# This file is the result of combining several RDB files, specifically # TR454.t06.str2.rdb (weight 1.54425) # TR454.t06.str4.rdb (weight 0.924988) # TR454.t06.pb.rdb (weight 0.789901) # TR454.t06.bys.rdb (weight 0.748322) # TR454.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 TR454.t06.str2.rdb # ============================================ # TARGET TR454 # 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 TR454.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 10175 # # ============================================ # Comments from TR454.t06.str4.rdb # ============================================ # TARGET TR454 # 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 TR454.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 10175 # # ============================================ # Comments from TR454.t06.pb.rdb # ============================================ # TARGET TR454 # 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 TR454.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 10175 # # ============================================ # Comments from TR454.t06.bys.rdb # ============================================ # TARGET TR454 # 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 TR454.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 10175 # # ============================================ # Comments from TR454.t06.alpha.rdb # ============================================ # TARGET TR454 # 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 TR454.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 10175 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.0951 0.3037 0.6012 2 C 0.0515 0.6638 0.2847 3 R 0.0124 0.8768 0.1108 4 S 0.0088 0.9107 0.0805 5 R 0.0083 0.9219 0.0698 6 L 0.0084 0.9189 0.0728 7 M 0.0083 0.9217 0.0700 8 E 0.0083 0.9243 0.0675 9 V 0.0083 0.9243 0.0675 10 A 0.0083 0.9245 0.0673 11 T 0.0083 0.9230 0.0687 12 E 0.0083 0.9242 0.0676 13 L 0.0083 0.9226 0.0690 14 F 0.0085 0.9175 0.0741 15 A 0.0088 0.9050 0.0862 16 Q 0.0154 0.7931 0.1915 17 K 0.0485 0.4529 0.4986 18 G 0.0462 0.2027 0.7511 19 F 0.1189 0.2607 0.6204 20 Y 0.1076 0.3547 0.5377 21 G 0.1258 0.3816 0.4926 22 V 0.2287 0.2735 0.4977 23 S 0.1793 0.2074 0.6132 24 I 0.0140 0.7706 0.2154 25 R 0.0091 0.8749 0.1161 26 E 0.0083 0.9236 0.0681 27 L 0.0084 0.9233 0.0684 28 A 0.0084 0.9178 0.0739 29 Q 0.0085 0.9172 0.0744 30 A 0.0111 0.8308 0.1580 31 A 0.0575 0.3290 0.6135 32 G 0.0412 0.0914 0.8673 33 A 0.1598 0.0542 0.7860 34 S 0.1746 0.0931 0.7322 35 I 0.0482 0.5253 0.4265 36 S 0.0738 0.6679 0.2584 37 M 0.1684 0.6749 0.1567 38 I 0.2364 0.6263 0.1373 39 S 0.2511 0.5818 0.1672 40 Y 0.2269 0.5115 0.2616 41 H 0.2130 0.3764 0.4106 42 F 0.1742 0.1954 0.6304 43 G 0.1031 0.1842 0.7127 44 G 0.1320 0.1432 0.7248 45 K 0.0156 0.7361 0.2482 46 E 0.0104 0.8599 0.1297 47 G 0.0092 0.9149 0.0759 48 L 0.0083 0.9222 0.0695 49 Y 0.0083 0.9213 0.0704 50 A 0.0083 0.9242 0.0675 51 A 0.0083 0.9234 0.0683 52 V 0.0083 0.9244 0.0673 53 L 0.0083 0.9223 0.0694 54 Q 0.0083 0.9222 0.0695 55 E 0.0084 0.9180 0.0736 56 Q 0.0086 0.9117 0.0798 57 F 0.0087 0.9048 0.0864 58 A 0.0089 0.8992 0.0919 59 C 0.0114 0.8647 0.1239 60 F 0.0225 0.7976 0.1799 61 G 0.0232 0.7470 0.2298 62 Q 0.0456 0.6814 0.2730 63 L 0.0710 0.6309 0.2981 64 D 0.0618 0.6245 0.3138 65 D 0.0735 0.6024 0.3241 66 I 0.0840 0.5694 0.3466 67 R 0.1026 0.4411 0.4563 