% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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.YEL012W.t2k-100-30-dssp-ehl2 Host: farm09 Fri Nov 18 19:40:19 2005 % karplus Dir: /projects/compbiousr/compbio0404/experiments/protein-predict/yeast/YEL0/YEL012W % --------------------------------------------------------------------- % 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 +1.5*ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YEL012W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL012W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13048 sequences, 3092733 residues, 219 nodes, 339.91 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 (10000.00) % E-value on N (=11000) sequences: % N / (1 + exp(-(lambda(=1.1818) * Reverse)^tau(=0.8714))) % Calculated when Simple < simple_threshold (10000.00) % 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 1x23A 155 -198.95 -180.90 2.99e-43 1z2uA 150 -201.47 -178.72 9.21e-43 2ayvA 166 -195.20 -176.66 2.68e-42 1y6lA 149 -186.59 -170.25 7.48e-41 2bepA 159 -174.75 -157.28 6.62e-38 1jbbA 153 -176.14 -156.31 1.10e-37 1jatA 155 -175.27 -156.04 1.27e-37 1yh2A 175 -171.30 -155.74 1.49e-37 1u9aA 160 -171.58 -154.21 3.33e-37 2e2c 156 -169.10 -153.23 5.59e-37 1fzyA 149 -168.66 -151.96 1.09e-36 2ucz 165 -175.18 -149.56 3.88e-36 1fxtA 149 -166.19 -149.42 4.17e-36 1i7kA 179 -161.12 -147.01 1.50e-35 1zdnA 158 -159.61 -141.85 2.33e-34 1yh6A 179 -153.72 -140.24 5.49e-34 1yf9A 171 -147.61 -133.79 1.74e-32 1yrvA 169 -143.76 -132.24 3.99e-32 1wzvA 155 -146.62 -129.32 1.92e-31 2awfA 172 -145.17 -125.72 1.34e-30 2a4dA 160 -126.35 -107.62 2.66e-26 1jatB 138 -118.89 -104.63 1.39e-25 1j7dA 145 -121.24 -101.29 8.88e-25 1zuoA 186 -84.07 -70.09 4.57e-17 1s1qA 145 -42.04 -27.12 1.35e-05 1uzxA 169 -38.67 -24.13 9.85e-05 1kppA 145 -37.28 -22.95 2.17e-04 2ac3A 316 -25.74 -13.77 1.27e-01 1l0qA 391 -22.17 -11.85 5.12e-01 1i8kB 124 -20.35 -11.59 6.20e-01 2ac5A 316 -22.87 -11.32 7.57e-01 1ukxA 137 -22.58 -11.32 7.60e-01 2es9A 115 -25.40 -11.17 8.48e-01 1eqfA 280 -25.21 -10.75 1.15e+00 1srqA 341 -22.02 -10.71 1.19e+00 1a2yB 116 -19.65 -10.22 1.71e+00 1g7jB 116 -19.67 -10.18 1.77e+00 1vfaB 116 -19.72 -10.14 1.82e+00 1um0A 365 -21.71 -9.92 2.14e+00 1h3fA 432 -21.51 -9.91 2.16e+00 1ny9A 143 -22.45 -9.83 2.29e+00 1eyvA 156 -22.00 -9.83 2.30e+00 6gsvA 217 -22.12 -9.68 2.57e+00 1tgoA 773 -24.02 -9.54 2.86e+00 1ks8A 433 -24.40 -9.42 3.14e+00 1usuA 260 -22.96 -9.41 3.14e+00 1nekC 129 -21.09 -9.23 3.62e+00 1vhzA 198 -18.80 -9.19 3.71e+00 1qhtA 775 -24.37 -8.88 4.69e+00 1ezvH 74 -21.42 -8.86 4.77e+00 1kb9F 74 -21.38 -8.86 4.79e+00 1ywzA 175 -21.89 -8.85 4.80e+00 