# TARGET T0302 # 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/T0302/T0302.t04-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 386 # 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 S 0.115 0.080 0.211 0.299 0.006 0.052 0.020 0.015 0.017 0.011 0.028 0.040 0.052 0.003 0.014 0.037 2 M 0.070 0.073 0.245 0.329 0.010 0.085 0.014 0.005 0.015 0.008 0.031 0.027 0.039 0.003 0.004 0.043 3 V 0.037 0.113 0.219 0.534 0.005 0.021 0.006 0.005 0.002 0.002 0.013 0.016 0.014 0.001 0.003 0.008 4 S 0.006 0.016 0.033 0.100 0.004 0.777 0.002 0.004 0.002 0.006 0.007 0.019 0.021 0.001 0.001 0.002 5 P 0.004 0.038 0.013 0.041 0.002 0.075 0.001 0.005 0.002 0.001 0.775 0.010 0.031 0.001 0.001 0.002 6 E 0.006 0.096 0.016 0.089 0.001 0.019 0.001 0.003 0.004 0.001 0.033 0.694 0.034 0.001 0.001 0.001 7 E 0.007 0.019 0.102 0.114 0.004 0.077 0.010 0.003 0.003 0.001 0.033 0.072 0.526 0.005 0.008 0.016 8 A 0.005 0.031 0.112 0.090 0.008 0.053 0.033 0.004 0.002 0.001 0.066 0.031 0.526 0.010 0.006 0.023 9 V 0.008 0.060 0.056 0.131 0.008 0.045 0.023 0.009 0.002 0.002 0.028 0.102 0.495 0.008 0.014 0.011 10 K 0.010 0.019 0.049 0.075 0.057 0.068 0.107 0.010 0.007 0.006 0.034 0.019 0.279 0.182 0.012 0.066 11 W 0.018 0.080 0.120 0.085 0.001 0.017 0.009 0.089 0.004 0.002 0.055 0.031 0.193 0.004 0.259 0.033 12 G 0.024 0.019 0.067 0.033 0.004 0.165 0.016 0.002 0.039 0.054 0.034 0.050 0.307 0.007 0.006 0.171 13 E 0.219 0.106 0.089 0.083 0.001 0.009 0.002 0.010 0.001 0.001 0.224 0.051 0.190 0.001 0.007 0.008 14 S 0.001 0.003 0.004 0.004 0.001 0.654 0.001 0.001 0.001 0.002 0.006 0.182 0.137 0.001 0.001 0.002 15 F 0.001 0.001 0.001 0.001 0.001 0.028 0.001 0.001 0.001 0.001 0.584 0.014 0.368 0.001 0.001 0.001 16 D 0.001 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.010 0.746 0.235 0.001 0.001 0.001 17 K 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.004 0.990 0.001 0.001 0.001 18 L 0.001 0.001 0.014 0.001 0.001 0.001 0.014 0.001 0.001 0.001 0.003 0.003 0.925 0.017 0.004 0.018 19 L 0.001 0.002 0.015 0.002 0.001 0.001 0.022 0.001 0.001 0.001 0.002 0.005 0.894 0.016 0.017 0.022 20 S 0.005 0.006 0.076 0.014 0.001 0.002 0.020 0.003 0.001 0.001 0.002 0.002 0.563 0.055 0.026 0.223 21 H 0.006 0.002 0.017 0.002 0.001 0.125 0.011 0.001 0.001 0.002 0.008 0.005 0.782 0.003 0.016 0.020 22 R 0.002 0.003 0.005 0.001 0.001 0.006 0.006 0.001 0.001 0.001 0.747 0.007 0.204 0.013 0.001 0.004 23 D 0.001 0.008 0.001 0.001 0.001 0.002 0.001 0.002 0.001 0.001 0.015 0.877 0.081 0.001 0.012 0.001 24 G 0.001 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.023 0.020 0.934 0.001 0.001 0.017 25 L 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.009 0.055 0.934 0.001 0.001 0.001 26 E 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.033 0.963 0.001 0.001 0.001 27 A 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.006 0.992 0.001 0.001 0.001 28 F 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.998 0.001 0.001 0.001 29 T 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 30 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 0.998 0.001 0.001 0.001 31 F 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.959 0.009 0.002 0.025 32 L 0.001 0.001 0.005 0.001 0.001 0.001 0.005 0.001 0.001 0.001 