# This file is the result of combining several RDB files, specifically # T0454.t04.str2.rdb (weight 1.54425) # T0454.t04.str4.rdb (weight 0.924988) # T0454.t04.pb.rdb (weight 0.789901) # T0454.t04.bys.rdb (weight 0.748322) # T0454.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 T0454.t04.str2.rdb # ============================================ # TARGET T0454 # 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 T0454.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 2182 # # ============================================ # Comments from T0454.t04.str4.rdb # ============================================ # TARGET T0454 # 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 T0454.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 2182 # # ============================================ # Comments from T0454.t04.pb.rdb # ============================================ # TARGET T0454 # 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 T0454.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 2182 # # ============================================ # Comments from T0454.t04.bys.rdb # ============================================ # TARGET T0454 # 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 T0454.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 2182 # # ============================================ # Comments from T0454.t04.alpha.rdb # ============================================ # TARGET T0454 # 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 T0454.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 2182 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2385 0.0524 0.7091 2 T 0.1679 0.0390 0.7931 3 R 0.0737 0.4219 0.5044 4 A 0.0149 0.7268 0.2583 5 D 0.0240 0.7860 0.1900 6 C 0.0179 0.8610 0.1210 7 R 0.0091 0.8925 0.0984 8 S 0.0085 0.9134 0.0781 9 R 0.0083 0.9235 0.0682 10 L 0.0083 0.9224 0.0693 11 M 0.0083 0.9239 0.0678 12 E 0.0083 0.9252 0.0666 13 V 0.0083 0.9252 0.0666 14 A 0.0083 0.9246 0.0671 15 T 0.0083 0.9244 0.0674 16 E 0.0083 0.9241 0.0676 17 L 0.0083 0.9148 0.0769 18 F 0.0084 0.9093 0.0823 19 A 0.0088 0.8994 0.0918 20 Q 0.0122 0.8023 0.1856 21 K 0.0554 0.3605 0.5841 22 G 0.0584 0.1769 0.7647 23 F 0.1149 0.2987 0.5864 24 Y 0.1201 0.3130 0.5669 25 G 0.1413 0.2516 0.6071 26 V 0.2057 0.2133 0.5810 27 S 0.1989 0.1097 0.6914 28 I 0.0144 0.7453 0.2403 29 R 0.0092 0.8723 0.1185 30 E 0.0083 0.9217 0.0699 31 L 0.0084 0.9181 0.0735 32 A 0.0084 0.9108 0.0808 33 Q 0.0088 0.8967 0.0945 34 A 0.0132 0.8185 0.1683 35 A 0.0585 0.2899 0.6515 36 G 0.0392 0.0902 0.8705 37 A 0.1393 0.0890 0.7716 38 S 0.1782 0.0907 0.7311 39 I 0.1324 0.4761 0.3915 40 S 0.1596 0.5275 0.3129 41 M 0.2991 0.4797 0.2212 42 I 0.4431 0.3669 0.1900 43 S 0.4261 0.3881 0.1858 44 Y 0.4467 0.3320 0.2213 45 H 0.3272 0.2524 0.4204 46 F 0.1885 0.2002 0.6114 47 G 0.1143 0.1813 0.7044 48 G 0.1120 0.1720 0.7160 49 K 0.0179 0.6659 0.3162 50 E 0.0106 0.8363 0.1532 51 G 0.0086 0.9101 0.0813 52 L 0.0089 0.9191 0.0719 53 Y 0.0083 0.9218 0.0699 54 A 0.0083 0.9236 0.0681 55 A 0.0083 0.9237 0.0681 56 V 0.0083 0.9234 0.0683 57 L 0.0084 0.9175 0.0741 58 Q 0.0084 0.9196 0.0721 59 E 0.0087 0.9116 0.0797 60 Q 0.0102 0.8854 0.1045 61 F 0.0112 0.8606 0.1281 62 A 0.0111 0.7911 0.1978 63 C 0.0219 0.6864 0.2916 64 F 0.0496 0.5602 0.3902 65 G 0.0499 0.5281 0.4220 66 Q 0.0713 0.6163 0.3124 67 L 0.0436 0.7362 0.2202 68 D 0.0300 0.7985 0.1715 69 D 0.0273 0.8196 0.1531 70 I 0.0343 0.7625 0.2033 71 R 0.0588 0.6074 0.3338 72 G 0.0614 0.4362 0.5024 73 Q 0.0835 0.3095 0.6069 