# This file is the result of combining several RDB files, specifically # T0481.t06.str2.rdb (weight 1.54425) # T0481.t06.str4.rdb (weight 0.924988) # T0481.t06.pb.rdb (weight 0.789901) # T0481.t06.bys.rdb (weight 0.748322) # T0481.t06.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 T0481.t06.str2.rdb # ============================================ # TARGET T0481 # Using neural net dunbrack-40pc-3157-t06-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 T0481.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 882 # # ============================================ # Comments from T0481.t06.str4.rdb # ============================================ # TARGET T0481 # Using neural net dunbrack-40pc-3157-t06-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 T0481.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 882 # # ============================================ # Comments from T0481.t06.pb.rdb # ============================================ # TARGET T0481 # Using neural net dunbrack-40pc-3157-t06-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 T0481.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 882 # # ============================================ # Comments from T0481.t06.bys.rdb # ============================================ # TARGET T0481 # Using neural net dunbrack-40pc-3157-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 T0481.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 882 # # ============================================ # Comments from T0481.t06.alpha.rdb # ============================================ # TARGET T0481 # Using neural net dunbrack-40pc-3157-t06-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 T0481.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 882 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1754 0.1332 0.6914 2 C 0.1320 0.1848 0.6832 3 Q 0.0597 0.6172 0.3231 4 S 0.0172 0.8303 0.1524 5 N 0.0092 0.9038 0.0870 6 Q 0.0089 0.9161 0.0750 7 I 0.0087 0.9181 0.0732 8 V 0.0084 0.9169 0.0747 9 S 0.0085 0.9133 0.0782 10 H 0.0092 0.8997 0.0911 11 F 0.0107 0.8980 0.0912 12 L 0.0090 0.8967 0.0942 13 S 0.0103 0.8755 0.1142 14 H 0.0145 0.8595 0.1260 15 R 0.0096 0.8903 0.1001 16 N 0.0090 0.9033 0.0877 17 V 0.0094 0.9087 0.0819 18 T 0.0092 0.9149 0.0759 19 N 0.0084 0.9169 0.0747 20 E 0.0085 0.9183 0.0732 21 L 0.0093 0.9088 0.0819 22 A 0.0109 0.8730 0.1161 23 E 0.0123 0.7136 0.2741 24 K 0.0241 0.3631 0.6127 25 I 0.1852 0.0616 0.7531 26 S 0.1587 0.0350 0.8063 27 K 0.0150 0.6967 0.2883 28 D 0.0157 0.7611 0.2232 29 H 0.0336 0.7166 0.2498 30 Y 0.1134 0.4928 0.3938 31 S 0.1227 0.3033 0.5740 32 Y 0.2276 0.1367 0.6357 33 K 0.2311 0.0382 0.7307 34 P 0.2120 0.0736 0.7144 35 A 0.1644 0.1406 0.6950 36 E 0.0762 0.3245 0.5993 37 T 0.0919 0.3072 0.6009 38 S 0.1215 0.2820 0.5965 39 M 0.1536 0.2139 0.6324 40 S 0.1712 0.1511 0.6777 41 A 0.0128 0.7557 0.2314 42 E 0.0091 0.8712 0.1196 43 E 0.0083 0.9227 0.0690 44 L 0.0083 0.9221 