# 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.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 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 0.249 0.166 0.261 0.096 0.087 0.022 0.056 0.021 0.028 0.013 0.001 2 K 0.374 0.181 0.299 0.060 0.023 0.027 0.016 0.003 0.013 0.003 0.002 3 M 0.304 0.197 0.264 0.128 0.016 0.047 0.014 0.004 0.025 0.002 0.001 4 A 0.198 0.278 0.329 0.067 0.041 0.028 0.022 0.003 0.029 0.004 0.001 5 N 0.165 0.091 0.351 0.151 0.017 0.115 0.055 0.007 0.041 0.003 0.005 6 H 0.053 0.218 0.574 0.005 0.033 0.021 0.016 0.001 0.075 0.003 0.001 7 P 0.235 0.005 0.660 0.022 0.001 0.021 0.001 0.001 0.001 0.001 0.056 8 R 0.033 0.268 0.454 0.003 0.069 0.019 0.008 0.001 0.141 0.003 0.001 9 P 0.407 0.003 0.500 0.027 0.001 0.018 0.001 0.001 0.001 0.001 0.045 10 G 0.405 0.005 0.055 0.023 0.038 0.001 0.006 0.284 0.002 0.181 0.001 11 D 0.664 0.018 0.153 0.081 0.009 0.049 0.007 0.004 0.006 0.001 0.006 12 I 0.813 0.056 0.070 0.034 0.002 0.015 0.001 0.001 0.007 0.001 0.001 13 I 0.851 0.039 0.033 0.055 0.004 0.013 0.001 0.001 0.003 0.001 0.001 14 Q 0.950 0.014 0.018 0.007 0.004 0.002 0.002 0.001 0.001 0.001 0.001 15 E 0.965 0.005 0.007 0.016 0.002 0.002 0.001 0.001 0.001 0.001 0.001 16 S 0.915 0.004 0.005 0.073 0.001 0.002 0.001 0.001 0.001 0.001 0.001 17 L 0.847 0.031 0.057 0.027 0.003 0.010 0.004 0.002 0.018 0.001 0.001 18 D 0.956 0.009 0.018 0.006 0.002 0.004 0.003 0.001 0.001 0.001 0.001 19 E 0.934 0.005 0.010 0.046 0.001 0.002 0.001 0.001 0.001 0.001 0.001 20 L 0.290 0.006 0.034 0.663 0.001 0.001 0.004 0.001 0.001 0.001 0.001 21 N 0.003 0.001 0.001 0.047 0.001 0.004 0.767 0.173 0.003 0.001 0.001 22 V 0.002 0.500 0.456 0.002 0.014 0.021 0.001 0.001 0.005 0.001 0.001 23 S 0.004 0.133 0.741 0.001 0.042 0.067 0.001 0.001 0.009 0.002 0.001 24 L 0.995 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 0.001 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 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 0.999 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 30 A 0.975 0.001 0.001 0.024 0.001 0.001 0.001 0.001 0.001 0.001 0.001 31 M 0.206 0.001 0.003 0.788 0.001 0.001 0.001 0.001 0.001 0.001 0.001 32 E 0.019 0.001 0.004 0.018 0.001 0.009 0.901 0.042 0.002 0.002 0.001 33 I 0.022 0.402 0.504 0.012 0.015 0.031 0.001 0.001 0.012 0.001 0.001 34 A 0.009 0.025 0.859 0.001 0.004 0.071 0.001 0.001 0.030 0.001 0.001 35 P 0.991 0.001 0.004 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 36 S 0.985 0.001 0.001 0.012 0.001 0.001 0.001 0.001 0.001 0.001 0.001 37 T 0.958 0.001 0.003 0.036 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 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 41 L 0.996 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 42 L 0.977 0.003 0.002 0.016 0.001 0.001 0.001 0.001 0.001 0.001 0.001 43 T 0.599 0.003 0.007 0.387 0.001 0.001 0.002 0.001 0.001 0.001 0.001 44 G 0.134 0.002 0.014 0.044 0.009 0.002 0.176 0.597 0.002 0.020 0.001 45 K 0.567 0.052 0.153 0.188 0.006 0.022 0.006 0.001 0.004 0.001 0.001 46 A 0.420 0.118 0.350 0.049 0.023 0.011 0.013 0.003 0.012 0.002 0.001 47 A 0.384 0.045 0.309 0.142 0.021 0.051 0.020 0.010 0.009 0.005 0.004 48 L 0.072 0.398 0.445 0.028 0.031 0.019 0.002 0.001 0.005 0.001 0.001 49 T 0.044 