# This file is the result of combining several RDB files, specifically # T0454.t2k.str2.rdb (weight 1.54425) # T0454.t2k.str4.rdb (weight 0.924988) # T0454.t2k.pb.rdb (weight 0.789901) # T0454.t2k.bys.rdb (weight 0.748322) # T0454.t2k.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.t2k.str2.rdb # ============================================ # TARGET T0454 # Using neural net dunbrack-40pc-3157-t2k-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.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 4992 # # ============================================ # Comments from T0454.t2k.str4.rdb # ============================================ # TARGET T0454 # Using neural net dunbrack-40pc-3157-t2k-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.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 4992 # # ============================================ # Comments from T0454.t2k.pb.rdb # ============================================ # TARGET T0454 # Using neural net dunbrack-40pc-3157-t2k-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.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 4992 # # ============================================ # Comments from T0454.t2k.bys.rdb # ============================================ # TARGET T0454 # Using neural net dunbrack-40pc-3157-t2k-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.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 4992 # # ============================================ # Comments from T0454.t2k.alpha.rdb # ============================================ # TARGET T0454 # Using neural net dunbrack-40pc-3157-t2k-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.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 4992 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2893 0.0697 0.6409 2 T 0.1772 0.0577 0.7651 3 R 0.0700 0.5027 0.4273 4 A 0.0168 0.7685 0.2147 5 D 0.0196 0.8099 0.1705 6 C 0.0141 0.8740 0.1119 7 R 0.0089 0.9087 0.0824 8 S 0.0083 0.9224 0.0693 9 R 0.0084 0.9236 0.0680 10 L 0.0083 0.9227 0.0690 11 M 0.0083 0.9239 0.0678 12 E 0.0083 0.9248 0.0670 13 V 0.0083 0.9246 0.0671 14 A 0.0083 0.9224 0.0693 15 T 0.0083 0.9225 0.0692 16 E 0.0083 0.9242 0.0675 17 L 0.0083 0.9226 0.0690 18 F 0.0085 0.9143 0.0773 19 A 0.0091 0.8880 0.1029 20 Q 0.0150 0.7946 0.1905 21 K 0.0472 0.3299 0.6230 22 G 0.0486 0.1185 0.8329 23 F 0.1398 0.1841 0.6761 24 Y 0.1865 0.2717 0.5417 25 G 0.1833 0.3509 0.4658 26 V 0.1987 0.3877 0.4136 27 S 0.1538 0.3608 0.4855 28 I 0.0142 0.7855 0.2003 29 R 0.0092 0.8785 0.1123 30 E 0.0083 0.9236 0.0681 31 L 0.0083 0.9235 0.0682 32 A 0.0083 0.9217 0.0700 33 Q 0.0084 0.9149 0.0766 34 A 0.0142 0.8179 0.1679 35 A 0.0563 0.4105 0.5332 36 G 0.0466 0.0769 0.8765 37 A 0.1483 0.0858 0.7660 38 S 0.1968 0.0870 0.7162 39 I 0.0970 0.5157 0.3873 40 S 0.1015 0.5799 0.3186 41 M 0.2692 0.5349 0.1959 42 I 0.2896 0.5372 0.1733 43 S 0.2777 0.5395 0.1828 44 Y 0.2223 0.5285 0.2492 45 H 0.2028 0.3796 0.4176 46 F 0.1736 0.2475 0.5789 47 G 0.0966 0.2084 0.6950 48 G 0.1037 0.1863 0.7101 49 K 0.0219 0.7185 0.2596 50 E 0.0118 0.8415 0.1467 51 G 0.0090 0.9028 0.0883 52 L 0.0084 0.9205 0.0711 53 Y 0.0083 0.9217 0.0700 54 A 0.0083 0.9238 0.0679 55 A 0.0083 0.9247 0.0671 56 V 0.0083 0.9237 0.0680 57 L 0.0083 0.9219 0.0698 58 Q 0.0084 0.9193 0.0724 59 E 0.0084 0.9183 0.0733 60 Q 0.0087 0.9110 0.0803 61 F 0.0087 0.9059 0.0854 62 A 0.0088 0.9009 0.0903 63 C 0.0116 0.8578 0.1306 64 F 0.0221 0.7964 0.1815 65 G 0.0230 0.7539 0.2232 66 Q 0.0360 0.7295 0.2346 67 L 0.0432 0.7219 0.2349 68 D 0.0374 0.7555 0.2071 69 D 0.0380 0.7641 0.1978 70 I 0.0509 0.7097 