% 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.YGR032W.t2k-100-30-str Host: cc53 Fri Nov 8 23:19:29 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR032W % --------------------------------------------------------------------- % 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 YGR032W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR032W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 1896 nodes, 1778.29 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(=1.6301) * Reverse)^tau(=0.7232))) % 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 1h2vC 771 -62.33 -17.13 1.09e-01 1fkmA 396 -56.63 -16.93 1.20e-01 1qbkB 890 -64.66 -16.41 1.54e-01 1cjaA 342 -43.15 -15.04 2.96e-01 1h6kA 757 -61.44 -14.61 3.66e-01 1e8yA 966 -55.02 -12.05 1.33e+00 1jcqA 382 -48.08 -11.96 1.39e+00 1ld8A 382 -48.09 -11.79 1.52e+00 1e7uA 961 -54.67 -11.51 1.76e+00 1iapA 211 -40.12 -11.33 1.93e+00 1mhyB 395 -51.80 -11.17 2.11e+00 1jipA 403 -44.42 -11.10 2.18e+00 1eupA 403 -46.60 -10.86 2.48e+00 1t7pA 698 -54.67 -10.76 2.62e+00 1mhyG 169 -36.67 -10.46 3.07e+00 1gw9A 388 -41.19 -10.21 3.51e+00 1j4nA 271 -47.52 -10.20 3.52e+00 1keyA 235 -47.04 -10.15 3.63e+00 4xis 387 -40.67 -10.09 3.75e+00 1xis 387 -40.65 -10.07 3.79e+00 1rmi 160 -41.08 -10.07 3.80e+00 1jk0B 345 -43.68 -9.96 4.01e+00 1kqfC 217 -52.58 -9.95 4.03e+00 1ah7 245 -47.43 -9.82 4.34e+00 1d6mA 653 -49.55 -9.71 4.60e+00 1be3C 379 -59.56 -9.68 4.69e+00 2xis 387 -40.46 -9.61 4.86e+00 1tubA 440 -38.59 -9.57 4.97e+00 6cts 433 -45.40 -9.53 5.09e+00 1iqrA 420 -39.24 -9.44 5.35e+00 1jb0A 755 -57.87 -9.17 6.21e+00 1b43A 340 -36.58 -9.16 6.25e+00 1gaxA 862 -47.38 -9.12 6.40e+00 3xis 387 -39.64 -9.09 6.51e+00 2bidA 197 -38.09 -9.04 6.69e+00 1lnh 857 -50.77 -9.03 6.72e+00 2pflA 759 -46.29 -8.83 7.51e+00 1ezfA 340 -49.87 -8.80 7.64e+00 1qjbA 245 -43.25 -8.66 8.29e+00 1a76 326 -36.70 -8.58 8.67e+00 1fjgD 209 -33.93 -8.57 8.69e+00 1d8dA 377 -45.59 -8.55 8.81e+00 1ft1A 377 -45.72 -8.51 9.02e+00 1ca1 370 -46.12 -8.48 9.16e+00 1eguA 731 -45.59 -8.44 9.38e+00 1oxa 403 -43.08 -8.44 9.39e+00 1ir6A 424 -35.58 -8.41 9.51e+00 1amoA 615 -37.61 -8.39 9.64e+00 1br2A 791 -40.92 -8.37 9.74e+00 1mmoG 162 -34.48 -8.37 9.75e+00 1pot 325 -36.10 -8.32 1.00e+01 1j8rA 196 -31.34 -8.30 1.02e+01 1io7A 368 -40.73 -8.29 1.02e+01 1ayx 492 -47.50 -8.23 1.06e+01 1kmmA 424 -35.18 -8.20 1.08e+01 1mtyG 162 -34.19 -8.18 1.09e+01 1l9hA 349 -58.21 -8.17 1.09e+01 1i7dA 659 -48.40 -8.15 1.11e+01 1gw5B 591 -50.24 -8.14 1.11e+01 1dugA 234 -41.27 -8.02 1.19e+01 1csc 433 -44.11 -7.91 1.27e+01 1ja1A 622 -38.38 -7.90 1.28e+01 1jcrA 377 -45.24 -7.85 1.32e+01 1rpa 342 -35.65 -7.84 1.33e+01 1hmcB 148 -33.78 -7.82 1.34e+01 1csmA 256 -41.92 -7.80 1.35e+01 