% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 09/03/03_16:30:36 % (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. % --------------------------------------------------------------------- % dssp-ehl2foo.1.YGR038C-B.t2k-100-30-dssp-ehl2 Host: cc55 Mon Nov 17 22:43:12 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR038C-B % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.dssps % % 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-B.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR038C-B.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8940 sequences, 2116673 residues, 1756 nodes, 2019.05 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 (=8162) sequences: % N / (1 + exp(-(lambda(=1.0033) * 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 1asu 162 -115.10 -88.66 8.91e-13 1vsd 152 -112.33 -87.61 1.26e-12 1cxqA 162 -110.12 -85.40 2.65e-12 2itg 163 -87.45 -59.99 1.77e-08 1hyvA 166 -80.00 -51.96 3.30e-07 1b9dA 163 -79.18 -51.89 3.39e-07 1exqA 154 -78.97 -50.35 5.99e-07 1bl3A 160 -76.45 -48.68 1.12e-06 1itg 166 -71.46 -43.84 7.00e-06 1hvc 203 -55.33 -25.37 1.17e-02 1mfs 55 -45.02 -22.60 3.86e-02 1difA 99 -46.97 -22.39 4.23e-02 1kzkA 99 -47.16 -22.15 4.70e-02 5hvpA 99 -47.17 -22.13 4.74e-02 1aaf 55 -43.31 -20.60 9.28e-02 1k1tA 99 -46.29 -20.18 1.12e-01 1a1tA 55 -41.22 -20.04 1.19e-01 1dazC 99 -45.97 -19.96 1.23e-01 1f6uA 55 -40.47 -19.83 1.31e-01 1bveA 99 -43.75 -19.72 1.38e-01 1dlc 584 -55.17 -19.65 1.42e-01 4fiv 113 -48.49 -19.60 1.45e-01 1fivA 113 -48.21 -18.96 1.94e-01 1idaA 99 -44.87 -18.14 2.80e-01 1nc8 29 -36.18 -17.89 3.14e-01 2fivA 116 -46.56 -17.47 3.82e-01 3fivA 116 -45.72 -16.45 6.10e-01 1dsqA 21 -32.10 -15.25 1.07e+00 1a6bB 40 -41.47 -15.06 1.17e+00 1lxkA 721 -60.45 -14.89 1.27e+00 1qksA 567 -59.29 -14.87 1.28e+00 1mml 265 -43.27 -14.60 1.45e+00 1aoqA 567 -59.23 -14.59 1.46e+00 1n7oA 721 -60.12 -14.57 1.47e+00 1vns 609 -58.86 -14.45 1.56e+00 1fmb 104 -36.76 -14.45 1.56e+00 1eguA 731 -60.09 -14.33 1.65e+00 1floA 422 -44.77 -13.63 2.31e+00 1vnc 609 -57.29 -12.91 3.28e+00 1a7cA 379 -40.26 -12.81 3.44e+00 1jmoA 480 -47.58 -12.54 3.91e+00 1lj5A 379 -39.86 -12.53 3.93e+00 1ciy 590 -49.39 -12.46 4.07e+00 1djxB 624 -49.74 -12.29 4.43e+00 1qmyA 167 -38.35 -11.99 5.14e+00 1dvpA 220 -42.19 -11.52 6.49e+00 1kwkA 645 -49.69 -11.17 7.73e+00 1gnlA 544 -52.02 -11.06 8.15e+00 1kwgA 645 -49.60 -11.05 8.20e+00 3psg 370 -45.11 -10.90 8.83e+00 1h0oA 390 -51.23 -10.65 1.00e+01 1o86A 589 -47.63 -10.52 1.07e+01 1xsm 390 -50.02 -10.46 1.10e+01 2rspB 124 -36.05 -10.44 1.12e+01 1hm2A 700 -56.56 -10.37 1.16e+01 1jj22 92 -31.94 -9.95 1.43e+01 1h1hA 134 -32.96 -9.94 1.43e+01 1qmtA 134 -32.96 -9.94 1.43e+01 2rspA 124 -35.01 -9.79 1.55e+01 1i1iP 681 -52.81 -9.77 1.57e+01 1ehkA 562 -46.47 -9.75 1.58e+01 1ffkZ 92 -31.93 -9.73 1.60e+01 1mhyD 521 -47.75 -9.61 1.70e+01 1e2uA 553 -52.06 -9.61 1.70e+01 1gntA 553 -52.06 -9.61 1.70e+01 1e1dA 553 -51.59 -9.58 1.73e+01 1mkeA 152 -35.74 -9.57 1.74e+01 1cb8A 678 -55.52 -9.51 1.79e+01 1dytA 133 -32.40 -9.42 1.88e+01 1ds6B 180 -35.20 -9.34 1.96e+01 1gpl 432 -47.21 -9.18 2.12e+01 1aocA 175 -33.04 -9.18 2.13e+01 1kanA 253 -40.16 -9.15 2.16e+01 1cg2A 393 -44.58 -9.09 2.22e+01 1qasA 622 -46.70 -9.09 2.23e+01 1jmxA 494 -50.16 -9.08 2.24e+01 1dc1A 323 -40.82 -8.99 2.35e+01 1djxA 624 -45.49 -8.93 2.42e+01 1nqcA 217 -34.05 -8.89 2.47e+01 1go3E 187 -35.89 -8.84 2.53e+01 1j79A 347 -36.11 -8.84 2.53e+01 1jjuA 489 -53.34 -8.83 2.55e+01 1mhyG 169 -39.13 -8.82 2.57e+01 1eybA 471 -49.04 -8.81 2.58e+01 1pbyA 489 -53.65 -8.78 2.62e+01 1n6zA 105 -34.54 -8.71 2.71e+01 1mvpA 124 -33.82 -8.70 2.73e+01 1scfA 273 -40.98 -8.62 2.85e+01 1di1A 300 -47.25 -8.59 2.90e+01 1cqxA 403 -43.03 -8.51 3.01e+01 16vpA 366 -41.45 -8.46 3.10e+01 1jsqA 582 -42.34 -8.45 3.12e+01 1i5pA 633 -50.08 -8.42 3.16e+01 1giqA 413 -48.64 -8.42 3.17e+01 1nr0A 611 -54.27 -8.38 3.22e+01 1dupA 152 -34.20 -8.35 3.29e+01 1euwA 152 -34.20 -8.35 3.29e+01 1smpI 101 -30.68 -8.29 3.38e+01 3pghA 587 -47.64 -8.22 3.52e+01 1f1oA 431 -40.42 -8.17 3.61e+01 1f2eA 201 -36.08 -8.15 3.65e+01 1mo9A 523 -51.13 -8.13 3.69e+01 1miqA 375 -42.44 -8.08 3.79e+01 1oi0A 124 -30.67 -8.07 3.81e+01 1bg1A 722 -54.15 -8.05 3.84e+01 1h09A 338 -45.36 -8.05 3.84e+01 1toh 343 -37.82 -8.04 3.86e+01 1gcyA 527 -50.18 -8.02 3.91e+01