% 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. % --------------------------------------------------------------------- % dsspfoo.1.YGR029W.t2k-100-30-dssp-ebghstl Host: cc57 Sat Oct 11 21:28:54 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.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 YGR029W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR029W.t2k.dssp-ebghstl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 8763 sequences, 2072585 residues, 190 nodes, 179.82 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 (0.00) % E-value on N (=8162) sequences: % N / (1 + exp(-(lambda(=2.5980) * Reverse)^tau(=0.7063))) % 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 -161.84 -137.52 2.02e-24 1jraA 117 -139.29 -117.60 1.56e-21 1jr8A 117 -138.50 -116.64 2.16e-21 1euvA 221 -33.13 -12.64 6.28e-02 1eyvA 156 -30.14 -10.88 2.05e-01 1ku1A 230 -31.15 -10.86 2.07e-01 1p8cA 145 -30.35 -10.45 2.76e-01 1dgjA 907 -33.35 -9.43 5.65e-01 1jvr 137 -32.79 -9.33 6.09e-01 4enl 436 -30.47 -8.67 9.79e-01 1ciy 590 -31.37 -8.35 1.25e+00 1bev1 281 -28.87 -7.93 1.71e+00 1g4yR 148 -26.62 -7.75 1.95e+00 1je8A 82 -25.31 -7.63 2.14e+00 1ngkA 128 -27.14 -7.63 2.15e+00 1iwhA 141 -26.24 -7.54 2.29e+00 1cc8A 73 -23.77 -7.51 2.36e+00 1oneA 436 -28.89 -7.17 3.04e+00 1a32 88 -24.88 -7.16 3.08e+00 1q8cA 151 -26.60 -7.09 3.25e+00 2abk 211 -27.35 -7.02 3.42e+00 1fxxA 482 -28.93 -6.92 3.71e+00 1fd8A 73 -23.32 -6.82 4.00e+00 2oneA 436 -28.60 -6.81 4.05e+00 1pbwA 216 -27.27 -6.78 4.14e+00 1agi 125 -24.96 -6.74 4.28e+00 1ky9A 448 -28.73 -6.73 4.30e+00 1hlrA 907 -30.57 -6.71 4.36e+00 1o6eA 235 -26.48 -6.59 4.81e+00 1gg3A 279 -27.79 -6.48 5.25e+00 1mlwA 301 -27.64 -6.32 5.96e+00 1m6bA 621 -31.72 -6.26 6.26e+00 1guzA 310 -27.00 -6.23 6.45e+00 1okgA 373 -27.49 -6.17 6.76e+00 1o98A 511 -28.30 -6.14 6.93e+00 1eqjA 511 -28.14 -6.06 7.37e+00 1jjfA 268 -26.86 -6.06 7.38e+00 1hxs1 302 -27.94 -6.05 7.44e+00 1ejjA 511 -28.17 -5.98 7.86e+00 1pov1 302 -27.69 -5.98 7.91e+00 1hyvA 166 -24.55 -5.91 8.33e+00 1b9dA 163 -24.51 -5.86 8.71e+00 1pyp 285 -29.86 -5.84 8.81e+00 1a04A 215 -26.00 -5.83 8.89e+00 1jenB 67 -23.23 -5.83 8.94e+00 1jroB 777 -31.01 -5.74 9.61e+00 1hyeA 313 -26.14 -5.68 1.01e+01 1eyeA 280 -25.59 -5.62 1.06e+01 1kgnA 329 -26.60 -5.61 1.07e+01 1jwwA 80 -22.51 -5.59 1.09e+01 1bg0 356 -27.17 -5.57 1.10e+01 1fua 215 -26.12 -5.54 1.14e+01 1irdA 141 -24.37 -5.51 1.17e+01 1tbgE 68 -22.70 -5.48 1.19e+01 1m15A 357 -27.08 -5.46 1.22e+01 2fua 215 -26.04 -5.46 1.22e+01 1g8iA 190 -25.28 -5.43 1.24e+01 1abwA 283 -25.78 -5.43 1.25e+01 1itg 166 -24.50 -5.39 1.29e+01 1ngvA 534 -27.80 -5.34 1.34e+01 1dszA 86 -23.90 -5.32 1.36e+01 1j7yA 141 -24.18 -5.30 1.38e+01 1babA 143 -24.19 -5.30 1.39e+01 1auk 489 -27.55 -5.29 1.41e+01 1ha2A 585 -27.90 -5.21 1.50e+01 1dw9A 156 -24.16 -5.21 1.50e+01 1bl3A 160 -23.80 -5.18 1.54e+01 1sw6A 327 -26.23 -5.18 1.54e+01 1b75A 94 -23.20 -5.16 1.56e+01 1dwtA 153 -24.31 -5.13 1.60e+01 1b9xB 68 -22.46 -5.12 1.62e+01 1f4tA 368 -25.84 -5.12 1.62e+01 1ah7 245 -25.52 -5.12 1.62e+01 1dwkA 156 -23.94 -5.08 1.67e+01 1qnoA 344 -25.94 -5.07 1.69e+01 1qnrA 344 -25.94 -5.06 1.70e+01 1mkaA 171 -24.30 -5.06 1.71e+01 1ystH 260 -28.34 -5.05 1.72e+01 1aw0 72 -21.40 -5.04 1.73e+01 2sas 185 -24.56 -5.04 1.73e+01 1toh 343 -26.01 -5.04 1.74e+01 1gjnA 153 -24.20 -5.03 1.74e+01 1oxjA 173 -25.95 -5.01 1.79e+01 1f6dA 376 -25.98 -4.96 1.86e+01 3cln 148 -23.89 -4.95 1.88e+01 1gotG 73 -22.41 -4.93 1.91e+01 1itf 165 -25.17 -4.92 1.93e+01 1iu8A 206 -24.58 -4.90 1.95e+01 4rxn 54 -24.86 -4.90 1.96e+01 1oaa 259 -24.60 -4.90 1.96e+01 1kw4A 89 -22.84 -4.89 1.97e+01 1fe0A 68 -20.94 -4.86 2.03e+01 1sep 261 -24.61 -4.84 2.05e+01 1g8lA 411 -25.82 -4.82 2.10e+01 4rnpA 883 -28.88 -4.82 2.10e+01 1if1A 113 -23.95 -4.78 2.17e+01 1ez3A 127 -23.69 -4.77 2.20e+01 1lnh 857 -29.49 -4.76 2.21e+01 1gio 125 -22.97 -4.75 2.23e+01 1bj5 585 -27.73 -4.73 2.28e+01 1vaoA 560 -27.89 -4.69 2.34e+01 1myf 153 -24.31 -4.69 2.34e+01 1iapA 211 -24.76 -4.63 2.48e+01 1ee8A 266 -25.31 -4.62 2.50e+01 1qsdA 106 -23.30 -4.61 2.52e+01 1emvB 134 -24.14 -4.59 2.58e+01 1ebmA 317 -26.27 -4.58 2.58e+01 1ka3A 90 -22.42 -4.57 2.62e+01 1fr2B 134 -24.10 -4.56 2.64e+01 1cnt2 187 -25.01 -4.55 2.66e+01 1c1dA 355 -24.90 -4.50 2.78e+01 1n9bA 265 -24.65 -4.50 2.79e+01 1qhtA 775 -27.31 -4.49 2.80e+01 1iro 54 -24.34 -4.47 2.85e+01 1jtkA 136 -22.52 -4.45 2.91e+01 1lwyA 324 -26.28 -4.44 2.93e+01 1f3vA 179 -23.52 -4.42 2.98e+01 1ko9A 345 -26.45 -4.42 2.99e+01 1e4cP 215 -24.99 -4.41 3.02e+01 1cg5B 141 -23.22 -4.40 3.04e+01 1cjwA 166 -24.00 -4.40 3.04e+01 1no1A 126 -23.95 -4.39 3.07e+01 1m2tA 254 -24.34 -4.39 3.07e+01 1dttA 560 -27.99 -4.35 3.17e+01 1bxm 99 -22.29 -4.35 3.18e+01 1lriA 98 -22.23 -4.32 3.26e+01 2cblA 305 -25.44 -4.32 3.27e+01 1tgoA 773 -26.92 -4.32 3.28e+01 1mhqA 148 -25.67 -4.28 3.38e+01 1isuA 62 -22.68 -4.28 3.39e+01 1jj2P 95 -24.76 -4.27 3.41e+01 1hdlA 55 -22.89 -4.26 3.45e+01 1e7wA 291 -24.46 -4.25 3.47e+01 3lynA 136 -24.59 -4.25 3.48e+01 1l1zA 274 -24.68 -4.24 3.51e+01 1j5sA 463 -26.66 -4.23 3.53e+01 1f45B 197 -27.35 -4.23 3.54e+01 1gzsB 165 -23.15 -4.22 3.57e+01 1mgn 154 -23.82 -4.21 3.60e+01 1exqA 154 -23.99 -4.20 3.64e+01 1jidA 128 -23.52 -4.19 3.66e+01 1dfuP 94 -20.85 -4.19 3.67e+01 1pnkA 209 -23.83 -4.19 3.67e+01 1dceB 331 -27.22 -4.19 3.68e+01 1dn1B 267 -24.49 -4.18 3.72e+01 2nllA 66 -22.59 -4.17 3.72e+01 1bbhA 131 -24.37 -4.17 3.73e+01 1jl0A 334 -24.87 -4.16 3.78e+01 1j5rA 371 -25.32 -4.16 3.78e+01 1h2wA 710 -26.52 -4.15 3.80e+01 1beo 98 -22.19 -4.15 3.80e+01 1pn1A 176 -23.91 -4.15 3.81e+01 1e8nA 710 -26.51 -4.12 3.91e+01 1aol 228 -26.78 -4.12 3.91e+01 1h2xA 710 -26.52 -4.12 3.91e+01 1jhb 106 -21.97 -4.11 3.94e+01 1qfmA 710 -26.51 -4.11 3.95e+01 1br0A 120 -22.82 -4.11 3.96e+01