# TARGET TR454 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment TR454.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 2159 # Pos AA H E P G Y N L T D S C 10N 1S 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 5N 1 D 0.256 0.077 0.220 0.199 0.050 0.090 0.061 0.016 0.019 0.011 0.002 2 C 0.576 0.066 0.130 0.128 0.044 0.025 0.009 0.002 0.016 0.004 0.001 3 R 0.924 0.010 0.029 0.027 0.002 0.004 0.002 0.001 0.001 0.001 0.001 4 S 0.974 0.003 0.005 0.016 0.001 0.001 0.001 0.001 0.001 0.001 0.001 5 R 0.984 0.004 0.004 0.004 0.001 0.001 0.001 0.001 0.001 0.001 0.001 6 L 0.997 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 7 M 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 8 E 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 9 V 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 10 A 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 11 T 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 12 E 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 13 L 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 14 F 0.992 0.001 0.001 0.006 0.001 0.001 0.001 0.001 0.001 0.001 0.001 15 A 0.990 0.001 0.001 0.007 0.001 0.001 0.001 0.001 0.001 0.001 0.001 16 Q 0.961 0.002 0.001 0.033 0.001 0.001 0.001 0.001 0.001 0.001 0.001 17 K 0.506 0.008 0.016 0.424 0.004 0.002 0.033 0.001 0.005 0.001 0.001 18 G 0.141 0.003 0.022 0.047 0.044 0.004 0.118 0.497 0.003 0.122 0.001 19 F 0.535 0.087 0.172 0.148 0.010 0.023 0.012 0.002 0.009 0.001 0.001 20 Y 0.463 0.108 0.133 0.217 0.017 0.017 0.031 0.002 0.011 0.001 0.001 21 G 0.252 0.041 0.128 0.059 0.128 0.033 0.098 0.200 0.004 0.056 0.001 22 V 0.590 0.184 0.113 0.050 0.035 0.016 0.003 0.001 0.007 0.001 0.001 23 S 0.245 0.087 0.386 0.016 0.061 0.134 0.004 0.001 0.064 0.002 0.001 24 I 0.995 0.001 0.002 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 25 R 0.998 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 26 E 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 27 L 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 28 A 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 29 Q 0.996 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 30 A 0.985 0.001 0.001 0.014 0.001 0.001 0.001 0.001 0.001 0.001 0.001 31 A 0.223 0.002 0.007 0.754 0.001 0.001 0.010 0.001 0.001 0.001 0.001 32 G 0.012 0.001 0.004 0.006 0.007 0.001 0.368 0.553 0.001 0.048 0.001 33 A 0.263 0.128 0.383 0.151 0.016 0.039 0.009 0.002 0.006 0.002 0.001 34 S 0.195 0.125 0.417 0.108 0.019 0.098 0.006 0.002 0.027 0.002 0.001 35 I 0.776 0.043 0.098 0.050 0.008 0.014 0.004 0.001 0.005 0.001 0.001 36 S 0.776 0.061 0.051 0.039 0.033 0.010 0.017 0.006 0.004 0.002 0.001 37 M 0.638 0.211 0.057 0.026 0.044 0.010 0.003 0.001 0.010 0.001 0.001 38 I 0.671 0.240 0.051 0.010 0.006 0.010 0.002 0.001 0.010 0.001 0.001 39 S 0.677 0.195 0.060 0.019 0.017 0.019 0.004 0.001 0.008 0.001 0.001 40 Y 0.522 0.250 0.063 0.080 0.040 0.013 0.008 0.001 0.023 0.001 0.001 41 H 0.392 0.149 0.178 0.155 0.029 0.045 0.024 0.003 0.022 0.002 0.002 42 F 0.217 0.147 0.171 0.278 0.050 0.019 0.073 0.004 0.034 0.006 0.001 43 G 0.199 0.014 0.138 0.101 0.069 0.017 0.099 0.110 0.007 0.243 0.004 44 G 0.212 0.025 0.224 0.167 0.095 0.051 0.047 0.073 0.018 0.085 0.002 45 K 0.929 0.005 0.040 0.017 0.002 0.003 0.001 0.001 0.001 0.001 0.001 46 E 0.990 0.001 0.003 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 