68 G 0.0925 0.3926 0.5149 69 Q 0.0972 0.3130 0.5897 70 A 0.1002 0.2125 0.6873 71 G 0.1126 0.1276 0.7598 72 D 0.1570 0.0541 0.7889 73 P 0.0143 0.7433 0.2424 74 L 0.0092 0.8674 0.1234 75 A 0.0083 0.9224 0.0693 76 V 0.0083 0.9238 0.0679 77 M 0.0083 0.9229 0.0688 78 T 0.0083 0.9238 0.0679 79 A 0.0083 0.9243 0.0675 80 Y 0.0083 0.9243 0.0674 81 L 0.0083 0.9232 0.0685 82 R 0.0083 0.9231 0.0686 83 W 0.0084 0.9222 0.0694 84 T 0.0084 0.9201 0.0715 85 I 0.0085 0.9120 0.0795 86 Q 0.0091 0.8962 0.0947 87 R 0.0124 0.8434 0.1443 88 H 0.0219 0.7629 0.2152 89 R 0.0258 0.6660 0.3082 90 N 0.0465 0.4203 0.5332 91 N 0.1336 0.2383 0.6281 92 P 0.0164 0.7138 0.2698 93 Q 0.0114 0.8345 0.1541 94 L 0.0125 0.8967 0.0908 95 L 0.0095 0.9117 0.0788 96 R 0.0100 0.9123 0.0778 97 F 0.0129 0.9012 0.0859 98 Y 0.0228 0.8700 0.1072 99 T 0.0288 0.8327 0.1384 100 S 0.0247 0.7880 0.1873 101 E 0.0328 0.6755 0.2917 102 L 0.0606 0.4878 0.4516 103 T 0.0815 0.3121 0.6065 104 N 0.1531 0.1292 0.7177 105 P 0.1107 0.2035 0.6858 106 T 0.1610 0.1440 0.6949 107 P 0.0261 0.6617 0.3122 108 C 0.0229 0.7689 0.2082 109 F 0.0291 0.8180 0.1529 110 A 0.0152 0.8701 0.1146 111 A 0.0140 0.8633 0.1228 112 I 0.0210 0.8244 0.1546 113 V 0.0336 0.7727 0.1937 114 S 0.0313 0.7939 0.1748 115 P 0.0107 0.8676 0.1217 116 A 0.0103 0.8920 0.0977 117 I 0.0088 0.9122 0.0790 118 A 0.0084 0.9187 0.0729 119 S 0.0083 0.9233 0.0684 120 V 0.0083 0.9232 0.0685 121 I 0.0083 0.9230 0.0687 122 R 0.0083 0.9241 0.0677 123 L 0.0083 0.9243 0.0675 124 L 0.0083 0.9235 0.0682 125 A 0.0083 0.9210 0.0707 126 E 0.0083 0.9238 0.0679 127 S 0.0083 0.9222 0.0694 128 I 0.0083 0.9217 0.0699 129 E 0.0085 0.9125 0.0790 130 A 0.0092 0.8634 0.1274 131 G 0.0146 0.8127 0.1727 132 M 0.0216 0.8148 0.1636 133 T 0.0285 0.6778 0.2937 134 R 0.0570 0.2627 0.6803 135 G 0.0534 0.1240 0.8225 136 L 0.2018 0.1450 0.6532 137 F 0.2989 0.1255 0.5756 138 R 0.2074 0.1471 0.6455 139 R 0.0926 0.4238 0.4835 140 D 0.1067 0.3615 0.5318 141 L 0.1448 0.3641 0.4910 142 H 0.1320 0.3086 0.5595 143 A 0.0148 0.7745 0.2107 144 V 0.0092 0.8750 0.1158 145 N 0.0083 0.9222 0.0695 146 S 0.0083 0.9237 0.0680 147 A 0.0083 0.9247 0.0670 148 L 0.0083 0.9248 0.0669 149 A 0.0083 0.9245 0.0672 150 L 0.0083 0.9240 0.0677 151 A 0.0083 0.9240 0.0677 152 G 0.0083 0.9231 0.0686 153 M 0.0083 0.9215 0.0702 154 V 0.0084 0.9146 0.0769 155 N 0.0087 0.9051 0.0862 156 Y 0.0092 0.9004 0.0904 157 F 0.0108 0.9010 0.0881 158 F 0.0144 0.8876 0.0980 159 L 0.0210 0.8580 0.1209 160 S 0.0270 0.8206 0.1524 161 T 0.0365 0.7828 0.1807 162 L 0.0533 0.7101 0.2367 163 A 0.0701 0.6018 0.3281 164 T 0.0857 0.4791 0.4352 165 E 0.0737 0.3567 0.5696 166 G 0.0763 0.2224 0.7013 167 L 0.1654 0.1502 0.6844 168 T 0.1923 0.1510 0.6567 169 S 0.1700 0.1685 0.6615 170 H 0.1763 0.1197 0.7040 171 S 0.1920 0.0408 0.7672 172 P 0.0541 0.3827 0.5632 173 D 0.0599 0.3702 0.5700 174 Q 0.0975 0.3585 0.5440 175 D 0.0194 0.7853 0.1953 176 E 0.0088 0.8948 0.0965 177 E 0.0084 0.9195 0.0721 178 L 0.0083 0.9242 0.0675 179 I 0.0083 0.9228 0.0689 180 R 0.0083 0.9242 0.0675 181 Q 0.0083 0.9242 0.0675 182 Y 0.0083 0.9248 0.0669 183 V 0.0083 0.9231 0.0687 184 A 0.0083 0.9237 0.0680 185 I 0.0084 0.9202 0.0713 186 F 0.0087 0.9087 0.0826 187 T 0.0113 0.8450 0.1437 188 R 0.0242 0.5857 0.3901 189 G 0.0437 0.2900 0.6662 190 I 0.1374 0.1455 0.7171 191 M 0.1445 0.1463 0.7092 192 A 0.1192 0.1925 0.6882