# 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.t06-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 12.359 # 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 0.072 0.036 0.141 0.197 0.005 0.048 0.012 0.003 0.011 0.007 0.030 0.066 0.306 0.004 0.004 0.057 2 I 0.039 0.033 0.157 0.155 0.026 0.119 0.030 0.007 0.001 0.003 0.035 0.069 0.301 0.011 0.004 0.010 3 S 0.002 0.016 0.014 0.023 0.003 0.359 0.002 0.035 0.001 0.003 0.107 0.048 0.370 0.002 0.010 0.003 4 N 0.002 0.010 0.004 0.010 0.001 0.023 0.001 0.003 0.005 0.004 0.427 0.096 0.402 0.003 0.002 0.007 5 A 0.004 0.005 0.003 0.005 0.001 0.004 0.001 0.001 0.001 0.001 0.023 0.395 0.554 0.001 0.004 0.001 6 K 0.001 0.001 0.002 0.001 0.001 0.006 0.001 0.001 0.001 0.001 0.008 0.019 0.954 0.001 0.001 0.006 7 I 0.001 0.001 0.001 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.010 0.017 0.967 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 0.004 0.024 0.967 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 0.004 0.991 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 0.003 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 0.006 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 0.992 0.001 0.003 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 0.974 0.011 0.002 0.010 16 K 0.002 0.001 0.008 0.001 0.001 0.001 0.013 0.001 0.001 0.001 0.002 0.001 0.842 0.070 0.027 0.033 17 A 0.002 0.001 0.025 0.001 0.001 0.004 0.017 0.001 0.001 0.001 0.002 0.004 0.810 0.014 0.073 0.046 18 K 0.006 0.006 0.016 0.001 0.003 0.006 0.104 0.001 0.001 0.001 0.026 0.004 0.393 0.332 0.007 0.096 19 A 0.021 0.104 0.054 0.007 0.001 0.005 0.045 0.018 0.001 0.001 0.012 0.056 0.253 0.027 0.368 0.029 20 G 0.009 0.030 0.203 0.021 0.001 0.008 0.031 0.003 0.015 0.007 0.008 0.014 0.208 0.004 0.044 0.395 21 V 0.302 0.046 0.295 0.072 0.001 0.019 0.014 0.001 0.004 0.001 0.011 0.009 0.097 0.002 0.005 0.121 22 I 0.036 0.055 0.634 0.173 0.001 0.031 0.004 0.002 0.001 0.001 0.010 0.012 0.031 0.001 0.002 0.007 23 T 0.001 0.008 0.012 0.015 0.001 0.910 0.001 0.001 0.001 0.001 0.005 0.018 0.026 0.001 0.001 0.001 24 E 0.001 0.002 0.001 0.001 0.001 0.018 0.001 0.001 0.001 0.001 0.956 0.004 0.018 0.001 0.001 0.001 25 E 0.001 0.006 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.016 0.939 0.036 0.001 0.001 0.001 26 E 0.001 0.001 0.001 0.001 0.001 0.005 0.001 0.001 0.001 0.001 0.003 0.042 0.947 0.001 0.001 0.001 27 K 0.001 0.001 0.001 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.011 0.005 0.980 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 0.007 0.025 0.968 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 0.009 0.990 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 0.999 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 0.999 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 0.999 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 0.999 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 0.001 0.998 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 0.997 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 0.001 0.975 0.002 0.001 0.020 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 0.994 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 0.991 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 0.006 0.005 0.984 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 0.019 0.928 0.007 0.001 0.037 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 0.003 0.004 0.001 0.001 0.001 0.004 0.001 0.001 0.001 0.005 0.007 0.964 0.005 0.004 0.004 47 N 0.001 0.002 0.002 0.004 0.001 0.001 0.002 0.001 0.001 0.001 0.003 0.008 0.952 0.001 0.012 0.010 48 T 0.006 0.005 0.029 0.004 0.001 0.004 0.010 0.001 0.001 0.001 0.005 0.006 0.763 0.027 0.005 0.135 49 L 0.007 0.003 0.035 