# TARGET T0335 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment /projects/compbio/experiments/protein-predict/casp7/T0335/T0335.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 10.3373 # Pos AA A B C D E F G H I J K L M N O P 10N 1S 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 1 M 0.057 0.035 0.132 0.162 0.005 0.039 0.015 0.002 0.014 0.007 0.024 0.064 0.342 0.006 0.005 0.093 2 I 0.047 0.032 0.208 0.144 0.022 0.081 0.037 0.008 0.001 0.003 0.027 0.051 0.308 0.013 0.007 0.012 3 S 0.002 0.013 0.016 0.016 0.003 0.450 0.002 0.030 0.001 0.004 0.072 0.036 0.340 0.001 0.010 0.004 4 N 0.002 0.008 0.003 0.006 0.001 0.021 0.001 0.002 0.004 0.003 0.578 0.065 0.298 0.003 0.001 0.005 5 A 0.004 0.005 0.002 0.003 0.001 0.003 0.001 0.001 0.001 0.001 0.022 0.568 0.387 0.001 0.003 0.001 6 K 0.001 0.001 0.002 0.001 0.001 0.005 0.001 0.001 0.001 0.001 0.007 0.017 0.961 0.001 0.001 0.005 7 I 0.001 0.001 0.001 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.008 0.015 0.971 0.001 0.001 0.001 8 A 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.023 0.970 0.001 0.001 0.001 9 R 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.992 0.001 0.001 0.001 10 I 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.002 0.993 0.001 0.001 0.001 11 N 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.005 0.992 0.001 0.001 0.001 12 E 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.995 0.001 0.001 0.001 13 L 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.995 0.001 0.001 0.001 14 A 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.993 0.001 0.002 0.001 15 A 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.981 0.007 0.002 0.007 16 K 0.001 0.001 0.006 0.001 0.001 0.001 0.012 0.001 0.001 0.001 0.003 0.001 0.860 0.063 0.022 0.029 17 A 0.002 0.001 0.023 0.001 0.001 0.004 0.015 0.001 0.001 0.001 0.002 0.004 0.820 0.013 0.075 0.040 18 K 0.005 0.005 0.013 0.001 0.003 0.005 0.100 0.001 0.001 0.001 0.020 0.003 0.342 0.405 0.006 0.090 19 A 0.018 0.079 0.046 0.006 0.001 0.005 0.037 0.019 0.001 0.001 0.011 0.045 0.241 0.021 0.445 0.024 20 G 0.009 0.027 0.168 0.017 0.001 0.008 0.028 0.002 0.017 0.008 0.008 0.013 0.207 0.004 0.033 0.452 21 V 0.371 0.048 0.260 0.075 0.001 0.013 0.012 0.001 0.003 0.001 0.010 0.009 0.086 0.002 0.005 0.105 22 I 0.029 0.043 0.676 0.166 0.001 0.029 0.004 0.001 0.001 0.001 0.006 0.010 0.024 0.001 0.002 0.006 23 T 0.002 0.011 0.018 0.024 0.001 0.894 0.001 0.001 0.001 0.001 0.006 0.014 0.026 0.001 0.001 0.001 24 E 0.001 0.002 0.001 0.003 0.001 0.030 0.001 0.001 0.001 0.001 0.940 0.005 0.018 0.001 0.001 0.001 25 E 0.001 0.012 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.022 0.919 0.040 0.001 0.001 0.001 26 E 0.001 0.001 0.002 0.001 0.001 0.009 0.001 0.001 0.001 0.001 0.004 0.056 0.924 0.001 0.001 0.001 27 K 0.001 0.001 0.001 0.001 0.001 0.005 0.001 0.001 0.001 0.001 0.021 0.006 0.966 0.001 0.001 0.001 28 A 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.013 0.041 0.944 0.001 0.001 0.001 29 E 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.013 0.985 0.001 0.001 0.001 30 Q 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.998 0.001 0.001 0.001 31 Q 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.998 0.001 0.001 0.001 32 K 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.998 0.001 0.001 0.001 33 L 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.999 0.001 0.001 0.001 34 R 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.999 0.001 0.001 0.001 35 Q 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.998 0.001 0.001 0.001 36 E 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.997 0.001 0.001 0.001 37 Y 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.998 0.001 0.001 0.001 38 L 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.998 0.001 0.001 0.001 39 K 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.996 0.001 0.001 0.001 40 G 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.962 0.003 0.001 0.030 41 F 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.993 0.001 0.001 0.001 42 R 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.990 0.003 0.001 0.001 43 S 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.008 0.006 0.979 0.001 0.002 0.001 44 S 