# TARGET T0353 # 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/T0353/T0353.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 4.37346 # 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 0.071 0.015 0.202 0.647 0.001 0.013 0.001 0.001 0.006 0.003 0.006 0.003 0.012 0.001 0.001 0.018 2 Q 0.020 0.012 0.356 0.603 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 3 I 0.002 0.003 0.043 0.943 0.001 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 4 H 0.001 0.005 0.019 0.957 0.005 0.012 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 5 V 0.001 0.012 0.004 0.754 0.089 0.129 0.001 0.002 0.001 0.001 0.005 0.001 0.001 0.001 0.001 0.001 6 Y 0.001 0.157 0.013 0.665 0.022 0.067 0.001 0.043 0.002 0.002 0.018 0.005 0.002 0.001 0.001 0.001 7 D 0.004 0.064 0.012 0.207 0.023 0.545 0.005 0.016 0.026 0.034 0.027 0.025 0.010 0.001 0.001 0.002 8 T 0.020 0.212 0.042 0.192 0.002 0.068 0.001 0.034 0.008 0.003 0.359 0.035 0.017 0.001 0.004 0.003 9 Y 0.019 0.079 0.129 0.445 0.003 0.025 0.003 0.003 0.026 0.003 0.041 0.170 0.028 0.002 0.002 0.022 10 V 0.025 0.028 0.325 0.488 0.005 0.017 0.007 0.002 0.002 0.001 0.008 0.014 0.066 0.001 0.002 0.009 11 K 0.004 0.068 0.109 0.628 0.020 0.092 0.010 0.003 0.001 0.001 0.004 0.006 0.045 0.002 0.001 0.008 12 A 0.003 0.009 0.010 0.054 0.219 0.625 0.011 0.009 0.001 0.002 0.018 0.004 0.030 0.003 0.001 0.001 13 K 0.001 0.050 0.008 0.013 0.244 0.011 0.059 0.065 0.003 0.003 0.364 0.008 0.009 0.156 0.003 0.002 14 D 0.003 0.033 0.005 0.020 0.001 0.004 0.001 0.247 0.026 0.004 0.004 0.049 0.006 0.001 0.591 0.005 15 G 0.024 0.006 0.045 0.013 0.001 0.002 0.002 0.001 0.230 0.030 0.003 0.002 0.012 0.001 0.002 0.627 16 H 0.852 0.017 0.079 0.039 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.002 0.001 0.001 0.003 17 V 0.015 0.009 0.624 0.315 0.002 0.027 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 18 M 0.002 0.026 0.101 0.844 0.002 0.018 0.001 0.002 0.001 0.001 0.002 0.001 0.002 0.001 0.001 0.001 19 H 0.001 0.014 0.011 0.961 0.002 0.006 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 20 F 0.005 0.004 0.028 0.843 0.005 0.101 0.001 0.003 0.001 0.001 0.004 0.001 0.003 0.001 0.001 0.001 21 D 0.002 0.287 0.037 0.543 0.006 0.096 0.001 0.003 0.002 0.002 0.007 0.009 0.005 0.001 0.001 0.001 22 V 0.002 0.012 0.007 0.917 0.001 0.022 0.001 0.004 0.001 0.001 0.029 0.002 0.002 0.001 0.001 0.001 23 F 0.005 0.060 0.272 0.571 0.021 0.032 0.007 0.001 0.002 0.001 0.004 0.009 0.008 0.001 0.001 0.005 24 T 0.004 0.032 0.040 0.888 0.004 0.014 0.002 0.004 0.001 0.001 0.002 0.001 0.004 0.001 0.001 0.002 25 D 0.002 0.015 0.012 0.105 0.016 0.818 0.003 0.003 0.002 0.005 0.006 0.003 0.007 0.001 0.001 0.002 26 V 0.006 0.088 0.008 0.036 0.033 0.097 0.008 0.014 0.002 0.002 0.675 0.013 0.012 0.004 0.001 0.001 27 R 0.004 0.185 0.024 0.041 0.007 0.025 