% 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.YGR036C.t2k-100-30-alpha Host: cc50 Fri Nov 8 19:38:12 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR036C % --------------------------------------------------------------------- % 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 YGR036C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR036C.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 240 nodes, 166.13 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(=3.7433) * Reverse)^tau(=0.6526))) % 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 1d2tA 231 -61.99 -40.82 1.99e-08 1vns 609 -55.89 -31.76 1.11e-06 1vnc 609 -55.61 -31.65 1.17e-06 1qi9A 556 -52.86 -29.12 3.86e-06 1qhbA 596 -49.31 -24.77 3.27e-05 1e19A 314 -33.51 -11.57 6.07e-02 1s01 283 -28.62 -8.74 4.32e-01 1li5A 461 -31.22 -8.48 5.22e-01 1b7bA 310 -28.88 -7.51 1.08e+00 1kzhA 555 -29.60 -6.53 2.33e+00 1jw9B 249 -26.30 -6.15 3.16e+00 1rypK 198 -26.47 -6.13 3.23e+00 1ewqA 765 -29.92 -6.10 3.30e+00 1h2vC 771 -32.58 -6.08 3.36e+00 1m55A 197 -25.59 -5.97 3.68e+00 1be3D 241 -29.24 -5.96 3.70e+00 1h6kA 757 -32.56 -5.91 3.88e+00 1lw6E 281 -25.62 -5.80 4.24e+00 1sup 275 -25.48 -5.65 4.82e+00 1csbB 205 -25.87 -5.63 4.91e+00 1bccD 241 -28.66 -5.35 6.21e+00 1avpA 204 -25.20 -5.08 7.87e+00 1lqtA 456 -26.97 -4.77 1.03e+01 1k7qA 479 -26.01 -4.68 1.12e+01 2abd 86 -23.20 -4.59 1.22e+01 1aca 86 -22.96 -4.56 1.25e+01 1kutA 230 -25.18 -4.50 1.32e+01 1lr0A 129 -24.23 -4.50 1.33e+01 1gkxA 388 -28.22 -4.46 1.37e+01 1ekeA 230 -28.34 -4.44 1.40e+01 1jplA 171 -25.74 -4.40 1.45e+01 1jihA 531 -28.28 -4.34 1.53e+01 1bf5A 545 -29.32 -4.31 1.58e+01 1ppa 121 -24.02 -4.26 1.66e+01 1tlfA 301 -24.56 -4.23 1.69e+01 1mc2A 122 -23.92 -4.14 1.85e+01 1fe8A 196 -23.37 -4.07 1.97e+01 1l7vA 326 -34.68 -4.05 2.01e+01 1i7xB 151 -24.99 -3.99 2.13e+01 1hb6A 86 -22.76 -3.98 2.15e+01 1qspA 165 -26.01 -3.97 2.17e+01 1lqpA 135 -22.27 -3.90 2.32e+01 1kqfC 217 -30.45 -3.84 2.45e+01 4rnpA 883 -28.25 -3.83 2.47e+01 1jbuH 254 -23.45 -3.83 2.47e+01 1ae7 119 -25.49 -3.79 2.57e+01 1bxm 99 -21.12 -3.74 2.71e+01 1fsiA 189 -23.52 -3.70 2.81e+01 1rypH 205 -23.22 -3.65 2.96e+01 1a0cA 438 -26.83 -3.64 2.99e+01 1bjt 793 -27.99 -3.63 2.99e+01 1flcA 432 -24.86 -3.62 3.04e+01 1gkzA 388 -27.23 -3.62 3.05e+01 1k7gA 479 -25.11 -3.61 3.08e+01 1a6dA 545 -28.39 -3.58 3.17e+01 1h2eA 207 -23.52 -3.55 3.26e+01 1fbaA 361 -25.31 -3.54 3.30e+01 1jh6A 189 -23.50 -3.53 3.32e+01 1exg 110 -20.43 -3.51 3.37e+01 1sfcA 96 -23.96 -3.51 3.38e+01 1a8l 226 -24.04 -3.51 3.39e+01 1gu9A 177 -25.58 -3.50 3.42e+01 1hxmD 242 -23.62 -3.50 3.43e+01 1go7P 462 -24.74 -3.49 3.45e+01 1lriA 98 -20.93 -3.47 3.51e+01 1ordA 730 -27.08 -3.46 3.55e+01 1c02A 166 -25.40 -3.45 3.61e+01 1kncA 177 -25.59 -3.44 3.63e+01 1go8P 462 -24.68 -3.42 3.69e+01 1b3qA 379 -25.79 -3.41 3.73e+01 1theA 260 -23.77 -3.41 3.75e+01 1beo 98 -20.93 -3.38 3.84e+01 1atzA 189 -22.56 -3.38 3.86e+01 1ebbA 202 -23.51 -3.37 3.89e+01 1qd1A 325 -24.06 -3.37 3.89e+01