% 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.YGR027W-A.t2k-100-30-alpha Host: cc51 Fri Nov 8 19:32:12 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR027W-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 YGR027W-A.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR027W-A.t2k.alpha.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 441 nodes, 303.91 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(=2.2050) * Reverse)^tau(=0.7384))) % 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 1l5zA 155 -32.71 -13.35 3.87e-02 1qkkA 155 -32.77 -13.33 3.93e-02 1fonA 240 -33.74 -11.88 1.05e-01 1hizA 379 -34.94 -10.40 2.99e-01 1f4qA 165 -30.86 -9.55 5.55e-01 1hw1A 239 -30.52 -8.96 8.57e-01 1e2xA 243 -30.52 -8.82 9.49e-01 1g8iA 190 -32.78 -8.76 9.98e-01 1ltm 320 -30.66 -8.73 1.02e+00 1klt 226 -30.42 -8.70 1.04e+00 1qusA 322 -30.67 -8.69 1.05e+00 1h5uA 842 -34.21 -8.28 1.43e+00 1har 216 -28.88 -8.22 1.50e+00 1eh2 106 -28.85 -8.09 1.65e+00 1kxpD 458 -32.13 -8.08 1.67e+00 1a8i 842 -33.77 -7.98 1.80e+00 1cghA 224 -28.62 -7.96 1.83e+00 1j78A 458 -31.24 -7.91 1.90e+00 1aisA 182 -27.94 -7.87 1.97e+00 1xsm 390 -31.85 -7.84 2.00e+00 2hmiA 558 -30.82 -7.76 2.14e+00 1fs1B 141 -28.52 -7.70 2.24e+00 1cqxA 403 -30.61 -7.62 2.37e+00 1qoyA 318 -32.10 -7.62 2.38e+00 1h0oA 390 -31.78 -7.42 2.78e+00 1vrtA 560 -30.93 -7.41 2.79e+00 1clxA 347 -31.00 -7.34 2.96e+00 1h67A 108 -27.64 -7.32 3.00e+00 1mhyG 169 -28.05 -7.26 3.15e+00 1go3F 107 -27.15 -7.26 3.16e+00 1bg4 302 -29.06 -7.25 3.19e+00 1e9lA 377 -30.03 -7.24 3.21e+00 1iq3A 110 -26.82 -7.22 3.25e+00 1f5sA 211 -28.46 -7.20 3.30e+00 1l2qA 458 -29.89 -7.16 3.42e+00 1b31A 302 -29.01 -7.14 3.47e+00 1l2rA 458 -29.87 -7.09 3.61e+00 1j97A 211 -28.21 -7.04 3.76e+00 1ihoA 283 -29.79 -6.92 4.11e+00 1cm7A 363 -29.08 -6.68 5.00e+00 1rthA 560 -29.79 -6.65 5.10e+00 1h99A 224 -29.63 -6.62 5.25e+00 1iow 306 -27.88 -6.60 5.32e+00 1mroA 548 -29.06 -6.59 5.40e+00 1el6A 219 -27.88 -6.55 5.55e+00 1rec 201 -28.40 -6.55 5.56e+00 1dttA 560 -29.66 -6.54 5.61e+00 1k94A 165 -29.25 -6.50 5.78e+00 1fftC 204 -28.11 -6.50 5.78e+00 1spgB 147 -27.17 -6.48 5.87e+00 2dln 306 -27.80 -6.44 6.07e+00 1kfuS 184 -29.24 -6.43 6.11e+00 1f5qB 252 -28.85 -6.37 6.45e+00 1ejbA 168 -26.31 -6.36 6.51e+00 1spgA 144 -28.73 -6.33 6.67e+00 1hlvA 131 -25.84 -6.28 6.92e+00 1el6B 219 -27.73 -6.27 6.97e+00 1dekA 241 -28.61 -6.25 7.11e+00 1a05A 358 -28.13 -6.23 7.22e+00 1keaA 221 -29.60 -6.16 7.67e+00 1ebmA 317 -27.99 -6.14 7.78e+00 3lynA 136 -26.46 -6.11 7.94e+00 1ig5A 75 -25.10 -6.10 8.04e+00 2tct 207 -28.52 -6.09 8.12e+00 1dgsA 667 -31.42 -6.06 8.28e+00 1qgjA 300 -27.62 -6.06 8.31e+00 1axn 323 -28.90 -6.06 8.31e+00 1ahpA 797 -30.89 -6.04 8.44e+00 1cpt 412 -29.36 -6.04 8.45e+00 1hh8A 213 -27.58 -6.03 8.53e+00 1qc7A 101 -26.54 -5.98 8.83e+00 1l7mA 211 -27.25 -5.97 8.93e+00 1hdiA 413 -28.90 -5.96 8.98e+00 1hbnA 549 -28.43 -5.93 9.27e+00 6paxA 133 -25.28 -5.91 9.40e+00 1d0bA 213 -25.79 -5.87 9.74e+00 1cnzA 363 -28.29 -5.84 9.94e+00 1i50F 155 -26.57 -5.84 9.97e+00 1h6yA 170 -25.78 -5.82 1.01e+01 1bjz 207 -28.19 -5.82 1.01e+01 1alvA 173 -29.13 -5.80 1.03e+01 1om2A 95 -25.58 -5.80 1.03e+01 1ax4A 467 -28.68 -5.77 1.05e+01 1ewaA 137 -27.31 -5.70 1.12e+01 1f82A 424 -31.22 -5.68 1.14e+01 1dw0A 112 -24.00 -5.68 1.14e+01 1mgtA 174 -25.61 -5.68 1.14e+01 1dyoA 160 -25.64 -5.67 1.14e+01 1ew6A 137 -27.29 -5.67 1.15e+01 1ccg 291 -28.77 -5.61 1.21e+01 1h7cA 108 -25.94 -5.58 1.23e+01 1g2iA 166 -25.51 -5.56 1.25e+01 1pbv 195 -27.62 -5.56 1.26e+01 1fkmA 396 -31.41 -5.56 1.26e+01 4icb 76 -24.64 -5.55 1.27e+01 1k04A 162 -29.05 -5.52 1.30e+01 1l2iA 261 -29.88 -5.51 1.32e+01 2end 138 -26.32 -5.51 1.32e+01 1m8aA 70 -23.72 -5.50 1.32e+01 2cyp 294 -28.66 -5.50 1.32e+01 1fxmA 302 -26.89 -5.50 1.33e+01 1myt 146 -27.42 -5.49 1.34e+01 1delA 241 -27.75 -5.45 1.38e+01 1ew6B 137 -27.00 -5.43 1.40e+01 1wdcC 156 -25.89 -5.39 1.45e+01 1dseA 292 -28.45 -5.39 1.46e+01 1e3oC 160 -26.77 -5.34 1.52e+01 1gkxA 388 -28.48 -5.33 1.53e+01 2occA 514 -28.75 -5.33 1.53e+01 1e96B 203 -26.97 -5.33 1.54e+01 1a28A 256 -27.81 -5.32 1.55e+01 1jgsA 138 -25.65 -5.29 1.58e+01 1guxB 152 -26.17 -5.27 1.60e+01 3icb 75 -24.22 -5.27 1.61e+01 5pal 109 -24.62 -5.25 1.63e+01 1gqeA 365 -30.00 -5.25 1.64e+01 1gkgA 136 -25.14 -5.23 1.67e+01 1ryc 294 -28.41 -5.23 1.67e+01 1gvkB 240 -26.40 -5.21 1.69e+01 1octC 156 -25.89 -5.20 1.71e+01 1k6aA 303 -26.56 -5.20 1.71e+01 1cg5B 141 -26.92 -5.19 1.73e+01 1btu 240 -26.41 -5.18 1.74e+01 1qnjA 240 -26.46 -5.16 1.76e+01 1gokA 303 -26.52 -5.16 1.77e+01 1qi6A 475 -27.49 -5.15 1.78e+01 1ds4A 292 -28.51 -5.15 1.79e+01 1innA 166 -24.94 -5.12 1.83e+01 1vaoA 560 -28.19 -5.11 1.85e+01 1k8eA 345 -27.22 -5.11 1.85e+01 1c8kA 842 -30.65 -5.09 1.88e+01 1e44B 96 -23.59 -5.09 1.89e+01 1ko9A 345 -27.38 -5.08 1.90e+01 1pvaA 110 -24.91 -5.08 1.90e+01 1l5wA 796 -29.87 -5.05 1.95e+01 1fqvD 149 -26.66 -5.04 1.97e+01 1jdrA 294 -28.50 -5.04 1.97e+01 1ak5 503 -29.13 -5.01 2.01e+01 1lkvX 232 -28.78 -5.01 2.02e+01 1iqrA 420 -27.60 -4.99 2.06e+01 1f4pA 147 -24.80 -4.96 2.10e+01 1ash 150 -27.43 -4.96 2.10e+01 