% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 09/03/03_16:30:36 % (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. % --------------------------------------------------------------------- % alphafoo.1.YGR029W.t2k-100-30-alpha Host: cc57 Sat Oct 11 21:37:56 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR029W % --------------------------------------------------------------------- % 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 YGR029W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR029W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 190 nodes, 180.00 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 (=8162) sequences: % N / (1 + exp(-(lambda(=4.3962) * Reverse)^tau(=0.6067))) % 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 1oqcA 125 -158.89 -137.20 6.17e-18 1jraA 117 -136.19 -116.22 6.51e-16 1jr8A 117 -136.25 -115.81 7.15e-16 1euvA 221 -30.67 -10.19 3.55e-01 1eyvA 156 -28.12 -9.45 5.56e-01 1dgjA 907 -32.31 -9.33 6.01e-01 1ngkA 128 -27.36 -9.18 6.56e-01 1jjfA 268 -29.24 -8.85 8.06e-01 1p8cA 145 -27.81 -8.64 9.24e-01 1dmhA 311 -28.59 -8.14 1.27e+00 1iwhA 141 -25.27 -7.24 2.32e+00 1je8A 82 -24.36 -7.24 2.33e+00 1ku1A 230 -26.59 -7.03 2.68e+00 1fd8A 73 -23.86 -6.66 3.49e+00 1fw9A 164 -25.16 -6.54 3.78e+00 1cc8A 73 -23.24 -6.54 3.80e+00 1hlrA 907 -29.33 -6.46 4.01e+00 1q8cA 151 -24.95 -6.45 4.05e+00 1ciy 590 -29.78 -6.42 4.14e+00 1mhqA 148 -25.79 -6.34 4.39e+00 1jvr 137 -25.80 -6.24 4.70e+00 2abk 211 -25.16 -6.02 5.53e+00 1a04A 215 -25.39 -5.95 5.81e+00 1mlwA 301 -26.19 -5.94 5.84e+00 1gxqA 106 -23.79 -5.76 6.68e+00 1cg5B 141 -24.12 -5.72 6.90e+00 1cokA 68 -22.69 -5.68 7.13e+00 1guzA 310 -26.07 -5.55 7.83e+00 1agi 125 -24.29 -5.52 8.00e+00 1qfmA 710 -27.72 -5.52 8.04e+00 1g8lA 411 -27.10 -5.52 8.05e+00 1dxsA 80 -23.05 -5.43 8.62e+00 1h2xA 710 -27.57 -5.35 9.11e+00 1e8nA 710 -27.51 -5.31 9.44e+00 1iatA 557 -27.14 -5.31 9.46e+00 1h2wA 710 -27.33 -5.16 1.06e+01 1qqiA 104 -22.98 -5.16 1.06e+01 1okgA 373 -26.01 -5.08 1.13e+01 1fg7A 356 -25.67 -4.98 1.22e+01 1abwA 283 -24.64 -4.97 1.23e+01 1chd 203 -24.58 -4.96 1.23e+01 1gotG 73 -21.93 -4.96 1.24e+01 1iapA 211 -24.27 -4.85 1.36e+01 1babA 143 -22.91 -4.67 1.56e+01 1dgmA 363 -25.32 -4.66 1.57e+01 1hyeA 313 -24.92 -4.65 1.59e+01 1fnhA 271 -25.43 -4.64 1.61e+01 1itg 166 -23.44 -4.61 1.64e+01 1tbgE 68 -21.39 -4.61 1.64e+01 1fbmC 46 -21.00 -4.60 1.66e+01 1hm5A 558 -26.49 -4.60 1.66e+01 1irdA 141 -22.79 -4.60 1.66e+01 1gewA 356 -25.24 -4.58 1.68e+01 1jwhA 337 -24.99 -4.55 1.72e+01 1vdfA 46 -20.94 -4.55 1.73e+01 1j7yA 141 -22.70 -4.51 1.79e+01 1b9xB 68 -21.37 -4.49 1.81e+01 1eo9B 241 -25.79 -4.48 1.82e+01 1b75A 94 -21.88 -4.47 1.84e+01 1kgsA 225 -23.82 -4.46 1.85e+01 1cjwA 166 -23.29 -4.43 1.91e+01 1h6qA 168 -23.21 -4.40 1.96e+01 1iu8A 206 -23.82 -4.37 2.00e+01 1aw0 72 -20.88 -4.34 2.05e+01 1dqrA 557 -26.18 -4.31 2.10e+01 1hxs1 302 -24.63 -4.25 2.21e+01 1kw4A 89 -21.61 -4.23 2.26e+01 1pov1 302 -24.94 -4.22 2.27e+01 1f45B 197 -24.97 -4.16 2.39e+01 1bev1 281 -24.05 -4.16 2.39e+01 1ajqA 209 -23.17 -4.13 2.45e+01 1j5sA 463 -25.54 -4.11 2.50e+01 1dioA 554 -25.56 -4.10 2.50e+01 1e5kA 201 -23.36 -4.10 2.51e+01 1ush 550 -26.30 -4.08 2.56e+01 1pbwA 216 -23.80 -4.05 2.61e+01 1ai7A 209 -23.06 -4.02 2.69e+01 1kuxA 207 -23.52 -3.99 2.76e+01 1rrpB 134 -22.90 -3.97 2.81e+01 1btkA 169 -23.26 -3.95 2.85e+01 1gdc 72 -21.03 -3.95 2.86e+01 1oyzA 280 -24.22 -3.95 2.87e+01 1btmA 252 -23.50 -3.92 2.93e+01 1mz9A 45 -19.99 -3.92 2.95e+01 1pvdA 537 -25.56 -3.91 2.96e+01 1pn1A 176 -22.95 -3.89 3.01e+01 1gg3A 279 -24.05 -3.88 3.04e+01 1e3jA 352 -24.76 -3.87 3.05e+01 1toh 343 -24.29 -3.85 3.12e+01 1o58A 303 -23.89 -3.85 3.12e+01 1f6dA 376 -24.70 -3.84 3.15e+01 1jwgA 147 -22.42 -3.83 3.17e+01 1blr 137 -22.74 -3.82 3.21e+01 1jenB 67 -21.19 -3.80 3.26e+01 1pnkA 209 -22.81 -3.77 3.36e+01 1eexA 554 -25.21 -3.74 3.45e+01 1eujA 166 -23.26 -3.71 3.54e+01 1jwwA 80 -20.89 -3.69 3.60e+01 1k3xA 262 -24.07 -3.68 3.61e+01 1aol 228 -24.39 -3.67 3.65e+01 1dwtA 153 -22.23 -3.66 3.69e+01 2nllA 66 -20.99 -3.65 3.71e+01 1dszB 85 -21.57 -3.65 3.71e+01 1bw9A 356 -24.06 -3.65 3.71e+01 1g60A 260 -23.85 -3.64 3.77e+01 1ee8A 266 -23.55 -3.63 3.80e+01 1j6nA 303 -23.71 -3.62 3.82e+01 1ngvA 534 -25.30 -3.60 3.89e+01