% 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.YGR038C-A.t2k-100-30-alpha Host: cc86 Fri Nov 8 20:33:28 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR038C-A % --------------------------------------------------------------------- % 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 YGR038C-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR038C-A.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 441 nodes, 301.41 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(=2.3379) * Reverse)^tau(=0.7186))) % 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 1fonA 240 -35.21 -12.57 8.58e-02 1qkkA 155 -31.01 -11.69 1.53e-01 1l5zA 155 -30.83 -11.58 1.64e-01 1klt 226 -32.54 -11.47 1.78e-01 1hw1A 239 -32.06 -10.73 2.92e-01 1e2xA 243 -32.08 -10.62 3.15e-01 1f4qA 165 -31.32 -9.94 5.01e-01 1g8iA 190 -33.32 -9.30 7.83e-01 1exeA 99 -27.31 -8.68 1.22e+00 1hizA 379 -33.06 -8.57 1.32e+00 1cghA 224 -29.19 -8.46 1.43e+00 1ltm 320 -29.84 -8.10 1.85e+00 1qusA 322 -29.84 -8.08 1.89e+00 1fs1B 141 -28.70 -7.99 2.02e+00 1har 216 -28.92 -7.97 2.05e+00 1k7hA 476 -30.35 -7.96 2.06e+00 1l2qA 458 -30.76 -7.86 2.22e+00 1f5sA 211 -28.60 -7.86 2.22e+00 1eh2 106 -28.71 -7.85 2.23e+00 1l2rA 458 -30.73 -7.81 2.30e+00 1kxpD 458 -31.84 -7.79 2.34e+00 2hmiA 558 -30.65 -7.69 2.51e+00 1bg4 302 -29.34 -7.68 2.54e+00 1b31A 302 -29.28 -7.64 2.61e+00 1j97A 211 -28.35 -7.62 2.65e+00 1kfuS 184 -30.70 -7.62 2.66e+00 1e44B 96 -26.00 -7.61 2.68e+00 1k94A 165 -30.47 -7.58 2.73e+00 1j78A 458 -30.83 -7.56 2.78e+00 1vrtA 560 -30.91 -7.47 2.98e+00 1mhyG 169 -27.85 -7.44 3.03e+00 1el6A 219 -28.34 -7.42 3.08e+00 1ebmA 317 -29.15 -7.41 3.12e+00 1xsm 390 -31.17 -7.38 3.17e+00 1aisA 182 -27.89 -7.35 3.25e+00 1dw0A 112 -25.70 -7.31 3.35e+00 1spgB 147 -27.88 -7.31 3.36e+00 1qoyA 318 -31.48 -7.29 3.40e+00 1dekA 241 -29.72 -7.27 3.46e+00 1e9lA 377 -30.16 -7.27 3.46e+00 1h6yA 170 -27.01 -7.26 3.49e+00 1el6B 219 -28.42 -7.24 3.54e+00 1alvA 173 -31.04 -7.23 3.55e+00 1rec 201 -29.16 -7.21 3.61e+00 1dyoA 160 -26.79 -7.16 3.75e+00 1fkmA 396 -32.26 -7.11 3.91e+00 1h0oA 390 -31.10 -7.08 4.00e+00 1dgsA 667 -31.56 -7.00 4.25e+00 1hh8A 213 -27.89 -6.85 4.75e+00 3rp2A 224 -29.55 -6.83 4.82e+00 1ihoA 283 -29.68 -6.83 4.82e+00 1b25A 619 -30.73 -6.77 5.04e+00 1l7mA 211 -27.39 -6.75 5.14e+00 1h99A 224 -29.42 -6.73 5.21e+00 1hlvA 131 -25.84 -6.73 5.23e+00 1kgsA 225 -32.69 -6.63 5.65e+00 1iow 306 -27.91 -6.62 5.69e+00 2dln 306 -27.86 -6.53 6.09e+00 1iq3A 110 -26.91 -6.53 6.11e+00 1bowA 159 -26.75 -6.52 6.14e+00 1cm7A 363 -28.90 -6.51 6.20e+00 1hdiA 413 -28.87 -6.49 6.27e+00 1ejbA 168 -26.39 -6.47 6.36e+00 1dttA 560 -29.55 -6.41 