# TARGET T0311 # 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/T0311/T0311.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 48.7579 # 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 0.061 0.020 0.184 0.330 0.010 0.062 0.018 0.004 0.013 0.007 0.026 0.031 0.181 0.006 0.005 0.044 2 K 0.045 0.066 0.316 0.305 0.010 0.055 0.009 0.010 0.002 0.002 0.023 0.020 0.113 0.003 0.008 0.013 3 M 0.013 0.032 0.080 0.335 0.103 0.154 0.040 0.010 0.007 0.006 0.044 0.021 0.079 0.051 0.004 0.020 4 A 0.019 0.202 0.129 0.378 0.015 0.034 0.018 0.051 0.006 0.002 0.019 0.019 0.055 0.006 0.036 0.011 5 N 0.018 0.072 0.110 0.417 0.014 0.054 0.027 0.012 0.054 0.034 0.017 0.025 0.050 0.007 0.009 0.078 6 H 0.170 0.050 0.211 0.279 0.020 0.079 0.018 0.013 0.011 0.007 0.038 0.016 0.044 0.003 0.007 0.034 7 P 0.038 0.137 0.250 0.442 0.009 0.029 0.003 0.006 0.006 0.008 0.017 0.022 0.019 0.001 0.002 0.011 8 R 0.012 0.009 0.020 0.067 0.285 0.462 0.048 0.003 0.001 0.012 0.014 0.033 0.020 0.011 0.001 0.002 9 P 0.002 0.035 0.008 0.027 0.001 0.071 0.001 0.321 0.001 0.001 0.463 0.014 0.036 0.001 0.018 0.001 10 G 0.002 0.010 0.003 0.019 0.001 0.020 0.001 0.001 0.108 0.064 0.117 0.565 0.077 0.001 0.001 0.012 11 D 0.078 0.009 0.015 0.029 0.001 0.007 0.001 0.001 0.001 0.001 0.066 0.308 0.484 0.001 0.001 0.001 12 I 0.001 0.002 0.024 0.013 0.001 0.053 0.001 0.001 0.001 0.001 0.016 0.059 0.829 0.001 0.001 0.002 13 I 0.001 0.009 0.002 0.006 0.001 0.019 0.001 0.001 0.001 0.001 0.006 0.034 0.922 0.001 0.001 0.001 14 Q 0.001 0.001 0.001 0.009 0.001 0.007 0.001 0.001 0.001 0.001 0.014 0.014 0.950 0.001 0.001 0.001 15 E 0.001 0.002 0.002 0.006 0.001 0.001 0.001 0.001 0.001 0.001 0.006 0.015 0.960 0.001 0.003 0.002 16 S 0.001 0.003 0.009 0.008 0.001 0.003 0.007 0.001 0.001 0.001 0.001 0.006 0.845 0.033 0.004 0.080 17 L 0.002 0.008 0.059 0.018 0.001 0.003 0.030 0.001 0.001 0.001 0.002 0.003 0.842 0.002 0.019 0.012 18 D 0.002 0.003 0.017 0.005 0.003 0.115 0.012 0.001 0.001 0.001 0.007 0.006 0.796 0.008 0.004 0.020 19 E 0.002 0.004 0.001 0.001 0.012 0.002 0.040 0.001 0.001 0.001 0.079 0.002 0.035 0.816 0.001 0.003 20 L 0.001 0.009 0.003 0.001 0.001 0.001 0.003 0.027 0.001 0.001 0.002 0.050 0.019 0.001 0.880 0.002 21 N 0.001 0.002 0.011 0.001 0.001 0.001 0.001 0.001 0.018 0.004 0.001 0.001 0.036 0.001 0.002 0.920 22 V 0.845 0.009 0.083 0.016 0.001 0.001 0.001 0.001 0.001 0.001 0.004 0.007 0.027 0.001 0.001 0.006 23 S 0.001 0.001 0.002 0.001 0.001 0.976 0.001 0.001 0.001 0.001 0.001 0.005 0.016 0.001 0.001 0.001 24 L 0.001 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.985 0.001 0.012 0.001 0.001 0.001 25 R 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.989 0.009 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 0.001 0.001 0.998 0.001 0.001 0.001 27 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 0.996 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 0.001 0.001 0.996 0.001 0.001 0.001 29 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 0.993 0.001 0.001 0.001 30 A 0.001 0.001 0.001 0.001 0.001 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.026 0.965 0.001 0.004 31 M 0.001 0.001 0.004 0.001 0.001 0.001 0.005 0.001 0.001 0.001 0.001 0.001 0.058 0.001 0.929 0.001 32 E 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.030 