% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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.YEL013W.t2k-100-30-CB_burial_14_7 Host: farm07 Tue Aug 2 12:20:23 2005 % karplus Dir: /projects/compbiousr/compbio0404/experiments/protein-predict/yeast/YEL0/YEL013W % --------------------------------------------------------------------- % 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 YEL013W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL013W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 12248 sequences, 2901007 residues, 579 nodes, 875.20 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 (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=1.2014) * Reverse)^tau(=0.8295))) % Calculated when Simple < simple_threshold (10000.00) % 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 1i7wA 538 -348.89 -330.48 7.56e-59 1bk6A 422 -350.24 -328.86 1.36e-58 1jdhA 529 -346.42 -328.05 1.82e-58 1g3jA 532 -343.98 -325.51 4.52e-58 1bk5A 422 -345.98 -325.48 4.58e-58 1ee4A 423 -345.25 -324.76 5.94e-58 1wa5B 530 -339.74 -314.39 2.52e-56 3bct 457 -315.36 -297.22 1.30e-53 1xm9A 457 -224.62 -205.14 1.54e-38 1gw5B 591 -229.67 -183.81 6.76e-35 1b3uA 588 -153.21 -111.67 5.87e-22 1qgrA 876 -156.87 -106.09 6.63e-21 1qbkB 890 -171.13 -101.42 5.11e-20 2bptA 861 -137.03 -94.40 1.14e-18 1xqsA 280 -107.74 -92.60 2.54e-18 1xqrA 296 -105.88 -89.49 1.02e-17 1ibrB 462 -112.70 -79.48 9.55e-16 1gw5A 621 -102.67 -71.32 4.14e-14 1ho8A 480 -89.83 -60.88 5.78e-12 1upkA 341 -61.71 -46.17 7.84e-09 1oyzA 280 -71.70 -46.09 8.17e-09 1z2cB 383 -61.30 -36.77 9.65e-07 2bnxA 386 -62.10 -34.48 3.21e-06 1wa5C 960 -87.42 -29.25 5.28e-05 1dvpA 220 -36.21 -20.54 6.88e-03 1l5jA 865 -74.48 -17.40 4.31e-02 1r6fA 310 -38.57 -16.41 7.80e-02 1pujA 282 -34.93 -16.20 8.82e-02 1lshA 1056 -58.18 -15.66 1.22e-01 1mhqA 148 -31.38 -14.76 2.11e-01 1vdyA 140 -28.97 -13.05 6.07e-01 1ft1B 437 -34.57 -10.96 2.27e+00 1lrv 244 -26.19 -10.94 2.29e+00 1jplA 171 -29.99 -10.41 3.24e+00 1bkdS 439 -37.05 -10.36 3.35e+00 1d8dB 437 -35.09 -10.27 3.54e+00 1w9cA 321 -34.87 -9.92 4.45e+00 1fchA 368 -25.01 -9.84 4.69e+00 1jcrB 437 -34.61 -9.83 4.71e+00 1yvrA 538 -33.55 -9.83 4.73e+00 1rz4A 226 -23.79 -9.72 5.06e+00 3xis 387 -36.54 -9.65 5.32e+00 1q5dA 419 -29.67 -9.62 5.43e+00 4xis 387 -36.46 -9.53 5.75e+00 1ld8B 437 -33.92 -9.47 6.00e+00 2xis 387 -36.48 -9.42 6.16e+00 1tn6B 437 -34.22 -9.42 6.18e+00 1hg2A 289 -24.47 -9.39 6.29e+00 1np3A 338 -29.22 -9.25 6.92e+00 1hf8A 289 -24.67 -9.21 7.08e+00 1hg5A 289 -24.59 -9.19 7.18e+00 1dciA 275 -25.70 -9.19 7.19e+00 1xo5A 183 -23.14 -9.15 7.39e+00 1dguA 183 -24.29 -9.15 7.39e+00 1xis 387 -36.16 -9.14 7.46e+00 1mnzA 388 -36.16 -9.12 7.53e+00 1fqiA 147 -24.27 -9.10 7.63e+00 1gw9A 388 -36.51 -9.04 7.94e+00 1w33A 181 -25.72 -9.02 8.07e+00 1wovA 250 -23.88 -8.86 8.95e+00 1s8nA 205 -20.65 -8.85 9.03e+00 1muwA 386 -34.90 -8.73 9.74e+00 1elkA 157 -24.92 -8.53 1.12e+01 1sd4A 126 -24.92 -8.47 1.16e+01 1c3d 294 -25.33 -8.35 1.26e+01 1ihgA 370 -41.66 -8.35 1.26e+01 1ounA 127 -23.07 -8.20 1.40e+01 1n4qB 377 -30.18 -8.19 1.40e+01 1eduA 149 -23.56 -8.19 1.40e+01 1ujkA 147 -27.58 -8.17 1.42e+01 1jwgA 147 -26.74 -8.14 1.45e+01 1b0pA 1231 -87.39 -8.09 1.50e+01 1yacA 208 -22.47 -8.03 1.57e+01 1ff9A 450 -35.97 -7.98 1.62e+01 1kekA 1231 -87.26 -7.97 1.63e+01 1f5nA 592 -36.22 -7.95 1.65e+01 1oshA 232 -26.72 -7.94 1.66e+01 1sva1 361 -35.33 -7.88 1.73e+01 1nvvS 481 -36.20 -7.82 1.80e+01 1gy6A 127 -22.38 -7.81 1.82e+01 1ar0A 127 -22.74 -7.71 1.94e+01 1h0aA 158 -22.41 -7.60 2.10e+01 1k92A 455 -35.57 -7.49 2.25e+01 1q16B 512 -43.67 -7.49 2.26e+01 1r4vA 171 -23.29 -7.47 2.29e+01 1eyhA 144 -23.37 -7.44 2.33e+01 1sz9A 144 -23.69 -7.42 2.37e+01 1vjxA 157 -23.66 -7.40 2.40e+01 1o77D 146 -21.47 -7.39 2.41e+01 1y5iB 512 -43.37 -7.24 2.68e+01 1bcsA 263 -26.25 -7.14 2.87e+01 1dg3A 592 -35.40 -7.09 2.98e+01 1zavA 180 -20.57 -7.00 3.15e+01 1o9iA 266 -25.96 -6.99 3.18e+01 1inzA 148 -23.98 -6.97 3.22e+01 1apyA 162 -21.80 -6.95 3.26e+01 1je0A 236 -20.25 -6.95 3.27e+01 1wr8A 231 -21.66 -6.92 3.33e+01 1q52A 314 -26.60 -6.92 3.35e+01 1oz9A 150 -20.11 -6.91 3.36e+01 1whsA 255 -25.78 -6.88 3.44e+01 1j9jA 247 -26.81 -6.87 3.47e+01 1azwA 313 -27.45 -6.87 3.47e+01 1ku2A 241 -21.32 -6.85 3.51e+01 1jb2A 127 -21.71 -6.83 3.56e+01 1y8oA 419 -32.03 -6.70 3.89e+01 1jf2A 195 -26.53 -6.68 3.94e+01 1v1rA 400 -30.18 -6.68 3.94e+01