0.006 0.036 0.010 0.003 0.070 0.541 0.016 0.005 0.023 0.004 28 D 0.014 0.024 0.058 0.020 0.004 0.108 0.013 0.023 0.016 0.027 0.089 0.139 0.340 0.005 0.050 0.070 29 D 0.036 0.019 0.024 0.005 0.001 0.076 0.005 0.005 0.007 0.006 0.303 0.103 0.358 0.004 0.009 0.037 30 K 0.023 0.019 0.025 0.007 0.001 0.011 0.001 0.002 0.002 0.001 0.147 0.412 0.338 0.001 0.005 0.006 31 K 0.003 0.002 0.009 0.003 0.001 0.025 0.001 0.001 0.001 0.001 0.016 0.175 0.760 0.001 0.001 0.004 32 A 0.001 0.001 0.001 0.001 0.001 0.008 0.001 0.001 0.001 0.001 0.040 0.019 0.930 0.001 0.001 0.001 33 I 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.004 0.069 0.925 0.001 0.001 0.001 34 E 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.004 0.994 0.001 0.001 0.001 35 F 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 36 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 0.998 0.001 0.001 0.001 37 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 38 Q 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 39 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 0.974 0.007 0.001 0.016 40 L 0.001 0.001 0.001 0.001 0.001 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.988 0.002 0.002 0.001 41 S 0.001 0.002 0.004 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.002 0.954 0.005 0.008 0.020 42 S 0.003 0.001 0.005 0.002 0.002 0.001 0.047 0.001 0.001 0.001 0.002 0.001 0.301 0.566 0.007 0.061 43 I 0.006 0.017 0.149 0.007 0.001 0.002 0.023 0.008 0.001 0.001 0.005 0.004 0.258 0.007 0.492 0.024 44 G 0.011 0.013 0.091 0.025 0.006 0.041 0.028 0.003 0.018 0.025 0.012 0.017 0.351 0.016 0.007 0.338 45 E 0.241 0.029 0.036 0.023 0.078 0.025 0.162 0.004 0.001 0.001 0.065 0.020 0.106 0.193 0.005 0.012 46 E 0.005 0.103 0.081 0.046 0.004 0.033 0.012 0.221 0.005 0.002 0.029 0.057 0.060 0.010 0.321 0.012 47 G 0.011 0.060 0.098 0.103 0.006 0.039 0.029 0.009 0.151 0.059 0.033 0.033 0.094 0.009 0.024 0.242 48 A 0.496 0.069 0.126 0.142 0.001 0.012 0.008 0.008 0.006 0.003 0.026 0.030 0.039 0.002 0.011 0.022 49 T 0.042 0.034 0.529 0.157 0.003 0.122 0.008 0.002 0.007 0.005 0.008 0.024 0.029 0.001 0.003 0.025 50 V 0.037 0.146 0.264 0.390 0.009 0.050 0.009 0.003 0.001 0.001 0.040 0.011 0.023 0.001 0.002 0.012 51 T 0.008 0.140 0.090 0.355 0.004 0.285 0.002 0.011 0.003 0.003 0.009 0.058 0.024 0.001 0.002 0.003 52 S 0.002 0.006 0.012 0.027 0.004 0.681 0.002 0.003 0.002 0.004 0.192 0.010 0.053 0.001 0.001 0.001 53 E 0.004 0.281 0.012 0.036 0.001 0.011 0.001 0.006 0.002 0.001 0.371 0.226 0.042 0.001 0.002 0.002 54 E 0.011 0.069 0.082 0.183 0.001 0.017 0.007 0.003 0.012 0.001 0.007 0.366 0.195 0.004 0.012 0.029 55 C 0.008 0.003 0.369 0.042 0.004 0.078 0.022 0.001 0.001 0.001 0.017 0.007 0.429 0.002 0.004 0.013 56 R 0.009 0.164 0.066 0.110 0.005 0.053 0.016 0.009 0.001 0.001 0.107 0.037 0.396 0.006 0.003 0.016 57 