% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YBL103C.t2k-100-30-CB_burial_14_7 Host: farm12 Wed Dec 29 04:46:16 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YBL1/YBL103C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YBL103C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YBL103C.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 11147 sequences, 2640567 residues, 487 nodes, 543.76 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 (=10700) sequences: % N / (1 + exp(-(lambda(=1.5214) * Reverse)^tau(=0.7548))) % 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 1nkpA 88 -101.06 -73.06 6.59e-12 1an2A 86 -94.11 -71.33 1.24e-11 1nkpB 83 -92.35 -69.73 2.21e-11 1hloA 150 -92.50 -68.07 4.08e-11 1am9A 82 -89.94 -67.51 5.01e-11 1nlwB 76 -88.54 -67.34 5.34e-11 1an4A 65 -76.65 -51.82 1.97e-08 1uklC 61 -65.71 -44.78 3.30e-07 1a0aA 63 -60.52 -38.90 3.78e-06 1nlwA 80 -61.47 -35.61 1.54e-05 1mdyA 68 -54.24 -30.55 1.42e-04 1kddA 36 -33.10 -13.50 5.99e-01 1j8bA 112 -32.21 -12.31 1.16e+00 1e7tA 59 -31.51 -11.78 1.56e+00 1lq7A 67 -27.39 -10.80 2.73e+00 1au1A 166 -22.88 -10.70 2.89e+00 1dh3A 55 -32.59 -10.41 3.42e+00 1bg1A 722 -30.47 -10.17 3.94e+00 1a1iA 90 -30.38 -10.03 4.28e+00 1aayA 90 -30.11 -9.97 4.44e+00 1p9iA 31 -27.32 -9.94 4.51e+00 1lj2A 110 -29.75 -9.66 5.32e+00 1kd9A 36 -31.42 -9.44 6.07e+00 1kd8A 36 -30.18 -9.39 6.26e+00 1zaaC 87 -29.16 -9.28 6.70e+00 1fpqA 372 -26.08 -9.21 6.99e+00 1nfa 178 -24.34 -8.95 8.15e+00 1s58A 554 -28.51 -8.65 9.76e+00 1ce9A 34 -26.56 -8.42 1.13e+01 1ce9C 34 -26.56 -8.42 1.13e+01 1lslA 113 -38.85 -8.39 1.15e+01 1coi 31 -25.64 -8.26 1.24e+01 1gk7A 39 -26.60 -8.26 1.24e+01 1rocA 155 -23.14 -8.20 1.29e+01 1ci6B 63 -30.65 -8.11 1.37e+01 1m1jA 491 -50.90 -8.08 1.39e+01 1a93A 34 -31.26 -8.08 1.39e+01 2ztaA 34 -26.01 -8.05 1.41e+01 1ziiA 34 -25.56 -8.02 1.44e+01 1fp1D 372 -26.99 -7.97 1.48e+01 1dwnA 127 -32.15 -7.97 1.49e+01 1hg4A 279 -19.99 -7.84 1.61e+01 1m7lA 40 -26.84 -7.80 1.65e+01 1a93B 34 -23.99 -7.80 1.66e+01 1pwbA 177 -25.48 -7.79 1.66e+01 3fivA 116 -21.29 -7.72 1.74e+01 1junA 44 -27.05 -7.65 1.82e+01 1fivA 113 -20.78 -7.62 1.85e+01 4fiv 113 -20.99 -7.54 1.94e+01 1llmC 88 -29.15 -7.47 2.03e+01 1pkhA 204 -24.71 -7.41 2.12e+01 1uixA 71 -29.67 -7.39 2.15e+01 1go3F 107 -20.71 -7.32 2.24e+01 1vorW 173 -25.55 -7.30 2.26e+01 1ci6A 63 -31.28 -7.29 2.28e+01 1xfhA 422 -23.32 -7.19 2.44e+01 2fivA 116 -20.45 -7.17 2.46e+01 1wu3I 161 -20.99 -7.16 2.48e+01 1fmhA 33 -26.95 -7.15 2.49e+01 1rmi 160 -20.17 -7.07 2.62e+01 1bxeA 113 -20.54 -7.06 2.64e+01 1d8iA 311 -22.96 -6.99 2.77e+01 1a66A 178 -19.22 -6.97 2.79e+01 1kn0A 212 -23.78 -6.94 2.86e+01 1d8hA 311 -22.65 -6.92 2.89e+01 1f3hA 142 -26.43 -6.88 2.97e+01 2nllB 103 -26.54 -6.85 3.01e+01 1dipB 78 -31.54 -6.81 3.11e+01 1bjt 793 -23.52 -6.79 3.15e+01 1dipA 78 -32.10 -6.77 3.17e+01 1midA 91 -21.86 -6.69 3.35e+01 1taq 832 -19.54 -6.63 3.49e+01 1qu7A 227 -30.13 -6.60 3.55e+01 1vkcA 158 -21.56 -6.60 3.56e+01 1xlyA 234 -20.13 -6.59 3.57e+01 1fpxA 352 -22.06 -6.59 3.59e+01 1g40A 244 -30.61 -6.56 3.65e+01 1fp2A 352 -22.23 -6.55 3.66e+01 1p42A 270 -18.83 -6.46 3.90e+01 1g03A 134 -21.01 -6.44 3.95e+01 1ty9A 222 -19.20 -6.43 3.98e+01