47 G 0.993 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 48 L 0.997 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 49 Y 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 50 A 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 51 A 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 52 V 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 53 L 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 54 Q 0.996 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 55 E 0.993 0.001 0.001 0.007 0.001 0.001 0.001 0.001 0.001 0.001 0.001 56 Q 0.971 0.001 0.001 0.027 0.001 0.001 0.001 0.001 0.001 0.001 0.001 57 F 0.971 0.001 0.003 0.021 0.001 0.001 0.002 0.001 0.001 0.001 0.001 58 A 0.982 0.002 0.004 0.007 0.001 0.001 0.003 0.001 0.001 0.001 0.001 59 C 0.891 0.006 0.007 0.088 0.002 0.002 0.001 0.001 0.001 0.001 0.001 60 F 0.730 0.008 0.030 0.217 0.001 0.003 0.007 0.001 0.004 0.001 0.001 61 G 0.751 0.013 0.049 0.049 0.013 0.006 0.063 0.039 0.004 0.013 0.001 62 Q 0.730 0.041 0.076 0.113 0.008 0.015 0.010 0.001 0.004 0.001 0.001 63 L 0.747 0.040 0.079 0.109 0.005 0.008 0.003 0.001 0.007 0.001 0.001 64 D 0.797 0.039 0.078 0.048 0.007 0.011 0.009 0.003 0.006 0.002 0.001 65 D 0.807 0.025 0.044 0.090 0.010 0.008 0.008 0.002 0.003 0.001 0.001 66 I 0.731 0.055 0.069 0.115 0.008 0.008 0.003 0.001 0.011 0.001 0.001 67 R 0.517 0.080 0.146 0.191 0.006 0.016 0.025 0.001 0.017 0.001 0.001 68 G 0.319 0.025 0.131 0.076 0.069 0.016 0.078 0.149 0.009 0.124 0.004 69 Q 0.384 0.113 0.291 0.119 0.014 0.023 0.017 0.005 0.026 0.005 0.003 70 A 0.242 0.065 0.301 0.279 0.020 0.018 0.052 0.003 0.009 0.004 0.007 71 G 0.147 0.014 0.116 0.092 0.067 0.013 0.034 0.329 0.004 0.181 0.002 72 D 0.044 0.075 0.621 0.013 0.032 0.032 0.007 0.001 0.169 0.006 0.001 73 P 0.939 0.001 0.051 0.005 0.001 0.002 0.001 0.001 0.001 0.001 0.002 74 L 0.992 0.001 0.002 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 75 A 0.996 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 76 V 0.998 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 77 M 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 78 T 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 79 A 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 80 Y 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 81 L 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 82 R 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 83 W 0.996 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 84 T 0.993 0.001 0.001 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 85 I 0.995 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 86 Q 0.986 0.002 0.002 0.007 0.001 0.001 0.001 0.001 0.001 0.001 0.001 87 R 0.868 0.008 0.011 0.101 0.004 0.003 0.002 0.001 0.003 0.001 0.001 88 H 0.743 0.018 0.040 0.167 0.005 0.008 0.009 0.001 0.007 0.001 0.001 89 R 0.783 0.015 0.040 0.125 0.005 0.005 0.020 0.002 0.002 0.002 0.001 90 N 0.404 0.018 0.046 0.466 0.015 0.013 0.022 0.008 0.004 0.003 0.001 91 N 0.157 0.048 0.352 0.033 0.027 0.033 0.031 0.002 0.307 0.009 0.001 92 P 0.973 0.001 0.020 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 93 Q 0.962 0.003 0.005 0.025 0.001 0.001 0.002 0.001 0.001 0.001 0.001 94 L 0.965 0.004 0.006 0.022 0.001 0.001 0.001 0.001 0.001 0.001 0.001 95 L 0.980 0.007 0.004 0.007 0.001 0.001 0.001 0.001 0.001 0.001 0.001 96 R 0.979 0.014 