% 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.YGR008C.t2k-100-30-alpha Host: cc67 Fri Nov 8 16:00:10 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR008C % --------------------------------------------------------------------- % 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 YGR008C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR008C.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 85 nodes, 56.70 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(=2.7608) * Reverse)^tau(=0.7662))) % 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 1jyrA 96 -27.12 -9.92 2.38e-02 1zfpE 98 -27.59 -9.19 4.93e-02 1poiA 317 -27.33 -8.09 1.49e-01 1efdN 266 -27.06 -7.45 2.89e-01 1jjfA 268 -26.26 -7.25 3.55e-01 1ghtA 105 -24.22 -7.11 4.13e-01 1azwA 313 -26.82 -7.08 4.24e-01 1vih 71 -22.54 -6.59 7.16e-01 1bmbA 123 -27.06 -6.50 7.87e-01 1fnlA 175 -24.79 -6.33 9.46e-01 1griA 217 -27.25 -6.10 1.21e+00 1vig 71 -21.89 -5.98 1.39e+00 1ah6 220 -23.95 -5.47 2.45e+00 1gv9A 260 -26.57 -5.44 2.52e+00 1f5jA 199 -24.06 -5.32 2.89e+00 1a87 321 -24.52 -5.13 3.58e+00 1ha9A 34 -19.63 -5.09 3.77e+00 1ae7 119 -22.50 -5.08 3.78e+00 1le6A 123 -22.22 -5.07 3.82e+00 2prd 174 -24.09 -4.99 4.19e+00 1jcv 153 -23.00 -4.99 4.22e+00 1aho 64 -20.76 -4.95 4.38e+00 1b06A 210 -23.44 -4.93 4.50e+00 2pth 193 -23.24 -4.88 4.75e+00 1k8cA 322 -24.73 -4.83 5.05e+00 1gkkA 297 -25.29 -4.81 5.18e+00 1pir 124 -22.77 -4.78 5.33e+00 2rslA 140 -22.22 -4.78 5.35e+00 1ayaA 101 -21.82 -4.75 5.54e+00 1gklA 297 -25.18 -4.71 5.78e+00 1a0i 348 -25.09 -4.69 5.92e+00 1iwgA 1053 -26.87 -4.58 6.72e+00 2hrvA 142 -22.07 -4.53 7.18e+00 1poa 118 -21.88 -4.49 7.47e+00 1bfeA 119 -22.80 -4.47 7.66e+00 1qf9A 194 -23.04 -4.40 8.33e+00 1ordA 730 -27.30 -4.37 8.63e+00 5ukdA 194 -22.94 -4.35 8.88e+00 1hn4A 131 -21.98 -4.29 9.54e+00 1iknD 236 -22.90 -4.22 1.04e+01 1d2kA 392 -24.22 -4.20 1.06e+01 1rl2A 137 -22.35 -4.19 1.07e+01 1gr5A 547 -25.39 -4.14 1.14e+01 1derA 547 -25.39 -4.12 1.16e+01 1l6uA 128 -22.21 -4.09 1.21e+01 1mil 104 -20.97 -4.08 1.23e+01 1iyu 79 -20.45 -4.07 1.23e+01 2hfh 109 -22.09 -4.04 1.28e+01 1g4uS 383 -23.98 -4.02 1.31e+01 4cms 323 -23.47 -4.02 1.31e+01 1gs5A 258 -23.68 -3.99 1.36e+01 1i39A 225 -22.54 -3.97 1.39e+01 1ayfA 105 -21.97 -3.96 1.41e+01 1ayfB 105 -22.01 -3.94 1.45e+01 1am2 199 -23.10 -3.92 1.48e+01 1g4iA 123 -21.08 -3.91 1.50e+01 1pdr 99 -21.33 -3.90 1.53e+01 1gw0A 559 -25.52 -3.86 1.60e+01 1be9A 119 -22.09 -3.85 1.61e+01 1fas 61 -20.24 -3.83 1.64e+01 1exeA 99 -20.29 -3.82 1.66e+01 1esgA 213 -22.77 -3.82 1.67e+01 3pvaA 335 -23.87 -3.82 1.67e+01 1rhs 296 -23.23 -3.81 1.70e+01 1by2 119 -21.16 -3.80 1.70e+01 1mku 123 -21.00 -3.79 1.74e+01 3cms 323 -23.20 -3.79 1.74e+01 1smnA 245 -22.46 -3.78 1.75e+01 1une 123 -20.91 -3.77 1.78e+01 1aun 208 -23.02 -3.76 1.80e+01 1c1lA 136 -21.45 -3.75 1.82e+01 1a6wL 109 -20.87 -3.75 1.82e+01 1f7wA 144 -22.12 -3.73 1.86e+01 3aprE 325 -24.40 -3.73 1.87e+01 2pspA 106 -20.57 -3.72 1.89e+01 4bp2 130 -20.86 -3.67 2.00e+01 1a4iB 301 -22.85 -3.65 2.05e+01 1sltA 134 -21.33 -3.65 2.06e+01 1ppfE 218 -23.29 -3.62 2.14e+01 1slaA 134 -21.26 -3.60 2.20e+01 1ql0A 241 -22.24 -3.57 2.26e+01 1sltB 134 -21.23 -3.57 2.27e+01 1kkeA 210 -22.77 -3.57 2.28e+01 1b6a 478 -24.85 -3.57 2.28e+01 3bamB 213 -22.39 -3.56 2.31e+01 1bam 213 -22.09 -3.55 2.32e+01 1qvcA 145 -22.04 -3.55 2.32e+01 1mh1 186 -21.25 -3.51 2.46e+01 1aapA 58 -19.04 -3.50 2.47e+01 1g8tA 245 -22.23 -3.50 2.48e+01 1a4iA 301 -22.63 -3.48 2.53e+01 1f4kA 122 -20.39 -3.46 2.59e+01 2pvaA 345 -23.88 -3.45 2.62e+01 1diaA 306 -22.60 -3.45 2.62e+01 2apr 325 -24.07 -3.44 2.65e+01 1qaeA 245 -22.15 -3.44 2.66e+01 1colA 204 -22.48 -3.44 2.66e+01 2pldA 105 -20.41 -3.43 2.68e+01 1bm9A 122 -20.29 -3.41 2.77e+01 1qr4B 186 -22.25 -3.40 2.80e+01 1mfa 247 -22.78 -3.39 2.85e+01 1mdc 133 -22.15 -3.32 3.08e+01 1ffkM 148 -20.81 -3.32 3.10e+01 1pta 318 -22.89 -3.29 3.20e+01 1ek6A 348 -23.24 -3.25 3.40e+01 1c2aA 120 -20.18 -3.22 3.51e+01 1ce3A 54 -18.85 -3.22 3.51e+01 1c4kA 730 -26.67 -3.22 3.53e+01 2tgf 50 -19.12 -3.17 3.72e+01 1i3kA 348 -23.14 -3.17 3.74e+01 1jj2O 148 -20.74 -3.17 3.75e+01 1ihjA 98 -20.75 -3.17 3.76e+01 1h65A 270 -22.23 -3.15 3.85e+01 1ppn 212 -22.81 -3.15 3.86e+01 1ei5A 520 -26.99 -3.13 3.92e+01 1fybA 111 -19.97 -3.13 3.94e+01 1pcp 106 -19.87 -3.13 3.95e+01