% SAM: /projects/compbio/bin/i686/hmmscore v3.3.2 (February, 2001) compiled 06/24/02_10:50:12 % (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-T99, 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, C. Barrett, R. Hughey, Hidden Markov models for detecting % remote protein homologies, Bioinformatics 14(10):846-856, 1998. % A. Krogh et al., Hidden Markov models in computational biology: % Applications to protein modeling, JMB 235:1501-1531, Feb 1994. % --------------------------------------------------------------------- % strfoo.1.YGR017W.t2k-100-30-str Host: cc71 Fri Nov 8 17:17:36 2002 % 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.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 YGR017W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR017W.t2k.str.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7310 sequences, 1706072 residues, 298 nodes, 202.96 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 (=7316) sequences: % N / (1 + exp(-(lambda(=1.3648) * Reverse)^tau(=0.8249))) % 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 1g79A 218 -72.56 -50.06 5.06e-11 1dnlA 199 -72.40 -49.86 5.61e-11 1ci0A 228 -63.84 -39.51 1.64e-08 1egxA 115 -37.37 -17.23 9.77e-03 1d8iA 311 -33.82 -11.13 5.86e-01 1d8hA 311 -33.41 -10.86 7.07e-01 1a65A 504 -37.60 -10.37 9.97e-01 2ucz 165 -31.95 -10.03 1.27e+00 1f8gA 384 -31.30 -9.83 1.46e+00 1i7qA 519 -33.81 -9.70 1.61e+00 1aol 228 -32.84 -9.69 1.62e+00 1hfuA 503 -36.70 -9.68 1.63e+00 1k6wA 426 -31.89 -9.32 2.11e+00 1gtfA 74 -29.46 -9.12 2.44e+00 1pysA 350 -32.64 -9.07 2.53e+00 1qawF 74 -29.36 -9.04 2.59e+00 1jbbA 153 -30.38 -8.97 2.73e+00 1jatA 155 -30.07 -8.91 2.84e+00 1evhA 112 -29.78 -8.76 3.16e+00 3thiA 371 -31.09 -8.49 3.86e+00 1b7yA 350 -32.25 -8.42 4.06e+00 2thiA 379 -31.53 -8.05 5.34e+00 1wapA 75 -27.92 -8.01 5.50e+00 1tmcA 175 -28.19 -7.72 6.84e+00 1gv4A 528 -31.94 -7.67 7.08e+00 1fl0A 171 -29.47 -7.50 8.06e+00 1qfoA 119 -28.20 -7.40 8.64e+00 1gbg 214 -28.78 -7.37 8.87e+00 1i4fA 275 -29.73 -7.36 8.93e+00 1duzA 275 -29.73 -7.32 9.20e+00 1ksgB 152 -28.08 -7.32 9.21e+00 1g9mG 321 -30.48 -7.31 9.25e+00 1qtsA 247 -29.60 -7.28 9.47e+00 1b9kA 238 -29.05 -7.27 9.55e+00 1f6bA 198 -28.33 -7.25 9.73e+00 1kshB 152 -27.49 -7.24 9.81e+00 2mtaC 147 -28.50 -7.23 9.82e+00 2prd 174 -29.56 -7.14 1.05e+01 1kyfA 247 -29.38 -7.13 1.06e+01 1e8nA 710 -35.20 -7.12 1.07e+01 1pnkB 557 -31.25 -7.11 1.08e+01 1ajqB 557 -31.20 -7.10 1.09e+01 1e3aB 560 -31.17 -7.06 1.12e+01 1b0uA 262 -27.67 -7.03 1.14e+01 1gm7B 557 -31.08 -7.01 1.16e+01 1gkfB 557 -31.07 -6.97 1.20e+01 1jhnA 424 -40.54 -6.96 1.21e+01 1gm9B 557 -31.06 -6.95 1.21e+01 1gk9B 557 -31.03 -6.93 1.23e+01 1l1eA 287 -29.29 -6.93 1.23e+01 1j8uA 325 -29.57 -6.76 1.40e+01 1pah 308 -28.92 -6.75 1.42e+01 1ds1A 324 -29.60 -6.71 1.46e+01 1if1A 113 -27.25 -6.71 1.46e+01 1kyaA 499 -34.03 -6.65 1.53e+01 1gywA 128 -27.76 -6.64 1.54e+01 1qu0A 191 -29.69 -6.63 1.55e+01 7ceiB 206 -32.18 -6.56 1.64e+01 1eujA 166 -28.56 -6.56 1.64e+01 1jb7A 495 -30.75 -6.50 1.71e+01 1dmtA 696 -30.16 -6.48 1.74e+01 1tbgA 340 -30.25 -6.47 1.76e+01 7ahlA 293 -28.68 -6.44 1.79e+01 1fl9A 161 -27.54 -6.43 1.81e+01 1kq1A 77 -24.79 -6.42 1.83e+01 1dmwA 307 -28.47 -6.36 1.91e+01 1jdc 429 -33.03 -6.35 1.93e+01 1hsbA 270 -28.67 -6.35 1.93e+01 1qrjB 199 -27.17 -6.34 1.94e+01 4pah 308 -28.46 -6.28 2.03e+01 1iknA 286 -30.51 -6.28 2.03e+01 1e7uA 961 -33.60 -6.24 2.10e+01 1qfoC 119 -27.25 -6.19 2.17e+01 1bunB 61 -25.44 -6.12 2.30e+01 1gkpA 458 -31.16 -6.12 2.30e+01 1k8kA 418 -28.42 -6.10 2.34e+01 2bbkL 125 -28.08 -6.07 2.39e+01 1llwA 1520 -32.72 -6.03 2.47e+01 1dykA 394 -30.93 -6.01 2.50e+01 1gcyA 527 -33.63 -5.97 2.57e+01 1htwA 158 -26.42 -5.95 2.62e+01 1otcA 495 -30.85 -5.93 2.66e+01 1fn9A 365 -29.47 -5.92 2.68e+01 1jlnA 297 -29.57 -5.92 2.68e+01 1b3qA 379 -28.80 -5.88 2.76e+01 1sacA 204 -28.76 -5.85 2.84e+01 1gotB 340 -29.94 -5.85 2.84e+01 1b9wA 89 -25.52 -5.79 2.96e+01 1bu6O 501 -28.68 -5.79 2.96e+01 1jj7A 260 -28.21 -5.79 2.97e+01 1a81A 254 -28.32 -5.74 3.09e+01 1glcG 501 -28.75 -5.73 3.10e+01 1toh 343 -30.01 -5.71 3.17e+01 1qfmA 710 -33.77 -5.68 3.23e+01 1jj2E 177 -26.63 -5.66 3.29e+01 1jqgA 433 -28.49 -5.66 3.29e+01 1vkxA 273 -29.21 -5.65 3.32e+01 1ef8A 261 -27.53 -5.59 3.46e+01 1ndh 272 -30.98 -5.56 3.56e+01 2arcA 164 -26.97 -5.53 3.65e+01 1dyqA 234 -28.38 -5.52 3.66e+01 1kluD 239 -28.33 -5.52 3.66e+01 1e5uI 187 -25.59 -5.52 3.67e+01 1j7dA 145 -28.40 -5.50 3.73e+01 1fts 295 -27.47 -5.47 3.82e+01 1kopA 223 -28.65 -5.45 3.87e+01 2arcB 164 -26.88 -5.45 3.88e+01 1h3nA 878 -30.94 -5.45 3.88e+01 2aaiB 262 -28.69 -5.44 3.90e+01