% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 06/01/06_09:03:53 % (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.YGR017W.t2k-100-30-dssp-ehl2 Host: farm03-10.kilokluster.ucsc.edu Fri Oct 6 04:43:09 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR017W % --------------------------------------------------------------------- % 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 YGR017W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR017W.t2k.dssp-ehl2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 15583 sequences, 3659059 residues, 298 nodes, 456.82 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(=1.4046) * Reverse)^tau(=0.8151))) % 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 2i51A 195 -238.59 -226.01 3.23e-44 1t9mA 214 -80.33 -69.61 6.94e-15 1ty9A 222 -70.78 -60.19 7.49e-13 1nrgA 261 -64.85 -49.74 1.60e-10 1g79A 218 -55.97 -44.54 2.48e-09 1dnlA 199 -56.09 -44.34 2.76e-09 1ci0A 228 -50.71 -36.79 1.66e-07 2a2jA 246 -47.84 -36.32 2.15e-07 2i02A 148 -29.81 -19.34 4.29e-03 2aq6A 147 -26.27 -15.84 3.95e-02 1xxoA 147 -26.23 -15.77 4.12e-02 1w9aA 147 -26.19 -15.68 4.38e-02 1rfeA 162 -26.55 -14.69 8.33e-02 2fhqA 141 -24.36 -13.12 2.35e-01 1egxA 115 -23.54 -12.84 2.85e-01 2dafA 118 -23.02 -12.29 4.12e-01 2asfA 137 -23.18 -11.87 5.47e-01 1d8hA 311 -21.97 -11.27 8.21e-01 1e1hA 287 -23.89 -11.27 8.25e-01 2b25A 336 -22.62 -11.08 9.36e-01 1d8iA 311 -21.14 -10.52 1.39e+00 2hhzA 150 -21.92 -10.29 1.63e+00 1l7dA 384 -20.08 -9.69 2.48e+00 2iutA 574 -23.62 -9.62 2.60e+00 1ywnA 316 -21.90 -9.20 3.50e+00 1hfuA 503 -22.37 -9.19 3.53e+00 2ac1A 541 -23.39 -9.11 3.74e+00 1z9tA 255 -20.29 -9.09 3.78e+00 2g9zA 348 -21.30 -9.08 3.82e+00 1oflA 481 -24.51 -8.99 4.07e+00 1qawF 74 -20.20 -8.84 4.53e+00 1gtfA 74 -20.20 -8.84 4.53e+00 1iknA 286 -21.61 -8.74 4.88e+00 1vkxA 273 -20.76 -8.57 5.50e+00 2b5lC 222 -20.69 -8.57 5.52e+00 1a65A 504 -21.61 -8.49 5.84e+00 1mz5A 638 -23.33 -8.48 5.88e+00 1f8gA 384 -18.32 -8.44 6.04e+00 2extA 77 -19.98 -8.37 6.35e+00 1llwA 1520 -20.87 -8.35 6.47e+00 1duzA 275 -18.95 -8.31 6.66e+00 2av1A 275 -18.95 -8.25 6.93e+00 2av7A 275 -18.91 -8.25 6.94e+00 1wapA 75 -19.20 -8.19 7.26e+00 1tmcA 175 -18.49 -8.19 7.26e+00 1i4fA 275 -18.95 -8.10 7.73e+00 1n1tA 641 -22.90 -8.05 8.03e+00 1ej6D 418 -19.78 -8.04 8.11e+00 1m4uA 206 -20.64 -7.97 8.51e+00 1kjqA 391 -18.19 -7.79 9.74e+00 1eyzA 392 -18.57 -7.67 1.06e+01 1ez1A 392 -18.59 -7.65 1.07e+01 2fg9A 178 -17.87 -7.65 1.08e+01 1sacA 204 -19.26 -7.54 1.17e+01 1f6bA 