# This file is the result of combining several RDB files, specifically # T0454.t06.str2.rdb (weight 1.54425) # T0454.t06.str4.rdb (weight 0.924988) # T0454.t06.pb.rdb (weight 0.789901) # T0454.t06.bys.rdb (weight 0.748322) # T0454.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 T0454.t06.str2.rdb # ============================================ # TARGET T0454 # 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 T0454.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 10199 # # ============================================ # Comments from T0454.t06.str4.rdb # ============================================ # TARGET T0454 # 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 T0454.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 10199 # # ============================================ # Comments from T0454.t06.pb.rdb # ============================================ # TARGET T0454 # 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 T0454.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 10199 # # ============================================ # Comments from T0454.t06.bys.rdb # ============================================ # TARGET T0454 # 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 T0454.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 10199 # # ============================================ # Comments from T0454.t06.alpha.rdb # ============================================ # TARGET T0454 # 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 T0454.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 10199 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1876 0.0782 0.7342 2 T 0.1649 0.0688 0.7662 3 R 0.1138 0.3707 0.5155 4 A 0.0358 0.6852 0.2790 5 D 0.0309 0.7600 0.2090 6 C 0.0285 0.8086 0.1629 7 R 0.0102 0.8926 0.0972 8 S 0.0084 0.9147 0.0769 9 R 0.0083 0.9235 0.0682 10 L 0.0083 0.9217 0.0700 11 M 0.0083 0.9219 0.0698 12 E 0.0083 0.9244 0.0674 13 V 0.0083 0.9243 0.0674 14 A 0.0083 0.9245 0.0672 15 T 0.0083 0.9230 0.0687 16 E 0.0083 0.9241 0.0677 17 L 0.0083 0.9226 0.0690 18 F 0.0085 0.9174 0.0742 19 A 0.0088 0.9049 0.0864 20 Q 0.0154 0.7928 0.1918 21 K 0.0485 0.4534 0.4981 22 G 0.0463 0.2037 0.7501 23 F 0.1187 0.2616 0.6197 24 Y 0.1074 0.3567 0.5359 25 G 0.1254 0.3845 0.4901 26 V 0.2290 0.2777 0.4933 27 S 0.1801 0.2112 0.6087 28 I 0.0140 0.7707 0.2152 29 R 0.0091 0.8748 0.1161 30 E 0.0083 0.9236 0.0681 31 L 0.0084 0.9233 0.0684 32 A 0.0084 0.9178 0.0738 33 Q 0.0085 0.9172 0.0744 34 A 0.0111 0.8304 0.1584 35 A 0.0575 0.3297 0.6128 36 G 0.0412 0.0916 0.8672 37 A 0.1598 0.0545 0.7857 38 S 0.1748 0.0931 0.7321 39 I 0.0482 0.5248 0.4270 40 S 0.0736 0.6667 0.2597 41 M 0.1688 0.6740 0.1572 42 I 0.2382 0.6241 0.1377 43 S 0.2536 0.5796 0.1668 44 Y 0.2293 0.5100 0.2606 45 H 0.2150 0.3754 0.4095 46 F 0.1752 0.1957 0.6291 47 G 0.1027 0.1845 0.7128 48 G 0.1315 0.1438 0.7247 49 K 0.0156 0.7360 0.2484 50 E 0.0104 0.8594 0.1302 51 G 0.0092 0.9148 0.0760 52 L 0.0083 0.9222 0.0695 53 Y 0.0083 0.9212 0.0704 54 A 0.0083 0.9242 0.0676 55 A 0.0083 0.9234 0.0683 56 V 0.0083 0.9243 0.0674 57 L 0.0083 0.9221 0.0696 58 Q 0.0083 0.9217 0.0700 59 E 0.0085 0.9154 0.0762 60 Q 0.0089 0.9041 0.0870 61 F 0.0096 0.8876 0.1027 62 A 0.0109 0.8635 0.1255 63 C 0.0182 0.7716 0.2102 64 F 0.0355 0.6660 0.2985 65 G 0.0302 0.6779 0.2919 66 Q 0.0541 0.6500 0.2959 67 L 0.0507 0.7506 0.1987 68 D 0.0283 0.8228 0.1490 69 D 0.0302 0.8138 0.1560 70 I 0.0411 0.7446 0.2143 71 R 0.0536 0.6375 0.3090 72 G 0.0496 0.5391 0.4113 73 Q 0.0715 0.3806 