0.001 0.001 0.958 33 I 0.896 0.013 0.044 0.016 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.012 0.001 0.002 0.012 34 A 0.002 0.001 0.079 0.001 0.001 0.883 0.002 0.001 0.001 0.001 0.001 0.002 0.026 0.001 0.001 0.001 35 P 0.001 0.005 0.001 0.001 0.001 0.018 0.001 0.001 0.001 0.001 0.966 0.001 0.008 0.001 0.001 0.001 36 S 0.001 0.030 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.959 0.003 0.001 0.001 0.001 37 T 0.001 0.001 0.017 0.005 0.001 0.032 0.003 0.001 0.001 0.001 0.006 0.033 0.892 0.001 0.001 0.006 38 A 0.001 0.002 0.013 0.002 0.001 0.026 0.002 0.001 0.001 0.001 0.052 0.015 0.886 0.001 0.001 0.001 39 S 0.001 0.019 0.003 0.012 0.001 0.003 0.002 0.001 0.001 0.001 0.013 0.176 0.766 0.001 0.002 0.002 40 R 0.001 0.001 0.001 0.009 0.001 0.002 0.002 0.001 0.001 0.001 0.003 0.005 0.970 0.002 0.002 0.004 41 L 0.001 0.002 0.030 0.004 0.001 0.003 0.011 0.001 0.001 0.001 0.002 0.004 0.903 0.010 0.003 0.025 42 L 0.001 0.001 0.004 0.002 0.019 0.001 0.175 0.001 0.001 0.001 0.001 0.001 0.074 0.714 0.003 0.004 43 T 0.001 0.003 0.008 0.003 0.001 0.002 0.004 0.080 0.001 0.001 0.001 0.001 0.055 0.002 0.832 0.007 44 G 0.004 0.005 0.007 0.005 0.001 0.004 0.003 0.001 0.090 0.059 0.020 0.003 0.084 0.004 0.003 0.708 45 K 0.857 0.022 0.029 0.009 0.001 0.002 0.009 0.001 0.001 0.001 0.004 0.027 0.026 0.003 0.003 0.007 46 A 0.019 0.042 0.666 0.072 0.001 0.041 0.012 0.005 0.001 0.001 0.015 0.026 0.060 0.002 0.016 0.019 47 A 0.022 0.131 0.285 0.257 0.009 0.123 0.014 0.002 0.008 0.003 0.013 0.013 0.060 0.002 0.003 0.057 48 L 0.025 0.180 0.115 0.588 0.001 0.020 0.001 0.003 0.001 0.001 0.017 0.018 0.025 0.001 0.001 0.004 49 T 0.001 0.001 0.003 0.004 0.001 0.948 0.001 0.001 0.001 0.002 0.003 0.015 0.021 0.001 0.001 0.001 50 P 0.001 0.001 0.001 0.001 0.001 0.012 0.001 0.001 0.001 0.001 0.970 0.003 0.014 0.001 0.001 0.001 51 E 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.985 0.009 0.001 0.001 0.001 52 M 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.002 0.006 0.989 0.001 0.001 0.002 53 A 0.001 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.003 0.988 0.001 0.001 0.001 54 I 0.001 0.002 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.007 0.982 0.001 0.001 0.001 55 K 0.001 0.001 0.001 0.007 0.001 0.010 0.001 0.001 0.001 0.001 0.002 0.003 0.967 0.003 0.001 0.004 56 L 0.001 0.001 0.001 0.001 0.001 0.005 0.001 0.001 0.001 0.001 0.008 0.003 0.978 0.001 0.001 0.001 57 S 0.001 0.006 0.001 0.003 0.001 0.001 0.002 0.001 0.001 0.001 0.003 0.016 0.962 0.001 0.001 0.003 58 V 0.001 0.001 0.001 0.003 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.003 0.982 0.001 0.001 0.004 59 V 0.001 0.002 0.017 0.002 0.011 0.002 0.101 0.001 0.001 0.001 0.001 0.001 0.208 0.620 0.003 0.031 60 I 0.002 0.007 0.026 0.010 0.001 0.003 0.010 0.055 0.001 0.001 0.003 0.002 0.156 0.005 0.710 0.011 61 G 0.007 0.010 0.022 0.011 0.003 0.020 0.014 0.002 0.055 0.064 0.006 0.005 0.194 0.010 0.004 0.575 62 S 0.655 0.029 0.027 0.029 0.001 0.008 0.002 0.007 0.001 0.002 0.060 0.029 0.132 0.001 0.008 0.010 63 S 0.005 0.021 0.051 0.009 0.001 0.299 0.003 0.001 0.002 0.005 0.047 0.194 0.353 0.001 0.002 0.006 64 P 0.002 0.003 0.004 0.005 0.001 0.041 0.001 0.001 0.001 0.001 0.510 0.070 0.363 0.001 0.001 0.001 65 Q 0.001 0.026 0.004 0.012 0.001 0.002 0.001 0.001 