0.005 0.002 0.041 0.098 0.001 0.001 0.001 0.011 0.013 0.734 0.034 0.011 0.005 50 K 0.002 0.435 0.074 0.029 0.001 0.005 0.009 0.010 0.001 0.001 0.006 0.020 0.305 0.003 0.064 0.036 51 S 0.030 0.017 0.061 0.341 0.001 0.008 0.004 0.001 0.027 0.002 0.007 0.007 0.219 0.008 0.009 0.260 52 V 0.045 0.004 0.873 0.038 0.001 0.004 0.004 0.001 0.001 0.001 0.001 0.001 0.022 0.001 0.001 0.006 53 K 0.003 0.016 0.224 0.732 0.001 0.006 0.001 0.001 0.001 0.001 0.003 0.001 0.009 0.001 0.001 0.003 54 I 0.004 0.011 0.031 0.738 0.030 0.162 0.004 0.001 0.001 0.001 0.002 0.002 0.012 0.001 0.001 0.003 55 I 0.001 0.161 0.021 0.798 0.002 0.005 0.001 0.005 0.001 0.001 0.003 0.001 0.002 0.001 0.001 0.001 56 D 0.001 0.001 0.001 0.002 0.001 0.992 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 57 P 0.001 0.003 0.001 0.001 0.011 0.001 0.003 0.001 0.001 0.001 0.978 0.001 0.001 0.003 0.001 0.001 58 E 0.001 0.015 0.001 0.002 0.001 0.003 0.001 0.039 0.001 0.001 0.001 0.664 0.001 0.002 0.269 0.001 59 G 0.001 0.001 0.012 0.001 0.001 0.001 0.012 0.001 0.033 0.016 0.008 0.001 0.042 0.010 0.017 0.844 60 N 0.745 0.022 0.018 0.009 0.001 0.005 0.014 0.008 0.005 0.002 0.022 0.055 0.041 0.002 0.021 0.031 61 D 0.122 0.057 0.442 0.026 0.001 0.040 0.020 0.003 0.018 0.011 0.015 0.034 0.079 0.004 0.011 0.116 62 V 0.066 0.091 0.419 0.320 0.001 0.008 0.003 0.003 0.002 0.002 0.009 0.014 0.031 0.001 0.003 0.028 63 T 0.002 0.002 0.015 0.013 0.001 0.924 0.001 0.001 0.001 0.002 0.002 0.009 0.030 0.001 0.001 0.001 64 P 0.001 0.001 0.001 0.001 0.001 0.074 0.001 0.001 0.001 0.001 0.880 0.005 0.036 0.001 0.001 0.001 65 E 0.001 0.011 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.026 0.929 0.031 0.001 0.001 0.001 66 K 0.001 0.001 0.004 0.002 0.001 0.002 0.004 0.001 0.001 0.001 0.004 0.049 0.897 0.011 0.002 0.023 67 L 0.001 0.001 0.054 0.001 0.001 0.002 0.009 0.001 0.001 0.001 0.004 0.006 0.912 0.001 0.007 0.004 68 K 0.001 0.002 0.009 0.003 0.001 0.005 0.003 0.001 0.001 0.001 0.005 0.007 0.951 0.002 0.002 0.010 69 R 0.003 0.001 0.003 0.006 0.001 0.008 0.004 0.001 0.001 0.001 0.019 0.010 0.923 0.012 0.002 0.007 70 E 0.001 0.007 0.012 0.005 0.001 0.004 0.007 0.001 0.001 0.001 0.015 0.022 0.885 0.014 0.014 0.013 71 Q 0.002 0.003 0.019 0.005 0.002 0.007 0.027 0.001 0.001 0.001 0.009 0.016 0.843 0.027 0.014 0.025 72 R 0.006 0.008 0.034 0.006 0.004 0.011 0.030 0.007 0.001 0.001 0.018 0.015 0.753 0.048 0.034 0.026 73 N 0.007 0.013 0.031 0.008 0.005 0.019 0.049 0.016 0.004 0.003 0.038 0.023 0.507 0.137 0.079 0.061 74 N 0.017 0.014 0.040 0.011 0.001 0.015 0.014 0.021 0.005 0.004 0.058 0.039 0.555 0.009 0.143 0.052 75 K 0.042 0.028 0.054 0.017 0.002 0.020 0.019 0.004 0.016 0.007 0.052 0.078 0.483 0.023 0.011 0.145 76 L 0.096 0.037 0.143 0.043 0.005 0.033 0.040 0.009 0.003 0.001 0.030 0.084 0.397 0.026 0.027 0.028 77 H 0.007 0.032 0.198 0.046 0.004 0.110 0.021 0.015 0.003 0.003 0.031 0.042 0.414 0.008 0.036 0.030 78 L 0.015 0.033 0.067 0.065 0.010 0.065 0.024 0.012 0.007 0.005 0.162 0.047 0.417 0.018 0.010 0.041 79 E 0.038 0.076 0.090 0.094 0.005 0.040 0.016 0.024 0.008 0.003 0.061 0.158 0.315 0.020 0.029 0.025 80 H 0.014 0.028 0.130 0.057 0.010 0.085 0.046 0.009 0.008 0.006 0.035 0.056 0.401 0.029 0.027 0.057 81 H 0.021 0.046 0.141 0.057 0.013 0.049 0.048 0.018 0.004 0.002 0.106 0.042 0.366 0.017 0.032 0.037 82 H 0.026 0.080 0.119 0.086 0.016 0.053 0.039 0.032 0.015 0.008 0.051 0.098 0.245 0.039 0.030 0.062 83 H 0.042 0.048 0.121 0.073 0.022 0.087 0.055 0.024 0.016 0.011 0.056 0.054 0.261 0.029 0.047 0.054 84 H 0.028 0.063 0.136 0.045 0.035 0.072 0.085 0.025 0.011 0.008 0.119 0.055 0.192 0.041 0.034 0.050 85 H 0.044 0.093 0.115 0.065 0.018 0.058 0.046 0.061 0.017 0.009 0.079 0.118 0.139 0.026 0.067 0.045