2olbA 517 -27.34 -4.91 2.19e+01 1qltA 560 -28.04 -4.91 2.20e+01 1f83A 425 -29.94 -4.88 2.25e+01 1hg3A 225 -25.07 -4.88 2.25e+01 1iqcA 308 -27.63 -4.86 2.29e+01 1jykA 254 -26.39 -4.83 2.35e+01 1dpjB 33 -21.24 -4.82 2.37e+01 1bihA 395 -28.75 -4.82 2.38e+01 1dp5B 68 -24.24 -4.79 2.43e+01 1fdlH 218 -27.54 -4.79 2.43e+01 1iq0A 592 -28.81 -4.78 2.47e+01 1i1rB 181 -26.96 -4.77 2.48e+01 1fqvJ 149 -26.02 -4.75 2.52e+01 1mkp 144 -24.68 -4.75 2.53e+01 1hm6A 346 -27.18 -4.74 2.54e+01 1mjhB 162 -27.34 -4.73 2.58e+01 1k7hA 476 -27.10 -4.72 2.58e+01 1gpb 842 -30.21 -4.72 2.59e+01 1dbgA 506 -27.63 -4.71 2.61e+01 1vasA 137 -25.36 -4.69 2.65e+01 1e8gA 560 -27.87 -4.69 2.67e+01 1ihrA 76 -22.59 -4.69 2.67e+01 1e9xA 455 -27.88 -4.68 2.69e+01 1hf2A 210 -24.82 -4.68 2.70e+01 1jhnA 424 -29.45 -4.65 2.76e+01 7catA 506 -28.33 -4.65 2.77e+01 1eazA 125 -23.88 -4.64 2.78e+01 1h6pA 203 -27.48 -4.64 2.79e+01 1cg2A 393 -26.72 -4.64 2.79e+01 1bed 181 -26.07 -4.64 2.79e+01 1bowA 159 -24.69 -4.63 2.81e+01 1qmhA 347 -26.51 -4.61 2.86e+01 1i37A 260 -27.69 -4.61 2.86e+01 1eia 207 -27.71 -4.60 2.87e+01 1gkzA 388 -27.88 -4.60 2.89e+01 1l7vA 326 -26.94 -4.60 2.89e+01 1aky 221 -25.04 -4.59 2.91e+01 1e5rA 290 -26.84 -4.59 2.91e+01 1k7iA 479 -27.98 -4.58 2.94e+01 1jk0A 419 -27.79 -4.58 2.94e+01 1go7P 462 -27.91 -4.56 2.99e+01 1ddzA 496 -28.99 -4.55 3.00e+01 1be3A 446 -27.57 -4.54 3.05e+01 1lshA 1056 -29.60 -4.52 3.10e+01 1afrA 345 -27.32 -4.52 3.10e+01 1pbp 321 -25.79 -4.50 3.15e+01 1csn 298 -25.73 -4.49 3.17e+01 1kcmA 270 -27.12 -4.48 3.21e+01 1jevA 517 -26.86 -4.47 3.23e+01 1llp 343 -27.90 -4.47 3.23e+01 1jpnA 296 -30.16 -4.46 3.26e+01 1e42A 258 -26.11 -4.46 3.27e+01 1qbzA 123 -26.91 -4.45 3.29e+01 3grx 82 -22.01 -4.45 3.29e+01 1jetA 517 -26.85 -4.44 3.32e+01 1cr6B 554 -28.83 -4.44 3.34e+01 1ho1A 242 -26.02 -4.41 3.43e+01 1k7qA 479 -27.87 -4.40 3.43e+01 1li5A 461 -28.75 -4.37 3.53e+01 1eemA 241 -25.65 -4.37 3.53e+01 1je8A 82 -22.99 -4.37 3.54e+01 1f7cA 231 -26.22 -4.37 3.55e+01 1ek1A 554 -28.38 -4.36 3.57e+01 1ezwA 349 -26.22 -4.34 3.63e+01 1k30A 368 -26.20 -4.33 3.68e+01 1m1cA 680 -27.65 -4.31 3.74e+01 1go8P 462 -27.67 -4.30 3.77e+01 1i1gA 141 -24.20 -4.30 3.77e+01 1ea1A 455 -27.76 -4.29 3.79e+01 1mjhA 162 -27.19 -4.29 3.80e+01 1euhA 475 -26.57 -4.29 3.80e+01 1fvzA 271 -26.61 -4.29 3.81e+01 1j6rA 214 -25.76 -4.26 3.90e+01 1am7A 158 -24.46 -4.26 3.92e+01 1chuA 540 -28.00 -4.25 3.94e+01 1iawA 317 -26.03 -4.24 3.96e+01 1k7gA 479 -27.83 -4.24 3.97e+01 1dboA 506 -27.24 -4.24 3.98e+01 1h6tA 291 -25.53 -4.23 4.00e+01