% 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. % --------------------------------------------------------------------- % w0.5foo.1.YGR223C.t2k-w0.5.mod Host: cc74 Tue Nov 12 17:36:35 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR223C % --------------------------------------------------------------------- % Inserted Files: YGR223C.t2k-w0.5.mod % Database Files: /projects/compbio/experiments/protein-predict/SAM_T02/data/pdbaa % % 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)) % Single Track Model: YGR223C.t2k-w0.5.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13975 sequences, 3107935 residues, 449 nodes, 477.84 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(=1.6671) * Reverse)^tau(=0.8100))) % 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 1erjA 393 -213.36 -182.77 1.71e-41 1gotB 340 -189.86 -163.51 1.21e-37 1a0rB 340 -189.86 -163.51 1.21e-37 1tbgA 340 -189.88 -163.48 1.23e-37 1gxrA 337 -137.84 -111.57 8.72e-27 1k8kC 372 -106.26 -75.99 8.70e-19 1crzA 403 -51.93 -22.11 6.29e-05 1c5kA 439 -51.70 -19.52 3.74e-04 1flgA 582 -63.94 -18.49 7.69e-04 1jmxB 349 -45.04 -12.98 4.22e-02 1k32A 1045 -96.18 -10.75 2.33e-01 1jjuB 337 -41.68 -10.74 2.34e-01 2bbkH 355 -46.99 -9.89 4.59e-01 1ibhA 151 -31.63 -9.77 5.04e-01 1yaiA 151 -31.29 -9.70 5.32e-01 1ibbA 151 -31.43 -9.66 5.51e-01 1bzoA 151 -31.20 -9.37 6.94e-01 1ib5A 151 -30.95 -9.18 8.04e-01 2mtaH 373 -47.11 -9.18 8.06e-01 1ibdA 151 -31.10 -9.15 8.26e-01 1xyzA 347 -42.61 -8.55 1.35e+00 1e1aA 314 -45.46 -8.47 1.43e+00 1ibfA 151 -29.75 -8.13 1.90e+00 1ddnA 226 -35.02 -7.87 2.34e+00 1bj4A 470 -41.21 -7.83 2.43e+00 1g3yA 226 -34.92 -7.82 2.44e+00 1c0wB 225 -34.66 -7.79 2.50e+00 2dtr 226 -34.67 -7.78 2.53e+00 1fwzA 226 -34.72 -7.64 2.84e+00 1bi0 226 -34.74 -7.63 2.87e+00 1g3tA 226 -34.46 -7.60 2.93e+00 1b6e 128 -27.98 -7.58 2.99e+00 2aaiB 262 -30.36 -7.56 3.04e+00 1qbhA 101 -28.06 -7.50 3.18e+00 1eqbB 417 -44.98 -7.46 3.29e+00 1dfoA 417 -44.90 -7.45 3.32e+00 1hdhA 536 -51.28 -7.43 3.38e+00 1e2rB 567 -55.84 -7.41 3.44e+00 1qksA 567 -55.70 -7.41 3.44e+00 1aoqA 567 -55.70 -7.41 3.44e+00 1aomA 567 -55.70 -7.41 3.44e+00 1ejiA 478 -39.83 -7.30 3.78e+00 1lenA 181 -28.27 -7.20 4.11e+00 1ft9A 222 -32.14 -7.02 4.77e+00 7fabL 208 -29.40 -7.00 4.87e+00 1cruA 454 -44.09 -6.87 5.42e+00 1c9uA 454 -44.09 -6.87 5.42e+00 1qbiA 454 -44.09 -6.87 5.42e+00 1cj0A 470 -41.66 -6.77 5.89e+00 1at0 145 -28.76 -6.74 6.05e+00 2ltnA 181 -27.91 -6.69 6.31e+00 1rinA 180 -28.00 -6.69 6.31e+00 1hj5A 567 -55.84 -6.65 6.53e+00 2mllB 255 -31.50 -6.51 7.35e+00 1f1cA 129 -26.88 -6.49 7.48e+00 1lgcA 181 -28.67 -6.34 8.51e+00 1nplA 109 -31.74 -6.29 8.91e+00 1efrC 510 -50.19 -6.20 9.66e+00 1e79A 510 -50.19 -6.19 9.71e+00 1bmfA 510 -50.19 -6.19 9.71e+00 1h8eA 510 -50.19 -6.19 9.71e+00 1lofC 181 -27.84 -6.19 9.74e+00 2bqpA 234 -28.50 -6.15 1.01e+01 1mabA 510 -49.49 -6.06 1.08e+01 1gq2A 555 -49.47 -5.97 1.18e+01 1qba 858 -73.19 -5.96 1.19e+01 1c7sA 858 -72.32 -5.95 1.20e+01 1c7tA 858 -72.70 -5.95 1.20e+01 1abrB 267 -29.45 -5.94 1.21e+01 2pelA 236 -30.95 -5.80 1.36e+01 1loeC 181 -27.26 -5.76 1.41e+01 1lgbA 181 -27.86 -5.76 1.41e+01 1gz4A 551 -52.22 -5.73 1.46e+01 1bzwA 232 -30.80 -5.72 1.47e+01 1gnyA 153 -26.82 -5.70 1.48e+01 1do8A 564 -52.65 -5.56 1.68e+01 1hy3A 294 -38.37 -5.48 1.80e+01 1tme3 236 -27.24 -5.45 1.86e+01 1g5qA 181 -29.43 -5.44 1.87e+01 1f3vB 171 -27.09 -5.44 1.87e+01 1g16C 170 -30.15 -5.43 1.90e+01 1lo9A 141 -26.86 -5.41 1.93e+01 3btaA 1295 -93.17 -5.40 1.94e+01 2sttA 96 -25.69 -5.39 1.96e+01 1lo7A 141 -26.91 -5.38 1.98e+01 1bvqA 141 -26.91 -5.38 1.98e+01 1jw9B 249 -30.78 -5.31 2.11e+01 7catA 506 -45.73 -5.29 2.13e+01 1d0aB 168 -26.96 -5.26 2.20e+01 1czyA 168 -26.96 -5.26 2.20e+01 1czyC 168 -26.96 -5.26 2.20e+01 1eqyS 125 -26.47 -5.25 2.21e+01 1qnwB 242 -29.19 -5.24 2.24e+01 1k6oC 103 -24.05 -5.23 2.25e+01 1kznA 205 -30.00 -5.23 2.26e+01 1c0gS 127 -26.51 -5.22 2.27e+01 1mafL 126 -26.12 -5.19 2.34e+01 1a79A 171 -29.14 -5.19 2.35e+01 1gyhA 318 -35.12 -5.18 2.37e+01 1bev1 281 -27.77 -5.16 2.41e+01 1g33A 73 -24.42 -5.12 2.49e+01 1gydB 315 -35.36 -5.11 2.51e+01 1wbfA 242 -30.01 -5.09 2.56e+01 1wblA 241 -30.00 -5.09 2.56e+01 1g63A 181 -29.30 -5.08 2.58e+01 1jndA 420 -42.34 -5.06 2.63e+01 1rtp1 109 -25.81 -5.01 2.76e+01 1cqdA 221 -28.21 -5.00 2.78e+01 1duxC 94 -25.08 -4.97 2.85e+01 1hxmD 242 -31.58 -4.96 2.89e+01 1lkfA 299 -29.17 -4.95 2.89e+01 1gtqA 140 -27.31 -4.90 3.04e+01 1b66A 140 -27.31 -4.90 3.04e+01 1jhwA 347 -40.92 -4.87 3.13e+01 1czzA 187 -27.14 -4.85 3.16e+01 1yagG 125 -26.04 -4.85 3.18e+01 1d4xG 126 -26.06 -4.85 3.19e+01 1ca4A 168 -26.51 -4.82 3.26e+01 1jq5A 370 -39.12 -4.76 3.45e+01 1jqaA 370 -39.12 -4.76 3.45e+01 1e8eA 124 -24.52 -4.73 3.53e+01 1g17A 170 -29.91 -4.72 3.57e+01 1hbxG 157 -27.70 -4.72 3.58e+01 1gff1 426 -36.13 -4.70 3.65e+01 1c9iA 359 -39.49 -4.69 3.66e+01 1c9lA 357 -39.45 -4.68 3.71e+01 1gyeB 315 -34.46 -4.67 3.72e+01 1bg4 302 -30.05 -4.67 3.73e+01 1b31A 302 -30.05 -4.67 3.73e+01 1do5A 154 -29.01 -4.65 3.80e+01 1xys 347 -33.92 -4.63 3.88e+01 1clxA 347 -34.22 -4.63 3.88e+01 1e5nA 348 -33.92 -4.63 3.89e+01 1qscC 191 -26.81 -4.62 3.92e+01 1pmr 80 -24.22 -4.60 3.99e+01