% 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. % --------------------------------------------------------------------- % stridefoo.1.YGR007W.t2k-100-30-stride-ebghtl Host: cc61 Sat Oct 11 21:04:06 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR007W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds % % 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 YGR007W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR007W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 324 nodes, 305.93 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(=1.2458) * Reverse)^tau(=0.8162))) % 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 1cozA 129 -147.84 -125.24 1.34e-23 1od6A 160 -55.72 -35.15 2.61e-06 1mrzA 293 -65.30 -34.93 2.92e-06 1b6tA 159 -51.44 -31.23 1.95e-05 1qjcA 158 -51.09 -30.90 2.32e-05 1f9aA 168 -46.87 -23.21 1.40e-03 1ihoA 283 -46.96 -21.69 3.24e-03 1oi7A 288 -46.39 -19.79 9.33e-03 1mopA 300 -42.40 -18.93 1.52e-02 1n2eA 300 -42.40 -18.88 1.56e-02 1ej2A 181 -41.49 -17.72 3.04e-02 1k4mA 213 -40.33 -17.62 3.23e-02 3uagA 437 -42.91 -15.22 1.31e-01 1uag 437 -42.55 -14.68 1.80e-01 4uagA 437 -42.45 -14.68 1.81e-01 1gdhA 320 -40.32 -14.16 2.46e-01 2scuA 288 -43.43 -14.07 2.59e-01 1scuA 288 -43.61 -14.07 2.60e-01 1j1iA 296 -38.78 -12.86 5.40e-01 1k8wA 327 -38.94 -12.22 8.00e-01 1jbwA 428 -38.42 -12.11 8.55e-01 1fsz 372 -44.97 -11.78 1.05e+00 1kqnA 279 -35.71 -11.76 1.06e+00 1kkuA 279 -35.60 -11.76 1.07e+00 1f6dA 376 -37.87 -11.71 1.10e+00 1dvjA 246 -35.40 -11.17 1.54e+00 1j09A 468 -37.45 -11.12 1.59e+00 1dvjC 246 -35.31 -11.09 1.62e+00 1hybA 181 -34.90 -11.00 1.71e+00 1ecxA 384 -37.76 -10.96 1.75e+00 1km4A 247 -35.76 -10.83 1.90e+00 1fxjA 331 -36.64 -10.47 2.39e+00 1eg5A 384 -37.18 -10.40 2.50e+00 1h7eA 245 -33.90 -10.37 2.54e+00 1kamA 194 -34.92 -10.37 2.55e+00 1g59A 468 -36.47 -10.15 2.93e+00 1j6uA 469 -41.74 -10.12 2.99e+00 1fwyA 331 -36.43 -10.11 3.01e+00 1zid 268 -34.30 -10.10 3.03e+00 1k8eA 345 -37.41 -10.10 3.03e+00 1o17A 345 -37.41 -10.10 3.03e+00 1ez0A 510 -41.08 -10.00 3.23e+00 1eyyA 510 -40.98 -9.91 3.42e+00 1jjtA 228 -34.11 -9.84 3.56e+00 1eny 268 -34.14 -9.75 3.77e+00 1db3A 372 -35.92 -9.61 4.14e+00 1d9eA 284 -36.03 -9.56 4.27e+00 1gmlA 178 -32.70 -9.56 4.29e+00 1bykA 255 -33.16 -9.55 4.31e+00 1qdlB 195 -34.47 -9.48 4.51e+00 1cw0A 155 -34.08 -9.41 4.71e+00 