198 -18.44 -7.46 1.24e+01 1dbgA 506 -22.73 -7.40 1.29e+01 1vqoE 178 -18.05 -7.37 1.32e+01 2htdA 140 -18.25 -7.33 1.36e+01 1cb8A 678 -20.16 -7.31 1.39e+01 1hm2A 700 -20.23 -7.28 1.41e+01 1a1nA 276 -18.01 -7.22 1.49e+01 1xh3A 276 -18.09 -7.21 1.49e+01 1i6pA 220 -18.22 -7.15 1.56e+01 1hsbA 270 -18.09 -7.13 1.58e+01 1b9kA 238 -17.55 -7.09 1.63e+01 1qtsA 247 -17.63 -7.06 1.67e+01 1gpmA 525 -18.13 -7.01 1.73e+01 1l1eA 287 -18.43 -6.99 1.76e+01 1k6wA 426 -18.11 -6.96 1.80e+01 1i7qA 519 -19.54 -6.91 1.88e+01 1jj2E 177 -17.61 -6.90 1.89e+01 2bvpA 276 -17.76 -6.87 1.93e+01 1kfuS 184 -17.79 -6.87 1.93e+01 1h6rA 236 -18.30 -6.86 1.94e+01 1pz7A 204 -17.69 -6.86 1.94e+01 1o65A 246 -18.49 -6.80 2.03e+01 2bi7A 384 -16.86 -6.79 2.05e+01 1ra0A 430 -18.14 -6.79 2.05e+01 1s72E 178 -17.55 -6.77 2.07e+01 1agdA 276 -17.83 -6.72 2.16e+01 1kyfA 247 -17.25 -6.72 2.16e+01 2gp5A 349 -17.85 -6.72 2.16e+01 1a81A 254 -18.41 -6.68 2.22e+01 1dyqA 234 -17.43 -6.66 2.25e+01 1mg2D 155 -19.23 -6.64 2.28e+01 1a9eA 277 -17.60 -6.64 2.28e+01 1sqnA 261 -16.62 -6.62 2.33e+01 1x1fA 149 -18.79 -6.62 2.33e+01 1waaA 93 -17.24 -6.61 2.33e+01 1v4sA 455 -17.57 -6.59 2.37e+01 1rewA 114 -16.27 -6.56 2.44e+01 1dykA 394 -19.44 -6.54 2.48e+01 3thiA 371 -18.24 -6.50 2.55e+01 1sr7A 259 -16.46 -6.50 2.55e+01 1w3oA 216 -16.87 -6.48 2.59e+01 1dboA 506 -21.25 -6.47 2.60e+01 1q67A 231 -22.62 -6.46 2.62e+01 2bfdA 400 -17.43 -6.44 2.66e+01 1a1mA 278 -17.55 -6.43 2.68e+01 1a1oA 276 -17.55 -6.43 2.69e+01 1k5nA 276 -17.43 -6.42 2.72e+01 7ahlA 293 -16.72 -6.33 2.90e+01 1hocA 272 -18.82 -6.33 2.91e+01 1mvcA 240 -16.30 -6.32 2.92e+01 1mznA 240 -16.19 -6.32 2.92e+01 2thiA 379 -18.71 -6.30 2.96e+01 1g5yA 238 -16.32 -6.28 3.01e+01 1esfA 233 -17.12 -6.28 3.02e+01 1ofdA 1520 -19.04 -6.27 3.04e+01 1b1xA 689 -17.54 -6.26 3.07e+01 1okgA 373 -17.74 -6.25 3.09e+01 1ffk1 177 -16.92 -6.20 3.20e+01 1a45 173 -17.70 -6.19 3.23e+01 1ecfA 504 -17.12 -6.19 3.23e+01 1x7yA 400 -17.32 -6.15 3.32e+01 1rp4A 389 -17.97 -6.13 3.38e+01 1if1A 113 -18.23 -6.12 3.40e+01 1jlnA 297 -17.02 -6.12 3.41e+01 1tqnA 486 -17.97 -6.10 3.46e+01 1qu0A 191 -18.51 -6.10 3.46e+01 2hq9A 149 -16.78 -6.09 3.47e+01 1evhA 112 -17.30 -6.09 3.47e+01 1o5uA 101 -16.88 -6.09 3.48e+01 1dkfA 233 -16.37 -6.09 3.49e+01 1z5bA 469 -18.62 -6.08 3.50e+01 1ecfB 504 -16.83 -6.01 3.71e+01 2clbA 188 -15.92 -6.00 3.75e+01 1a5dA 173 -16.47 -5.99 3.75e+01 1vjoA 393 -18.96 -5.99 3.77e+01 1vjpA 394 -17.30 -5.96 3.84e+01 1mlwA 301 -17.15 -5.93 3.93e+01 1ocvA 125 -15.31 -5.92 3.97e+01