% SAM: /projects/compbio/bin/i686/hmmscore v3.4 (July 31, 2003) compiled 08/05/03_15:14:38 % (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. % --------------------------------------------------------------------- % strfoo.1.YEL012W.t2k-100-30-str Host: cc75 Mon Aug 18 10:55:57 2003 % karplus Dir: /projects/compbio/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.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 YEL012W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YEL012W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8565 sequences, 2028471 residues, 219 nodes, 202.72 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(=1.1993) * Reverse)^tau(=0.8392))) % 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 1jatA 155 -201.52 -171.20 1.10e-34 1jbbA 153 -201.77 -170.58 1.43e-34 2e2c 156 -193.73 -169.55 2.22e-34 1fzyA 149 -192.97 -165.65 1.18e-33 1u9aA 160 -195.49 -163.73 2.71e-33 1i7kA 179 -186.37 -163.65 2.79e-33 2ucz 165 -199.49 -163.44 3.07e-33 1fxtA 149 -185.70 -158.32 2.79e-32 1jatB 138 -136.03 -108.73 1.09e-22 1j7dA 145 -140.15 -108.13 1.43e-22 1kppA 145 -48.76 -23.47 5.82e-04 1tgoA 773 -39.81 -12.14 6.32e-01 1qhtA 775 -40.28 -11.84 7.70e-01 6gsvA 217 -33.93 -11.36 1.06e+00 1eqfA 280 -36.57 -11.05 1.30e+00 1h3fA 432 -35.26 -10.44 1.95e+00 1ej8A 140 -29.76 -10.44 1.96e+00 1gtkA 313 -32.03 -10.37 2.05e+00 1ezvH 74 -31.88 -10.28 2.18e+00 1kb9F 74 -31.62 -10.22 2.26e+00 1jpzA 473 -36.81 -9.99 2.64e+00 1qnrA 344 -33.15 -9.86 2.89e+00 1qupA 222 -29.87 -9.73 3.15e+00 1chrA 370 -33.38 -9.72 3.16e+00 1qnoA 344 -33.18 -9.68 3.25e+00 1fohA 664 -35.79 -9.38 3.98e+00 1kbhB 59 -27.59 -9.28 4.27e+00 1i8kB 124 -28.23 -9.26 4.32e+00 1jw3A 140 -30.18 -9.18 4.59e+00 1go3E 187 -29.72 -9.10 4.83e+00 1a2yB 116 -28.61 -9.08 4.90e+00 1vfaB 116 -28.62 -9.07 4.93e+00 1jj2L 194 -31.11 -8.97 5.29e+00 1aa0 113 -29.18 -8.92 5.48e+00 1pda 315 -30.83 -8.85 5.76e+00 1mmoB 384 -35.65 -8.76 6.11e+00 1mtyB 384 -35.65 -8.75 6.17e+00 1eyvA 156 -30.52 -8.63 6.68e+00 1g7jB 116 -28.62 -8.61 6.78e+00 1lvmA 229 -29.56 -8.50 7.30e+00 1fm4A 159 -31.25 -8.50 7.33e+00 1k38A 254 -35.79 -8.45 7.58e+00 1c1kA 217 -33.43 -8.43 7.65e+00 1bu7A 455 -36.18 -8.39 7.91e+00 2ms2A 129 -27.52 -8.31 8.37e+00 1htrB 329 -29.30 -8.25 8.68e+00 1vpsA 289 -29.82 -8.07 9.83e+00 1h3oB 76 -29.38 -8.01 1.03e+01 1cd9C 175 -32.94 -7.87 1.14e+01 1qgiA 259 -30.04 -7.80 1.19e+01 1phk 298 -30.73 -7.80 1.19e+01 1dypA 271 -30.70 -7.78 1.20e+01 1i5nA 146 -31.34 -7.78 1.21e+01 1lm8V 160 -30.07 -7.77 1.22e+01 1brwA 433 -30.80 -7.70 1.27e+01 1krhA 338 -29.94 -7.65 1.32e+01 1rcd 173 -34.74 -7.63 1.34e+01 1kqwA 134 -28.17 -7.57 1.40e+01 2bmhA 455 -35.54 -7.50 1.47e+01 1vcbC 160 -28.80 -7.41 1.57e+01 1c4kA 730 -31.98 -7.40 1.58e+01 1ordA 730 -32.17 -7.37 1.61e+01 1hwwA 1015 -34.47 -7.36 1.63e+01 1iknD 236 -29.53 -7.36 1.63e+01 1jb9A 316 -31.74 -7.32 1.67e+01 1ezfA 340 -31.32 -7.27 1.73e+01 1oebA 62 -24.54 -7.22 1.79e+01 1nekC 129 -29.14 -7.21 1.80e+01 1ir6A 424 -30.67 -7.18 1.85e+01 1fz1C 389 -34.12 -7.15 1.88e+01 8prkA 287 -29.28 -7.13 1.92e+01 1iapA 211 -29.33 -7.09 1.97e+01 1fm2A 169 -31.89 -7.09 1.97e+01 1jyhA 157 -26.85 -7.08 1.98e+01 1humA 69 -24.39 -7.07 2.00e+01 1es2A 262 -28.46 -7.06 2.01e+01 1qfhA 212 -29.36 -7.04 2.04e+01 1xnaA 183 -27.81 -7.01 2.08e+01 1ks8A 433 -35.36 -6.98 2.12e+01 1seiA 130 -28.91 -6.98 2.12e+01 1bea 127 -27.61 -6.97 2.14e+01 2abk 211 -29.10 -6.89 2.27e+01 1bfa 134 -27.75 -6.82 2.38e+01 1pnsB 234 -30.97 -6.80 2.41e+01 1l9mA 692 -32.58 -6.79 2.44e+01 1wwcA 118 -27.90 -6.66 2.68e+01 1lqbC 162 -29.55 -6.62 2.76e+01 1e9gA 286 -28.73 -6.58 2.84e+01 1qrdA 273 -29.82 -6.56 2.86e+01 1j5eB 256 -31.06 -6.56 2.88e+01 1ev0A 58 -25.28 -6.54 2.91e+01 1tafA 68 -25.89 -6.52 2.95e+01 1bs0A 384 -29.34 -6.50 3.00e+01 1bp3B 211 -28.44 -6.45 3.11e+01 1iu4A 331 -28.83 -6.39 3.24e+01 1hs6A 611 -31.63 -6.37 3.30e+01 1jl0A 334 -29.76 -6.32 3.40e+01 1es4A 262 -27.12 -6.31 3.43e+01 1b87A 181 -26.89 -6.31 3.43e+01 1n71A 180 -26.90 -6.29 3.48e+01 1llnA 262 -30.41 -6.27 3.55e+01 1mqkH 127 -25.00 -6.22 3.66e+01 1dseA 292 -30.53 -6.22 3.67e+01 1vpsB 289 -29.00 -6.21 3.71e+01 2hmx 133 -26.57 -6.20 3.71e+01 1jmxA 494 -32.04 -6.20 3.73e+01 1foeA 377 -30.39 -6.20 3.73e+01 1htyA 1015 -33.93 -6.20 3.73e+01 1hxkA 1015 -33.93 -6.20 3.74e+01 1g9mC 185 -27.09 -6.19 3.74e+01 1mntA 76 -25.55 -6.18 3.78e+01 1b7yB 785 -31.70 -6.18 3.78e+01 1jpnA 296 -29.84 -6.16 3.85e+01 1ls1A 295 -29.83 -6.11 3.97e+01 1es5A 262 -27.49 -6.11 3.99e+01