# TARGET T0311 # Using neural net t06-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.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 56.9073 # 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 0.101 0.352 0.288 0.059 0.108 0.025 0.022 0.010 0.027 0.009 0.001 2 K 0.086 0.351 0.385 0.027 0.054 0.044 0.014 0.002 0.031 0.004 0.001 3 M 0.179 0.272 0.373 0.065 0.016 0.057 0.009 0.002 0.025 0.002 0.001 4 A 0.243 0.277 0.234 0.076 0.065 0.029 0.029 0.006 0.032 0.008 0.001 5 N 0.150 0.152 0.301 0.151 0.024 0.115 0.048 0.005 0.048 0.003 0.003 6 H 0.035 0.284 0.461 0.003 0.031 0.023 0.032 0.001 0.129 0.001 0.001 7 P 0.147 0.004 0.723 0.019 0.001 0.033 0.001 0.001 0.001 0.001 0.073 8 R 0.023 0.270 0.517 0.002 0.072 0.017 0.004 0.001 0.089 0.006 0.001 9 P 0.486 0.002 0.408 0.034 0.001 0.018 0.001 0.001 0.001 0.001 0.051 10 G 0.533 0.006 0.044 0.056 0.026 0.002 0.007 0.258 0.002 0.067 0.001 11 D 0.650 0.031 0.171 0.051 0.010 0.047 0.012 0.007 0.015 0.003 0.002 12 I 0.762 0.058 0.097 0.031 0.004 0.030 0.002 0.001 0.013 0.001 0.001 13 I 0.876 0.023 0.034 0.042 0.004 0.011 0.002 0.001 0.004 0.001 0.001 14 Q 0.969 0.007 0.011 0.007 0.002 0.002 0.001 0.001 0.001 0.001 0.001 15 E 0.975 0.003 0.005 0.013 0.001 0.001 0.001 0.001 0.001 0.001 0.001 16 S 0.930 0.002 0.003 0.061 0.001 0.002 0.001 0.001 0.001 0.001 0.001 17 L 0.868 0.033 0.049 0.026 0.002 0.008 0.002 0.001 0.010 0.001 0.001 18 D 0.969 0.006 0.011 0.005 0.002 0.003 0.003 0.001 0.001 0.001 0.001 19 E 0.910 0.007 0.007 0.071 0.001 0.002 0.001 0.001 0.001 0.001 0.001 20 L 0.163 0.006 0.020 0.803 0.001 0.002 0.003 0.001 0.002 0.001 0.001 21 N 0.003 0.001 0.001 0.026 0.001 0.006 0.860 0.098 0.004 0.001 0.001 22 V 0.001 0.504 0.442 0.002 0.019 0.024 0.001 0.001 0.007 0.001 0.001 23 S 0.002 0.135 0.732 0.001 0.067 0.054 0.001 0.001 0.007 0.002 0.001 24 L 0.992 0.001 0.001 0.003 0.001 0.002 0.001 0.001 0.001 0.001 0.001 25 R 0.995 0.001 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.001 0.001 26 E 0.996 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 27 F 0.997 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 28 A 0.998 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 29 R 0.996 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 30 A 0.925 0.001 0.001 0.071 0.001 0.001 0.001 0.001 0.001 0.001 0.001 31 M 0.192 0.004 0.010 0.791 0.001 0.001 0.001 0.001 0.001 0.001 0.001 32 E 0.017 0.002 0.006 0.016 0.002 0.022 0.883 0.044 0.005 0.003 0.001 33 I 0.026 0.512 0.381 0.016 0.033 0.020 0.001 0.001 0.011 0.001 0.001 34 A 0.006 0.039 0.869 0.001 0.009 0.051 0.001 0.001 0.022 0.002 0.001 35 P 0.985 0.001 0.007 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 36 S 0.976 0.001 0.001 0.020 0.001 0.001 0.001 0.001 0.001 0.001 0.001 37 T 0.948 0.003 0.006 0.039 0.001 0.001 0.001 0.001 0.002 0.001 0.001 38 A 0.996 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 39 S 0.998 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 40 R 0.996 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 41 L 0.990 0.001 0.001 0.008 0.001 0.001 0.001 0.001 0.001 0.001 0.001 42 L 0.937 0.007 0.005 0.047 0.001 0.002 0.001 0.001 0.002 0.001 0.001 43 T 0.531 0.014 0.024 0.413 0.002 0.002 0.006 0.001 0.005 0.001 0.001 44 G 0.084 0.002 0.015 0.022 0.013 0.003 0.232 0.589 0.002 0.039 0.001 45 K 0.444 0.068 0.108 0.328 0.011 0.025 0.006 0.002 0.006 0.001 