1g5cA 170 -33.28 -9.32 5.00e+00 1gln 468 -35.48 -9.13 5.65e+00 1rboC 123 -29.73 -9.05 5.94e+00 8rucI 123 -29.61 -8.94 6.38e+00 1i39A 225 -33.10 -8.91 6.50e+00 1owxA 121 -31.67 -8.91 6.53e+00 1vsrA 136 -32.82 -8.90 6.56e+00 1g5pA 289 -36.03 -8.89 6.59e+00 1oatA 439 -40.78 -8.80 7.02e+00 1eo1A 124 -29.26 -8.76 7.19e+00 1f3aA 222 -31.59 -8.76 7.21e+00 1ig0A 319 -34.06 -8.68 7.56e+00 1o4vA 183 -32.70 -8.67 7.64e+00 1ycsB 239 -32.42 -8.64 7.79e+00 1j0aA 325 -38.14 -8.60 7.99e+00 1h3fA 432 -33.54 -8.57 8.14e+00 1j5sA 463 -37.83 -8.56 8.21e+00 1hjzA 192 -32.03 -8.52 8.41e+00 1hqcA 324 -31.11 -8.52 8.42e+00 1qs0B 338 -36.29 -8.49 8.57e+00 1f0jA 377 -31.91 -8.44 8.86e+00 1gr0A 367 -35.92 -8.40 9.12e+00 1uteA 313 -32.36 -8.34 9.47e+00 1o4sA 389 -38.04 -8.33 9.55e+00 1rlr 761 -47.92 -8.30 9.74e+00 1kanA 253 -36.13 -8.29 9.78e+00 1dd6A 228 -32.67 -8.22 1.03e+01 1fl9A 161 -30.83 -8.09 1.12e+01 2gar 212 -30.79 -8.07 1.14e+01 1e39A 571 -45.59 -8.06 1.14e+01 1m64A 571 -45.64 -8.05 1.15e+01 1mqsA 671 -45.11 -7.98 1.20e+01 1ma3A 253 -31.64 -7.94 1.24e+01 1rpxA 230 -34.58 -7.90 1.27e+01 1kgdA 180 -32.93 -7.89 1.28e+01 1fgs 428 -34.76 -7.89 1.28e+01 1hg3A 225 -33.34 -7.87 1.30e+01 2fokA 579 -43.31 -7.77 1.38e+01 1qfcA 306 -34.09 -7.74 1.42e+01 1nuuA 252 -31.70 -7.72 1.43e+01 1ajsA 412 -33.89 -7.72 1.43e+01 2cmd 312 -32.36 -7.68 1.47e+01 1k8kF 168 -29.58 -7.67 1.48e+01 1k77A 260 -30.37 -7.66 1.49e+01 1nqzA 194 -29.42 -7.57 1.58e+01 1k5hA 398 -32.49 -7.56 1.59e+01 1iqrA 420 -31.91 -7.53 1.63e+01 1n2zA 245 -30.53 -7.53 1.63e+01 1poiA 317 -35.27 -7.52 1.64e+01 1a5t 334 -29.95 -7.49 1.67e+01 1cz3A 168 -29.74 -7.48 1.68e+01 1o1yA 239 -32.72 -7.44 1.72e+01 1fp6A 289 -34.70 -7.44 1.73e+01 1qjdA 571 -44.90 -7.43 1.74e+01 1ixkA 315 -34.41 -7.42 1.75e+01 1lj1A 571 -45.09 -7.41 1.77e+01 1ki1B 352 -36.79 -7.40 1.78e+01 1fnnA 389 -35.77 -7.39 1.78e+01 1jp3A 253 -30.17 -7.38 1.79e+01 1a2zA 220 -30.22 -7.37 1.81e+01 1p3wA 404 -36.39 -7.37 1.81e+01 2oatA 439 -39.08 -7.36 1.82e+01 1n08A 163 -30.85 -7.34 1.85e+01 1h5yA 253 -34.90 -7.34 1.85e+01 1nb9A 147 -28.71 -7.29 1.91e+01 1garA 212 -29.97 -7.27 1.94e+01 1pujA 282 -33.76 -7.24 1.98e+01 1kssA 571 -44.80 -7.21 2.02e+01 1byrA 155 -28.54 -7.20 2.03e+01 1i8tA 367 -37.33 -7.18 2.05e+01 1h5qA 265 -30.26 -7.17 2.08e+01 1n40A 396 -34.11 -7.17 2.08e+01 1tig 94 -26.63 -7.16 2.09e+01 