6.68e+00 1ko9A 345 -28.54 -6.38 6.87e+00 1qrjB 199 -27.50 -6.38 6.87e+00 1rthA 560 -29.63 -6.38 6.88e+00 2tct 207 -28.47 -6.32 7.21e+00 1i50F 155 -26.67 -6.25 7.61e+00 1qgjA 300 -27.67 -6.23 7.72e+00 1ewaA 137 -27.37 -6.20 7.88e+00 1e96B 203 -27.33 -6.20 7.90e+00 1ew6A 137 -27.35 -6.18 8.02e+00 1a05A 358 -28.13 -6.17 8.09e+00 1cpt 412 -29.27 -6.14 8.29e+00 1axn 323 -28.84 -6.09 8.61e+00 1delA 241 -28.47 -6.08 8.70e+00 1a8i 842 -31.68 -6.07 8.78e+00 1bjz 207 -28.18 -6.06 8.84e+00 1hm6A 346 -28.25 -6.06 8.84e+00 1eaxA 241 -28.04 -6.05 8.92e+00 1qc7A 101 -26.46 -6.03 9.01e+00 1keaA 221 -29.46 -6.03 9.01e+00 1gqeA 365 -30.25 -6.01 9.20e+00 1om2A 95 -25.53 -6.00 9.23e+00 1jgsA 138 -26.11 -5.95 9.66e+00 1ew6B 137 -27.09 -5.92 9.84e+00 1h5uA 842 -31.66 -5.92 9.84e+00 1ig5A 75 -24.89 -5.91 9.95e+00 2ptd 298 -27.50 -5.87 1.02e+01 1mgtA 174 -25.85 -5.87 1.03e+01 1f5qB 252 -28.79 -5.85 1.04e+01 1fxmA 302 -27.19 -5.83 1.06e+01 6paxA 133 -25.23 -5.82 1.07e+01 1gvkB 240 -27.37 -5.82 1.07e+01 1myt 146 -27.71 -5.81 1.08e+01 1pjcA 361 -26.75 -5.78 1.10e+01 1btu 240 -27.38 -5.78 1.11e+01 1g2iA 166 -25.70 -5.75 1.13e+01 1dp4A 435 -28.56 -5.74 1.14e+01 1qnjA 240 -27.32 -5.73 1.15e+01 1ax4A 467 -28.45 -5.66 1.22e+01 1cnzA 363 -28.07 -5.64 1.24e+01 1clxA 347 -30.65 -5.57 1.30e+01 1k6aA 303 -26.86 -5.53 1.35e+01 1sayA 361 -26.46 -5.52 1.37e+01 1gokA 303 -26.82 -5.50 1.38e+01 1ak5 503 -29.67 -5.49 1.40e+01 1ccg 291 -28.63 -5.48 1.41e+01 1qi6A 475 -27.91 -5.48 1.41e+01 1itkA 731 -30.49 -5.47 1.42e+01 1vaoA 560 -28.41 -5.45 1.44e+01 1tfe 145 -26.84 -5.43 1.47e+01 5ptp 223 -26.96 -5.41 1.49e+01 1hg3A 225 -25.63 -5.40 1.51e+01 4icb 76 -24.48 -5.38 1.53e+01 1guxB 152 -26.14 -5.37 1.54e+01 2cyp 294 -28.51 -5.32 1.61e+01 1l2iA 261 -29.51 -5.31 1.61e+01 5pal 109 -24.52 -5.29 1.64e+01 1mkp 144 -24.97 -5.26 1.69e+01 1go3F 107 -25.11 -5.24 1.71e+01 1k8eA 345 -27.30 -5.24 1.72e+01 1h7cA 108 -25.62 -5.23 1.72e+01 1iq0A 592 -28.98 -5.21 1.76e+01 1fqvD 149 -26.75 -5.20 1.77e+01 1e3oC 160 -26.50 -5.20 1.77e+01 1ordA 730 -30.27 -5.19 1.78e+01 1dseA 292 -28.38 -5.19 1.79e+01 1e8gA 560 -28.29 -5.18 1.80e+01 1ithA 141 -26.44 -5.18 1.80e+01 1pjbA 361 -26.10 -5.14 1.86e+01 3icb 75 -24.07 -5.12 1.90e+01 1e3sA 261 -26.35 -5.11 1.91e+01 1fs0G 230 -27.47 -5.11 1.91e+01 1qltA 560 -28.22 -5.11 1.91e+01 1m8aA 70 -23.49 -5.11 1.91e+01 1bqyA 234 -27.09 -5.10 1.93e+01 1oyb 400 -27.18 -5.08 1.95e+01 1ash 150 -27.13 -5.06 2.00e+01 1ddzA 496 -29.48 -5.05 2.02e+01 1hj9A 226 -26.37 -5.04 2.02e+01 1ryc 294 -28.28 -5.04 2.03e+01 1octC 156 -25.72 -5.03 2.04e+01 1e5rA 290 -27.60 -5.02 2.06e+01 1cyx 205 -26.05 -5.01 2.08e+01 1ihrA 76 -22.61 -4.99 2.12e+01 1jykA 254 -26.40 -4.97 2.14e+01 1fqvJ 149 -26.16 -4.97 2.15e+01 1huw 166 -26.46 -4.97 2.16e+01 1ds4A 292 -28.37 -4.96 2.16e+01 3inkC 133 -26.16 -4.94 2.20e+01 1lkvX 232 -28.72 -4.94 2.21e+01 1pvaA 110 -24.75 -4.93 2.23e+01 1dm5A 315 -27.66 -4.92 2.24e+01 2pkaB 152 -26.07 -4.92 2.25e+01 2end 138 -25.70 -4.87 2.33e+01 1jdrA 294 -28.35 -4.87 2.34e+01 1hmpA 217 -25.92 -4.87 2.34e+01 1je8A 82 -23.45 -4.86 2.35e+01 1be3A 446 -27.48 -4.76 2.58e+01 1eazA 125 -23.97 -4.74 2.60e+01 1dpuA 99 -23.25 -4.72 2.66e+01 1e9xA 455 -27.87 -4.66 2.80e+01 1ddf 127 -24.14 -4.65 2.81e+01 1eemA 241 -25.98 -4.64 2.85e+01 1oya 400 -26.72 -4.62 2.89e+01 1chuA 540 -28.01 -4.62 2.90e+01 1jpnA 296 -30.39 -4.61 2.91e+01 1kyqA 274 -26.19 -4.61 2.91e+01 1mjhB 162 -27.50 -4.61 2.91e+01 1lshA 1056 -29.59 -4.60 2.94e+01 1a28A 256 -27.53 -4.58 2.98e+01 1sfcA 96 -25.00 -4.58 2.98e+01 1euhA 475 -26.94 -4.58 3.00e+01 1t7pA 698 -28.70 -4.57 3.03e+01 1lqbC 162 -26.05 -4.56 3.05e+01 1wdcC 156 -25.02 -4.55 3.08e+01 1egr 85 -22.39 -4.55 3.09e+01 1dpjB 33 -20.93 -4.54 3.09e+01 1oyc 400 -26.67 -4.54 3.09e+01 1lm8V 160 -26.05 -4.54 3.10e+01 1b6g 310 -26.43 -4.52 3.14e+01 2sas 185 -27.07 -4.52 3.16e+01 1csn 298 -25.90 -4.52 3.16e+01 1cqxA 403 -27.75 -4.51 3.19e+01 1kcmA 270 -27.29 -4.50 3.21e+01 1jk0A 419 -27.63 -4.50 3.21e+01 1hmcA 148 -25.87 -4.50 3.22e+01 1gkxA 388 -27.27 -4.49 3.23e+01 1spgA 144 -27.09 -4.49 3.25e+01 1ezwA 349 -26.19 -4.48 3.25e+01 1dbgA 506 -27.77 -4.47 3.28e+01 1ebuA 358 -26.27 -4.47 3.28e+01 1f47B 144 -24.77 -4.47 3.30e+01 1cg2A 393 -26.45 -4.46 3.31e+01 1aky 221 -24.97 -4.46 3.32e+01 1dvbA 191 -27.19 -4.46 3.33e+01 1fvzA 271 -26.89 -4.45 3.34e+01 1dp5B 68 -23.91 -4.43 3.40e+01 1b3aA 67 -24.34 -4.42 3.43e+01 1k30A 368 -26.24 -4.42 3.43e+01 1e1dA 553 -27.85 -4.42 3.44e+01 1k04A 162 -27.76 -4.41 3.46e+01 1h6pA 203 -27.38 -4.41 3.48e+01 7odcA 424 -26.47 -4.41 3.48e+01 1a04A 215 -25.03 -4.40 3.49e+01 1ho1A 242 -25.95 -4.40 3.49e+01 1gyzA 60 -23.39 -4.40 3.49e+01 1hf2A 210 -24.79 -4.39 3.52e+01 1f46A 140 -24.90 -4.38 3.55e+01 1i5nA 146 -25.86 -4.38 3.56e+01 1cb6A 691 -27.47 -4.37 3.60e+01 1bed 181 -25.91 -4.37 3.60e+01 1hx1B 114 -28.92 -4.36 3.63e+01 1cwyA 500 -28.26 -4.34 3.70e+01 1kf6A 602 -27.32 -4.32 3.74e+01 1e2uA 553 -27.84 -4.32 3.75e+01 1ryt 190 -27.11 -4.30 3.82e+01 1eia 207 -27.71 -4.30 3.82e+01 1ea1A 455 -27.83 -4.29 3.84e+01 1bihA 395 -27.95 -4.29 3.84e+01 1pmt 203 -25.00 -4.29 3.85e+01 1ede 310 -26.24 -4.28 3.87e+01 1ego 85 -22.21 -4.28 3.90e+01 2mysB 166 -27.01 -4.27 3.93e+01 1iqrA 420 -27.08 -4.26 3.95e+01 1gntA 553 -27.65 -4.26 3.96e+01 1jilA 420 -28.24 -4.25 3.97e+01