% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 09/03/03_16:30:36 % (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.YGR212W.t2k-100-30-alpha Host: cc50 Sun Oct 12 01:11:11 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR212W % --------------------------------------------------------------------- % 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 YGR212W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR212W.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 469 nodes, 439.82 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 (=8162) sequences: % N / (1 + exp(-(lambda(=2.2126) * Reverse)^tau(=0.7570))) % 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 8pchA 220 -29.49 -8.78 6.44e-01 1uc8A 280 -29.57 -8.20 1.03e+00 8acn 754 -31.96 -7.49 1.88e+00 1amj 754 -31.96 -7.48 1.89e+00 1n99A 166 -27.97 -7.30 2.20e+00 1fljA 260 -29.00 -7.08 2.66e+00 1c96A 753 -31.47 -6.98 2.90e+00 1mr7A 209 -30.21 -6.93 3.03e+00 7acn 754 -31.54 -6.92 3.06e+00 1e2kA 331 -28.64 -6.82 3.32e+00 1bmlC 362 -29.83 -6.71 3.65e+00 1bgp 309 -28.71 -6.59 4.08e+00 1kk6A 209 -30.02 -6.53 4.28e+00 1qniA 581 -30.09 -6.52 4.31e+00 1b0jA 754 -31.08 -6.46 4.56e+00 6acn 754 -31.20 -6.44 4.65e+00 1f8rA 498 -29.93 -6.37 4.93e+00 1dmuA 299 -28.46 -6.27 5.38e+00 1ubkL 534 -29.32 -6.23 5.56e+00 1h2aL 567 -29.42 -6.16 5.91e+00 1hyt 316 -27.95 -6.06 6.48e+00 1jk0B 345 -28.43 -6.06 6.52e+00 1keiA 316 -27.86 -6.00 6.86e+00 1jkgA 140 -25.99 -5.95 7.16e+00 1icxA 155 -27.14 -5.87 7.72e+00 1gosA 520 -29.61 -5.82 8.07e+00 1l5aA 436 -28.31 -5.81 8.11e+00 1h2rL 534 -28.91 -5.80 8.17e+00 1ojaA 520 -29.47 -5.71 8.86e+00 1fgyA 127 -25.73 -5.70 8.94e+00 1jn5A 140 -25.72 -5.70 9.00e+00 6tmnE 316 -27.51 -5.70 9.00e+00 8tlnE 316 -27.49 -5.67 9.21e+00 1kxlA 199 -27.04 -5.64 9.45e+00 3vtk 343 -27.62 -5.62 9.66e+00 1a3c 181 -26.97 -5.57 1.01e+01 2tmnE 316 -27.38 -5.53 1.05e+01 1jeiA 53 -22.58 -5.51 1.07e+01 2dri 271 -26.39 -5.46 1.11e+01 1qhiA 366 -27.68 -5.46 1.11e+01 1jhnA 424 -28.64 -5.42 1.16e+01 1jndA 420 -29.57 -5.36 1.22e+01 1jb2A 127 -25.18 -5.33 1.25e+01 1gk8A 475 -28.36 -5.29 1.31e+01 1iz7A 295 -27.01 -5.22 1.38e+01 1a31A 538 -31.01 -5.21 1.40e+01 1pb1A 416 -28.19 -5.21 1.40e+01 1a15A 67 -23.45 -5.18 1.44e+01 1en7A 157 -25.01 -5.18 1.45e+01 1dcfA 136 -26.38 -5.16 1.47e+01 1asu 162 -25.82 -5.13 1.51e+01 1cv2A 296 -26.89 -5.12 1.52e+01 1bmv1 198 -26.29 -5.12 