1mldA 314 -31.90 -7.15 2.10e+01 1gdtA 183 -31.12 -7.11 2.16e+01 1i6uA 130 -28.54 -7.10 2.17e+01 3pmgA 561 -46.90 -7.07 2.21e+01 1b7fA 168 -30.29 -7.05 2.24e+01 1nipA 289 -34.21 -7.05 2.26e+01 1m2xA 223 -33.07 -7.04 2.27e+01 1i3kA 348 -36.95 -7.03 2.28e+01 1k07A 263 -32.15 -7.02 2.29e+01 1uehA 253 -30.10 -7.02 2.30e+01 1f6kA 293 -34.34 -7.00 2.32e+01 1jr3E 334 -29.27 -6.99 2.34e+01 1edzA 320 -35.29 -6.98 2.36e+01 1iu8A 206 -31.62 -6.91 2.48e+01 1d1gA 168 -29.39 -6.89 2.52e+01 1kdgA 546 -43.06 -6.88 2.52e+01 1efdN 266 -32.09 -6.88 2.53e+01 1gnwA 211 -29.68 -6.83 2.61e+01 1augA 215 -32.77 -6.83 2.62e+01 1taq 832 -38.55 -6.81 2.64e+01 1kewA 361 -34.19 -6.81 2.65e+01 1gpmA 525 -42.44 -6.80 2.67e+01 1jvsA 400 -31.65 -6.79 2.68e+01 1k7yA 577 -37.85 -6.79 2.68e+01 1pgvA 197 -28.86 -6.77 2.72e+01 1k92A 455 -36.15 -6.77 2.72e+01 1itxA 419 -38.86 -6.75 2.76e+01 1qlzA 210 -30.02 -6.75 2.77e+01 1ek6A 348 -36.15 -6.71 2.84e+01 1fokA 568 -43.62 -6.68 2.90e+01 1knyA 253 -32.83 -6.67 2.91e+01 1qhsA 178 -29.49 -6.66 2.93e+01 1f89A 291 -33.13 -6.65 2.95e+01 1g6hA 257 -32.72 -6.65 2.95e+01 1ghj 79 -27.19 -6.62 3.01e+01 1hm2A 700 -40.66 -6.62 3.01e+01 1jg8A 347 -32.74 -6.61 3.04e+01 1m6sA 347 -32.74 -6.61 3.04e+01 1ko3A 230 -31.32 -6.59 3.07e+01 3adk 195 -30.14 -6.58 3.10e+01 1qklA 127 -26.87 -6.57 3.12e+01 1e69B 322 -35.08 -6.55 3.17e+01 1qhxA 178 -29.48 -6.54 3.18e+01 1jr3A 373 -29.83 -6.54 3.20e+01 1jpmA 366 -31.73 -6.53 3.20e+01 1ee9A 320 -35.33 -6.52 3.22e+01 2aacA 177 -29.66 -6.51 3.25e+01 2tmkA 216 -30.03 -6.51 3.25e+01 1tyfA 193 -28.28 -6.49 3.29e+01 1gp1A 198 -29.82 -6.48 3.32e+01 1aym3 238 -29.01 -6.48 3.33e+01 1c0nA 406 -32.70 -6.47 3.35e+01 1eemA 241 -31.14 -6.46 3.37e+01 1psdA 409 -36.49 -6.45 3.39e+01 2arcB 164 -29.25 -6.41 3.49e+01 1k0nA 241 -28.68 -6.40 3.50e+01 1cl2A 395 -33.65 -6.39 3.53e+01 1brwA 433 -33.40 -6.38 3.56e+01 1f74A 293 -33.84 -6.37 3.57e+01 1jc7A 131 -27.75 -6.36 3.60e+01 1dmr 823 -51.42 -6.35 3.63e+01 1io2A 213 -30.00 -6.35 3.65e+01 1ofuA 320 -33.19 -6.34 3.66e+01 1lxtA 561 -46.36 -6.34 3.67e+01 1nsj 205 -29.77 -6.33 3.69e+01 1cb8A 678 -40.08 -6.31 3.73e+01 1dc1A 323 -32.95 -6.28 3.82e+01 1nnwA 252 -33.97 -6.27 3.83e+01 1sxl 97 -27.20 -6.25 3.89e+01 2cbf 234 -31.53 -6.24 3.91e+01 1hyeA 313 -34.72 -6.24 3.93e+01 3tmkA 216 -30.29 -6.23 3.95e+01 1a8q 274 -33.55 -6.22 3.98e+01