1ihgA 370 -45.19 -7.78 1.37e+01 1ecrA 309 -32.90 -7.76 1.39e+01 1sftA 388 -31.49 -7.74 1.40e+01 1e8xA 961 -50.98 -7.72 1.42e+01 1bd0A 388 -31.49 -7.72 1.42e+01 1qjaA 245 -41.51 -7.69 1.45e+01 1hzxA 349 -57.78 -7.66 1.47e+01 1dofA 403 -44.98 -7.65 1.48e+01 1h7eA 245 -30.66 -7.59 1.53e+01 1by2 119 -29.18 -7.59 1.53e+01 1fvzA 271 -35.24 -7.56 1.56e+01 1lkxA 697 -41.93 -7.56 1.56e+01 5csmA 256 -43.10 -7.52 1.60e+01 1j78A 458 -42.95 -7.51 1.61e+01 1amz 435 -46.37 -7.48 1.63e+01 1j99A 293 -35.49 -7.48 1.64e+01 1b9zA 516 -38.57 -7.41 1.71e+01 1ndk 155 -29.47 -7.35 1.76e+01 1hmcA 148 -34.30 -7.33 1.78e+01 1npk 154 -29.44 -7.33 1.79e+01 1lpuA 332 -34.39 -7.29 1.83e+01 1qhbA 596 -44.42 -7.26 1.86e+01 1aisB 200 -33.93 -7.23 1.89e+01 2hpaA 342 -34.90 -7.23 1.89e+01 1ea3A 164 -33.96 -7.20 1.93e+01 1dvkA 173 -36.52 -7.17 1.96e+01 1ifa 158 -33.44 -7.13 2.02e+01 4crxA 322 -36.83 -7.11 2.04e+01 1f3fA 155 -29.28 -7.11 2.04e+01 1i36A 264 -35.60 -7.08 2.07e+01 1envA 123 -43.05 -7.06 2.10e+01 3pflA 759 -43.68 -7.04 2.12e+01 3crxA 343 -38.72 -7.03 2.13e+01 1fz1C 389 -45.54 -7.02 2.15e+01 1byb 495 -38.62 -7.00 2.18e+01 1i5nA 146 -36.22 -6.89 2.32e+01 1crxA 322 -36.70 -6.89 2.32e+01 1csh 435 -45.80 -6.87 2.35e+01 1gcvA 140 -33.03 -6.82 2.42e+01 1cnsA 243 -34.93 -6.78 2.48e+01 1xsm 390 -45.11 -6.75 2.52e+01 1cm5A 759 -44.20 -6.75 2.52e+01 2pgd 482 -45.12 -6.74 2.53e+01 1d3uB 201 -33.69 -6.73 2.56e+01 1h3qA 140 -29.49 -6.72 2.56e+01 1i37A 260 -38.32 -6.70 2.60e+01 1c0aA 585 -37.96 -6.69 2.62e+01 1taq 832 -43.20 -6.63 2.71e+01 1avc 673 -47.01 -6.61 2.75e+01 1g71A 347 -33.97 -6.58 2.80e+01 1fm9D 272 -38.97 -6.57 2.83e+01 1qusA 322 -37.83 -6.54 2.87e+01 1ltm 320 -37.67 -6.54 2.87e+01 1f2fA 104 -26.68 -6.53 2.88e+01 1mdaH 368 -29.43 -6.51 2.91e+01 1b77A 228 -29.62 -6.49 2.96e+01 1de6A 426 -34.94 -6.47 2.99e+01 1dkiA 371 -37.66 -6.44 3.06e+01 1f8mA 429 -34.32 -6.43 3.07e+01 1f61A 429 -34.30 -6.40 3.13e+01 1ahpA 797 -44.57 -6.39 3.14e+01 1ddbA 195 -36.37 -6.37 3.19e+01 1lxkA 721 -43.55 -6.37 3.19e+01 1prgA 270 -38.21 -6.35 3.23e+01 1dxjA 242 -35.50 -6.33 3.27e+01 1kiyA 374 -44.11 -6.32 3.29e+01 1deoA 233 -31.60 -6.31 3.30e+01 1f4tA 368 -38.04 -6.31 3.31e+01 1aw9 216 -33.87 -6.31 3.31e+01 1b79A 119 -31.37 -6.30 3.31e+01 1kbuA 349 -38.64 -6.29 3.35e+01 1h3nA 878 -45.89 -6.26 3.40e+01 1l7vA 326 -59.58 -6.26 3.40e+01 1jfgA 374 -43.60 -6.25 3.43e+01 1lrv 244 -34.03 -6.23 3.46e+01 1shdA 107 -26.72 -6.23 3.46e+01 1ytfC 79 -26.01 -6.23 3.47e+01 1k7cA 233 -31.41 -6.14 3.67e+01 1kz7A 353 -41.04 -6.09 3.79e+01 1e3oC 160 -34.81 -6.08 3.81e+01 2baa 243 -33.60 -6.05 3.89e+01 1dkqA 410 -33.78 -6.04 3.89e+01 1a36A 592 -43.90 -6.04 3.91e+01 1qbqA 333 -42.86 -6.03 3.92e+01 1aa7A 158 -32.46 -6.03 3.94e+01