1.53e+01 1vsd 152 -25.74 -5.08 1.59e+01 1ldjB 90 -23.50 -5.07 1.59e+01 1m1hA 248 -27.39 -5.06 1.62e+01 1a36A 592 -30.68 -5.01 1.69e+01 1iso 416 -27.81 -5.00 1.71e+01 1acc 735 -29.32 -4.99 1.73e+01 1cxqA 162 -25.69 -4.98 1.74e+01 1g6oA 330 -27.92 -4.98 1.74e+01 1g4wR 383 -27.51 -4.97 1.75e+01 1azo 232 -26.27 -4.97 1.76e+01 1k0mA 241 -26.03 -4.97 1.76e+01 2ki5A 366 -27.15 -4.95 1.78e+01 1kimA 366 -27.23 -4.95 1.78e+01 1bowA 159 -27.21 -4.95 1.79e+01 1k6xA 352 -28.18 -4.91 1.86e+01 1ipaA 274 -26.27 -4.90 1.88e+01 1a8s 273 -26.24 -4.89 1.88e+01 1jvpP 298 -27.56 -4.89 1.89e+01 1omzA 293 -26.96 -4.88 1.91e+01 7icd 416 -28.00 -4.88 1.91e+01 1mkiA 330 -27.24 -4.87 1.93e+01 1bxvA 91 -24.22 -4.86 1.94e+01 1qjoA 80 -23.34 -4.83 1.99e+01 2sil 381 -27.57 -4.82 2.02e+01 1k6iA 352 -28.42 -4.79 2.08e+01 1qg7A 67 -23.36 -4.77 2.12e+01 1smd 496 -28.33 -4.76 2.13e+01 1mj5A 302 -26.70 -4.76 2.13e+01 1dz3A 130 -24.13 -4.76 2.14e+01 1parA 53 -22.83 -4.75 2.15e+01 1fzvA 132 -24.32 -4.74 2.17e+01 1dim 381 -27.37 -4.72 2.21e+01 1bdtA 53 -22.69 -4.71 2.24e+01 1cozA 129 -26.28 -4.71 2.24e+01 1mykA 53 -22.74 -4.65 2.37e+01 1o7fA 469 -27.15 -4.65 2.38e+01 1f7dA 136 -24.39 -4.55 2.61e+01 1broA 277 -26.02 -4.54 2.64e+01 1h3gA 601 -27.84 -4.53 2.65e+01 1lvl 458 -28.79 -4.52 2.68e+01 1iuz 98 -24.40 -4.49 2.75e+01 1gfsA 321 -26.27 -4.48 2.79e+01 1kewA 361 -27.13 -4.45 2.85e+01 1qmpA 130 -23.75 -4.45 2.86e+01 1oe4A 247 -26.38 -4.45 2.86e+01 3sil 379 -27.16 -4.44 2.89e+01 1gz8A 299 -26.90 -4.43 2.92e+01 1fh0A 221 -25.43 -4.42 2.96e+01 1bsvA 321 -26.24 -4.40 3.01e+01 1o5hA 214 -26.28 -4.36 3.13e+01 1mxmA 254 -26.21 -4.35 3.16e+01 1e7lA 157 -24.06 -4.34 3.19e+01 2fnbA 95 -24.73 -4.31 3.27e+01 1m1nB 522 -28.02 -4.30 3.30e+01 1g3p 217 -26.10 -4.29 3.34e+01 1g4uS 383 -26.67 -4.29 3.35e+01 1eh8A 207 -25.93 -4.28 3.38e+01 1bwsA 321 -25.96 -4.27 3.41e+01 2minB 522 -28.07 -4.24 3.52e+01 1jbeA 128 -23.80 -4.23 3.54e+01 1kdj 102 -23.20 -4.22 3.59e+01 3ldh 330 -26.34 -4.21 3.62e+01 1lbvA 252 -25.79 -4.20 3.63e+01 3minB 522 -27.82 -4.20 3.65e+01 1odkA 235 -25.03 -4.19 3.68e+01 1pymA 295 -25.93 -4.19 3.68e+01 1gy6A 127 -24.09 -4.17 3.75e+01 1o54A 277 -26.21 -4.16 3.77e+01 1k0nA 241 -25.94 -4.15 3.82e+01 1k94A 165 -24.74 -4.14 3.85e+01 1e6uA 321 -25.92 -4.14 3.86e+01 1hcl 298 -26.71 -4.13 3.90e+01 1ir3A 306 -26.21 -4.12 3.95e+01 1mxiA 160 -24.20 -4.12 3.96e+01 1mp8A 281 -26.08 -4.11 3.97e+01