% 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. % --------------------------------------------------------------------- % alphafoo.1.YGR009C.t2k-100-30-alpha Host: farm20 Wed Nov 17 17:08:25 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR009C % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR009C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR009C.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10772 sequences, 2550165 residues, 652 nodes, 706.34 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(=1.6237) * Reverse)^tau(=0.7725))) % 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 1n7sC 79 -104.91 -85.04 3.08e-16 1sfcC 83 -104.21 -84.87 3.30e-16 1l4aD 87 -97.91 -81.48 1.32e-15 1sfcD 87 -101.49 -80.13 2.31e-15 1jthA 82 -98.84 -77.90 5.85e-15 1n7sD 66 -94.14 -72.20 6.44e-14 1kilD 66 -92.78 -71.04 1.05e-13 1gl2C 65 -63.95 -48.87 1.96e-09 1gl2D 65 -63.76 -43.84 2.06e-08 1n7sB 68 -36.27 -19.42 6.09e-03 1jthD 77 -35.00 -18.89 8.25e-03 1hvvA 75 -36.34 -18.88 8.31e-03 1jthB 77 -36.38 -18.87 8.37e-03 1sfcB 83 -36.07 -18.75 8.93e-03 1gl2B 65 -34.24 -18.27 1.18e-02 1dn1B 267 -34.64 -13.61 1.93e-01 1tqhA 247 -24.70 -12.26 4.49e-01 1n7zA 334 -24.05 -12.12 4.89e-01 1s9aA 257 -25.88 -12.12 4.90e-01 1r1dA 247 -23.88 -11.39 7.85e-01 1ab4 477 -23.87 -11.00 1.01e+00 1h0oA 390 -23.87 -10.98 1.02e+00 1auiA 521 -25.79 -10.97 1.03e+00 1w68A 390 -23.18 -10.72 1.21e+00 1auwA 468 -25.05 -10.65 1.27e+00 1qpxA 218 -22.57 -10.38 1.52e+00 1xsm 390 -22.85 -10.31 1.58e+00 1k7wA 468 -24.00 -10.11 1.81e+00 1psdA 409 -20.88 -9.97 1.98e+00 1vcaA 202 -20.97 -9.84 2.16e+00 1k47A 337 -22.40 -9.81 2.21e+00 1sziA 247 -26.85 -9.79 2.25e+00 1qppA 218 -21.56 -9.57 2.59e+00 1hy0A 466 -23.08 -9.47 2.78e+00 1ic2A 81 -25.55 -9.35 3.01e+00 1rurL 217 -21.07 -9.16 3.41e+00 1n0lA 224 -20.72 -9.05 3.69e+00 1keyA 235 -24.18 -9.03 3.73e+00 1pfzA 380 -20.76 -9.01 3.78e+00 1ni3A 392 -21.40 -9.01 3.78e+00 1iyjB 817 -22.85 -8.90 4.09e+00 1jadA 251 -28.22 -8.85 4.23e+00 1vl6A 388 -21.70 -8.81 4.34e+00 1d7uA 433 -21.16 -8.78 4.43e+00 1s35A 214 -22.39 -8.70 4.69e+00 1smeA 329 -21.48 -8.66 4.81e+00 1ih7A 903 -23.78 -8.61 4.99e+00 1m0qA 433 -20.86 -8.59 5.05e+00 1kv7A 488 -21.73 -8.49 5.40e+00 1aozA 552 -23.32 -8.46 5.53e+00 1xfjA 261 -20.05 -8.41 5.73e+00 1tz9A 367 -20.64 -8.31 6.14e+00 1oxjA 173 -20.23 -8.25 6.41e+00 1bg7 176 -21.96 -8.20 6.60e+00 1dcnD 436 -22.14 -8.19 6.67e+00 1wduA 245 -18.97 -8.05 7.35e+00 1a3lL 217 -19.82 -7.98 7.73e+00 1nrlA 316 -21.09 -7.92 8.04e+00 2dkb 433 -20.14 -7.88 8.29e+00 1fcqA 350 -19.93 -7.86 8.42e+00 1prgA 270 -19.83 -7.83 8.55e+00 1ca4A 168 -19.22 -7.80 8.75e+00 1dtwB 342 -19.50 -7.74 9.12e+00 1umwA 237 -19.80 -7.74 9.16e+00 1iw7C 1119 -21.83 -7.69 9.43e+00 1gy8A 397 -19.29 -7.67 9.61e+00 1fm9D 272 -19.67 -7.65 9.70e+00 1pvc2 271 -19.00 -7.64 9.82e+00 1rdr 461 -20.75 -7.57 1.03e+01 1czyA 168 -19.02 -7.55 1.05e+01 1czyC 168 -19.06 -7.52 1.06e+01 1d0aB 168 -18.83 -7.48 1.10e+01 1v1rB 342 -19.06 -7.47 1.10e+01 1m13A 316 -20.72 -7.37 1.19e+01 1m3kA 392 -18.30 -7.32 1.23e+01 1lf2A 331 -19.99 -7.23 1.31e+01 1art 396 -18.71 -7.19 1.35e+01 1ahxA 396 -18.82 -7.17 1.37e+01 1qflA 389 -18.09 -7.15 1.39e+01 1kamA 194 -19.12 -7.14 1.39e+01 1dcnA 424 -21.43 -7.11 1.43e+01 1txuA 273 -19.23 -7.08 1.46e+01 1g8jA 825 -19.47 -7.06 1.48e+01 1j1jA 240 -22.45 -7.04 1.51e+01 1m4tA 392 -18.02 -7.03 1.51e+01 1olsB 342 -18.54 -7.02 1.52e+01 1ewqA 765 -19.20 -7.01 1.54e+01 2prgA 271 -19.06 -6.95 1.60e+01 1lrzA 426 -21.27 -6.95 1.60e+01 1rz1A 161 -17.58 -6.94 1.62e+01 1clqA 903 -22.47 -6.92 1.64e+01 1fxkA 107 -24.59 -6.91 1.65e+01 1spa 396 -18.76 -6.89 1.68e+01 1pp7U 131 -17.91 -6.89 1.68e+01 1lvfA 110 -23.39 -6.88 1.68e+01 1umnA 165 -20.66 -6.88 1.69e+01 1fxkB 109 -23.25 -6.87 1.70e+01 1qisA 396 -18.69 -6.87 1.71e+01 5reqA 727 -19.03 -6.86 1.72e+01 1h0cA 392 -19.92 -6.85 1.72e+01 1aho 64 -17.10 -6.85 1.73e+01 1ars 396 -18.60 -6.84 1.73e+01 1p8kZ 254 -17.95 -6.83 1.74e+01 1ex7A 186 -19.79 -6.83 1.75e+01 1sqjA 789 -20.54 -6.81 1.77e+01 1reqA 727 -18.96 -6.73 1.89e+01 1j5rA 371 -19.18 -6.70 1.92e+01 1eljA 381 -19.16 -6.70 1.93e+01 7reqA 727 -18.86 -6.66 1.98e+01 1us0A 316 -18.82 -6.64 2.01e+01 1glcG 501 -18.58 -6.63 2.03e+01 2sns 149 -17.39 -6.61 2.06e+01 1gky 187 -19.70 -6.60 2.07e+01 2eifA 136 -17.30 -6.59 2.08e+01 1pwmA 316 -18.67 -6.58 2.10e+01 1o2dA 371 -19.23 -6.53 2.17e+01 1jokA 149 -17.35 -6.53 2.17e+01 1hziA 129 -18.21 -6.50 2.22e+01 1m7vA 363 -19.28 -6.50 2.22e+01 1rcb 