0.002 0.001 0.001 0.001 0.002 0.001 0.001 0.001 0.001 97 F 0.958 0.026 0.007 0.002 0.001 0.003 0.001 0.001 0.002 0.001 0.001 98 Y 0.882 0.033 0.030 0.035 0.006 0.007 0.001 0.001 0.006 0.001 0.001 99 T 0.859 0.024 0.027 0.067 0.003 0.009 0.004 0.001 0.005 0.001 0.001 100 S 0.872 0.026 0.017 0.057 0.012 0.005 0.006 0.001 0.003 0.001 0.001 101 E 0.748 0.038 0.036 0.154 0.006 0.006 0.006 0.001 0.005 0.001 0.001 102 L 0.506 0.079 0.104 0.222 0.019 0.018 0.034 0.003 0.012 0.001 0.001 103 T 0.324 0.108 0.105 0.389 0.016 0.015 0.027 0.003 0.011 0.001 0.001 104 N 0.034 0.114 0.427 0.022 0.055 0.043 0.060 0.003 0.229 0.013 0.001 105 P 0.505 0.004 0.415 0.039 0.002 0.010 0.001 0.001 0.001 0.003 0.020 106 T 0.187 0.076 0.517 0.019 0.015 0.033 0.016 0.002 0.130 0.005 0.001 107 P 0.936 0.001 0.051 0.009 0.001 0.001 0.001 0.001 0.001 0.001 0.002 108 C 0.865 0.013 0.020 0.088 0.002 0.006 0.003 0.001 0.003 0.001 0.001 109 F 0.927 0.006 0.012 0.049 0.002 0.002 0.001 0.001 0.001 0.001 0.001 110 A 0.970 0.008 0.011 0.006 0.001 0.001 0.002 0.001 0.001 0.001 0.001 111 A 0.969 0.008 0.006 0.012 0.001 0.001 0.001 0.001 0.001 0.001 0.001 112 I 0.872 0.013 0.033 0.071 0.002 0.007 0.001 0.001 0.002 0.001 0.001 113 V 0.824 0.033 0.046 0.080 0.003 0.007 0.002 0.001 0.005 0.001 0.001 114 S 0.652 0.047 0.189 0.013 0.004 0.030 0.017 0.001 0.045 0.002 0.001 115 P 0.960 0.001 0.025 0.012 0.001 0.001 0.001 0.001 0.001 0.001 0.001 116 A 0.870 0.009 0.039 0.065 0.003 0.007 0.002 0.001 0.004 0.001 0.001 117 I 0.980 0.001 0.007 0.011 0.001 0.001 0.001 0.001 0.001 0.001 0.001 118 A 0.992 0.001 0.002 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 119 S 0.993 0.001 0.001 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 120 V 0.993 0.001 0.001 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 121 I 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 122 R 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 123 L 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 124 L 0.998 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 125 A 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 126 E 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 127 S 0.997 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 128 I 0.998 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 129 E 0.998 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 130 A 0.965 0.001 0.001 0.031 0.001 0.001 0.001 0.001 0.001 0.001 0.001 131 G 0.950 0.002 0.009 0.028 0.002 0.002 0.003 0.003 0.001 0.001 0.001 132 M 0.959 0.005 0.013 0.017 0.001 0.002 0.002 0.001 0.001 0.001 0.001 133 T 0.932 0.008 0.011 0.041 0.001 0.002 0.003 0.001 0.001 0.001 0.001 134 R 0.265 0.011 0.026 0.660 0.004 0.002 0.026 0.002 0.004 0.001 0.001 135 G 0.018 0.002 0.009 0.008 0.028 0.002 0.097 0.779 0.001 0.057 0.001 136 L 0.220 0.229 0.398 0.079 0.014 0.035 0.011 0.001 0.011 0.001 0.001 137 F 0.108 0.287 0.406 0.087 0.017 0.069 0.004 0.001 0.019 0.001 0.001 138 R 0.152 0.292 0.342 0.038 0.042 0.073 0.010 0.002 0.043 0.004 0.002 139 R 0.518 0.078 0.246 0.076 0.027 0.027 0.009 0.003 0.006 0.006 0.004 140 D 0.139 0.081 0.147 0.330 0.085 0.096 0.080 0.016 0.018 0.007 0.001 141 L 0.447 0.096 0.245 0.148 0.021 0.017 0.006 0.001 0.016 0.002 0.001 142 H 0.162 0.084 0.501 0.031 0.025 0.071 0.018 0.001 0.097 0.009 0.001 143 A 0.976 0.001 0.015 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 