0.001 0.001 0.963 0.004 0.011 0.006 33 K 0.001 0.003 0.015 0.003 0.001 0.003 0.006 0.001 0.001 0.001 0.003 0.001 0.894 0.014 0.009 0.047 34 T 0.013 0.009 0.015 0.007 0.001 0.013 0.028 0.001 0.001 0.001 0.020 0.013 0.792 0.034 0.016 0.036 35 E 0.014 0.054 0.093 0.013 0.001 0.015 0.024 0.005 0.002 0.001 0.036 0.028 0.542 0.026 0.052 0.094 36 F 0.015 0.068 0.159 0.052 0.001 0.015 0.014 0.004 0.003 0.002 0.018 0.072 0.457 0.004 0.027 0.088 37 S 0.010 0.002 0.018 0.003 0.001 0.297 0.002 0.001 0.001 0.003 0.029 0.029 0.598 0.001 0.002 0.005 38 E 0.002 0.005 0.003 0.001 0.001 0.014 0.001 0.001 0.001 0.001 0.647 0.049 0.275 0.001 0.001 0.001 39 E 0.001 0.007 0.001 0.002 0.001 0.003 0.001 0.001 0.001 0.001 0.014 0.753 0.218 0.001 0.002 0.001 40 N 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.011 0.980 0.001 0.001 0.003 41 I 0.001 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.004 0.017 0.976 0.001 0.001 0.001 42 E 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.004 0.007 0.986 0.001 0.001 0.001 43 F 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.007 0.991 0.001 0.001 0.001 44 W 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.997 0.001 0.001 0.001 45 I 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 46 A 0.001 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.980 0.003 0.001 0.011 47 C 0.001 0.001 0.001 0.001 0.001 0.002 0.004 0.001 0.001 0.001 0.003 0.001 0.969 0.014 0.005 0.001 48 E 0.001 0.003 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.007 0.007 0.949 0.007 0.016 0.007 49 D 0.002 0.001 0.002 0.003 0.001 0.001 0.005 0.001 0.002 0.001 0.001 0.006 0.770 0.061 0.012 0.133 50 F 0.008 0.002 0.090 0.002 0.001 0.002 0.051 0.001 0.001 0.001 0.003 0.003 0.754 0.015 0.037 0.032 51 K 0.006 0.015 0.132 0.011 0.002 0.015 0.043 0.004 0.001 0.001 0.009 0.009 0.627 0.024 0.022 0.082 52 K 0.064 0.045 0.073 0.065 0.007 0.041 0.040 0.010 0.011 0.005 0.038 0.035 0.374 0.062 0.028 0.104 53 S 0.033 0.070 0.125 0.032 0.022 0.066 0.135 0.007 0.007 0.004 0.062 0.032 0.240 0.060 0.030 0.074 54 K 0.024 0.226 0.338 0.097 0.001 0.007 0.010 0.034 0.003 0.002 0.024 0.035 0.090 0.003 0.063 0.045 55 G 0.017 0.007 0.031 0.025 0.004 0.589 0.008 0.003 0.008 0.044 0.016 0.070 0.161 0.002 0.002 0.013 56 P 0.009 0.016 0.010 0.005 0.001 0.033 0.001 0.004 0.001 0.001 0.783 0.017 0.119 0.001 0.001 0.001 57 Q 0.001 0.017 0.004 0.012 0.001 0.006 0.001 0.001 0.001 0.001 0.019 0.875 0.062 0.001 0.001 0.001 58 Q 0.004 0.003 0.022 0.019 0.001 0.010 0.002 0.001 0.001 0.001 0.017 0.053 0.862 0.001 0.001 0.005 59 I 0.001 0.001 0.007 0.003 0.001 0.020 0.001 0.001 0.001 0.001 0.028 0.019 0.919 0.001 0.001 0.001 60 H 0.001 0.002 0.001 0.002 0.001 0.008 0.001 0.001 0.001 0.001 0.013 0.043 0.927 0.001 0.001 0.001 61 L 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.006 0.021 0.967 0.001 0.001 0.001 62 K 0.001 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.009 0.984 0.001 0.001 0.003 63 A 0.001 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.004 0.004 0.990 0.001 0.001 0.001 64 K 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.009 0.987 0.001 0.001 0.001 65 A 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 66 I 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.997 