% 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. % --------------------------------------------------------------------- % str2foo.1.YGR029W.t2k-100-30-str2 Host: cc57 Sat Oct 11 21:22:52 2003 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR029W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.str2s % % 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 YGR029W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR029W.t2k.str2.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 190 nodes, 179.42 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(=2.5516) * Reverse)^tau(=0.7195))) % 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 1oqcA 125 -159.01 -134.46 8.60e-26 1jraA 117 -136.78 -115.77 7.81e-23 1jr8A 117 -136.57 -115.38 9.05e-23 1eyvA 156 -32.77 -13.93 1.74e-02 1ku1A 230 -34.09 -13.43 2.45e-02 1euvA 221 -33.69 -13.13 3.01e-02 1dgjA 907 -36.22 -11.98 6.70e-02 1p8cA 145 -30.23 -10.01 2.76e-01 1iwhA 141 -28.50 -9.68 3.54e-01 1ngkA 128 -29.00 -9.36 4.49e-01 1hlrA 907 -33.45 -9.31 4.66e-01 1jjfA 268 -28.77 -8.19 1.11e+00 1cc8A 73 -24.44 -8.02 1.26e+00 1fd8A 73 -24.67 -7.95 1.33e+00 1irdA 141 -26.63 -7.78 1.52e+00 1mlwA 301 -28.77 -7.52 1.88e+00 1agi 125 -25.82 -7.51 1.89e+00 1j7yA 141 -26.34 -7.49 1.93e+00 1abwA 283 -27.83 -7.48 1.93e+00 1babA 143 -26.34 -7.47 1.95e+00 2abk 211 -27.98 -7.43 2.01e+00 1fxxA 482 -29.22 -7.26 2.31e+00 1je8A 82 -24.92 -7.24 2.34e+00 1ciy 590 -31.31 -7.03 2.79e+00 1g4yR 148 -26.34 -6.88 3.15e+00 1q8cA 151 -26.35 -6.83 3.28e+00 1okgA 373 -28.03 -6.77 3.44e+00 1iweA 457 -28.25 -6.73 3.57e+00 1m6bA 621 -31.28 -6.64 3.84e+00 1g8lA 411 -27.37 -6.58 4.05e+00 1mhqA 148 -28.53 -6.54 4.16e+00 1h2wA 710 -28.84 -6.45 4.51e+00 1e8nA 710 -28.83 -6.44 4.53e+00 1qfmA 710 -28.83 -6.43 4.59e+00 1h2xA 710 -28.84 -6.42 4.60e+00 1hyvA 166 -24.87 -6.08 6.13e+00 4rnpA 883 -30.27 -6.01 6.52e+00 1b9dA 163 -24.86 -6.01 6.54e+00 1o6eA 235 -25.88 -5.95 6.85e+00 1ljrA 244 -27.62 -5.88 7.29e+00 1nn7A 105 -24.65 -5.86 7.44e+00 1a32 88 -23.65 -5.85 7.50e+00 1b9xB 68 -23.06 -5.76 8.07e+00 1iapA 211 -25.47 -5.76 8.07e+00 1b75A 94 -23.50 -5.73 8.29e+00 1ysc 421 -27.43 -5.70 8.48e+00 1myf 153 -25.33 -5.68 8.67e+00 1ko9A 345 -28.03 -5.67 8.74e+00 1dwtA 153 -24.92 -5.66 8.84e+00 1jwgA 147 -25.04 -5.63 9.02e+00 1pyp 285 -29.18 -5.63 9.04e+00 1gjnA 153 -24.84 -5.61 9.20e+00 1guzA 310 -26.38 -5.58 9.48e+00 1iu8A 206 -25.27 -5.50 1.01e+01 1ebmA 317 -27.63 -5.46 1.05e+01 1bl3A 160 -24.17 -5.44 1.07e+01 1jwwA 80 -22.50 -5.43 1.08e+01 1ngvA 534 -28.01 -5.42 1.08e+01 1bev1 281 -26.45 -5.42 1.09e+01 1gotG 73 -22.78 -5.41 1.10e+01 1ha2A 585 -28.81 -5.41 1.10e+01 1toh 343 -26.39 -5.40 1.11e+01 1pbwA 216 -26.18 -5.40 1.11e+01 2hpaA 342 -26.58 -5.39 1.11e+01 1itg 166 -24.60 -5.38 1.13e+01 1lwyA 324 -27.72 -5.37 1.14e+01 1gg3A 279 -27.73 -5.36 1.15e+01 1ky9A 448 -27.46 -5.35 1.15e+01 4enl 436 -27.21 -5.35 1.16e+01 1bg0 356 -26.64 -5.29 1.22e+01 1a04A 215 -25.78 -5.29 1.22e+01 1tbgE 68 -22.51 -5.25 1.26e+01 1cg5B 