% 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. % --------------------------------------------------------------------- % dsspfoo.1.YGR235C.t2k-100-30-dssp-ebghstl Host: cc86 Tue Nov 12 18:51:06 2002 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR2/YGR235C % --------------------------------------------------------------------- % 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 ln(seq len) (adjust_score = 2) % Track 0 FIMs added (geometric mean of match probabilities (6)) % Track 0 Coeff 1.000 File YGR235C.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR235C.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 7323 sequences, 1713023 residues, 234 nodes, 156.97 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(=1.8058) * Reverse)^tau(=0.7702))) % 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 1iq0A 592 -36.85 -14.02 4.27e-02 1iwhB 146 -34.02 -13.08 8.03e-02 1jevA 517 -35.39 -12.37 1.29e-01 2olbA 517 -35.18 -12.23 1.42e-01 1jetA 517 -34.81 -11.84 1.87e-01 1sig 339 -34.56 -11.31 2.68e-01 1ass 159 -31.43 -10.17 6.01e-01 1fliA 98 -28.71 -9.87 7.43e-01 1asx 159 -30.46 -9.24 1.17e+00 1g0u1 266 -30.41 -8.37 2.22e+00 1jenA 267 -28.30 -7.91 3.13e+00 1dxtB 147 -30.06 -7.88 3.22e+00 1babB 146 -30.04 -7.87 3.23e+00 1ryp2 233 -29.66 -7.71 3.65e+00 1kl7A 514 -31.52 -7.64 3.86e+00 1cyo 93 -25.04 -7.34 4.85e+00 1gd5A 130 -27.35 -7.27 5.11e+00 1fhjB 146 -30.79 -7.04 6.08e+00 1irdB 146 -28.74 -6.99 6.36e+00 1im4A 221 -27.85 -6.87 6.99e+00 2ctb 307 -28.25 -6.81 7.31e+00 1mgtA 174 -28.14 -6.80 7.36e+00 1yme 309 -28.27 -6.80 7.37e+00 1jl0A 334 -27.69 -6.79 7.44e+00 1eupA 403 -32.77 -6.78 7.45e+00 1necA 216 -29.58 -6.70 7.97e+00 1spgB 147 -28.37 -6.56 8.89e+00 1j5eC 239 -27.17 -6.55 8.92e+00 1a6dA 545 -32.82 -6.52 9.14e+00 2ctc 307 -27.73 -6.44 9.75e+00 1hw5A 210 -27.06 -6.36 1.04e+01 1lucB 324 -27.89 -6.23 1.15e+01 1ajsA 412 -29.14 -6.20 1.18e+01 1fjgC 239 -26.61 -6.19 1.19e+01 1b0zA 445 -29.13 -6.17 1.21e+01 2pgi 445 -29.13 -6.17 1.21e+01 1dhs 344 -28.92 -6.09 1.29e+01 1brlB 324 -27.62 -6.07 1.31e+01 1i37A 260 -28.36 -6.04 1.35e+01 1ci9A 392 -28.08 -6.01 1.38e+01 1c7qA 445 -28.94 -6.00 1.38e+01 2spcA 107 -28.03 -5.96 1.43e+01 1aisB 200 -27.06 -5.96 1.44e+01 1cem 363 -28.39 -5.92 1.47e+01 1jkiA 533 -28.83 -5.90 1.50e+01 1kwfA 363 -28.45 -5.79 1.64e+01 1avaA 403 -27.73 -5.78 1.65e+01 1j54A 186 -26.18 -5.78 1.65e+01 1ez0A 510 -28.33 -5.77 1.67e+01 1amuA 563 -28.26 -5.76 1.68e+01 1ib8A 164 -25.24 -5.75 1.70e+01 1f6dA 376 -30.58 -5.69 1.78e+01 1hcnA 92 -23.41 -5.64 1.86e+01 1g8yA 279 -27.78 -5.62 1.88e+01 1dz7A 92 -23.37 -5.62 1.89e+01 1h3nA 878 -30.25 -5.57 1.97e+01 6cpa 307 -26.72 -5.56 1.98e+01 1ci8A 392 -27.50 -5.52 2.04e+01 1lqxA 82 -22.93 -5.50 2.07e+01 2at9 247 -27.08 -5.49 2.10e+01 1h5wA 309 -27.90 -5.46 2.15e+01 1jfuA 186 -24.76 -5.44 2.18e+01 1chuA 540 -29.91 -5.41 2.23e+01 1smd 496 -27.85 -5.36 2.33e+01 1a99A 344 -26.95 -5.33 2.39e+01 1hu4A 288 -27.54 -5.30 2.45e+01 1nksA 194 -25.12 -5.28 2.49e+01 1i3dA 146 -28.34 -5.28 2.50e+01 1b16A 254 -27.51 -5.27 2.51e+01 1ldjA 760 -31.88 -5.27 2.51e+01 1a4uA 254 -27.48 -5.26 2.53e+01 1jigA 146 -27.37 -5.25 2.55e+01 3pghA 587 -28.81 -5.24 2.58e+01 1lfpA 249 -26.75 -5.24 2.58e+01 1k8kA 418 -28.63 -5.23 2.60e+01 1eyyA 510 -27.77 -5.22 2.63e+01 1jqhA 308 -27.52 -5.20 2.66e+01 1pymA 295 -26.76 -5.19 2.69e+01 1udh 244 -26.47 -5.15 2.77e+01 1i0hA 205 -28.75 -5.15 2.77e+01 2cgpA 210 -25.59 -5.13 2.82e+01 1wdb 104 -23.93 -5.12 2.84e+01 1zid 268 -26.66 -5.11 2.88e+01 1im5A 180 -25.28 -5.08 2.94e+01 1csn 298 -27.63 -5.05 3.01e+01 1aep 161 -29.05 -5.04 3.03e+01 1udg 244 -26.31 -5.04 3.05e+01 1pbv 195 -28.55 -5.03 3.06e+01 1bob 320 -26.95 -5.02 3.09e+01 1ijgA 309 -28.53 -4.98 3.20e+01 1icrA 217 -27.19 -4.97 3.23e+01 1jkfA 533 -27.71 -4.95 3.29e+01 1cot 129 -24.11 -4.92 3.36e+01 1ceo 343 -26.74 -4.89 3.44e+01 1reqD 637 -28.66 -4.89 3.45e+01 1eny 268 -26.47 -4.85 3.56e+01 1oxa 403 -30.65 -4.85 3.57e+01 1amk 251 -27.64 -4.82 3.65e+01 1fm2A 169 -25.68 -4.81 3.69e+01 1bi0 226 -26.01 -4.80 3.71e+01 1g7dA 106 -27.07 -4.76 3.83e+01 1fqiA 147 -27.16 -4.75 3.86e+01 1pmi 440 -27.65 -4.72 3.98e+01 1sur 215 -26.09 -4.72 3.98e+01