% 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. % --------------------------------------------------------------------- % strfoo.1.YGR038C-A.t2k-100-30-str Host: cc86 Fri Nov 8 20:03:07 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.strs % % 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.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 441 nodes, 303.35 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(=1.6144) * Reverse)^tau(=0.7804))) % 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 1fftC 204 -38.00 -14.37 6.50e-02 1hw1A 239 -34.66 -11.72 3.59e-01 1eemA 241 -33.04 -10.58 7.69e-01 1kfuS 184 -34.64 -10.26 9.54e-01 1ljrA 244 -32.50 -10.24 9.71e-01 1l5zA 155 -29.27 -10.00 1.14e+00 1kf6A 602 -34.82 -9.88 1.24e+00 1qkkA 155 -29.11 -9.85 1.27e+00 1ois 223 -33.17 -9.85 1.27e+00 1mhyG 169 -31.71 -9.73 1.37e+00 1ew6A 137 -31.40 -9.19 2.00e+00 1ewaA 137 -31.40 -9.19 2.00e+00 1f4qA 165 -32.76 -9.10 2.12e+00 1hlvA 131 -29.44 -9.05 2.21e+00 1e2xA 243 -32.56 -9.00 2.28e+00 1ltm 320 -31.30 -8.95 2.37e+00 1qusA 322 -31.25 -8.87 2.50e+00 1am7A 158 -30.14 -8.72 2.79e+00 1ew6B 137 -31.01 -8.60 3.03e+00 1k94A 165 -34.31 -8.56 3.12e+00 2lhb 149 -32.03 -8.53 3.18e+00 1eh2 106 -32.01 -8.45 3.35e+00 1klt 226 -30.90 -8.44 3.38e+00 1qqfA 277 -31.82 -8.43 3.41e+00 1dw0A 112 -27.45 -8.37 3.57e+00 1mhyB 395 -35.54 -8.29 3.76e+00 1hmcB 148 -30.89 -8.20 4.03e+00 1hizA 379 -33.61 -8.19 4.05e+00 1lnrI 134 -31.21 -8.11 4.29e+00 1kgsA 225 -33.70 -8.00 4.64e+00 1ko9A 345 -31.26 -7.97 4.73e+00 1i37A 260 -31.35 -7.92 4.89e+00 1iow 306 -29.31 -7.92 4.91e+00 1alvA 173 -35.13 -7.91 4.93e+00 1jk0A 419 -33.80 -7.75 5.53e+00 1seiA 130 -28.25 -7.62 6.08e+00 1g5gB 481 -33.03 -7.59 6.23e+00 1enfA 212 -29.26 -7.50 6.64e+00 1kwiA 101 -27.09 -7.48 6.73e+00 1a28A 256 -30.65 -7.42 7.06e+00 1k8eA 345 -30.29 -7.41 7.10e+00 1dseA 292 -31.08 -7.41 7.12e+00 1fqvD 149 -29.78 -7.40 7.13e+00 2cblA 305 -31.33 -7.40 7.16e+00 2dln 306 -28.95 -7.40 7.17e+00 1e96B 203 -29.93 -7.39 7.22e+00 1fs1B 141 -29.69 -7.37 7.32e+00 1guxB 152 -28.40 -7.33 7.53e+00 1hmcA 148 -29.96 -7.33 7.54e+00 1hh8A 213 -30.02 -7.28 7.83e+00 1ihoA 283 -30.58 -7.27 7.85e+00 1ryc 294 -31.09 -7.26 7.94e+00 2cyp 294 -31.09 -7.21 8.19e+00 2btvA 901 -34.09 -7.18 8.43e+00 1ds4A 292 -31.09 -7.17 8.44e+00 1fqvJ 149 -29.38 -7.15 8.58e+00 1ash 150 -31.28 -7.12 8.79e+00 1iq0A 592 -32.01 -7.08 9.04e+00 1m1cA 680 -33.09 -7.04 9.34e+00 1a05A 358 -29.22 -6.98 9.74e+00 1myt 146 -30.91 -6.98 9.77e+00 1a6dA 545 -32.77 -6.89 1.04e+01 1b47A 304 -30.94 -6.89 1.05e+01 1jdrA 294 -30.64 -6.86 1.07e+01 1k04A 162 -30.50 -6.86 1.07e+01 1iq3A 110 -29.44 -6.84 1.08e+01 1huw 166 -28.97 -6.83 1.08e+01 2vsgA 358 -35.00 -6.83 1.09e+01 1el6A 219 -29.14 -6.78 1.13e+01 1bed 181 -29.01 -6.78 1.13e+01 1qmhA 347 -29.12 -6.76 1.15e+01 1qgjA 300 -29.05 -6.76 1.15e+01 1bg4 302 -29.52 -6.75 1.16e+01 1b31A 302 -29.52 -6.72 1.18e+01 1j4nA 271 -31.36 -6.70 1.20e+01 1el6B 219 -29.09 -6.68 1.22e+01 2hmiA 558 -31.34 -6.65 1.24e+01 1ewcA 214 -28.40 -6.65 1.24e+01 1ccg 291 -30.57 -6.65 1.24e+01 1gqeA 365 -34.40 -6.63 1.26e+01 1exeA 99 -29.24 -6.63 1.26e+01 1ng1 294 -33.50 -6.62 1.28e+01 1aisA 182 -28.00 -6.61 1.28e+01 1l2iA 261 -32.58 -6.61 1.29e+01 2end 138 -28.42 -6.59 1.30e+01 1dp4A 435 -30.32 -6.55 1.34e+01 1lea 84 -25.45 -6.53 1.37e+01 1j8uA 325 -29.40 -6.52 1.37e+01 1cm7A 363 -29.09 -6.50 1.40e+01 1ii7A 333 -28.75 -6.47 1.42e+01 1iyjB 817 -33.13 -6.47 1.42e+01 1fonA 240 -31.00 -6.43 1.47e+01 1om2A 95 -26.60 -6.41 1.48e+01 1jpnA 296 -33.11 -6.41 1.49e+01 1g8iA 190 -34.04 -6.37 1.54e+01 1lshA 1056 -31.99 -6.36 1.55e+01 1g13A 162 -28.27 -6.35 1.56e+01 1mgtA 174 -26.96 -6.34 1.57e+01 1ig6A 107 -25.72 -6.31 1.61e+01 1qrjB 199 -30.56 -6.31 1.61e+01 1b4aA 149 -27.38 -6.28 1.64e+01 1hx1B 114 -31.82 -6.27 1.65e+01 1dn1A 594 -32.29 -6.24 1.70e+01 1g7oA 215 -30.16 -6.23 1.70e+01 1ig5A 75 -25.68 -6.20 1.74e+01 1l7mA 211 -27.46 -6.20 1.75e+01 3sdhA 146 -28.70 -6.16 1.79e+01 1gulA 222 -32.13 -6.16 1.79e+01 1g5yA 238 -28.56 -6.12 1.85e+01 1a4pA 96 -26.27 -6.11 1.86e+01 1f5sA 211 -27.43 -6.11 1.87e+01 1ax4A 467 -29.41 -6.11 1.87e+01 1j97A 211 -27.43 -6.11 1.87e+01 2ng1 293 -32.78 -6.11 1.87e+01 1h99A 224 -31.40 -6.09 1.89e+01 1har 216 -28.72 -6.07 1.93e+01 1csn 298 -29.30 -6.07 1.93e+01 1dmwA 307 -28.61 -6.06 1.95e+01 1k30A 368 -29.49 -6.03 1.99e+01 1dgsA 667 -30.97 -6.03 1.99e+01 1jdpA 441 -28.67 -6.01 2.02e+01 1ebmA 317 -28.74 -5.98 2.06e+01 3icb 75 -26.51 -5.98 2.07e+01 1gseA 221 -32.61 -5.98 2.07e+01 1spgA 144 -31.39 -5.97 2.08e+01 1k3lA 221 -32.61 -5.96 2.09e+01 1pah 308 -28.69 -5.96 2.10e+01 1vasA 137 -28.10 -5.95 2.11e+01 4icb 76 -25.67 -5.95 2.11e+01 1g2iA 166 -25.47 -5.94 2.13e+01 4pah 308 -28.52 -5.93 2.15e+01 1f5qB 252 -31.04 -5.92 2.16e+01 1f82A 424 -33.16 -5.92 2.16e+01 1xsm 390 -33.40 -5.92 2.16e+01 1go4E 100 -26.69 -5.90 2.19e+01 1k7hA 476 -29.80 -5.88 2.23e+01 1tfe 145 -30.06 -5.87 2.24e+01 1wer 334 -30.94 -5.87 2.25e+01 1dk8A 147 -27.13 -5.82 2.34e+01 1lfpA 249 -28.25 -5.81 2.34e+01 1ddzA 496 -30.17 -5.81 2.36e+01 1dgjA 907 -30.62 -5.77 2.42e+01 5pal 109 -25.72 -5.77 2.42e+01 1dkgD 383 -29.33 -5.77 2.42e+01 1pvaA 110 -26.51 -5.76 2.44e+01 2tct 207 -29.54 -5.75 2.47e+01 1sfcA 96 -27.93 -5.75 2.47e+01 1dp5B 68 -24.92 -5.74 2.48e+01 3vtk 343 -27.86 -5.74 2.48e+01 1gumA 222 -31.54 -5.68 2.59e+01 1axn 323 -29.60 -5.68 2.61e+01 1rec 201 -28.09 -5.66 2.65e+01 1be3C 379 -31.60 -5.63 2.70e+01 1an7A 136 -25.72 -5.63 2.71e+01 1i50F 155 -28.91 -5.62 2.72e+01 2sas 185 -28.92 -5.59 2.78e+01 1chuA 540 -29.86 -5.57 2.83e+01 1ku1A 230 -29.28 -5.56 2.86e+01 1knyA 253 -28.48 -5.55 2.87e+01 1cf9A 753 -33.11 -5.55 2.88e+01 1qb2A 109 -25.53 -5.54 2.91e+01 1dlyA 164 -26.34 -5.53 2.91e+01 1kxpD 458 -32.37 -5.51 2.96e+01 1e8aA 91 -26.72 -5.49 3.01e+01 1bolA 222 -26.95 -5.47 3.05e+01 1ejbA 168 -26.11 -5.46 3.08e+01 1dcnD 436 -30.44 -5.46 3.08e+01 1h0oA 390 -33.58 -5.44 3.12e+01 1fyhA 258 -34.44 -5.44 3.13e+01 1ae9A 179 -26.45 -5.44 3.13e+01 1sly 618 -29.70 -5.44 3.14e+01 1e3aB 560 -32.41 -5.44 3.14e+01 1j77A 209 -28.51 -5.41 3.20e+01 3erdA 261 -31.32 -5.41 3.21e+01 1gyzA 60 -24.03 -5.40 3.24e+01 1bhb 71 -23.94 -5.38 3.28e+01 1gk9B 557 -32.17 -5.36 3.34e+01 1f3aA 222 -30.46 -5.33 3.41e+01 1gkxA 388 -29.22 -5.31 3.46e+01 1go3F 107 -26.39 -5.31 3.47e+01 1i5nA 146 -29.07 -5.30 3.48e+01 1gnlA 544 -29.42 -5.30 3.48e+01 1e79D 482 -29.48 -5.30 3.49e+01 1eia 207 -30.95 -5.27 3.56e+01 1gkfB 557 -32.34 -5.23 3.67e+01 1gm9B 557 -32.08 -5.19 3.80e+01 2eiaB 206 -30.71 -5.19 3.80e+01 1dttA 560 -30.46 -5.18 3.85e+01 1euhA 475 -28.41 -5.15 3.91e+01 1hlb 158 -26.88 -5.13 3.98e+01 1yveJ 524 -29.17 -5.13 3.99e+01