129 -18.03 -6.50 2.23e+01 1ovnA 248 -18.28 -6.49 2.23e+01 1eg5A 384 -19.38 -6.47 2.28e+01 1k92A 455 -18.07 -6.47 2.28e+01 1i9bA 217 -18.41 -6.46 2.29e+01 1qs8A 329 -19.14 -6.46 2.29e+01 1orjA 130 -20.55 -6.45 2.30e+01 1klo 162 -18.28 -6.45 2.30e+01 1hxs2 272 -17.50 -6.45 2.31e+01 1r8iA 213 -20.88 -6.45 2.31e+01 1kjvA 284 -18.41 -6.44 2.32e+01 1ads 315 -18.59 -6.42 2.36e+01 2acr 315 -18.33 -6.38 2.43e+01 1qh7A 207 -18.18 -6.36 2.47e+01 1segA 64 -17.48 -6.36 2.47e+01 1po5A 476 -18.69 -6.32 2.53e+01 1ogsA 497 -17.76 -6.27 2.64e+01 1bbpA 173 -20.50 -6.25 2.67e+01 2int 129 -18.08 -6.22 2.73e+01 1gyhA 318 -18.57 -6.21 2.76e+01 1mrzA 293 -19.08 -6.20 2.78e+01 1floA 422 -17.78 -6.20 2.78e+01 1jalA 363 -20.08 -6.18 2.82e+01 1sty 150 -16.89 -6.18 2.82e+01 1odmA 331 -17.31 -6.17 2.84e+01 1afwA 393 -17.81 -6.17 2.85e+01 1wp1A 474 -19.70 -6.16 2.85e+01 1l5zA 155 -16.90 -6.11 2.96e+01 1miuA 738 -19.27 -6.10 2.99e+01 1j9bA 141 -16.90 -6.09 3.01e+01 1bk0 331 -17.21 -6.09 3.01e+01 1o5kA 306 -18.51 -6.08 3.03e+01 1oj6A 151 -16.60 -6.08 3.03e+01 1w0pA 781 -19.55 -6.06 3.07e+01 1gp1A 198 -17.71 -6.04 3.12e+01 1m6kA 251 -17.55 -6.04 3.13e+01 1qg3A 195 -17.38 -6.02 3.18e+01 5eat 548 -19.84 -6.00 3.22e+01 1s4nA 348 -17.63 -5.99 3.23e+01 1gdeA 389 -19.87 -5.98 3.27e+01 1h4gA 207 -17.64 -5.98 3.27e+01 1dixA 208 -17.37 -5.97 3.29e+01 1dkxA 219 -18.12 -5.97 3.29e+01 1j3vA 289 -18.38 -5.96 3.32e+01 1snc 149 -16.74 -5.96 3.32e+01 1acc 735 -18.22 -5.95 3.34e+01 1a73A 163 -17.20 -5.95 3.34e+01 1uypA 432 -18.54 -5.94 3.36e+01 1rrmA 386 -16.75 -5.94 3.37e+01 1utwA 432 -18.52 -5.92 3.41e+01 1az3A 244 -19.83 -5.88 3.53e+01 1v8gA 329 -16.65 -5.87 3.54e+01 1kwsA 261 -17.26 -5.87 3.55e+01 1gd9A 389 -19.72 -5.86 3.58e+01 1oglA 283 -21.07 -5.84 3.63e+01 1smoA 119 -18.06 -5.84 3.63e+01 1vi6A 208 -16.54 -5.83 3.65e+01 1e8cA 498 -17.72 -5.83 3.65e+01 1et0A 269 -18.18 -5.81 3.70e+01 1ecxA 384 -18.71 -5.81 3.71e+01 1sup 275 -19.12 -5.79 3.76e+01 1kit 757 -19.19 -5.79 3.76e+01 1kl9A 182 -17.42 -5.78 3.81e+01 1feuA 206 -16.95 -5.77 3.81e+01 1bywA 110 -15.96 -5.77 3.83e+01 1ehkA 562 -18.73 -5.76 3.84e+01 1itkA 731 -18.30 -5.75 3.88e+01 1kxoA 184 -18.97 -5.75 3.89e+01 1ei5A 520 -17.27 -5.74 3.92e+01 1el3A 316 -18.00 -5.71 3.99e+01