% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (May 1, 2004) compiled 08/09/04_15:52:12 % (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-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. % --------------------------------------------------------------------- % dsspfoo.1.YGR213C.t2k-100-30-dssp-ebghstl Host: farm01 Wed Dec 1 18:30:40 2004 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR213C % --------------------------------------------------------------------- % 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 YGR213C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR213C.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 10944 sequences, 2597075 residues, 318 nodes, 340.09 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 (=10700) sequences: % N / (1 + exp(-(lambda(=2.2630) * Reverse)^tau(=0.7290))) % 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 1tlqA 189 -24.37 -12.02 1.59e-01 1jalA 363 -21.90 -10.24 5.42e-01 1fqyA 269 -25.93 -9.85 7.16e-01 6prcH 258 -21.77 -9.17 1.17e+00 1dxrH 258 -21.74 -9.12 1.21e+00 1jb0A 755 -31.13 -9.11 1.22e+00 1dofA 403 -24.84 -8.92 1.40e+00 1t7rA 269 -21.10 -8.39 2.07e+00 1i37A 260 -21.08 -8.22 2.35e+00 1gkmA 509 -22.01 -8.19 2.40e+00 1fc6A 388 -17.94 -7.94 2.90e+00 1qlaC 256 -27.93 -7.62 3.69e+00 1v54A 514 -31.23 -7.45 4.19e+00 1j4nA 271 -29.04 -7.45 4.21e+00 1b8fA 509 -21.27 -7.39 4.41e+00 1oshA 232 -20.78 -7.31 4.70e+00 1dl5A 317 -17.15 -7.29 4.76e+00 1ih7A 903 -20.27 -6.94 6.25e+00 1ks9A 291 -19.25 -6.90 6.42e+00 1ldfA 281 -26.48 -6.88 6.54e+00 1p8cA 145 -17.42 -6.53 8.59e+00 1fx8A 281 -26.06 -6.44 9.25e+00 1eia 207 -19.21 -6.41 9.48e+00 1fcyA 236 -21.55 -6.38 9.68e+00 2lbd 267 -21.77 -6.36 9.86e+00 1hw1A 239 -19.65 -6.34 1.00e+01 1rzhL 281 -24.50 -6.30 1.03e+01 4lbd 267 -21.65 -6.30 1.04e+01 1be3C 379 -29.20 -6.29 1.04e+01 1vkeA 133 -17.31 -6.27 1.06e+01 1dxrM 323 -21.98 -6.22 1.11e+01 1lw3A 657 -18.64 -6.21 1.11e+01 2occA 514 -29.41 -6.19 1.13e+01 1f1oA 431 -20.24 -6.18 1.14e+01 1rcuA 195 -17.01 -6.18 1.14e+01 1oa4A 222 -15.46 -6.16 1.16e+01 1e2xA 243 -19.05 -6.10 1.21e+01 1noyA 388 -19.50 -6.07 1.25e+01 1vns 609 -20.66 -5.99 1.33e+01 1mjgM 729 -19.84 -5.97 1.35e+01 1ass 159 -15.57 -5.96 1.36e+01 1rzhM 307 -25.94 -5.92 1.40e+01 2sfa 191 -15.33 -5.92 1.41e+01 6prcM 323 -21.82 -5.90 1.43e+01 1jffA 451 -17.15 -5.90 1.44e+01 1rfzA 168 -17.78 -5.84 1.51e+01 1upvA 257 -21.64 -5.82 1.53e+01 1vnc 609 -20.71 -5.81 1.54e+01 1eagA 342 -15.29 -5.81 1.55e+01 1d2kA 392 -17.74 -5.76 1.61e+01 1m0uA 249 -17.99 -5.72 1.66e+01 2eiaB 206 -17.78 -5.70 1.68e+01 1pdz 434 -19.09 -5.70 1.69e+01 1oaoC 729 -19.47 -5.67 1.73e+01 1g8iA 190 -19.23 -5.62 1.80e+01 1vmgA 95 -18.81 -5.62 1.81e+01 1bcfA 158 -20.88 -5.58 1.86e+01 1fp1D 372 -17.38 -5.56 1.90e+01 1tk1A 260 -18.82 -5.53 1.94e+01 1clqA 903 -18.74 -5.53 1.95e+01 1eysH 259 -18.67 -5.52 1.96e+01 1dt6A 473 -18.87 -5.51 1.97e+01 2hmx 133 -18.65 -5.48 2.03e+01 1kwsA 261 -14.97 -5.42 2.13e+01 1asx 159 -14.66 -5.39 2.18e+01 1fggA 261 -14.97 -5.38 2.20e+01 1aijL 281 -24.76 -5.35 2.25e+01 1pq9A 253 -22.68 -5.33 2.30e+01 1v8bA 479 -18.42 -5.28 2.40e+01 1rifA 282 -15.52 -5.23 2.50e+01 1ghpA 258 -16.25 -5.23 2.50e+01 4tmkA 213 -15.98 -5.17 2.62e+01 1swxA 209 -19.89 -5.16 2.65e+01 1ll7A 392 -16.87 -5.14 2.70e+01 1v7zA 260 -17.99 -5.12 2.73e+01 1jpzA 473 -20.58 -5.09 2.82e+01 1ithA 141 -17.19 -5.06 2.89e+01 1a8h 500 -16.79 -4.97 3.12e+01 1nozA 388 -17.93 -4.96 3.14e+01 1nyhA 166 -19.44 -4.89 3.32e+01 1cqxA 403 -18.16 -4.84 3.48e+01 1pjcA 361 -16.71 -4.84 3.48e+01 1sayA 361 -16.69 -4.84 3.49e+01 1dbhA 354 -16.96 -4.81 3.56e+01 1l58 164 -15.58 -4.81 3.56e+01 1pjbA 361 -16.64 -4.81 3.57e+01 1ukvG 453 -16.81 -4.77 3.69e+01 1iomA 377 -18.08 -4.76 3.72e+01 1ufzA 83 -14.66 -4.75 3.75e+01 1w36C 1122 -17.55 -4.75 3.76e+01 1gtrA 553 -15.52 -4.71 3.90e+01 1pl5A 142 -19.62 -4.69 3.96e+01