74 A 0.0800 0.2384 0.6815 75 G 0.0777 0.1532 0.7691 76 D 0.1587 0.0656 0.7757 77 P 0.0176 0.6941 0.2883 78 L 0.0093 0.8619 0.1287 79 A 0.0083 0.9217 0.0700 80 V 0.0083 0.9224 0.0692 81 M 0.0083 0.9226 0.0691 82 T 0.0083 0.9240 0.0677 83 A 0.0083 0.9247 0.0671 84 Y 0.0083 0.9249 0.0668 85 L 0.0083 0.9239 0.0679 86 R 0.0083 0.9245 0.0672 87 W 0.0083 0.9237 0.0680 88 T 0.0084 0.9211 0.0706 89 I 0.0085 0.9186 0.0729 90 Q 0.0087 0.9157 0.0755 91 R 0.0125 0.8782 0.1092 92 H 0.0240 0.7858 0.1902 93 R 0.0247 0.6382 0.3371 94 N 0.0416 0.4232 0.5352 95 N 0.1326 0.2626 0.6047 96 P 0.0147 0.7420 0.2433 97 Q 0.0134 0.8250 0.1616 98 L 0.0212 0.8674 0.1113 99 L 0.0187 0.8927 0.0885 100 R 0.0186 0.9017 0.0797 101 F 0.0269 0.8890 0.0840 102 Y 0.0401 0.8554 0.1045 103 T 0.0359 0.8394 0.1248 104 S 0.0332 0.8141 0.1528 105 E 0.0514 0.6718 0.2768 106 L 0.0875 0.4193 0.4932 107 T 0.1028 0.2496 0.6476 108 N 0.1513 0.1162 0.7325 109 P 0.1138 0.1960 0.6902 110 T 0.1437 0.1584 0.6980 111 P 0.0174 0.7160 0.2666 112 C 0.0166 0.7977 0.1856 113 F 0.0159 0.8604 0.1237 114 A 0.0139 0.8785 0.1077 115 A 0.0124 0.8810 0.1066 116 I 0.0192 0.8356 0.1452 117 V 0.0303 0.7544 0.2153 118 S 0.0439 0.7570 0.1991 119 P 0.0126 0.8660 0.1214 120 A 0.0149 0.8677 0.1174 121 I 0.0098 0.8998 0.0903 122 A 0.0085 0.9189 0.0727 123 S 0.0083 0.9206 0.0710 124 V 0.0083 0.9220 0.0697 125 I 0.0083 0.9240 0.0677 126 R 0.0083 0.9246 0.0672 127 L 0.0083 0.9242 0.0676 128 L 0.0083 0.9230 0.0687 129 A 0.0083 0.9243 0.0675 130 E 0.0083 0.9242 0.0676 131 S 0.0083 0.9236 0.0682 132 I 0.0083 0.9233 0.0684 133 E 0.0083 0.9210 0.0706 134 A 0.0087 0.9104 0.0809 135 G 0.0098 0.8850 0.1052 136 M 0.0107 0.8796 0.1097 137 T 0.0134 0.8133 0.1732 138 R 0.0566 0.2911 0.6523 139 G 0.0506 0.1098 0.8395 140 L 0.1667 0.1520 0.6813 141 F 0.2971 0.1466 0.5563 142 R 0.2321 0.1660 0.6019 143 R 0.1024 0.4515 0.4461 144 D 0.1084 0.2755 0.6161 145 L 0.1553 0.2496 0.5951 146 H 0.1712 0.1537 0.6751 147 A 0.0142 0.7508 0.2350 148 V 0.0092 0.8696 0.1212 149 N 0.0083 0.9212 0.0704 150 S 0.0083 0.9239 0.0678 151 A 0.0083 0.9241 0.0676 152 L 0.0083 0.9250 0.0668 153 A 0.0083 0.9247 0.0671 154 L 0.0083 0.9227 0.0690 155 A 0.0083 0.9215 0.0702 156 G 0.0083 0.9187 0.0730 157 M 0.0085 0.9135 0.0779 158 V 0.0093 0.8943 0.0964 159 N 0.0117 0.8676 0.1207 160 Y 0.0188 0.8453 0.1359 161 F 0.0317 0.8265 0.1419 162 F 0.0515 0.7715 0.1771 163 L 0.0655 0.6950 0.2395 164 S 0.0715 0.6265 0.3020 165 T 0.0593 0.6497 0.2910 166 L 0.0677 0.6378 0.2945 167 A 0.0906 0.5711 0.3383 168 T 0.1109 0.4943 0.3948 169 E 0.1177 0.4302 0.4521 170 G 0.1372 0.3362 0.5265 171 L 0.1856 0.2512 0.5632 172 T 0.2096 0.1728 0.6176 173 S 0.1761 0.1737 0.6502 174 H 0.1433 0.1425 0.7142 175 S 0.1773 0.0463 0.7764 176 P 0.0657 0.3724 0.5619 177 D 0.0777 0.3202 0.6021 178 Q 0.1197 0.2835 0.5969 179 D 0.0169 0.7415 0.2415 180 E 0.0091 0.8714 0.1195 181 E 0.0084 0.9185 0.0732 182 L 0.0083 0.9225 0.0692 183 I 0.0083 0.9222 0.0695 184 R 0.0083 0.9247 0.0670 185 Q 0.0083 0.9250 0.0667 186 Y 0.0083 0.9243 0.0675 187 V 0.0083 0.9242 0.0675 188 A 0.0083 0.9246 0.0671 189 I 0.0084 0.9169 0.0747 190 F 0.0087 0.9185 0.0728 191 T 0.0096 0.8993 0.0911 192 R 0.0163 0.8152 0.1685 193 G 0.0421 0.6247 0.3332 194 I 0.0950 0.4713 0.4337 195 M 0.1640 0.3011 0.5349 196 A 0.1544 0.2762 0.5694 197 D 0.1294 0.1877 0.6829 198 G 0.1020 0.1954 0.7027 199 G 0.1181 0.1948 0.6871 200 A 0.1944 0.1286 0.6769 201 A 0.2443 0.0487 0.7070 202 P 0.2030 0.0700 0.7271 203 A 0.1901 0.1350 0.6749