% 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. % --------------------------------------------------------------------- % CB_burial_14_7foo.1.YGR017W.t2k-100-40-40-str2+CB_burial_14_7 Host: farm03-10.kilokluster.ucsc.edu Fri Oct 6 05:15:07 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.str2s,/projects/compbio/experiments/models.97/indexes/t2k.CB-burial-14-7s % % 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 0.400 File YGR017W.t2k.str2.mod % Track 2 FIMs added (the generic node (5)) % Track 2 Coeff 0.400 File YGR017W.t2k.CB_burial_14_7.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 15583 sequences, 3659059 residues, 298 nodes, 493.00 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(=0.6853) * Reverse)^tau(=0.8417))) % 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 -304.22 -278.47 8.87e-33 1t9mA 214 -130.24 -113.05 1.38e-13 1ty9A 222 -120.61 -103.25 2.41e-12 1nrgA 261 -114.65 -92.27 6.27e-11 1dnlA 199 -106.94 -87.43 2.68e-10 1g79A 218 -104.48 -85.21 5.24e-10 1ci0A 228 -96.66 -70.47 4.88e-08 2a2jA 246 -91.31 -67.84 1.11e-07 2i02A 148 -65.30 -50.03 3.41e-05 2fhqA 141 -53.14 -37.72 2.15e-03 2aq6A 147 -55.05 -37.44 2.37e-03 2asfA 137 -48.96 -35.57 4.52e-03 1xxoA 147 -53.93 -34.53 6.51e-03 1rfeA 162 -53.39 -34.40 6.81e-03 1w9aA 147 -51.95 -32.28 1.43e-02 2hq7A 146 -49.01 -25.77 1.49e-01 2hhzA 150 -46.27 -25.76 1.49e-01 2iabA 155 -41.98 -20.81 9.44e-01 1vl7A 157 -38.50 -19.69 1.44e+00 1w3oA 216 -42.75 -19.62 1.48e+00 1jhnA 424 -74.81 -19.46 1.58e+00 2fg9A 178 -34.84 -19.06 1.84e+00 1otcA 495 -43.21 -19.02 1.87e+00 2ucz 165 -35.71 -18.90 1.96e+00 2htdA 140 -40.52 -18.83 2.01e+00 1a81A 254 -37.10 -18.76 2.06e+00 1c4zD 154 -35.97 -18.75 2.07e+00 1iznA 286 -38.02 -18.71 2.10e+00 1jbbA 153 -35.51 -18.54 2.24e+00 1gmnA 183 -35.39 -18.42 2.36e+00 1egxA 115 -36.21 -18.34 2.43e+00 1sacA 204 -35.33 -18.29 2.48e+00 1xccA 220 -35.82 -18.27 2.49e+00 1xhnA 184 -33.46 -18.25 2.51e+00 1ayzA 169 -34.20 -17.83 2.95e+00 1prxB 224 -36.65 -17.78 3.02e+00 1s4uX 407 -35.52 -17.66 3.16e+00 1ryp1 222 -35.03 -17.61 3.21e+00 1dykA 394 -34.04 -17.48 3.39e+00 1ywnA 316 -33.17 -17.20 3.77e+00 1yh2A 175 -33.03 -17.08 3.95e+00 1jb7A 495 -40.69 -16.99 4.09e+00 1prxA 224 -37.37 -16.97 4.13e+00 1jatA 155 -32.86 -16.95 4.17e+00 1cmxA 236 -33.69 -16.43 5.11e+00 2furA 209 -36.00 -16.41 5.14e+00 1p4uA 153 -36.02 -16.40 5.16e+00 1ww7A 160 -34.39 -16.26 5.46e+00 2hq9A 149 -36.19 -16.18 5.64e+00 1rypK 198 -29.22 -16.17 5.65e+00 2i1sA 188 -36.46 -16.13 5.74e+00 1avk 638 -35.61 -15.92 6.25e+00 2fimA 276 -46.15 -15.87 6.36e+00 1g0uL 241 -32.92 -15.69 6.84e+00 2d37A 176 -30.60 -15.60 7.07e+00 1vkxA 273 -33.60 -15.58 7.15e+00 1kyfA 247 -35.84 -15.22 8.22e+00 1qtsA 247 -35.81 -14.93 9.25e+00 1eujA 166 -31.26 -14.88 9.42e+00 1fl0A 171 -33.71 -14.74 9.96e+00 1rypJ 204 -27.65 -14.68 1.02e+01 1sq9A 397 -35.81 -14.60 1.05e+01 1dt9A 437 -37.18 -14.59 1.06e+01 2ar0A 541 -34.98 -14.53 1.08e+01 1zdnA 158 -28.76 -14.53 1.09e+01 2occD 147 -47.68 -14.47 1.11e+01 1slqA 278 -34.50 -14.44 1.12e+01 1kgyA 181 -38.60 -14.42 1.13e+01 1ocrD 147 -47.67 -14.42 1.13e+01 1v54D 147 -47.61 -14.40 1.14e+01 2dfkA 402 -37.77 -14.33 1.18e+01 1flcA 432 -33.92 -14.24 1.22e+01 1iknA 286 -34.18 -14.23 1.23e+01 1z5yE 149 -27.07 -14.21 1.23e+01 1qu0A 191 -34.19 -14.11 1.28e+01 2b29A 123 -31.08 -14.01 1.34e+01 1cojA 212 -33.00 -13.98 1.35e+01 2a7bA 120 -31.19 -13.95 1.37e+01 1s31A 273 -44.94 -13.85 1.43e+01 1xewX 182 -30.86 -13.78 1.46e+01 1iruK 201 -30.66 -13.78 1.47e+01 2ayvA 166 -28.83 -13.64 1.55e+01 1x23A 155 -30.21 -13.63 1.56e+01 1b9kA 238 -34.94 -13.57 1.60e+01 2awfA 172 -34.96 -13.53 1.62e+01 1mg2D 155 -28.80 -13.47 1.66e+01 1rjoA 646 -32.47 -13.45 1.68e+01 1q3iA 214 -29.66 -13.38 1.73e+01 2mtaC 147 -30.39 -13.37 1.73e+01 1gywA 128 -32.07 -13.28 1.80e+01 1m13A 316 -30.58 -13.27 1.80e+01 1bhtA 176 -29.85 -13.23 1.83e+01 1siiA 646 -32.10 -13.18 1.87e+01 1zh5A 195 -30.62 -13.14 1.90e+01 2fug5 207 -48.86 -13.02 1.99e+01 1z02A 446 -34.89 -13.01 2.01e+01 1ui7A 638 -30.69 -13.00 2.01e+01 1uz5A 402 -28.11 -13.00 2.01e+01 1wzvA 155 -28.17 -12.95 2.05e+01 2dafA 118 -30.91 -12.94 2.06e+01 1oqyA 368 -59.87 -12.93 2.07e+01 2bepA 159 -28.17 -12.88 2.12e+01 1tmcA 175 -33.35 -12.82 2.17e+01 1g0uI 205 -25.86 -12.79 2.19e+01 1w6gA 646 -31.35 -12.74 2.23e+01 1k32A 1045 -40.11 -12.69 2.28e+01 1if1A 113 -31.47 -12.62 2.35e+01 1z2uA 150 -28.47 -12.56 2.41e+01 1gweA 503 -40.18 -12.46 2.51e+01 1gnhA 206 -29.99 -12.44 2.53e+01 1i2hA 168 -39.05 -12.40 2.57e+01 1i7pA 274 -29.61 -12.38 2.60e+01 1i6pA 220 -28.61 -12.33 2.64e+01 1yfqA 342 -30.55 -12.33 2.65e+01 1iu1A 146 -29.65 -12.29 2.69e+01 1v7rA 186 -26.13 -12.20 2.79e+01 1shwB 181 -35.41 -12.20 2.79e+01 1n6eA 1071 -39.66 -12.07 2.94e+01 1te5A 257 -31.01 -11.98 3.06e+01 1cg7A 93 -35.67 -11.97 3.07e+01 1hbzA 498 -39.67 -11.96 3.08e+01 1otvA 259 -26.73 -11.92 3.13e+01 1htoA 477 -31.14 -11.91 3.14e+01 1u4cA 349 -27.03 -11.91 3.15e+01 1ve6A 582 -29.70 -11.89 3.17e+01 1ok8A 394 -30.68 -11.88 3.18e+01 1nuyA 337 -28.56 -11.86 3.21e+01 1kyqA 274 -27.09 -11.78 3.31e+01 2b1kA 168 -27.01 -11.76 3.34e+01 2i52A 121 -24.56 -11.75 3.37e+01 7ceiB 206 -34.61 -11.69 3.45e+01 1w0pA 781 -27.51 -11.65 3.50e+01 1m1hA 248 -30.68 -11.64 3.52e+01 1umkA 275 -29.56 -11.62 3.54e+01 1qwlA 505 -38.48 -11.57 3.63e+01 1g0uE 234 -26.56 -11.55 3.65e+01 1a8q 274 -24.08 -11.54 3.67e+01 2c1gA 431 -24.95 -11.52 3.70e+01 1mnnA 340 -34.93 -11.45 3.81e+01 1aab 83 -34.35 -11.42 3.85e+01 1fvzA 271 -32.89 -11.41 3.87e+01 1httA 423 -26.42 -11.38 3.91e+01 1pah 308 -26.27 -11.37 3.93e+01 1u9aA 160 -30.39 -11.37 3.93e+01