0.2394 71 R 0.0745 0.5383 0.3872 72 G 0.0725 0.3472 0.5803 73 Q 0.0944 0.2644 0.6411 74 A 0.0972 0.1874 0.7154 75 G 0.0889 0.1370 0.7741 76 D 0.1496 0.0535 0.7968 77 P 0.0172 0.7296 0.2532 78 L 0.0095 0.8674 0.1231 79 A 0.0084 0.9196 0.0720 80 V 0.0083 0.9228 0.0689 81 M 0.0083 0.9238 0.0680 82 T 0.0083 0.9237 0.0680 83 A 0.0083 0.9242 0.0675 84 Y 0.0083 0.9238 0.0679 85 L 0.0083 0.9227 0.0690 86 R 0.0083 0.9223 0.0694 87 W 0.0083 0.9229 0.0688 88 T 0.0084 0.9188 0.0728 89 I 0.0085 0.9135 0.0780 90 Q 0.0087 0.9073 0.0841 91 R 0.0109 0.8568 0.1322 92 H 0.0215 0.7416 0.2369 93 R 0.0342 0.5947 0.3711 94 N 0.0547 0.3713 0.5740 95 N 0.1292 0.2082 0.6626 96 P 0.0209 0.6919 0.2872 97 Q 0.0204 0.7606 0.2190 98 L 0.0282 0.8370 0.1349 99 L 0.0252 0.8788 0.0960 100 R 0.0288 0.8794 0.0918 101 F 0.0344 0.8692 0.0965 102 Y 0.0482 0.8297 0.1221 103 T 0.0497 0.8011 0.1493 104 S 0.0415 0.7781 0.1804 105 E 0.0511 0.6760 0.2729 106 L 0.0745 0.5070 0.4185 107 T 0.0978 0.2826 0.6197 108 N 0.1543 0.1350 0.7107 109 P 0.1143 0.1920 0.6937 110 T 0.1325 0.1375 0.7300 111 P 0.0218 0.6533 0.3249 112 C 0.0240 0.7441 0.2319 113 F 0.0290 0.8263 0.1447 114 A 0.0188 0.8689 0.1123 115 A 0.0153 0.8674 0.1173 116 I 0.0214 0.8241 0.1544 117 V 0.0417 0.7544 0.2040 118 S 0.0353 0.7615 0.2032 119 P 0.0108 0.8605 0.1288 120 A 0.0111 0.8860 0.1029 121 I 0.0092 0.9116 0.0793 122 A 0.0084 0.9151 0.0765 123 S 0.0083 0.9221 0.0695 124 V 0.0083 0.9214 0.0702 125 I 0.0083 0.9231 0.0686 126 R 0.0083 0.9242 0.0675 127 L 0.0083 0.9245 0.0672 128 L 0.0083 0.9225 0.0692 129 A 0.0083 0.9210 0.0707 130 E 0.0083 0.9244 0.0673 131 S 0.0083 0.9225 0.0691 132 I 0.0084 0.9186 0.0730 133 E 0.0084 0.9185 0.0731 134 A 0.0088 0.9089 0.0823 135 G 0.0116 0.8704 0.1180 136 M 0.0134 0.8346 0.1520 137 T 0.0210 0.7245 0.2546 138 R 0.0586 0.2983 0.6431 139 G 0.0475 0.1207 0.8318 140 L 0.1777 0.1257 0.6966 141 F 0.2838 0.1055 0.6107 142 R 0.2006 0.1345 0.6649 143 R 0.0846 0.3964 0.5190 144 D 0.0947 0.3010 0.6043 145 L 0.1356 0.3088 0.5556 146 H 0.1316 0.2679 0.6005 147 A 0.0122 0.7655 0.2223 148 V 0.0091 0.8757 0.1152 149 N 0.0083 0.9226 0.0691 150 S 0.0083 0.9228 0.0690 151 A 0.0083 0.9241 0.0676 152 L 0.0083 0.9247 0.0670 153 A 0.0083 0.9244 0.0673 154 L 0.0083 0.9232 0.0685 155 A 0.0083 0.9232 0.0685 156 G 0.0083 0.9214 0.0703 157 M 0.0085 0.9141 0.0774 158 V 0.0091 0.8993 0.0916 159 N 0.0099 0.8891 0.1010 160 Y 0.0139 0.8802 0.1058 161 F 0.0196 0.8663 0.1141 162 F 0.0297 0.8378 0.1325 163 L 0.0454 0.7959 0.1587 164 S 0.0713 0.7144 0.2143 165 T 0.0990 0.6255 0.2755 166 L 0.1218 0.5116 0.3666 167 A 0.1340 0.3783 0.4877 168 T 0.1372 0.2634 0.5994 169 E 0.1010 0.2334 0.6656 170 G 0.1041 0.1531 0.7429 171 L 0.1669 0.1517 0.6814 172 T 0.1962 0.1270 0.6768 173 S 0.1709 0.1524 0.6767 174 H 0.1590 0.1323 0.7087 175 S 0.1645 0.0660 0.7695 176 P 0.0481 0.4518 0.5000 177 D 0.0502 0.5161 0.4337 178 Q 0.0398 0.6998 0.2604 179 D 0.0154 0.8561 0.1285 180 E 0.0088 0.9052 0.0860 181 E 0.0083 0.9216 0.0701 182 L 0.0083 0.9215 0.0702 183 I 0.0083 0.9235 0.0682 184 R 0.0083 0.9236 0.0681 185 Q 0.0083 0.9229 0.0688 186 Y 0.0084 0.9198 0.0718 187 V 0.0084 0.9177 0.0739 188 A 0.0088 0.9138 0.0773 189 I 0.0124 0.8878 0.0998 190 F 0.0296 0.8051 0.1653 191 T 0.0585 0.6410 0.3005 192 R 0.0676 0.4191 0.5133 193 G 0.0847 0.2456 0.6698 194 I 0.1955 0.1976 0.6070 195 M 0.2675 0.1208 0.6117 196 A 0.2382 0.1414 0.6204 197 D 0.1439 0.1620 0.6940 198 G 0.0880 0.1552 0.7568 199 G 0.1170 0.1555 0.7275 200 A 0.1789 0.1584 0.6627 201 A 0.2182 0.0867 0.6951 202 P 0.1988 0.1821 0.6191 203 A 0.2130 0.2470 0.5401