144 V 0.996 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 145 N 0.997 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 146 S 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 147 A 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 148 L 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 149 A 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 150 L 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 151 A 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 152 G 0.998 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 153 M 0.998 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 154 V 0.998 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 155 N 0.986 0.001 0.001 0.011 0.001 0.001 0.001 0.001 0.001 0.001 0.001 156 Y 0.954 0.005 0.003 0.030 0.003 0.001 0.002 0.001 0.001 0.001 0.001 157 F 0.968 0.011 0.006 0.009 0.001 0.002 0.003 0.001 0.001 0.001 0.001 158 F 0.938 0.020 0.014 0.014 0.003 0.005 0.003 0.001 0.002 0.001 0.001 159 L 0.883 0.024 0.019 0.057 0.003 0.007 0.004 0.001 0.004 0.001 0.001 160 S 0.812 0.027 0.031 0.089 0.015 0.009 0.009 0.002 0.005 0.001 0.001 161 T 0.805 0.048 0.037 0.078 0.008 0.010 0.008 0.001 0.006 0.001 0.001 162 L 0.800 0.059 0.050 0.058 0.006 0.011 0.008 0.001 0.007 0.001 0.001 163 A 0.708 0.059 0.088 0.091 0.018 0.014 0.009 0.002 0.010 0.001 0.001 164 T 0.534 0.072 0.080 0.253 0.014 0.014 0.012 0.002 0.016 0.001 0.001 165 E 0.341 0.055 0.106 0.297 0.024 0.016 0.122 0.013 0.017 0.006 0.002 166 G 0.204 0.020 0.080 0.062 0.093 0.014 0.094 0.281 0.009 0.142 0.002 167 L 0.433 0.100 0.255 0.140 0.014 0.023 0.015 0.003 0.012 0.002 0.004 168 T 0.280 0.176 0.224 0.196 0.040 0.026 0.022 0.005 0.025 0.004 0.003 169 S 0.281 0.109 0.234 0.156 0.067 0.036 0.055 0.019 0.018 0.017 0.008 170 H 0.176 0.109 0.246 0.338 0.030 0.044 0.023 0.009 0.015 0.005 0.005 171 S 0.017 0.139 0.479 0.008 0.045 0.029 0.012 0.001 0.262 0.007 0.001 172 P 0.597 0.002 0.336 0.029 0.001 0.004 0.001 0.001 0.001 0.002 0.028 173 D 0.423 0.061 0.147 0.275 0.019 0.021 0.025 0.017 0.010 0.002 0.001 174 Q 0.465 0.076 0.296 0.082 0.027 0.017 0.005 0.001 0.029 0.002 0.001 175 D 0.927 0.004 0.047 0.015 0.001 0.004 0.001 0.001 0.001 0.001 0.001 176 E 0.996 0.001 0.002 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 177 E 0.996 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 178 L 0.997 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 179 I 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 180 R 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 181 Q 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 182 Y 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 183 V 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 184 A 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 185 I 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 186 F 0.997 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 187 T 0.974 0.001 0.001 0.023 0.001 0.001 0.001 0.001 0.001 0.001 0.001 188 R 0.857 0.001 0.002 0.121 0.002 0.001 0.013 0.001 0.001 0.001 0.001 189 G 0.820 0.005 0.017 0.112 0.009 0.002 0.014 0.016 0.002 0.003 0.001 190 I 0.586 0.052 0.058 0.256 0.004 0.015 0.020 0.001 0.008 0.001 0.001 191 M 0.393 0.168 0.227 0.049 0.031 0.030 0.055 0.002 0.039 0.004 0.001 192 A 0.398 0.045 0.377 0.068 0.026 0.034 0.015 0.006 0.011 0.013 0.007