% 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. % --------------------------------------------------------------------- % dsspfoo.1.YGR230W.t2k-100-30-dssp-ebghstl Host: cc76 Tue Nov 12 18:20:21 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR230W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.dssps % % 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)) % Track 0 Coeff 1.000 File YGR230W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR230W.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 138 nodes, 94.15 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(=1.8588) * Reverse)^tau(=0.8422))) % 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 1ihuA 589 -34.60 -11.02 2.19e-02 1f48A 589 -34.06 -10.53 3.53e-02 1dszA 86 -27.85 -9.82 7.14e-02 1bza 262 -28.77 -8.48 2.72e-01 1nzyA 269 -29.25 -8.46 2.79e-01 1hra 81 -26.43 -7.99 4.47e-01 1fntc 245 -28.79 -7.65 6.36e-01 1kfiA 572 -30.24 -7.61 6.65e-01 1hyqA 263 -27.89 -7.55 7.01e-01 3pmgA 561 -31.02 -7.36 8.60e-01 1bn7A 294 -28.08 -7.09 1.14e+00 1bn6A 294 -28.01 -7.05 1.19e+00 1cqwA 295 -28.00 -6.98 1.27e+00 1gdtA 183 -28.05 -6.84 1.47e+00 1lxtA 561 -30.49 -6.68 1.74e+00 1jksA 294 -27.87 -6.58 1.94e+00 1aky 221 -27.65 -6.17 2.99e+00 1kwmA 402 -27.09 -5.88 4.08e+00 1k3eA 156 -25.90 -5.76 4.63e+00 2lfb 100 -25.50 -5.54 5.90e+00 1hzoA 271 -26.05 -5.51 6.03e+00 1gnwA 211 -26.20 -5.45 6.48e+00 1fslA 143 -25.61 -5.41 6.76e+00 1erp 38 -20.67 -5.37 7.08e+00 1i86A 389 -27.61 -5.35 7.25e+00 1bi5A 389 -27.61 -5.34 7.26e+00 1i88A 389 -27.52 -5.29 7.73e+00 1binA 143 -25.47 -5.29 7.74e+00 1gw5B 591 -31.77 -5.20 8.51e+00 3minC 491 -27.33 -5.15 8.96e+00 2nllB 103 -24.79 -5.13 9.23e+00 2fsp 124 -24.96 -5.11 9.38e+00 1bueA 265 -25.29 -5.07 9.79e+00 1dceB 331 -27.51 -5.05 1.00e+01 1bsg 266 -26.17 -5.04 1.01e+01 1g6zA 70 -22.07 -5.02 1.04e+01 1avmA 201 -25.74 -5.00 1.06e+01 1bsmA 201 -25.74 -4.99 1.07e+01 1ixxB 123 -23.45 -4.93 1.14e+01 1kxlA 199 -25.64 -4.91 1.17e+01 1g4wR 383 -26.86 -4.89 1.20e+01 1ekjA 221 -26.15 -4.88 1.21e+01 2aaa 484 -26.72 -4.87 1.22e+01 1qk8A 146 -23.49 -4.85 1.25e+01 1gyfA 62 -21.36 -4.80 1.32e+01 1hx0A 496 -26.96 -4.80 1.32e+01 1fyeA 229 -24.64 -4.78 1.35e+01 1h6pA 203 -26.58 -4.77 1.37e+01 1ekjB 221 -26.12 -4.74 1.42e+01 1pkn 530 -27.13 -4.65 1.56e+01 1lct 333 -25.99 -4.65 1.57e+01 1opp 38 -20.61 -4.60 1.65e+01 1ep3A 311 -27.61 -4.59 1.67e+01 1fy2A 229 -24.41 -4.56 1.73e+01 1a49A 530 -27.00 -4.54 1.76e+01 1pmi 440 -27.21 -4.54 1.76e+01 1cd0A 111 -21.29 -4.48 1.88e+01 1h67A 108 -24.50 -4.48 1.89e+01 1iieA 75 -22.92 -4.43 2.00e+01 4pgaA 337 -25.88 -4.39 2.08e+01 1ef8A 261 -26.32 -4.39 2.08e+01 1dl2A 511 -27.14 -4.34 2.20e+01 1tafB 70 -22.76 -4.33 2.22e+01 1fwp 139 -23.52 -4.33 2.23e+01 1j97A 211 -24.44 -4.30 2.29e+01 1kktA 511 -28.46 -4.30 2.31e+01 1dts 221 -23.81 -4.29 2.34e+01 2rslA 140 -24.69 -4.27 2.37e+01 1b0zA 445 -28.03 -4.27 2.39e+01 2pgi 445 -28.03 -4.27 2.39e+01 1fp6A 289 -24.76 -4.26 2.40e+01 1a5t 334 -25.96 -4.25 2.43e+01 1g5pA 289 -24.82 -4.24 2.46e+01 1nipA 289 -24.88 -4.24 2.46e+01 1dioG 173 -24.03 -4.23 2.49e+01 1dbs 224 -23.76 -4.21 2.54e+01 1volA 204 -26.95 -4.21 2.56e+01 1fbaA 361 -25.76 -4.20 2.57e+01 1isaA 192 -23.98 -4.20 2.57e+01 1iscA 192 -23.98 -4.20 2.57e+01 1crzA 403 -24.36 -4.20 2.59e+01 1hmcB 148 -25.49 -4.19 2.60e+01 1c7qA 445 -27.87 -4.19 2.61e+01 1l7mA 211 -24.27 -4.19 2.61e+01 1qgxA 357 -27.04 -4.15 2.74e+01 1hmcA 148 -26.28 -4.14 2.74e+01 1f5sA 211 -24.27 -4.14 2.77e+01 2ilk 160 -25.52 -4.12 2.82e+01 1jli 112 -24.35 -4.10 2.89e+01 2minA 491 -26.37 -4.09 2.92e+01 1vpt 348 -27.72 -4.08 2.94e+01 1fmtA 314 -25.65 -4.08 2.96e+01 1ks2A 219 -23.42 -4.03 3.11e+01 1ig8A 486 -27.50 -4.03 3.14e+01 1h99A 224 -26.76 -4.02 3.16e+01 1ka1A 357 -26.85 -3.97 3.36e+01 1aw9 216 -25.33 -3.95 3.41e+01 1jflA 228 -24.53 -3.95 3.43e+01 1csh 435 -26.75 -3.95 3.43e+01 1g6aA 271 -25.40 -3.93 3.52e+01 1g8kA 825 -27.86 -3.93 3.52e+01 1tfb 208 -26.41 -3.92 3.53e+01 1amz 435 -26.74 -3.92 3.54e+01 1e3jA 352 -26.25 -3.91 3.57e+01 1hr6B 443 -27.26 -3.91 3.57e+01 1byi 224 -23.37 -3.91 3.59e+01 1dad 224 -23.38 -3.91 3.59e+01 1g8jA 825 -27.84 -3.91 3.60e+01 1lshA 1056 -27.88 -3.90 3.64e+01 1sur 215 -24.00 -3.87 3.74e+01 1iciA 256 -24.66 -3.87 3.75e+01 1bpoA 494 -26.71 -3.86 3.79e+01 1eexG 173 -23.68 -3.86 3.81e+01 1d5tA 433 -28.04 -3.85 3.82e+01 1ewxA 146 -22.54 -3.85 3.83e+01 2cblA 305 -26.18 -3.84 3.87e+01