79 -4.57 1.51e+01 1bx4A 345 -26.05 -4.53 1.58e+01 1fjgR 88 -22.70 -4.44 1.73e+01 1g1xC 88 -22.70 -4.44 1.73e+01 1seiA 130 -23.47 -4.44 1.74e+01 1i94R 87 -22.67 -4.43 1.76e+01 1dnlA 199 -24.11 -4.39 1.83e+01 1dhkA 496 -26.66 -4.36 1.90e+01 1ose 496 -26.67 -4.35 1.91e+01 1ciu 683 -27.97 -4.35 1.91e+01 1jbsA 149 -23.29 -4.35 1.92e+01 1aqzB 149 -23.33 -4.33 1.95e+01 1aqzA 149 -23.33 -4.33 1.95e+01 1kgxA 496 -26.57 -4.31 2.01e+01 1lqxA 82 -21.66 -4.27 2.07e+01 3cpuA 496 -26.53 -4.26 2.10e+01 1b2yA 496 -26.53 -4.26 2.11e+01 1hny 496 -26.53 -4.26 2.11e+01 1kgwA 496 -26.53 -4.26 2.12e+01 1g08B 145 -24.25 -4.25 2.13e+01 1jnwA 218 -24.20 -4.24 2.15e+01 1bvnP 496 -26.52 -4.22 2.19e+01 1pig 496 -26.51 -4.22 2.21e+01 1kguA 496 -26.53 -4.21 2.23e+01 1ck4B 198 -24.34 -4.20 2.25e+01 1akz 223 -24.04 -4.18 2.29e+01 1sspE 223 -24.04 -4.18 2.29e+01 1kl7A 514 -26.45 -4.16 2.35e+01 1qk1A 379 -26.04 -4.14 2.39e+01 1lr6A 82 -21.55 -4.11 2.47e+01 1blj 114 -22.44 -4.11 2.49e+01 1hx0A 496 -26.36 -4.05 2.66e+01 1kxqA 496 -26.35 -4.03 2.70e+01 1jfh 496 -26.35 -4.03 2.70e+01 1ppi 496 -26.35 -4.02 2.72e+01 1qvaA 223 -24.15 -4.01 2.77e+01 1g6hA 257 -25.18 -3.98 2.85e+01 1ehbA 82 -21.43 -3.97 2.88e+01 1m20A 82 -21.51 -3.95 2.94e+01 1fpwA 190 -23.81 -3.93 3.01e+01 1im4A 221 -23.99 -3.89 3.16e+01 1qbgA 272 -25.76 -3.85 3.29e+01 1h69A 273 -25.77 -3.85 3.29e+01 1d4aA 273 -25.77 -3.85 3.30e+01 1kbqA 273 -25.77 -3.85 3.30e+01 1gajA 257 -25.00 -3.84 3.32e+01 1qmoE 133 -22.78 -3.80 3.46e+01 1jexA 94 -21.75 -3.80 3.48e+01 1gojA 355 -24.79 -3.79 3.53e+01 1i9cA 137 -23.65 -3.77 3.61e+01 1fawA 141 -22.77 -3.77 3.62e+01 1g0wA 380 -25.33 -3.72 3.78e+01 1chuA 540 -25.77 -3.70 3.87e+01 1e5eA 404 -25.34 -3.70 3.89e+01 1mgtA 174 -23.41 -3.69 3.94e+01 2sspE 223 -23.53 -3.68 3.95e+01