0.001 0.001 0.001 67 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 0.996 0.001 0.001 0.001 68 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 0.992 0.002 0.001 0.001 69 K 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.980 0.003 0.005 0.005 70 F 0.001 0.001 0.010 0.001 0.001 0.001 0.017 0.001 0.001 0.001 0.001 0.002 0.813 0.045 0.009 0.100 71 I 0.003 0.008 0.083 0.006 0.001 0.001 0.019 0.001 0.001 0.001 0.001 0.003 0.799 0.006 0.036 0.033 72 Q 0.007 0.005 0.061 0.009 0.010 0.043 0.142 0.002 0.001 0.002 0.004 0.003 0.406 0.199 0.009 0.097 73 T 0.025 0.037 0.040 0.015 0.003 0.050 0.026 0.062 0.001 0.001 0.226 0.009 0.279 0.016 0.189 0.020 74 D 0.009 0.341 0.065 0.030 0.001 0.005 0.007 0.004 0.053 0.006 0.020 0.069 0.051 0.009 0.015 0.318 75 A 0.359 0.015 0.184 0.060 0.003 0.078 0.050 0.002 0.005 0.003 0.010 0.048 0.142 0.004 0.012 0.025 76 P 0.017 0.124 0.579 0.035 0.001 0.083 0.016 0.004 0.001 0.001 0.036 0.010 0.068 0.002 0.005 0.017 77 K 0.021 0.186 0.073 0.509 0.002 0.024 0.005 0.005 0.008 0.002 0.049 0.062 0.031 0.002 0.004 0.016 78 E 0.040 0.034 0.351 0.459 0.006 0.015 0.021 0.001 0.008 0.001 0.003 0.010 0.021 0.006 0.002 0.022 79 V 0.012 0.013 0.373 0.568 0.001 0.006 0.005 0.002 0.001 0.001 0.002 0.001 0.008 0.001 0.003 0.006 80 N 0.009 0.020 0.081 0.604 0.016 0.232 0.004 0.001 0.003 0.005 0.003 0.003 0.008 0.001 0.001 0.012 81 L 0.017 0.097 0.033 0.715 0.008 0.047 0.001 0.007 0.001 0.002 0.059 0.004 0.007 0.001 0.001 0.001 82 D 0.001 0.010 0.003 0.013 0.003 0.916 0.001 0.002 0.001 0.003 0.005 0.037 0.004 0.001 0.001 0.001 83 F 0.001 0.006 0.001 0.003 0.001 0.007 0.001 0.002 0.001 0.001 0.965 0.003 0.012 0.001 0.001 0.001 84 H 0.001 0.009 0.001 0.003 0.001 0.004 0.001 0.001 0.001 0.001 0.008 0.958 0.014 0.001 0.001 0.001 85 T 0.001 0.001 0.009 0.002 0.001 0.020 0.001 0.001 0.001 0.001 0.031 0.047 0.885 0.001 0.001 0.001 86 K 0.001 0.002 0.003 0.001 0.001 0.007 0.001 0.001 0.001 0.001 0.043 0.035 0.907 0.001 0.001 0.001 87 E 0.001 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.004 0.046 0.943 0.001 0.001 0.001 88 V 0.001 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.007 0.981 0.001 0.001 0.003 89 I 0.001 0.001 0.002 0.001 0.001 0.002 0.002 0.001 0.001 0.001 0.002 0.002 0.985 0.001 0.001 0.001 90 T 0.001 0.002 0.002 0.002 0.001 0.002 0.004 0.001 0.001 0.001 0.003 0.004 0.962 0.011 0.004 0.004 91 N 0.001 0.002 0.004 0.007 0.001 0.002 0.004 0.001 0.001 0.001 0.004 0.005 0.897 0.014 0.032 0.026 92 S 0.006 0.004 0.026 0.005 0.001 0.004 0.015 0.001 0.001 0.001 0.004 0.008 0.748 0.032 0.020 0.126 93 I 0.019 0.011 0.087 0.011 0.003 0.016 0.089 0.001 0.001 0.001 0.016 0.009 0.611 0.054 0.021 0.052 94 T 0.018 0.166 0.285 0.078 0.001 0.005 0.024 0.014 0.003 0.001 0.008 0.019 0.191 0.016 0.074 0.097 95 Q 0.048 0.020 0.215 0.166 0.005 0.095 0.035 0.002 0.018 0.012 0.008 0.009 0.193 0.007 0.011 0.157 96 P 0.071 0.119 0.398 0.179 0.004 0.025 0.013 0.006 0.001 0.002 0.075 0.010 0.073 0.002 0.004 0.017 97 T 0.005 0.018 0.011 0.027 0.007 0.753 0.004 0.003 0.001 0.003 0.016 0.096 0.052 0.002 0.001 0.002 98 L 0.002 0.014 0.008 0.009 0.001 0.032 0.002 0.005 0.001 0.001 0.773 0.029 0.118 0.001 0.002 0.002 99 H 0.001 0.016 0.003 