% 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. % --------------------------------------------------------------------- % alphafoo.1.YGR230W.t2k-100-30-alpha Host: cc76 Tue Nov 12 18:26:45 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.alphas % % 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.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 138 nodes, 93.57 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(=2.4127) * Reverse)^tau(=0.7898))) % 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 -33.83 -11.30 9.01e-03 1f48A 589 -33.25 -10.70 1.60e-02 1dszA 86 -25.81 -8.73 1.10e-01 1nzyA 269 -27.34 -6.80 8.06e-01 1hyqA 263 -26.39 -6.37 1.27e+00 1aky 221 -26.83 -6.28 1.41e+00 1a49A 530 -28.06 -5.90 2.12e+00 1pkn 530 -28.05 -5.87 2.19e+00 1aw9 216 -26.54 -5.84 2.26e+00 1hstA 90 -24.47 -5.62 2.90e+00 1g6zA 70 -21.98 -5.51 3.24e+00 1gw5B 591 -30.10 -5.31 4.07e+00 1kktA 511 -29.09 -5.29 4.15e+00 1volA 204 -25.79 -5.25 4.35e+00 1g4wR 383 -27.38 -5.25 4.36e+00 1e3jA 352 -26.56 -5.23 4.44e+00 2mnr 357 -26.57 -5.19 4.65e+00 1ktgA 138 -23.02 -5.10 5.12e+00 1mdl 359 -26.49 -5.07 5.30e+00 1hra 81 -21.79 -5.02 5.61e+00 1sctB 151 -25.40 -4.98 5.92e+00 1a32 88 -24.39 -4.92 6.30e+00 1gdtA 183 -24.60 -4.90 6.48e+00 1g8jA 825 -27.76 -4.87 6.64e+00 1erp 38 -19.87 -4.86 6.78e+00 1lxtA 561 -27.11 -4.77 7.51e+00 2ilk 160 -24.84 -4.76 7.55e+00 1ehyA 294 -25.49 -4.70 8.09e+00 1kwmA 402 -25.40 -4.69 8.18e+00 1ioj 57 -21.95 -4.68 8.32e+00 1jksA 294 -25.60 -4.67 8.36e+00 1g8kA 825 -27.43 -4.62 8.89e+00 1ekjA 221 -24.91 -4.55 9.65e+00 1isaA 192 -23.81 -4.54 9.69e+00 1ddcA 247 -24.62 -4.52 9.95e+00 3pmgA 561 -26.87 -4.43 1.10e+01 1a8y 367 -26.15 -4.42 1.12e+01 1qk8A 146 -22.94 -4.42 1.12e+01 1fm0E 150 -24.37 -4.40 1.14e+01 1ekjB 221 -24.98 -4.39 1.16e+01 1iscA 192 -23.59 -4.38 1.18e+01 1k3rA 268 -24.19 -4.31 1.26e+01 1binA 143 -23.83 -4.30 1.28e+01 1kte 105 -22.91 -4.28 1.32e+01 2rslA 140 -24.35 -4.27 1.33e+01 1sqc 631 -27.09 -4.23 1.39e+01 1dt6A 473 -28.29 -4.20 1.44e+01 1gnwA 211 -23.96 -4.18 1.47e+01 1d7kA 421 -27.87 -4.16 1.51e+01 1ewxA 146 -22.56 -4.11 1.59e+01 1pmi 440 -26.35 -4.11 1.61e+01 1fmaE 150 -24.03 -4.05 1.72e+01 1iieA 75 -21.99 -4.03 1.76e+01 1fyeA 229 -23.68 -4.02 1.77e+01 1k92A 455 -25.78 -3.96 1.90e+01 1dofA 403 -26.13 -3.93 1.99e+01 1oacA 727 -25.49 -3.92 2.00e+01 1fslA 143 -23.63 -3.91 2.02e+01 1bsmA 201 -24.00 -3.91 2.03e+01 1h5qA 265 -24.54 -3.89 2.07e+01 1bza 262 -23.71 -3.89 2.08e+01 1tf3A 92 -22.08 -3.86 2.15e+01 1spuB 727 -25.44 -3.82 2.27e+01 1hx0A 496 -25.56 -3.80 2.32e+01 2cblA 305 -25.64 -3.80 2.32e+01 1cd0A 111 -20.71 -3.78 2.37e+01 4pgaA 337 -24.34 -3.76 2.42e+01 1d6zA 727 -25.34 -3.75 2.46e+01 1avmA 201 -23.82 -3.75 2.46e+01 1gjsA 65 -21.55 -3.73 2.51e+01 1lct 333 -24.63 -3.70 2.59e+01 1j54A 186 -23.13 -3.69 2.62e+01 1h67A 108 -22.17 -3.68 2.68e+01 1bpoA 494 -25.67 -3.67 2.69e+01 1gpmA 525 -26.71 -3.67 2.70e+01 1c7qA 445 -27.51 -3.67 2.71e+01 1qcrA 446 -28.00 -3.66 2.73e+01 1gteD 1025 -26.94 -3.66 2.74e+01 1bu8A 452 -24.52 -3.64 2.79e+01 1h7xA 1025 -26.95 -3.64 2.80e+01 1h7xD 1025 -26.88 -3.64 2.81e+01 1h7wD 1025 -26.94 -3.63 2.83e+01 1exzA 141 -25.16 -3.62 2.88e+01 2minA 491 -25.11 -3.62 2.88e+01 1jflA 228 -23.64 -3.61 2.89e+01 1h7xC 1025 -26.89 -3.60 2.93e+01 1h7wB 1025 -26.92 -3.59 2.97e+01 1kzhA 555 -27.79 -3.59 2.97e+01 2ay1A 394 -25.74 -3.59 2.99e+01 1h7xB 1025 -26.85 -3.58 3.00e+01 1h7wA 1025 -26.95 -3.56 3.08e+01 1gteA 1025 -26.99 -3.55 3.11e+01 1ks2A 219 -22.61 -3.55 3.12e+01 3minC 491 -25.07 -3.55 3.13e+01 1ck2A 104 -20.93 -3.54 3.14e+01 1ep3A 311 -25.94 -3.54 3.14e+01 1ecfB 504 -26.23 -3.54 3.16e+01 1dg9A 157 -22.46 -3.53 3.20e+01 1crzA 403 -23.43 -3.50 3.32e+01 1dl2A 511 -25.58 -3.50 3.34e+01 1ecfA 504 -26.15 -3.49 3.34e+01 1gthD 1025 -26.84 -3.49 3.34e+01 1b0zA 445 -27.44 -3.48 3.38e+01 2pgi 445 -27.44 -3.48 3.38e+01 1gthB 1025 -26.86 -3.48 3.40e+01 1e0tA 470 -25.84 -3.47 3.43e+01 1gt8B 1025 -26.78 -3.45 3.51e+01 1gt8A 1025 -26.78 -3.45 3.52e+01 1gthC 1025 -26.85 -3.45 3.54e+01 2sqcA 631 -26.25 -3.42 3.64e+01 1h6pA 203 -24.99 -3.40 3.74e+01 1i3kA 348 -24.19 -3.40 3.76e+01 1vid 221 -23.32 -3.39 3.78e+01 1fpqA 372 -25.69 -3.38 3.83e+01 1k8kE 178 -23.02 -3.37 3.88e+01 1hmcA 148 -23.02 -3.37 3.89e+01 1kewA 361 -24.40 -3.35 3.96e+01 1gthA 1025 -26.75 -3.35 3.97e+01