0.5479 74 A 0.0880 0.2290 0.6830 75 G 0.0906 0.1492 0.7602 76 D 0.1486 0.0706 0.7808 77 P 0.0156 0.7424 0.2420 78 L 0.0092 0.8680 0.1228 79 A 0.0083 0.9221 0.0696 80 V 0.0083 0.9239 0.0678 81 M 0.0083 0.9231 0.0686 82 T 0.0083 0.9238 0.0679 83 A 0.0083 0.9243 0.0675 84 Y 0.0083 0.9243 0.0674 85 L 0.0083 0.9232 0.0685 86 R 0.0083 0.9231 0.0686 87 W 0.0084 0.9222 0.0694 88 T 0.0084 0.9202 0.0713 89 I 0.0085 0.9126 0.0789 90 Q 0.0091 0.8967 0.0942 91 R 0.0124 0.8460 0.1416 92 H 0.0222 0.7667 0.2111 93 R 0.0255 0.6746 0.2999 94 N 0.0469 0.4350 0.5181 95 N 0.1363 0.2399 0.6238 96 P 0.0176 0.7026 0.2798 97 Q 0.0124 0.8284 0.1592 98 L 0.0131 0.8932 0.0937 99 L 0.0097 0.9104 0.0799 100 R 0.0101 0.9113 0.0786 101 F 0.0138 0.8998 0.0864 102 Y 0.0235 0.8692 0.1073 103 T 0.0297 0.8332 0.1370 104 S 0.0248 0.7884 0.1868 105 E 0.0325 0.6788 0.2887 106 L 0.0585 0.4967 0.4449 107 T 0.0812 0.3188 0.5999 108 N 0.1525 0.1335 0.7140 109 P 0.1113 0.1990 0.6896 110 T 0.1602 0.1442 0.6956 111 P 0.0255 0.6690 0.3055 112 C 0.0220 0.7768 0.2012 113 F 0.0282 0.8249 0.1470 114 A 0.0148 0.8739 0.1113 115 A 0.0134 0.8667 0.1198 116 I 0.0206 0.8273 0.1521 117 V 0.0338 0.7728 0.1934 118 S 0.0321 0.7906 0.1773 119 P 0.0107 0.8649 0.1244 120 A 0.0104 0.8897 0.0999 121 I 0.0088 0.9115 0.0796 122 A 0.0084 0.9182 0.0735 123 S 0.0083 0.9233 0.0684 124 V 0.0083 0.9231 0.0686 125 I 0.0083 0.9230 0.0687 126 R 0.0083 0.9240 0.0678 127 L 0.0083 0.9243 0.0675 128 L 0.0083 0.9235 0.0682 129 A 0.0083 0.9210 0.0707 130 E 0.0083 0.9239 0.0678 131 S 0.0083 0.9223 0.0694 132 I 0.0083 0.9221 0.0696 133 E 0.0085 0.9151 0.0765 134 A 0.0089 0.8805 0.1106 135 G 0.0122 0.8498 0.1380 136 M 0.0157 0.8546 0.1296 137 T 0.0215 0.7248 0.2537 138 R 0.0548 0.2723 0.6729 139 G 0.0501 0.1221 0.8278 140 L 0.1943 0.1386 0.6671 141 F 0.2839 0.1290 0.5872 142 R 0.1991 0.1704 0.6305 143 R 0.0841 0.4500 0.4659 144 D 0.1070 0.3823 0.5107 145 L 0.1542 0.3616 0.4842 146 H 0.1363 0.3033 0.5604 147 A 0.0148 0.7745 0.2107 148 V 0.0092 0.8739 0.1169 149 N 0.0083 0.9220 0.0697 150 S 0.0083 0.9235 0.0682 151 A 0.0083 0.9247 0.0671 152 L 0.0083 0.9248 0.0669 153 A 0.0083 0.9245 0.0672 154 L 0.0083 0.9240 0.0677 155 A 0.0083 0.9241 0.0676 156 G 0.0083 0.9231 0.0686 157 M 0.0083 0.9215 0.0702 158 V 0.0084 0.9144 0.0772 159 N 0.0087 0.9050 0.0863 160 Y 0.0092 0.9007 0.0901 161 F 0.0108 0.9020 0.0872 162 F 0.0142 0.8890 0.0968 163 L 0.0201 0.8616 0.1183 164 S 0.0262 0.8253 0.1485 165 T 0.0359 0.7904 0.1737 166 L 0.0528 0.7187 0.2284 167 A 0.0693 0.6080 0.3227 168 T 0.0848 0.4800 0.4351 169 E 0.0737 0.3545 0.5718 170 G 0.0748 0.2204 0.7048 171 L 0.1650 0.1463 0.6886 172 T 0.1921 0.1461 0.6618 173 S 0.1703 0.1646 0.6651 174 H 0.1746 0.1202 0.7052 175 S 0.1917 0.0411 0.7672 176 P 0.0532 0.3869 0.5599 177 D 0.0592 0.3761 0.5647 178 Q 0.0970 0.3680 0.5350 179 D 0.0183 0.7897 0.1920 180 E 0.0087 0.8961 0.0952 181 E 0.0083 0.9201 0.0716 182 L 0.0083 0.9242 0.0675 183 I 0.0083 0.9228 0.0689 184 R 0.0083 0.9244 0.0674 185 Q 0.0083 0.9241 0.0676 186 Y 0.0083 0.9248 0.0669 187 V 0.0083 0.9230 0.0687 188 A 0.0083 0.9240 0.0678 189 I 0.0084 0.9211 0.0705 190 F 0.0085 0.9158 0.0757 191 T 0.0097 0.8861 0.1042 192 R 0.0189 0.7382 0.2429 193 G 0.0418 0.5696 0.3886 194 I 0.0999 0.4844 0.4157 195 M 0.1601 0.3180 0.5219 196 A 0.1539 0.2490 0.5971 197 D 0.1156 0.1762 0.7082 198 G 0.0793 0.1786 0.7421 199 G 0.1021 0.1701 0.7278 200 A 0.1709 0.1147 0.7144 201 A 0.2367 0.0438 0.7195 202 P 0.2109 0.1001 0.6890 203 A 0.1917 0.1753 0.6330