0.006 0.001 0.014 0.001 0.001 0.002 0.001 0.020 0.835 0.095 0.001 0.002 0.002 100 S 0.003 0.001 0.005 0.002 0.001 0.007 0.001 0.001 0.001 0.001 0.079 0.039 0.850 0.001 0.001 0.008 101 F 0.001 0.001 0.003 0.001 0.001 0.008 0.001 0.001 0.001 0.001 0.035 0.113 0.838 0.001 0.001 0.001 102 D 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.010 0.026 0.961 0.001 0.001 0.001 103 A 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.015 0.983 0.001 0.001 0.001 104 A 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.004 0.995 0.001 0.001 0.001 105 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 0.001 106 S 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 0.001 107 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 0.998 0.001 0.001 0.001 108 V 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 0.001 109 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 0.001 110 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 0.997 0.001 0.001 0.001 111 L 0.001 0.001 0.003 0.001 0.001 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.960 0.007 0.005 0.018 112 M 0.001 0.002 0.020 0.005 0.001 0.002 0.016 0.001 0.001 0.001 0.001 0.002 0.886 0.017 0.016 0.031 113 E 0.003 0.004 0.023 0.004 0.003 0.018 0.030 0.002 0.001 0.001 0.005 0.003 0.775 0.070 0.019 0.040 114 Q 0.008 0.021 0.016 0.006 0.001 0.020 0.018 0.011 0.002 0.002 0.094 0.016 0.629 0.046 0.063 0.045 115 D 0.011 0.024 0.021 0.005 0.001 0.023 0.011 0.004 0.005 0.004 0.075 0.159 0.576 0.005 0.033 0.045 116 S 0.029 0.032 0.048 0.011 0.001 0.014 0.004 0.001 0.002 0.001 0.067 0.125 0.602 0.001 0.006 0.056 117 Y 0.014 0.010 0.071 0.014 0.001 0.038 0.004 0.001 0.001 0.001 0.033 0.154 0.649 0.001 0.002 0.007 118 T 0.001 0.003 0.011 0.004 0.001 0.061 0.003 0.001 0.001 0.001 0.060 0.045 0.809 0.001 0.001 0.001 119 R 0.001 0.022 0.001 0.007 0.001 0.010 0.001 0.001 0.001 0.001 0.066 0.094 0.796 0.001 0.001 0.001 120 F 0.001 0.005 0.003 0.007 0.001 0.004 0.011 0.001 0.001 0.001 0.003 0.133 0.819 0.003 0.002 0.010 121 L 0.001 0.003 0.037 0.005 0.001 0.003 0.009 0.001 0.001 0.001 0.002 0.005 0.915 0.001 0.006 0.012 122 K 0.003 0.010 0.049 0.019 0.001 0.008 0.007 0.002 0.001 0.001 0.005 0.008 0.816 0.014 0.007 0.051 123 S 0.003 0.001 0.004 0.002 0.001 0.112 0.002 0.001 0.001 0.001 0.017 0.011 0.837 0.001 0.005 0.002 124 D 0.001 0.004 0.002 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.438 0.023 0.523 0.001 0.001 0.003 125 I 0.001 0.002 0.001 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.007 0.529 0.455 0.001 0.001 0.001 126 Y 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.006 0.984 0.001 0.001 0.001 127 L 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.006 0.986 0.001 0.001 0.001 128 D 0.001 0.001 0.001 0.002 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.005 0.983 0.001 0.001 0.002 129 L 0.001 0.002 0.004 0.004 0.001 0.002 0.009 0.001 0.001 0.001 0.002 0.005 0.915 0.020 0.005 0.030 130 M 0.002 0.002 0.022 0.003 0.007 0.002 0.111 0.001 0.001 0.001 0.003 0.004 0.510 0.297 0.016 0.020 131 E 0.003 0.011 0.049 0.007 0.003 0.005 0.047 0.029 0.001 0.001 0.005 0.003 0.362 0.072 0.346 0.057 132 G 0.013 0.022 0.036 0.016 0.005 0.009 0.048 0.010 0.028 0.024 0.019 0.007 0.230 0.056 0.056 0.422