0.001 0.001 0.010 0.711 0.231 0.001 0.001 0.001 66 M 0.001 0.001 0.002 0.004 0.001 0.003 0.001 0.001 0.001 0.001 0.003 0.006 0.978 0.001 0.001 0.002 67 W 0.001 0.003 0.009 0.003 0.001 0.006 0.010 0.001 0.001 0.001 0.004 0.010 0.949 0.002 0.001 0.002 68 L 0.001 0.003 0.002 0.007 0.001 0.010 0.002 0.001 0.001 0.001 0.004 0.014 0.949 0.001 0.006 0.001 69 N 0.001 0.003 0.003 0.007 0.001 0.008 0.002 0.001 0.001 0.001 0.009 0.011 0.932 0.002 0.002 0.019 70 L 0.003 0.001 0.002 0.003 0.001 0.004 0.001 0.001 0.001 0.001 0.015 0.015 0.946 0.003 0.002 0.004 71 Q 0.001 0.004 0.015 0.003 0.001 0.003 0.006 0.001 0.001 0.001 0.009 0.027 0.910 0.010 0.004 0.007 72 N 0.001 0.002 0.004 0.003 0.001 0.006 0.004 0.001 0.001 0.001 0.005 0.014 0.947 0.002 0.007 0.005 73 A 0.002 0.011 0.015 0.006 0.001 0.006 0.012 0.001 0.001 0.001 0.017 0.010 0.859 0.010 0.005 0.046 74 W 0.010 0.013 0.057 0.028 0.001 0.006 0.004 0.003 0.001 0.001 0.008 0.047 0.783 0.001 0.025 0.014 75 S 0.002 0.002 0.007 0.003 0.001 0.151 0.002 0.001 0.001 0.002 0.008 0.015 0.798 0.001 0.001 0.008 76 L 0.001 0.004 0.001 0.002 0.001 0.013 0.001 0.001 0.001 0.001 0.308 0.018 0.649 0.001 0.001 0.001 77 A 0.001 0.008 0.003 0.003 0.001 0.002 0.001 0.001 0.001 0.001 0.009 0.417 0.550 0.001 0.003 0.002 78 E 0.001 0.001 0.003 0.002 0.001 0.001 0.002 0.001 0.001 0.001 0.002 0.005 0.970 0.003 0.002 0.009 79 A 0.001 0.001 0.013 0.002 0.001 0.004 0.005 0.001 0.001 0.001 0.004 0.006 0.952 0.003 0.003 0.005 80 E 0.001 0.005 0.014 0.006 0.001 0.005 0.010 0.001 0.001 0.001 0.007 0.007 0.912 0.008 0.008 0.015 81 K 0.005 0.009 0.026 0.023 0.001 0.008 0.008 0.002 0.001 0.001 0.011 0.015 0.825 0.009 0.016 0.041 82 T 0.013 0.015 0.065 0.017 0.006 0.031 0.053 0.001 0.002 0.001 0.016 0.012 0.577 0.084 0.010 0.096 83 V 0.015 0.111 0.187 0.051 0.001 0.018 0.013 0.016 0.001 0.001 0.040 0.025 0.408 0.003 0.087 0.025 84 D 0.009 0.031 0.061 0.032 0.001 0.255 0.007 0.002 0.009 0.009 0.019 0.058 0.443 0.002 0.004 0.057 85 V 0.031 0.028 0.032 0.026 0.001 0.036 0.004 0.002 0.001 0.001 0.411 0.029 0.391 0.002 0.002 0.005 86 S 0.004 0.076 0.042 0.043 0.001 0.044 0.004 0.002 0.002 0.001 0.027 0.462 0.279 0.003 0.004 0.006 87 R 0.004 0.012 0.042 0.042 0.003 0.048 0.013 0.002 0.001 0.001 0.039 0.027 0.734 0.011 0.007 0.015 88 L 0.004 0.052 0.111 0.064 0.003 0.025 0.022 0.005 0.001 0.001 0.026 0.054 0.595 0.007 0.018 0.014 89 R 0.009 0.029 0.079 0.146 0.001 0.023 0.010 0.009 0.004 0.002 0.026 0.020 0.561 0.007 0.019 0.056 90 R 0.035 0.044 0.223 0.257 0.003 0.020 0.014 0.003 0.006 0.002 0.014 0.014 0.263 0.009 0.009 0.084 91 L 0.027 0.036 0.331 0.328 0.005 0.046 0.014 0.003 0.002 0.001 0.009 0.008 0.153 0.004 0.007 0.025 92 V 0.012 0.094 0.216 0.451 0.008 0.089 0.011 0.004 0.001 0.001 0.011 0.007 0.070 0.004 0.003 0.016 93 T 0.014 0.044 0.055 0.362 0.027 0.323 0.014 0.011 0.003 0.004 0.049 0.017 0.061 0.006 0.004 0.007 94 Q 0.009 0.274 0.081 0.254 0.018 0.064 0.012 0.024 0.009 0.003 0.139 0.031 0.053 0.006 0.007 0.016 95 S 0.021 0.182 0.122 0.466 0.006 0.020 0.008 0.009 0.022 0.005 0.009 0.057 0.031 0.003 0.008 0.030 96 T 0.029 0.016 0.222 0.143 0.106 0.263 0.087 0.004 0.005 0.011 0.016 0.014 0.061 0.007 0.003 0.012 97 P 0.014 0.137 0.083 0.109 0.045 0.115 0.019 0.114 0.003 0.004 0.270 0.020 0.040 0.009 0.012 0.007