0.238 0.593 0.002 0.050 0.028 0.001 0.001 0.040 0.005 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 0.004 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 0.989 0.001 0.001 0.009 0.001 0.001 0.001 0.001 0.001 0.001 0.001 56 L 0.990 0.001 0.002 0.006 0.001 0.001 0.001 0.001 0.001 0.001 0.001 57 S 0.990 0.002 0.002 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 58 V 0.991 0.002 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.001 0.001 59 V 0.972 0.003 0.002 0.021 0.001 0.001 0.001 0.001 0.001 0.001 0.001 60 I 0.352 0.007 0.008 0.628 0.001 0.001 0.001 0.001 0.002 0.001 0.001 61 G 0.071 0.004 0.018 0.051 0.013 0.004 0.306 0.487 0.003 0.042 0.001 62 S 0.133 0.200 0.401 0.146 0.059 0.035 0.008 0.002 0.009 0.009 0.001 63 S 0.178 0.068 0.529 0.009 0.090 0.046 0.005 0.002 0.043 0.028 0.001 64 P 0.994 0.001 0.001 0.003 0.001 0.001 0.001 0.001 0.001 0.001 0.001 65 Q 0.982 0.001 0.001 0.016 0.001 0.001 0.001 0.001 0.001 0.001 0.001 66 M 0.974 0.001 0.001 0.022 0.001 0.001 0.001 0.001 0.001 0.001 0.001 67 W 0.991 0.001 0.001 0.004 0.001 0.001 0.001 0.001 0.001 0.001 0.001 68 L 0.991 0.001 0.001 0.005 0.001 0.001 0.001 0.001 0.001 0.001 0.001 69 N 0.983 0.001 0.001 0.014 0.001 0.001 0.001 0.001 0.001 0.001 0.001 70 L 0.956 0.001 0.001 0.040 0.001 0.001 0.001 0.001 0.001 0.001 0.001 71 Q 0.938 0.007 0.012 0.035 0.001 0.003 0.002 0.001 0.001 0.001 0.001 72 N 0.959 0.003 0.005 0.027 0.001 0.001 0.003 0.001 0.001 0.001 0.001 73 A 0.816 0.011 0.007 0.151 0.004 0.003 0.004 0.002 0.002 0.001 0.001 74 W 0.717 0.076 0.063 0.100 0.016 0.008 0.009 0.002 0.007 0.001 0.001 75 S 0.686 0.033 0.136 0.026 0.007 0.075 0.010 0.002 0.023 0.002 0.001 76 L 0.984 0.002 0.002 0.010 0.001 0.001 0.001 0.001 0.001 0.001 0.001 77 A 0.989 0.001 0.001 0.008 0.001 0.001 0.001 0.001 0.001 0.001 0.001 78 E 0.974 0.001 0.002 0.021 0.001 0.001 0.001 0.001 0.001 0.001 0.001 79 A 0.966 0.003 0.007 0.020 0.001 0.001 0.002 0.001 0.001 0.001 0.001 80 E 0.951 0.005 0.007 0.032 0.001 0.001 0.002 0.001 0.001 0.001 0.001 81 K 0.908 0.013 0.021 0.044 0.003 0.003 0.004 0.002 0.001 0.001 0.001 82 T 0.700 0.039 0.042 0.190 0.006 0.009 0.006 0.001 0.006 0.001 0.001 83 V 0.447 0.147 0.188 0.142 0.026 0.017 0.014 0.003 0.016 0.002 0.001 84 D 0.248 0.073 0.264 0.067 0.034 0.154 0.089 0.008 0.053 0.008 0.001 85 V 0.892 0.020 0.032 0.041 0.003 0.007 0.002 0.001 0.002 0.001 0.001 86 S 0.883 0.021 0.033 0.049 0.003 0.005 0.002 0.001 0.003 0.001 0.001 87 R 0.841 0.035 0.033 0.065 0.006 0.006 0.006 0.001 0.006 0.001 0.001 88 L 0.692 0.074 0.118 0.065 0.010 0.016 0.013 0.002 0.008 0.001 0.001 89 R 0.610 0.109 0.147 0.067 0.022 0.014 0.016 0.003 0.009 0.002 0.001 90 R 0.455 0.156 0.196 0.106 0.015 0.032 0.016 0.002 0.021 0.001 0.001 91 L 0.167 0.347 0.337 0.048 0.023 0.042 0.004 0.001 0.031 0.001 0.001 92 V 0.180 0.344 0.306 0.035 0.027 0.042 0.010 0.001 0.051 0.001 0.001 93 T 0.240 0.182 0.426 0.067 0.020 0.046 0.003 0.001 0.012 0.001 0.002 94 Q 0.305 0.265 0.171 0.150 0.052 0.025 0.008 0.003 0.020 0.002 0.001 95 S 0.181 0.154 0.282 0.225 0.066 0.039 0.016 0.010 0.017 0.009 0.002 96 T 0.028 0.315 0.359 0.004 0.052 0.012 0.009 0.001 0.215 0.004 0.001 97 P 0.228 0.004 0.648 0.010 0.001 0.019 0.001 0.001 0.001 0.001 0.088