141 -24.12 -5.24 1.27e+01 1avmA 201 -25.24 -5.23 1.29e+01 1qsdA 106 -24.03 -5.21 1.30e+01 1ixh 321 -26.56 -5.18 1.34e+01 1itf 165 -25.47 -5.16 1.36e+01 1dgmA 363 -25.41 -5.15 1.39e+01 1m15A 357 -26.58 -5.12 1.42e+01 1bsmA 201 -25.11 -5.11 1.43e+01 1aw0 72 -21.55 -5.10 1.45e+01 1dw9A 156 -24.35 -5.08 1.47e+01 1hyeA 313 -25.45 -5.07 1.48e+01 3kvt 115 -23.15 -5.04 1.53e+01 1dwkA 156 -24.17 -4.98 1.60e+01 1f6fA 199 -26.28 -4.94 1.66e+01 1f7tA 122 -23.24 -4.91 1.72e+01 1g8iA 190 -25.04 -4.86 1.79e+01 1cjwA 166 -24.29 -4.86 1.79e+01 1kgnA 329 -26.29 -4.83 1.83e+01 1aol 228 -27.52 -4.83 1.84e+01 1jenB 67 -22.13 -4.82 1.86e+01 1rpa 342 -26.17 -4.82 1.86e+01 1esxA 96 -24.50 -4.80 1.88e+01 1bj5 585 -28.32 -4.79 1.91e+01 1bbhA 131 -24.92 -4.76 1.96e+01 1mgn 154 -24.43 -4.75 1.99e+01 1ejjA 511 -26.88 -4.74 1.99e+01 1qhtA 775 -27.63 -4.74 2.00e+01 1kyoD 248 -27.16 -4.73 2.02e+01 1eqjA 511 -26.69 -4.72 2.03e+01 1gio 125 -22.97 -4.70 2.07e+01 1o98A 511 -26.76 -4.70 2.07e+01 5pal 109 -23.65 -4.70 2.08e+01 1sw6A 327 -26.06 -4.69 2.08e+01 1emvB 134 -24.22 -4.66 2.14e+01 1fr2B 134 -24.21 -4.64 2.20e+01 3cln 148 -24.00 -4.63 2.21e+01 1exqA 154 -24.45 -4.62 2.22e+01 1lis 136 -24.53 -4.62 2.23e+01 2lisA 136 -24.53 -4.62 2.23e+01 1ezvD 245 -27.13 -4.60 2.26e+01 1fe0A 68 -21.12 -4.56 2.36e+01 1dceA 567 -28.26 -4.55 2.36e+01 1g03A 134 -23.71 -4.53 2.42e+01 1pov1 302 -26.02 -4.52 2.45e+01 1jvr 137 -30.71 -4.51 2.46e+01 1bxiB 134 -23.87 -4.49 2.51e+01 1kw4A 89 -22.78 -4.49 2.52e+01 1oyzA 280 -25.65 -4.48 2.53e+01 1jfvA 131 -23.61 -4.48 2.54e+01 2spo 154 -24.13 -4.47 2.55e+01 1f3vA 179 -23.65 -4.46 2.58e+01 1n9bA 265 -25.12 -4.45 2.60e+01 1hxs1 302 -26.31 -4.40 2.73e+01 2oneA 436 -26.23 -4.40 2.74e+01 1kb9D 246 -27.13 -4.39 2.75e+01 1jtkA 136 -22.48 -4.38 2.77e+01 1be3D 241 -27.00 -4.37 2.81e+01 1j77A 209 -25.64 -4.36 2.82e+01 1pnkA 209 -24.14 -4.36 2.84e+01 4rxn 54 -24.90 -4.36 2.84e+01 1if1A 113 -23.71 -4.34 2.89e+01 1hqvA 191 -25.44 -4.31 2.97e+01 1mbd 153 -23.93 -4.30 3.00e+01 1h1oA 183 -24.93 -4.29 3.03e+01 1mg7A 417 -25.85 -4.29 3.03e+01 1ystH 260 -27.85 -4.28 3.04e+01 1kuxA 207 -24.14 -4.28 3.04e+01 1j5rA 371 -25.74 -4.28 3.05e+01 1ez3A 127 -23.39 -4.28 3.07e+01 1n5uA 585 -27.79 -4.27 3.08e+01 1o2dA 371 -25.75 -4.27 3.08e+01 1gzsB 165 -23.26 -4.26 3.11e+01 1tgoA 773 -27.08 -4.22 3.23e+01 1dszA 86 -23.06 -4.21 3.26e+01 1ai7A 209 -23.98 -4.19 3.32e+01 1a4uA 254 -24.12 -4.19 3.32e+01 1hzfA 367 -26.37 -4.18 3.34e+01 1b16A 254 -24.11 -4.16 3.43e+01 1iro 54 -24.44 -4.15 3.45e+01 1ajqA 209 -23.91 -4.14 3.48e+01 1k59A 123 -23.41 -4.14 3.49e+01 2occM 46 -21.24 -4.13 3.52e+01 1pn1A 176 -24.44 -4.13 3.52e+01 1oaa 259 -23.80 -4.12 3.56e+01 1a4yB 123 -23.93 -4.11 3.56e+01 1sep 261 -23.81 -4.11 3.57e+01 1oxjA 173 -24.94 -4.08 3.68e+01 1oneA 436 -25.82 -4.05 3.80e+01 1irk 306 -24.78 -4.04 3.82e+01 3lynA 136 -25.21 -4.02 3.88e+01 1nrvA 105 -21.76 -4.02 3.91e+01 1jroB 777 -29.85 -4.01 3.93e+01 1jhnA 424 -28.93 -4.01 3.95e+01 1gc5A 467 -25.26 -4.00 3.99e+01