% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-T2K, 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, et al., What is the value added by human intervention in protein % structure prediction, Proteins: Stucture, Function, Genetics 45(S5):86--91, 2001. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YDR030C.t2k-100-30-CB_burial_14_7 Host: farm15 Sat Nov 13 20:56:08 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YDR0/YDR030C % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % Subsequence-submodel (local) (SW = 2) % Simple scores adjusted by +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YDR030C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YDR030C.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10735 sequences, 2539893 residues, 507 nodes, 554.22 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 (=10700) sequences: % N / (1 + exp(-(lambda(=1.6782) * Reverse)^tau(=0.8031))) % 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 1gotB 340 -275.69 -255.51 3.74e-53 1tbgA 340 -275.44 -254.83 4.94e-53 1erjA 393 -262.88 -241.49 1.19e-50 1nr0A 611 -241.25 -213.28 1.58e-45 1gxrA 337 -192.47 -176.00 1.51e-38 1pguA 615 -184.94 -153.96 2.77e-34 1k8kC 372 -166.40 -145.71 1.17e-32 1sq9A 397 -134.19 -116.33 1.04e-26 1u4cA 349 -129.76 -108.62 4.24e-25 1l0qA 391 -88.49 -62.26 7.28e-15 1ri6A 343 -81.59 -52.58 1.47e-12 1q7fA 286 -66.14 -43.73 2.24e-10 1aomA 567 -77.41 -31.70 2.92e-07 1crzA 403 -56.26 -31.52 3.26e-07 1c5kA 439 -60.09 -31.21 3.95e-07 1suuA 312 -52.63 -30.55 5.93e-07 1pbyB 337 -55.12 -30.40 6.53e-07 1jmxB 349 -51.83 -30.34 6.78e-07 1jjuB 337 -54.69 -30.00 8.38e-07 1jofA 365 -55.96 -29.63 1.05e-06 1aoqA 567 -71.04 -26.06 1.01e-05 1qksA 567 -70.52 -24.87 2.16e-05 2bbkH 355 -54.83 -24.19 3.37e-05 1rwiA 270 -44.20 -22.98 7.44e-05 1k32A 1045 -101.25 -22.81 8.29e-05 1e1aA 314 -51.89 -22.24 1.21e-04 1pjxA 314 -51.92 -21.84 1.57e-04 1n6eA 1071 -101.99 -21.15 2.50e-04 1utcA 363 -47.60 -19.89 5.82e-04 1kb0A 677 -70.07 -16.98 4.28e-03 1wp5A 323 -43.83 -16.97 4.31e-03 1v04A 355 -39.64 -16.08 8.04e-03 1u6dX 308 -33.69 -15.46 1.24e-02 1c9uA 454 -43.83 -14.09 3.32e-02 1cruA 454 -43.80 -13.90 3.82e-02 1qbiA 454 -43.21 -13.69 4.43e-02 1npeA 267 -33.88 -13.27 6.03e-02 1bpoA 494 -50.47 -12.77 8.69e-02 1xfdA 723 -53.35 -11.23 2.75e-01 1orvA 728 -47.81 -10.34 5.42e-01 1n1mA 728 -48.76 -9.99 7.06e-01 1g72A 573 -51.04 -9.91 7.52e-01 1lrwA 600 -61.30 -9.91 7.53e-01 1qniA 581 -53.52 -9.80 8.21e-01 1ijqA 316 -27.85 -9.80 8.23e-01 1xm8A 254 -25.63 -9.51 1.03e+00 1s1dA 331 -34.84 -9.47 1.06e+00 1fwxA 595 -53.56 -9.44 1.08e+00 4aahA 571 -50.15 -9.19 1.32e+00 1kv9A 668 -61.38 -9.10 1.42e+00 1t6t1 118 -23.40 -8.27 2.74e+00 1q47A 495 -39.87 -8.20 2.91e+00 1oalA 151 -22.09 -8.15 3.02e+00 1yaiA 151 -21.57 -8.14 3.04e+00 1at0 145 -21.19 -8.11 3.11e+00 1vehA 92 -22.76 -8.00 3.42e+00 1m2oB 190 -23.94 -7.33 5.90e+00 2irfG 113 -23.14 -7.03 7.57e+00 2pooA 355 -38.19 -6.96 8.01e+00 1qlgA 355 -37.74 -6.93 8.19e+00 1gguA 731 -56.82 -6.69 1.00e+01 1irf 112 -23.27 -6.66 1.02e+01 1qrkA 731 -57.41 -6.64 1.04e+01 1cvmA 353 -37.05 -6.60 1.08e+01 1sqjA 789 -58.86 -6.55 1.13e+01 1eur 365 -29.79 -6.45 1.22e+01 1evuA 731 -56.61 -6.43 1.24e+01 1h6lA 353 -37.17 -6.43 1.25e+01 1gnuA 117 -21.04 -6.25 1.45e+01 1f13A 731 -57.72 -6.20 1.51e+01 1ex0A 731 -55.84 -6.14 1.59e+01 1ggtB 731 -56.63 -6.14 1.60e+01 1ohgA 282 -30.02 -6.09 1.67e+01 1mkfA 382 -27.20 -6.08 1.68e+01 1i1gA 141 -23.34 -6.07 1.69e+01 1fh6A 282 -30.19 -6.06 1.70e+01 1aym3 238 -23.72 -5.97 1.83e+01 1aym1 285 -28.01 -5.82 2.10e+01 1cojA 212 -26.79 -5.81 2.11e+01 1jguH 217 -16.72 -5.78 2.17e+01 2ltnA 181 -21.86 -5.74 2.24e+01 1jipA 403 -39.14 -5.72 2.28e+01 1am2 199 -23.33 -5.68 2.36e+01 1eupA 403 -38.70 -5.65 2.43e+01 1fvuB 125 -20.51 -5.63 2.46e+01 1oxa 403 -38.47 -5.55 2.64e+01 1rhi3 236 -24.38 -5.55 2.64e+01 1n99A 166 -20.98 -5.54 2.67e+01 1b35B 255 -26.14 -5.53 2.68e+01 1dg9A 157 -17.46 -5.47 2.84e+01 1g8lA 411 -37.68 -5.46 2.84e+01 1s28A 132 -23.41 -5.38 3.05e+01 1a12A 413 -32.21 -5.34 3.16e+01 1gxqA 106 -18.45 -5.31 3.26e+01 1w8oA 601 -42.08 -5.28 3.34e+01 1ugmA 125 -21.15 -5.27 3.38e+01 1enxA 190 -16.59 -5.20 3.57e+01 1iyjA 70 -22.58 -5.20 3.58e+01 1fneA 192 -25.09 -5.19 3.62e+01 1ixmA 192 -22.04 -5.17 3.67e+01 1qdlB 195 -22.21 -5.14 3.78e+01 1xypA 190 -16.51 -5.13 3.82e+01 1jtdB 273 -26.54 -5.12 3.85e+01 1dim 381 -23.32 -5.10 3.89e+01 1d5tA 433 -35.05 -5.10 3.92e+01