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.023 0.924 0.007 0.001 0.036 45 M 0.001 0.001 0.002 0.001 0.001 0.001 0.003 0.001 0.001 0.001 0.003 0.003 0.983 0.002 0.002 0.001 46 K 0.001 0.004 0.005 0.001 0.001 0.001 0.004 0.001 0.001 0.001 0.005 0.007 0.961 0.006 0.003 0.004 47 N 0.001 0.002 0.003 0.005 0.001 0.002 0.003 0.001 0.001 0.001 0.003 0.007 0.944 0.002 0.015 0.011 48 T 0.007 0.006 0.038 0.005 0.001 0.004 0.013 0.001 0.002 0.001 0.005 0.005 0.688 0.030 0.006 0.191 49 L 0.012 0.004 0.047 0.008 0.003 0.054 0.131 0.001 0.001 0.001 0.012 0.012 0.649 0.047 0.014 0.007 50 K 0.002 0.592 0.080 0.030 0.001 0.004 0.010 0.009 0.002 0.001 0.004 0.013 0.160 0.002 0.061 0.031 51 S 0.034 0.016 0.072 0.474 0.001 0.005 0.002 0.001 0.034 0.001 0.004 0.003 0.101 0.004 0.008 0.240 52 V 0.053 0.003 0.890 0.038 0.001 0.002 0.002 0.001 0.001 0.001 0.001 0.001 0.006 0.001 0.001 0.004 53 K 0.002 0.006 0.158 0.828 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 54 I 0.002 0.005 0.015 0.763 0.046 0.162 0.002 0.001 0.001 0.001 0.001 0.001 0.003 0.001 0.001 0.001 55 I 0.001 0.135 0.008 0.841 0.001 0.004 0.001 0.006 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 56 D 0.001 0.001 0.001 0.002 0.001 0.993 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 57 P 0.001 0.004 0.001 0.001 0.007 0.001 0.001 0.001 0.001 0.001 0.984 0.001 0.001 0.001 0.001 0.001 58 E 0.001 0.018 0.001 0.003 0.001 0.004 0.001 0.027 0.001 0.001 0.001 0.815 0.001 0.002 0.126 0.001 59 G 0.001 0.002 0.022 0.002 0.002 0.004 0.022 0.001 0.034 0.020 0.017 0.002 0.075 0.018 0.027 0.751 60 N 0.589 0.043 0.023 0.015 0.001 0.008 0.019 0.015 0.009 0.002 0.038 0.094 0.063 0.004 0.034 0.044 61 D 0.136 0.057 0.372 0.032 0.001 0.032 0.020 0.004 0.026 0.013 0.015 0.038 0.086 0.005 0.013 0.151 62 V 0.071 0.070 0.495 0.267 0.001 0.007 0.003 0.002 0.001 0.002 0.006 0.012 0.031 0.001 0.003 0.029 63 T 0.002 0.001 0.017 0.013 0.001 0.921 0.001 0.001 0.001 0.002 0.002 0.007 0.032 0.001 0.001 0.001 64 P 0.001 0.001 0.001 0.001 0.001 0.093 0.001 0.001 0.001 0.001 0.861 0.005 0.037 0.001 0.001 0.001 65 E 0.001 0.008 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.033 0.927 0.029 0.001 0.001 0.001 66 K 0.001 0.001 0.002 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.004 0.061 0.911 0.003 0.001 0.011 67 L 0.001 0.001 0.020 0.001 0.001 0.001 0.003 0.001 0.001 0.001 0.003 0.006 0.962 0.001 0.002 0.001 68 K 0.001 0.001 0.002 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.004 0.005 0.980 0.001 0.001 0.002 69 R 0.001 0.001 0.001 0.002 0.001 0.002 0.001 0.001 0.001 0.001 0.008 0.006 0.972 0.003 0.001 0.002 70 E 0.001 0.003 0.004 0.003 0.001 0.002 0.003 0.001 0.001 0.001 0.003 0.013 0.950 0.006 0.005 0.008 71 Q 0.001 0.001 0.011 0.003 0.001 0.003 0.017 0.001 0.001 0.001 0.003 0.005 0.925 0.010 0.008 0.014 72 R 0.002 0.004 0.018 0.003 0.003 0.005 0.024 0.002 0.001 0.001 0.010 0.006 0.838 0.047 0.016 0.019 73 N 0.003 0.005 0.009 0.002 0.007 0.005 0.084 0.005 0.001 0.001 0.010 0.005 0.157 0.635 0.045 0.026 74 N 0.006 0.009 0.023 0.004 0.001 0.004 0.010 0.028 0.003 0.001 0.012 0.008 0.150 0.004 0.705 0.035 75 K 0.033 0.020 0.047 0.009 0.001 0.003 0.009 0.001 0.045 0.008 0.008 0.012 0.084 0.006 0.004 0.710 76 L 0.622 0.017 0.183 0.048 0.001 0.012 0.014 0.002 0.001 0.001 0.006 0.019 0.058 0.003 0.005 0.011 77 H 0.007 0.065 0.527 0.104 0.004 0.167 0.008 0.007 0.002 0.002 0.009 0.012 0.067 0.002 0.005 0.011 78 L 0.010 0.045 0.048 0.282 0.022 0.211 0.009 0.010 0.004 0.004 0.225 0.020 0.093 0.004 0.003 0.008 79 E 0.015 0.187 0.089 0.234 0.013 0.064 0.009 0.024 0.008 0.003 0.077 0.174 0.082 0.007 0.008 0.008 80 H 0.013 0.049 0.112 0.207 0.019 0.135 0.028 0.017 0.014 0.008 0.043 0.087 0.208 0.013 0.017 0.031 81 H 0.020 0.067 0.180 0.118 0.023 0.081 0.041 0.022 0.007 0.005 0.101 0.045 0.223 0.012 0.020 0.033 82 H 0.031 0.101 0.122 0.163 0.020 0.069 0.031 0.040 0.017 0.010 0.062 0.086 0.159 0.022 0.023 0.045 83 H 0.038 0.060 0.133 0.133 0.030 0.114 0.043 0.024 0.021 0.015 0.059 0.062 0.177 0.020 0.029 0.044 84 H 0.031 0.073 0.127 0.075 0.049 0.089 0.074 0.027 0.011 0.009 0.120 0.056 0.163 0.034 0.024 0.039 85 H 0.036 0.100 0.103 0.089 0.022 0.071 0.039 0.070 0.018 0.010 0.084 0.118 0.126 0.024 0.054 0.035