0.001 46 A 0.223 0.227 0.329 0.048 0.076 0.028 0.028 0.007 0.025 0.010 0.001 47 A 0.270 0.064 0.410 0.106 0.016 0.074 0.024 0.008 0.013 0.008 0.009 48 L 0.099 0.375 0.406 0.045 0.050 0.016 0.002 0.001 0.005 0.001 0.001 49 T 0.081 0.147 0.654 0.003 0.052 0.030 0.001 0.001 0.025 0.007 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 0.997 0.001 0.001 0.002 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 0.991 0.001 0.002 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 57 S 0.996 0.001 0.001 0.002 0.001 0.001 0.001 0.001 0.001 0.001 0.001 58 V 0.991 0.001 0.001 0.007 0.001 0.001 0.001 0.001 0.001 0.001 0.001 59 V 0.964 0.002 0.001 0.032 0.001 0.001 0.001 0.001 0.001 0.001 0.001 60 I 0.264 0.005 0.005 0.721 0.001 0.001 0.001 0.001 0.003 0.001 0.001 61 G 0.062 0.003 0.017 0.025 0.012 0.004 0.297 0.500 0.003 0.078 0.001 62 S 0.190 0.147 0.420 0.123 0.067 0.026 0.007 0.003 0.006 0.011 0.001 63 S 0.207 0.050 0.575 0.008 0.054 0.052 0.004 0.002 0.026 0.020 0.002 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 0.991 0.001 0.001 0.008 0.001 0.001 0.001 0.001 0.001 0.001 0.001 66 M 0.987 0.001 0.001 0.011 0.001 0.001 0.001 0.001 0.001 0.001 0.001 67 W 0.996 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 68 L 0.996 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 69 N 0.992 0.001 0.001 0.007 0.001 0.001 0.001 0.001 0.001 0.001 0.001 70 L 0.973 0.001 0.001 0.025 0.001 0.001 0.001 0.001 0.001 0.001 0.001 71 Q 0.975 0.002 0.004 0.016 0.001 0.001 0.001 0.001 0.001 0.001 0.001 72 N 0.969 0.002 0.002 0.024 0.001 0.001 0.001 0.001 0.001 0.001 0.001 73 A 0.917 0.004 0.003 0.069 0.001 0.002 0.002 0.001 0.001 0.001 0.001 74 W 0.810 0.039 0.031 0.100 0.006 0.005 0.004 0.002 0.002 0.001 0.001 75 S 0.747 0.027 0.082 0.030 0.008 0.064 0.014 0.003 0.023 0.003 0.001 76 L 0.988 0.001 0.001 0.008 0.001 0.001 0.001 0.001 0.001 0.001 0.001 77 A 0.989 0.001 0.001 0.009 0.001 0.001 0.001 0.001 0.001 0.001 0.001 78 E 0.975 0.001 0.001 0.021 0.001 0.001 0.001 0.001 0.001 0.001 0.001 79 A 0.964 0.003 0.007 0.020 0.001 0.001 0.003 0.001 0.001 0.001 0.001 80 E 0.948 0.009 0.008 0.029 0.001 0.002 0.001 0.001 0.001 0.001 0.001 81 K 0.896 0.013 0.023 0.055 0.003 0.004 0.003 0.002 0.001 0.001 0.001 82 T 0.583 0.046 0.046 0.283 0.008 0.012 0.006 0.001 0.013 0.001 0.001 83 V 0.455 0.128 0.158 0.173 0.019 0.025 0.018 0.003 0.019 0.002 0.001 84 D 0.197 0.065 0.231 0.108 0.036 0.160 0.123 0.011 0.059 0.011 0.001 85 V 0.752 0.053 0.071 0.084 0.007 0.015 0.005 0.002 0.009 0.001 0.001 86 S 0.686 0.056 0.107 0.097 0.011 0.021 0.008 0.002 0.009 0.002 0.001 87 R 0.646 0.104 0.092 0.096 0.015 0.017 0.011 0.002 0.016 0.001 0.001 88 L 0.518 0.126 0.225 0.055 0.014 0.025 0.015 0.003 0.016 0.002 0.001 89 R 0.448 0.142 0.266 0.047 0.019 0.036 0.019 0.002 0.016 0.002 0.002 90 R 0.378 0.269 0.226 0.054 0.020 0.027 0.006 0.001 0.017 0.001 0.002 91 L 0.252 0.320 0.309 0.028 0.014 0.040 0.004 0.001 0.031 0.001 0.001 92 V 0.246 0.251 0.383 0.025 0.011 0.051 0.004 0.001 0.027 0.001 0.001 93 T 0.385 0.231 0.176 0.096 0.025 0.052 0.008 0.002 0.022 0.001 0.001 94 Q 0.258 0.362 0.165 0.075 0.080 0.020 0.011 0.002 0.022 0.003 0.001 95 S 0.239 0.155 0.324 0.146 0.035 0.051 0.016 0.006 0.020 0.005 0.002 96 T 0.024 0.326 0.281 0.002 0.038 0.021 0.015 0.001 0.289 0.002 0.001 97 P 0.329 0.003 0.523 0.014 0.001 0.024 0.001 0.001 0.001 0.001 0.104