% SAM: /projects/compbio/bin/i686/hmmscore v3.5 (July 15, 2005) compiled 07/18/05_14:54:13 % (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. % --------------------------------------------------------------------- % stridefoo.1.YGR006W.t2k-100-30-stride-ebghtl Host: farm20.cse.ucsc.edu Sun Feb 12 22:43:17 2006 % karplus Dir: /projects/compbio/experiments/protein-predict/yeast/YGR0/YGR006W % --------------------------------------------------------------------- % Inserted Files: % Database Files: /projects/compbio/experiments/models.97/indexes/t2k.x-seqs,/projects/compbio/experiments/models.97/indexes/t2k.2ds % % 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 YGR006W.t2k-w0.5.mod % Track 1 FIMs added (the generic node (5)) % Track 1 Coeff 0.300 File YGR006W.t2k.stride-ebghtl.mod % Score DP Method: forward all-paths (dpstyle = 0) % Align DP Method: viterbi (adpstyle = 1) % 13614 sequences, 3208521 residues, 252 nodes, 403.63 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(=2.3462) * Reverse)^tau(=0.6809))) % 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 1dvkA 173 -161.76 -142.49 2.07e-19 1mzwB 31 -21.50 -12.17 6.10e-01 1evyA 366 -31.69 -10.91 1.24e+00 1bg6 359 -28.98 -10.61 1.47e+00 1fchA 368 -32.89 -10.49 1.57e+00 1ef8A 261 -26.31 -10.35 1.70e+00 1xx4A 261 -26.31 -10.30 1.75e+00 1rtxA 123 -30.02 -10.30 1.75e+00 1spgB 147 -29.10 -10.10 1.97e+00 1uouA 474 -25.81 -9.80 2.34e+00 1vqrA 297 -34.14 -9.38 3.00e+00 1h96A 182 -30.83 -9.17 3.40e+00 1zbsA 291 -24.03 -9.16 3.42e+00 1eia 207 -27.70 -8.94 3.91e+00 1dxtB 147 -26.05 -8.89 4.02e+00 1j7yB 146 -25.89 -8.83 4.17e+00 1babB 146 -25.95 -8.82 4.19e+00 1sctB 151 -29.89 -8.80 4.26e+00 1n0qA 93 -20.14 -8.66 4.64e+00 1htjF 210 -32.89 -8.52 5.04e+00 3sdhA 146 -30.38 -8.47 5.19e+00 1vjxA 157 -30.89 -8.40 5.42e+00 1s69A 124 -28.66 -8.31 5.76e+00 1irdB 146 -25.36 -8.27 5.88e+00 1gjnA 153 -29.29 -8.27 5.90e+00 1myt 146 -27.07 -8.21 6.12e+00 1vf6C 72 -23.84 -8.08 6.62e+00 1fhjB 146 -28.09 -8.06 6.73e+00 2aa1B 146 -26.08 -8.03 6.84e+00 1k1aA 241 -20.71 -7.97 7.11e+00 2eiaB 206 -26.31 -7.93 7.28e+00 1gcb 454 -27.99 -7.78 8.00e+00 1dk5A 322 -31.65 -7.76 8.09e+00 1lb3A 182 -29.33 -7.66 8.64e+00 1mym 154 -28.38 -7.55 9.24e+00 1mgn 154 -28.02 -7.53 9.37e+00 103m 154 -27.83 -7.51 9.49e+00 1wp8A 89 -24.71 -7.47 9.74e+00 1mlo 154 -28.12 -7.42 1.01e+01 2spl 154 -28.00 -7.34 1.06e+01 1yhlA 362 -31.04 -7.32 1.08e+01 1mhyB 395 -31.46 -7.32 1.08e+01 1s4bP 674 -31.10 -7.29 1.09e+01 2spo 154 -27.83 -7.27 1.11e+01 1mod 154 -27.93 -7.24 1.13e+01 2myo 118 -18.55 -7.22 1.14e+01 1oyzA 280 -30.62 -7.21 1.15e+01 1rcd 173 -28.46 -7.19 1.16e+01 1mll 154 -27.96 -7.16 1.19e+01 1gnlA 544 -26.69 -7.14 1.20e+01 2ilk 160 -30.60 -7.13 1.21e+01 1myo 118 -18.49 -7.13 1.21e+01 1a6r 471 -28.29 -7.06 1.27e+01 3gcb 470 -28.30 -7.06 1.27e+01 1t98A 287 -35.13 -7.02 1.31e+01 1a1z 91 -24.74 -7.01 1.31e+01 1aew 174 -29.15 -7.01 1.31e+01 1r9dA 787 -31.55 -7.00 1.32e+01 1jk0B 345 -32.36 -6.90 1.41e+01 1iwhB 146 -25.59 -6.89 1.42e+01 1dat 174 -29.08 -6.89 1.42e+01 1hkbA 917 -22.58 -6.83 1.47e+01 1ygmA 118 -20.75 -6.81 1.49e+01 1ash 150 -28.16 -6.80 1.50e+01 2bs3C 256 -30.96 -6.79 1.52e+01 2mgb 154 -27.49 -6.77 1.53e+01 1xnfA 275 -34.01 -6.76 1.54e+01 1wy6A 172 -28.77 -6.74 1.56e+01 1bzpA 153 -27.21 -6.68 1.63e+01 1xwoA 465 -28.99 -6.68 1.63e+01 1a6m 151 -29.06 -6.67 1.64e+01 1mlg 154 -27.36 -6.61 1.71e+01 2mgg 154 -27.95 -6.60 1.72e+01 1bgf 124 -26.75 -6.59 1.73e+01 1n00A 321 -29.49 -6.55 1.78e+01 1f0jA 377 -27.11 -6.54 1.79e+01 1ilk 151 -30.00 -6.50 1.84e+01 1ift 263 -22.18 -6.47 1.87e+01 1xfhA 422 -31.95 -6.46 1.89e+01 1cn4C 166 -22.83 -6.45 1.90e+01 2frvA 264 -15.85 -6.44 1.91e+01 1s9uA 207 -26.18 -6.44 1.91e+01 1sgmA 191 -31.61 -6.41 1.95e+01 1v9vA 114 -26.08 -6.41 1.96e+01 1ap7 168 -17.56 -6.37 2.00e+01 1r03A 182 -28.18 -6.32 2.07e+01 1bd8 156 -18.09 -6.30 2.10e+01 1ribA 375 -30.90 -6.29 2.12e+01 1dwtA 153 -29.44 -6.28 2.12e+01 1muyA 225 -21.44 -6.28 2.13e+01 1u5pA 216 -35.36 -6.28 2.13e+01 1l6kA 77 -25.02 -6.16 2.31e+01 1dqeA 137 -22.33 -6.16 2.31e+01 1qlaC 256 -30.49 -6.15 2.33e+01 2vhbB 146 -24.54 -6.13 2.37e+01 1qhaA 917 -22.46 -6.12 2.38e+01 1dgkN 917 -22.63 -6.09 2.42e+01 1z0xA 220 -29.98 -6.09 2.43e+01 1mbd 153 -29.05 -6.08 2.44e+01 1c20A 128 -21.83 -6.07 2.46e+01 1r6fA 310 -24.11 -6.05 2.49e+01 1wmuB 146 -25.21 -6.02 2.54e+01 1l58 164 -24.86 -6.01 2.56e+01 1zx4A 192 -24.43 -5.99 2.59e+01 1czaN 917 -22.26 -5.96 2.66e+01 1jqcA 375 -30.42 -5.93 2.70e+01 1ezoA 370 -18.50 -5.93 2.71e+01 1mxrA 375 -30.42 -5.92 2.72e+01 1bor 56 -13.80 -5.88 2.79e+01 1v4sA 455 -23.52 -5.86 2.84e+01 1bdg 451 -20.82 -5.84 2.87e+01 1nwmX 142 -30.31 -5.83 2.90e+01 1o1yA 239 -20.53 -5.82 2.92e+01 2au5A 139 -27.57 -5.81 2.93e+01 1di1A 300 -31.24 -5.81 2.93e+01 1p36A 164 -24.35 -5.81 2.94e+01 1jli 112 -21.32 -5.80 2.96e+01 1y6nL 145 -29.45 -5.79 2.98e+01 1u35C 120 -21.99 -5.78 3.00e+01 1kncA 177 -25.69 -5.78 3.00e+01 1zgmA 248 -27.73 -5.76 3.04e+01 2cb5A 453 -27.42 -5.74 3.08e+01 1it2A 146 -27.44 -5.74 3.09e+01 1lw9A 164 -24.28 -5.73 3.11e+01 1nktA 922 -31.52 -5.72 3.13e+01 1eljA 381 -19.85 -5.70 3.16e+01 1uaaA 673 -24.61 -5.68 3.22e+01 1l92 164 -24.44 -5.68 3.22e+01 1ca1 370 -26.54 -5.68 3.23e+01 2avuE 192 -22.17 -5.66 3.25e+01 1uq5A 263 -21.07 -5.65 3.29e+01 1xorA 349 -26.77 -5.62 3.35e+01 2aaxA 275 -25.38 -5.56 3.51e+01 1bmtA 246 -21.02 -5.54 3.55e+01 1sknP 92 -21.98 -5.52 3.59e+01 1n9dA 199 -28.86 -5.51 3.62e+01 1t7pA 698 -23.79 -5.51 3.63e+01 1cwwA 102 -22.49 -5.49 3.66e+01 1tbbA 332 -26.94 -5.48 3.70e+01 1h6pA 203 -27.68 -5.48 3.71e+01 1y2kA 349 -26.61 -5.46 3.74e+01 119l 164 -24.29 -5.45 3.78e+01 1dbhA 354 -32.15 -5.44 3.82e+01 2bnxA 386 -32.39 -5.43 3.82e+01 2b49A 287 -17.47 -5.42 3.85e+01 1e9rA 437 -23.07 -5.41 3.88e+01 1x9mA 698 -23.75 -5.40 3.90e+01 1ukz 203 -19.86 -5.40 3.92e+01 1jjyA 636 -21.05 -5.39 3.94e+01 1su8A 636 -21.05 -5.39 3.95e+01 1tlqA 189 -28.14 -5.39 3.95e+01 1r4vA 171 -30.69 -5.38 3.98e+01 1knqA 175 -17.09 -5.37 3.99e+01 1rz4A 226 -22.87 -5.37 4.00e+01 1tfjA 219 -24.77 -5.37 4.00e+01