# This file is the result of combining several RDB files, specifically # T0489.t04.str2.rdb (weight 1.54425) # T0489.t04.str4.rdb (weight 0.924988) # T0489.t04.pb.rdb (weight 0.789901) # T0489.t04.bys.rdb (weight 0.748322) # T0489.t04.alpha.rdb (weight 0.678173) # These files were combined by translating their predictions into EHL # predictions with tables generated by compare-real, and then combining # those predictions with weights proportional to their mutual information # with the EHL alphabet. The comments from the individual files follow. # # Comments from T0489.t04.str2.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0489.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 23.1154 # # ============================================ # Comments from T0489.t04.str4.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0489.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 23.1154 # # ============================================ # Comments from T0489.t04.pb.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t04-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 T0489.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 23.1154 # # ============================================ # Comments from T0489.t04.bys.rdb # ============================================ # TARGET T0489 # 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 T0489.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 23.1154 # # ============================================ # Comments from T0489.t04.alpha.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t04-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0489.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 23.1154 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2736 0.2607 0.4657 2 M 0.3171 0.2335 0.4494 3 F 0.3676 0.1580 0.4744 4 K 0.3298 0.1210 0.5492 5 W 0.2779 0.0774 0.6447 6 P 0.1896 0.1927 0.6177 7 W 0.1898 0.2997 0.5105 8 K 0.1974 0.2418 0.5609 9 A 0.1651 0.3420 0.4929 10 D 0.1258 0.3737 0.5005 11 D 0.1031 0.4864 0.4105 12 E 0.0905 0.5118 0.3976 13 S 0.1041 0.3823 0.5136 14 G 0.1107 0.2394 0.6499 15 N 0.1307 0.1685 0.7008 16 A 0.1905 0.1183 0.6911 17 E 0.1756 0.1358 0.6886 18 M 0.2037 0.1438 0.6525 19 P 0.1254 0.2641 0.6105 20 W 0.0294 0.7385 0.2321 21 E 0.0156 0.8433 0.1411 22 Q 0.0157 0.8578 0.1265 23 A 0.0242 0.7806 0.1951 24 L 0.0463 0.6477 0.3059 25 A 0.0662 0.4525 0.4812 26 I 0.1647 0.2400 0.5953 27 P 0.1345 0.2920 0.5735 28 V 0.1072 0.5689 0.3239 29 L 0.1052 0.6185 0.2764 30 A 0.0914 0.5859 0.3227 31 H 0.1208 0.2923 0.5869 32 L 0.1894 0.1173 0.6932 33 S 0.1558 0.0498 0.7944 34 S 0.0227 0.6578 0.3196 35 T 0.0117 0.7950 0.1932 36 E 0.0104 0.8819 0.1077 37 Q 0.0091 0.9065 0.0844 38 H 0.0091 0.9139 0.0770 39 K 0.0090 0.9128 0.0782 40 L 0.0084 0.9188 0.0728 41 T 0.0083 0.9226 0.0691 42 Q 0.0083 0.9241 0.0676 43 M 0.0083 0.9245 0.0673 44 A 0.0083 0.9236 0.0681 45 A 0.0083 0.9247 0.0671 46 R 0.0084 0.9213 0.0704 47 F 0.0084 0.9152 0.0764 48 L 0.0086 0.9064 0.0850 49 Q 0.0096 0.8872 0.1032 50 Q 0.0184 0.7926 0.1889 51 K 0.0507 0.6423 0.3070 52 R 0.1166 0.4709 0.4125 53 L 0.2221 0.3467 0.4312 54 V 0.3175 0.2477 0.4348 55 A 0.3358 0.2103 0.4539 56 L 0.2841 0.1953 0.5206 57 Q 0.1673 0.1509 0.6818 58 G 0.1370 0.0889 0.7740 59 L 0.4049 0.0312 0.5639 60 E 0.5531 0.0281 0.4188 61 L 0.4656 0.0533 0.4811 62 T 0.2317 0.0504 0.7178 63 P 0.0239 0.6755 0.3006 64 L 0.0142 0.7960 0.1898 65 H 0.0222 0.8676 0.1102 66 Q 0.0232 0.8905 0.0864 67 A 0.0252 0.8975 0.0773 68 R 0.0233 0.9045 0.0722 69 I 0.0203 0.9084 0.0713 70 A 0.0143 0.9145 0.0713 71 M 0.0194 0.9034 0.0772 72 L 0.0215 0.8843 0.0942 73 F 0.0391 0.8196 0.1413 74 C 0.0451 0.7425 0.2124 75 L 0.0658 0.7426 0.1916 76 P 0.0300 0.8003 0.1697 77 V 0.0711 0.7465 0.1825 78 L 0.0756 0.7276 0.1969 79 E 0.0867 0.6052 0.3081 80 L 0.0991 0.3735 0.5274 81 G 0.0887 0.2335 0.6777 82 I 0.1112 0.3841 0.5047 83 E 0.1172 0.4811 0.4017 84 W 0.1416 0.4872 0.3711 85 L 0.1683 0.3574 0.4742 86 D 0.1211 0.2668 0.6121 87 G 0.0875 0.1475 0.7650 88 F 0.3066 0.0702 0.6232 89 H 0.4557 0.0634 0.4809 90 E 0.7348 0.0134 0.2518 91 V 0.7689 0.0067 0.2244 92 L 0.7974 0.0060 0.1966 93 I 0.7815 0.0079 0.2106 94 Y 0.5634 0.0122 0.4244 95 P 0.2809 0.0420 0.6771