F 0.018 0.040 0.029 0.414 0.005 0.048 0.009 0.008 0.013 0.003 0.029 0.087 0.256 0.009 0.011 0.021 58 C 0.012 0.039 0.150 0.173 0.006 0.078 0.017 0.007 0.004 0.005 0.020 0.032 0.404 0.006 0.012 0.036 59 H 0.008 0.025 0.023 0.050 0.003 0.229 0.005 0.010 0.001 0.002 0.068 0.043 0.511 0.005 0.007 0.010 60 S 0.004 0.006 0.008 0.010 0.003 0.081 0.011 0.004 0.002 0.002 0.312 0.094 0.426 0.029 0.004 0.005 61 Q 0.003 0.033 0.009 0.011 0.001 0.005 0.005 0.005 0.001 0.001 0.084 0.276 0.515 0.004 0.040 0.009 62 K 0.005 0.018 0.044 0.019 0.001 0.002 0.006 0.001 0.006 0.001 0.004 0.029 0.391 0.007 0.009 0.458 63 A 0.022 0.005 0.338 0.017 0.001 0.024 0.021 0.001 0.001 0.001 0.004 0.012 0.537 0.002 0.007 0.012 64 P 0.001 0.001 0.007 0.001 0.001 0.629 0.001 0.001 0.001 0.001 0.034 0.005 0.318 0.001 0.001 0.001 65 D 0.001 0.008 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.855 0.036 0.099 0.001 0.001 0.001 66 E 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.776 0.219 0.001 0.001 0.001 67 V 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.994 0.001 0.001 0.001 68 I 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.006 0.990 0.001 0.001 0.001 69 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 0.993 0.001 0.001 0.001 70 A 0.001 0.001 0.002 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.968 0.010 0.001 0.012 71 I 0.001 0.001 0.007 0.001 0.001 0.001 0.011 0.001 0.001 0.001 0.001 0.001 0.966 0.003 0.005 0.004 72 K 0.001 0.004 0.012 0.002 0.004 0.005 0.027 0.001 0.001 0.001 0.003 0.003 0.841 0.061 0.008 0.028 73 Q 0.003 0.002 0.004 0.002 0.008 0.001 0.081 0.004 0.001 0.001 0.006 0.001 0.075 0.763 0.031 0.017 74 N 0.002 0.018 0.036 0.003 0.001 0.001 0.006 0.025 0.002 0.001 0.002 0.002 0.031 0.001 0.840 0.029 75 G 0.070 0.011 0.078 0.024 0.001 0.003 0.002 0.001 0.078 0.008 0.002 0.002 0.020 0.001 0.002 0.699 76 Y 0.725 0.022 0.173 0.073 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.003 77 F 0.003 0.004 0.448 0.524 0.001 0.018 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 78 I 0.001 0.013 0.038 0.930 0.002 0.013 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 79 Y 0.001 0.007 0.005 0.983 0.002 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 80 K 0.001 0.005 0.020 0.909 0.026 0.034 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 81 M 0.001 0.002 0.002 0.034 0.909 0.035 0.011 0.001 0.001 0.001 0.002 0.001 0.001 0.004 0.001 0.001 82 E 0.001 0.056 0.001 0.055 0.007 0.014 0.001 0.836 0.001 0.001 0.010 0.002 0.001 0.001 0.016 0.001 83 G 0.001 0.022 0.003 0.032 0.011 0.014 0.003 0.004 0.539 0.308 0.008 0.010 0.002 0.001 0.001 0.042 84 C 0.588 0.030 0.033 0.040 0.042 0.047 0.041 0.025 0.005 0.007 0.059 0.050 0.018 0.004 0.008 0.003 85 N 0.010 0.107 0.155 0.041 0.018 0.121 0.016 0.148 0.015 0.019 0.134 0.104 0.042 0.010 0.041 0.019