# TARGET T0311 # Using neural net t04-2621-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 T0311.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 61.1882 # 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 M 0.110 0.235 0.357 0.095 0.084 0.033 0.037 0.014 0.025 0.009 0.001 2 K 0.100 0.375 0.337 0.044 0.043 0.036 0.023 0.003 0.035 0.004 0.001 3 M 0.192 0.225 0.405 0.067 0.017 0.051 0.010 0.004 0.023 0.003 0.001 4 A 0.168 0.308 0.295 0.071 0.047 0.034 0.031 0.005 0.034 0.005 0.001 5 N 0.136 0.112 0.365 0.147 0.019 0.114 0.054 0.007 0.039 0.003 0.005 6 H 0.033 0.253 0.547 0.003 0.038 0.021 0.016 0.001 0.086 0.002 0.001 7 P 0.176 0.004 0.717 0.015 0.001 0.023 0.001 0.001 0.001 0.001 0.063 8 R 0.026 0.266 0.480 0.003 0.075 0.019 0.007 0.001 0.120 0.003 0.001 9 P 0.431 0.004 0.481 0.027 0.001 0.018 0.001 0.001 0.001 0.001 0.037 10 G 0.460 0.007 0.065 0.028 0.043 0.001 0.006 0.234 0.002 0.153 0.001 11 D 0.700 0.017 0.129 0.080 0.009 0.042 0.007 0.005 0.005 0.002 0.004 12 I 0.837 0.044 0.058 0.036 0.002 0.014 0.002 0.001 0.007 0.001 0.001 13 I 0.866 0.031 0.029 0.053 0.004 0.012 0.001 0.001 0.003 0.001 0.001 14 Q 0.962 0.009 0.014 0.007 0.003 0.002 0.002 0.001 0.001 0.001 0.001 15 E 0.973 0.003 0.005 0.014 0.001 0.001 0.001 0.001 0.001 0.001 0.001 16 S 0.926 0.002 0.003 0.065 0.001 0.001 0.001 0.001 0.001 0.001 0.001 17 L 0.866 0.026 0.050 0.024 0.002 0.009 0.004 0.002 0.017 0.001 0.001 18 D 0.965 0.007 0.015 0.004 0.002 0.003 0.002 0.001 0.001 0.001 0.001 19 E 0.937 0.005 0.009 0.045 0.001 0.002 0.001 0.001 0.001 0.001 0.001 20 L 0.253 0.005 0.028 0.707 0.001 0.001 0.003 0.001 0.001 0.001 0.001 21 N 0.002 0.001 0.001 0.036 0.001 0.003 0.804 0.150 0.002 0.001 0.001 22 V 0.001 0.491 0.467 0.002 0.013 0.021 0.001 0.001 0.005 0.001 0.001 23 S 0.003 0.129 0.751 0.001 0.039 0.066 0.001 0.001 0.009 0.002 0.001 24 L 0.994 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 25 R 0.998 0.001 0.001 0.002 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 F 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 R 0.998 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 30 A 0.969 0.001 0.001 0.030 0.001 0.001 0.001 0.001 0.001 0.001 0.001 31 M 0.214 0.002 0.005 0.777 0.001 0.001 0.001 0.001 0.001 0.001 0.001 32 E 0.023 0.001 0.006 0.020 0.002 0.013 0.890 0.042 0.003 0.002 0.001 33 I 0.025 0.439 0.466 0.012 0.017 0.028 0.001 0.001 0.011 0.001 0.001 34 A 0.011 0.027 0.844 0.001 0.004 0.079 0.001 0.001 0.032 0.001 0.001 35 P 0.994 0.001 0.002 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 36 S 0.989 0.001 0.001 0.009 0.001 0.001 0.001 0.001 0.001 0.001 0.001 37 T 0.964 0.001 0.002 0.032 0.001 0.001 0.001 0.001 0.001 0.001 0.001 38 A 0.998 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 39 S 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 40 R 0.998 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 41 L 0.996 0.001 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.001 0.001 42 L 0.972 0.004 0.003 0.019 0.001 0.001 0.001 0.001 0.001 0.001 0.001 43 T 0.560 0.003 0.009 0.422 0.001 0.001 0.003 0.001 0.001 0.001 0.001 44 G 0.106 0.002 0.014 0.042 0.008 0.002 0.187 0.620 0.002 0.018 0.001 45 K 0.517 0.067 0.185 0.184 0.007 0.026 0.006 0.001 0.005 0.001 0.001 46 A 0.358 0.139 0.373 0.051 0.028 0.012 0.017 0.003 0.016 0.003 0.001 47 A 0.350 0.046 0.353 0.124 0.022 0.055 0.019 0.011 0.008 0.006 0.006 48 L 0.081 0.434 0.402 0.027 0.032 0.017 0.001 0.001 