0.0696 45 V 0.0083 0.9205 0.0712 46 K 0.0083 0.9205 0.0711 47 H 0.0085 0.9187 0.0729 48 I 0.0093 0.9147 0.0760 49 L 0.0102 0.9080 0.0818 50 T 0.0125 0.8902 0.0972 51 S 0.0133 0.8933 0.0934 52 F 0.0107 0.9020 0.0874 53 H 0.0113 0.9047 0.0840 54 L 0.0135 0.9013 0.0851 55 F 0.0171 0.8914 0.0914 56 A 0.0160 0.8859 0.0982 57 N 0.0162 0.8742 0.1096 58 V 0.0252 0.8274 0.1475 59 I 0.0609 0.6902 0.2488 60 K 0.0602 0.4932 0.4466 61 E 0.0587 0.2411 0.7002 62 G 0.0817 0.1577 0.7607 63 N 0.1548 0.1015 0.7437 64 A 0.1977 0.0773 0.7249 65 S 0.1952 0.0447 0.7600 66 P 0.1242 0.2706 0.6052 67 F 0.1490 0.2838 0.5671 68 Q 0.1484 0.3081 0.5435 69 N 0.1281 0.2671 0.6048 70 K 0.1100 0.2750 0.6150 71 Q 0.1358 0.2290 0.6352 72 E 0.1286 0.2669 0.6045 73 E 0.1459 0.2185 0.6356 74 T 0.1597 0.1188 0.7215 75 E 0.0160 0.7341 0.2499 76 T 0.0102 0.8669 0.1229 77 D 0.0094 0.9150 0.0756 78 L 0.0084 0.9207 0.0709 79 N 0.0084 0.9195 0.0721 80 V 0.0083 0.9228 0.0689 81 L 0.0085 0.9203 0.0712 82 A 0.0084 0.9194 0.0722 83 K 0.0084 0.9166 0.0750 84 T 0.0086 0.9162 0.0752 85 Y 0.0100 0.9089 0.0811 86 T 0.0084 0.9187 0.0729 87 E 0.0083 0.9211 0.0705 88 K 0.0083 0.9224 0.0693 89 T 0.0083 0.9230 0.0687 90 V 0.0084 0.9198 0.0719 91 A 0.0084 0.9209 0.0707 92 I 0.0089 0.9131 0.0780 93 L 0.0096 0.8888 0.1016 94 E 0.0108 0.7397 0.2495 95 Q 0.0207 0.4167 0.5626 96 L 0.1621 0.1098 0.7281 97 T 0.1564 0.0457 0.7979 98 E 0.0141 0.7162 0.2697 99 E 0.0122 0.7979 0.1899 100 Q 0.0205 0.7908 0.1887 101 L 0.0545 0.7023 0.2432 102 D 0.0555 0.5506 0.3938 103 R 0.1127 0.4029 0.4844 104 E 0.2216 0.2569 0.5215 105 I 0.3319 0.1116 0.5565 106 D 0.3354 0.1046 0.5600 107 L 0.3245 0.1431 0.5323 108 T 0.2944 0.1245 0.5811 109 S 0.1802 0.2528 0.5670 110 A 0.0983 0.3499 0.5518 111 F 0.0899 0.1582 0.7519 112 G 0.0710 0.0956 0.8335 113 R 0.2742 0.0453 0.6805 114 K 0.3766 0.0526 0.5708 115 V 0.3758 0.0618 0.5624 116 T 0.2032 0.0752 0.7215 117 G 0.0185 0.7452 0.2363 118 R 0.0099 0.8693 0.1208 119 A 0.0086 0.9214 0.0701 120 L 0.0083 0.9230 0.0687 121 L 0.0083 0.9231 0.0686 122 Q 0.0083 0.9218 0.0699 123 L 0.0085 0.9162 0.0753 124 A 0.0094 0.9082 0.0825 125 M 0.0107 0.8945 0.0948 126 E 0.0139 0.8532 0.1329 127 H 0.0259 0.8088 0.1654 128 E 0.0381 0.7701 0.1917 129 I 0.0578 0.7125 0.2298 130 H 0.0796 0.6170 0.3034 131 H 0.0970 0.5585 0.3445 132 K 0.0441 0.6754 0.2806 133 G 0.0395 0.7415 0.2190 134 N 0.0313 0.8445 0.1242 135 L 0.0216 0.8938 0.0847 136 F 0.0108 0.9170 0.0721 137 V 0.0099 0.9198 0.0703 138 Y 0.0098 0.9193 0.0710 139 V 0.0091 0.9161 0.0748 140 R 0.0091 0.9081 0.0828 141 E 0.0136 0.8093 0.1770 142 M 0.0613 0.3525 0.5862 143 G 0.0451 0.0929 0.8619 144 H 0.1549 0.0514 0.7938 145 T 0.2232 0.0624 0.7144 146 E 0.2367 0.0652 0.6980 147 L 0.2504 0.0747 0.6749 148 P 0.2014 0.2083 0.5903 149 F 0.2064 0.2374 0.5562 150 Y 0.1788 0.1914 0.6298 151 Q 0.0869 0.3957 0.5174 152 Q 0.1067 0.3722 0.5210 153 R 0.1538 0.2872 0.5590 154 M 0.1799 0.2222 0.5979