% 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.YGR036C.t2k-100-30-str Host: cc50 Fri Nov 8 19:19:43 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR036C % --------------------------------------------------------------------- % 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 YGR036C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR036C.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 240 nodes, 168.20 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(=2.3260) * Reverse)^tau(=0.7446))) % 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 1d2tA 231 -68.75 -43.34 2.44e-10 1vnc 609 -61.56 -35.54 1.73e-08 1vns 609 -61.35 -35.32 1.96e-08 1qi9A 556 -60.61 -34.75 2.71e-08 1qhbA 596 -56.40 -27.93 1.41e-06 1e19A 314 -34.62 -12.20 4.17e-02 1li5A 461 -34.76 -11.16 9.04e-02 1avpA 204 -30.45 -9.79 2.59e-01 1s01 283 -29.64 -9.01 4.80e-01 1rypK 198 -30.39 -8.97 4.94e-01 1b7bA 310 -30.31 -8.59 6.71e-01 1h2vC 771 -35.81 -8.10 9.98e-01 1h6kA 757 -35.23 -7.92 1.16e+00 1kqfC 217 -37.34 -7.88 1.20e+00 1bccD 241 -33.90 -7.75 1.33e+00 1kpkA 473 -38.72 -7.71 1.38e+00 1be3D 241 -33.92 -7.44 1.71e+00 1bjt 793 -32.52 -7.28 1.97e+00 1kplA 473 -38.75 -7.17 2.16e+00 1fqyA 269 -33.00 -7.13 2.22e+00 1kzhA 555 -30.85 -7.03 2.44e+00 1m55A 197 -27.53 -6.92 2.66e+00 1k7qA 479 -28.73 -6.62 3.45e+00 1ekeA 230 -31.10 -6.56 3.64e+00 1fftC 204 -32.23 -6.49 3.85e+00 1jw9B 249 -26.80 -6.36 4.31e+00 1gg3A 279 -29.39 -6.32 4.48e+00 1go7P 462 -27.88 -5.95 6.18e+00 1sup 275 -26.48 -5.89 6.53e+00 1ae7 119 -28.47 -5.88 6.57e+00 1lw6E 281 -26.42 -5.84 6.80e+00 1egdA 396 -30.44 -5.82 6.92e+00 1a0fA 201 -28.60 -5.75 7.40e+00 1csbB 205 -26.60 -5.73 7.52e+00 1lr0A 129 -25.95 -5.67 7.92e+00 1go8P 462 -27.55 -5.59 8.56e+00 1a6dA 545 -31.23 -5.52 9.05e+00 3vtk 343 -29.49 -5.51 9.18e+00 1k7gA 479 -27.69 -5.50 9.26e+00 1a0cA 438 -29.16 -5.49 9.35e+00 1ca1 370 -31.14 -5.45 9.66e+00 1rtu 114 -26.20 -5.34 1.07e+01 1k7iA 479 -27.36 -5.24 1.17e+01 1hyt 316 -27.58 -5.21 1.20e+01 1bxm 99 -23.30 -5.19 1.23e+01 1lriA 98 -23.29 -5.18 1.23e+01 8tlnE 316 -27.54 -5.17 1.25e+01 2tmnE 316 -27.45 -5.08 1.35e+01 1epuA 591 -29.43 -5.04 1.41e+01 1gu9A 177 -28.27 -5.02 1.43e+01 1lqtA 456 -27.66 -5.02 1.43e+01 1kncA 177 -28.28 -4.99 1.47e+01 6tmnE 316 -27.34 -4.99 1.48e+01 1sqc 631 -31.44 -4.93 1.55e+01 6prcM 323 -33.85 -4.83 1.72e+01 1dxrM 323 -33.93 -4.81 1.74e+01 1ewqA 765 -29.82 -4.80 1.76e+01 1sbp 310 -26.89 -4.79 1.77e+01 1aca 86 -24.81 -4.79 1.78e+01 1f3iA 481 -28.69 -4.78 1.78e+01 1fwkA 296 -27.55 -4.74 1.87e+01 1a16 440 -27.89 -4.73 1.87e+01 2abd 86 -24.40 -4.71 1.91e+01 1allA 160 -27.13 -4.70 1.92e+01 1az9 457 -27.96 -4.68 1.98e+01 1jplA 171 -27.39 -4.65 2.03e+01 1fa0B 537 -28.47 -4.58 2.17e+01 1beo 98 -23.00 -4.56 2.19e+01 1ixh 321 -25.67 -4.56 2.20e+01 1khdA 345 -26.42 -4.56 2.21e+01 1neq 74 -22.07 -4.39 2.58e+01 1kijA 390 -26.86 -4.39 2.58e+01 2occD 147 -27.20 -4.39 2.59e+01 1ocrD 147 -27.22 -4.39 2.59e+01 1dioG 173 -24.70 -4.36 2.66e+01 1exzA 141 -25.54 -4.35 2.69e+01 1k8kD 300 -27.41 -4.29 2.85e+01 1sfcA 96 -25.84 -4.27 2.89e+01 1plc 99 -22.17 -4.26 2.92e+01 2pcy 99 -22.17 -4.26 2.94e+01 1fbaA 361 -26.69 -4.21 3.08e+01 1e9xA 455 -29.84 -4.18 3.16e+01 1hb6A 86 -23.91 -4.18 3.16e+01 2ezl 99 -23.40 -4.12 3.35e+01 1tlfA 301 -24.84 -4.10 3.40e+01 1c02A 166 -27.55 -4.05 3.57e+01 1ekrA 161 -24.43 -4.05 3.60e+01 1f82A 424 -28.91 -4.02 3.71e+01 1pmi 440 -28.06 -4.01 3.74e+01 1lqpA 135 -22.92 -4.01 3.74e+01 1i1iP 681 -28.61 -4.00 3.75e+01 1jihA 531 -29.00 -3.99 3.79e+01 1kvkA 395 -28.01 -3.97 3.88e+01 2ezk 99 -23.28 -3.97 3.89e+01 1h72C 296 -27.78 -3.94 3.98e+01 1gdhA 320 -25.41 -3.94 3.99e+01