0.005 0.001 0.001 49 T 0.057 0.232 0.583 0.002 0.046 0.029 0.001 0.001 0.043 0.006 0.001 50 P 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 51 E 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 52 M 0.996 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 53 A 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 54 I 0.998 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 55 K 0.990 0.001 0.001 0.008 0.001 0.001 0.001 0.001 0.001 0.001 0.001 56 L 0.989 0.001 0.001 0.008 0.001 0.001 0.001 0.001 0.001 0.001 0.001 57 S 0.990 0.001 0.002 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 58 V 0.993 0.002 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 59 V 0.973 0.002 0.001 0.021 0.001 0.001 0.001 0.001 0.001 0.001 0.001 60 I 0.339 0.006 0.006 0.644 0.001 0.001 0.001 0.001 0.002 0.001 0.001 61 G 0.101 0.005 0.022 0.065 0.016 0.006 0.335 0.392 0.004 0.054 0.001 62 S 0.170 0.180 0.347 0.173 0.062 0.038 0.009 0.002 0.009 0.010 0.001 63 S 0.286 0.055 0.413 0.012 0.091 0.054 0.006 0.003 0.044 0.033 0.001 64 P 0.996 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 65 Q 0.990 0.001 0.001 0.009 0.001 0.001 0.001 0.001 0.001 0.001 0.001 66 M 0.986 0.001 0.001 0.013 0.001 0.001 0.001 0.001 0.001 0.001 0.001 67 W 0.996 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 68 L 0.997 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 69 N 0.993 0.001 0.001 0.006 0.001 0.001 0.001 0.001 0.001 0.001 0.001 70 L 0.969 0.001 0.001 0.030 0.001 0.001 0.001 0.001 0.001 0.001 0.001 71 Q 0.956 0.003 0.007 0.028 0.001 0.002 0.002 0.001 0.001 0.001 0.001 72 N 0.968 0.002 0.004 0.022 0.001 0.001 0.002 0.001 0.001 0.001 0.001 73 A 0.817 0.008 0.005 0.158 0.003 0.002 0.003 0.002 0.001 0.001 0.001 74 W 0.698 0.077 0.072 0.107 0.017 0.009 0.009 0.002 0.008 0.001 0.001 75 S 0.616 0.034 0.157 0.029 0.008 0.106 0.012 0.002 0.032 0.003 0.001 76 L 0.986 0.001 0.002 0.009 0.001 0.001 0.001 0.001 0.001 0.001 0.001 77 A 0.991 0.001 0.001 0.007 0.001 0.001 0.001 0.001 0.001 0.001 0.001 78 E 0.977 0.001 0.001 0.020 0.001 0.001 0.001 0.001 0.001 0.001 0.001 79 A 0.969 0.002 0.006 0.019 0.001 0.001 0.001 0.001 0.001 0.001 0.001 80 E 0.962 0.004 0.005 0.025 0.001 0.001 0.001 0.001 0.001 0.001 0.001 81 K 0.929 0.008 0.016 0.036 0.003 0.002 0.004 0.001 0.001 0.001 0.001 82 T 0.728 0.026 0.030 0.194 0.004 0.007 0.005 0.001 0.005 0.001 0.001 83 V 0.501 0.114 0.143 0.173 0.019 0.016 0.013 0.003 0.016 0.002 0.001 84 D 0.269 0.072 0.228 0.091 0.031 0.130 0.113 0.010 0.048 0.008 0.001 85 V 0.802 0.041 0.065 0.066 0.006 0.010 0.003 0.001 0.005 0.001 0.001 86 S 0.777 0.044 0.072 0.075 0.008 0.011 0.005 0.002 0.006 0.001 0.001 87 R 0.724 0.063 0.075 0.090 0.010 0.012 0.010 0.002 0.012 0.001 0.001 88 L 0.602 0.099 0.172 0.064 0.013 0.019 0.014 0.003 0.012 0.002 0.001 89 R 0.542 0.115 0.210 0.051 0.020 0.024 0.019 0.003 0.013 0.002 0.001 90 R 0.435 0.156 0.274 0.067 0.014 0.028 0.008 0.001 0.015 0.001 0.002 91 L 0.202 0.341 0.320 0.033 0.026 0.031 0.006 0.001 0.038 0.001 0.001 92 V 0.292 0.201 0.409 0.027 0.011 0.035 0.004 0.001 0.019 0.001 0.001 93 T 0.327 0.218 0.238 0.110 0.022 0.055 0.006 0.002 0.020 0.001 0.001 94 Q 0.274 0.323 0.174 0.098 0.071 0.019 0.011 0.003 0.025 0.004 0.001 95 S 0.224 0.113 0.356 0.166 0.033 0.055 0.018 0.010 0.017 0.006 0.004 96 T 0.029 0.346 0.318 0.005 0.030 0.019 0.010 0.001 0.241 0.001 0.001 97 P 0.238 0.006 0.661 0.012 0.001 0.023 0.001 0.001 0.001 0.002 0.055