1t5eA 360 -21.86 -8.82 4.92e+00 1chrA 370 -20.35 -8.63 5.69e+00 1su0B 159 -19.85 -8.56 6.00e+00 1xaoA 121 -20.02 -8.49 6.33e+00 2bnxA 386 -22.44 -8.48 6.39e+00 1hilB 220 -18.05 -8.33 7.18e+00 1t2jA 116 -16.96 -8.23 7.76e+00 1c1kA 217 -22.64 -8.07 8.76e+00 1mqkH 127 -17.65 -8.06 8.84e+00 1who 96 -18.94 -8.04 8.96e+00 2bi7A 384 -19.08 -7.92 9.85e+00 1w9hA 427 -21.50 -7.87 1.02e+01 2auaA 224 -18.60 -7.86 1.03e+01 1bp3B 211 -18.47 -7.83 1.05e+01 2bmhA 455 -23.10 -7.78 1.09e+01 1go3E 187 -17.98 -7.71 1.16e+01 1y4wA 518 -18.92 -7.61 1.24e+01 1nu5A 370 -18.58 -7.55 1.30e+01 1ornA 226 -20.75 -7.55 1.30e+01 1w27A 714 -20.53 -7.49 1.37e+01 1h3oB 76 -20.01 -7.43 1.43e+01 1ju2A 536 -18.50 -7.41 1.46e+01 1bu7A 455 -22.44 -7.37 1.50e+01 1cd9C 175 -20.85 -7.34 1.54e+01 1b2pA 119 -17.37 -7.29 1.60e+01 1ugjA 141 -17.31 -7.26 1.65e+01 1kbhB 59 -17.70 -7.14 1.79e+01 1g9mC 185 -18.47 -7.11 1.84e+01 8fabB 224 -16.79 -7.08 1.89e+01 1bihA 395 -16.54 -7.08 1.89e+01 1winA 143 -21.05 -7.06 1.92e+01 1fjgB 256 -21.15 -7.01 1.98e+01 1rt8A 513 -20.86 -6.99 2.02e+01 1ex1A 605 -18.26 -6.97 2.05e+01 2ar9A 278 -19.29 -6.95 2.09e+01 2biiA 424 -16.38 -6.94 2.10e+01 1ej8A 140 -15.81 -6.90 2.16e+01 1iexA 605 -18.26 -6.89 2.19e+01 1mlcB 218 -19.59 -6.83 2.29e+01 1mkeA 152 -16.83 -6.83 2.29e+01 1phk 298 -18.28 -6.83 2.30e+01 2abk 211 -18.89 -6.80 2.36e+01 1qnrA 344 -18.80 -6.78 2.38e+01 1cdi 179 -17.85 -6.76 2.43e+01 1vhnA 318 -18.67 -6.70 2.54e+01 1qupA 222 -15.73 -6.68 2.59e+01 1y7rA 133 -16.25 -6.66 2.63e+01 1h0aA 158 -19.31 -6.65 2.65e+01 1n67A 359 -17.23 -6.63 2.69e+01 1qgiA 259 -18.59 -6.61 2.73e+01 1aa0 113 -17.84 -6.60 2.75e+01 1px5A 349 -19.73 -6.59 2.78e+01 3cd4 182 -17.59 -6.56 2.85e+01 1jpzA 473 -20.81 -6.56 2.85e+01 1eyhA 144 -19.24 -6.52 2.92e+01 1eduA 149 -19.26 -6.52 2.94e+01 1xx1A 285 -17.53 -6.49 2.99e+01 1vixA 420 -18.37 -6.46 3.06e+01 2c1dA 264 -18.67 -6.45 3.09e+01 1oaqH 121 -15.60 -6.43 3.15e+01 1dvfD 120 -14.79 -6.42 3.16e+01 1bs0A 384 -17.47 -6.41 3.19e+01 1ee4A 423 -18.27 -6.40 3.21e+01 1tqgA 105 -19.74 -6.40 3.23e+01 1dypA 271 -16.86 -6.38 3.26e+01 1um5H 217 -15.67 -6.37 3.31e+01 1kf6D 119 -20.20 -6.36 3.32e+01 1vj7A 393 -18.87 -6.36 3.33e+01 2aqjA 538 -18.89 -6.36 3.34e+01 1ejbA 168 -16.95 -6.35 3.35e+01 1pnsB 234 -19.83 -6.35 3.35e+01 1yjsA 419 -19.25 -6.35 3.36e+01 1qnoA 344 -18.82 -6.32 3.42e+01 1j05B 121 -15.09 -6.32 3.42e+01 1c4kA 730 -18.26 -6.27 3.56e+01 1cdy 178 -16.17 -6.26 3.59e+01 1gz2A 142 -16.73 -6.25 3.62e+01 4pep 326 -17.03 -6.23 3.68e+01 1xkrA 206 -17.06 -6.23 3.69e+01 1j5eB 256 -19.74 -6.16 3.89e+01 1yqcA 170 -15.67 -6.16 3.91e+01 2occA 514 -21.37 -6.16 3.91e+01 1q0xH 221 -15.76 -6.14 3.95e+01