# 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 10160 # # ============================================ # 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 10160 # # ============================================ # 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 10160 # # ============================================ # 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 10160 # # ============================================ # 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 10160 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2134 0.0645 0.7221 2 T 0.1651 0.0616 0.7732 3 R 0.1004 0.4293 0.4704 4 A 0.0272 0.7295 0.2433 5 D 0.0244 0.8007 0.1749 6 C 0.0225 0.8459 0.1316 7 R 0.0094 0.9012 0.0894 8 S 0.0084 0.9168 0.0748 9 R 0.0083 0.9238 0.0680 10 L 0.0083 0.9219 0.0698 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 0.4539 0.4976 22 G 0.0464 0.2045 0.7492 23 F 0.1187 0.2614 0.6198 24 Y 0.1074 0.3579 0.5347 25 G 0.1257 0.3878 0.4865 26 V 0.2284 0.2827 0.4888 27 S 0.1792 0.2165 0.6043 28 I 0.0140 0.7713 0.2147 29 R 0.0091 0.8751 0.1159 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 0.8307 0.1581 35 A 0.0575 0.3298 0.6127 36 G 0.0412 0.0916 0.8672 37 A 0.1598 0.0545 0.7857 38 S 0.1747 0.0938 0.7315 39 I 0.0484 0.5251 0.4266 40 S 0.0736 0.6667 0.2596 41 M 0.1687 0.6740 0.1574 42 I 0.2369 0.6251 0.1380 43 S 0.2529 0.5803 0.1668 44 Y 0.2287 0.5104 0.2609 45 H 0.2140 0.3760 0.4100 46 F 0.1748 0.1955 0.6297 47 G 0.1029 0.1845 0.7126 48 G 0.1318 0.1436 0.7246 49 K 0.0156 0.7359 0.2484 50 E 0.0104 0.8599 0.1297 51 G 0.0092 0.9149 0.0759 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 0.0675 57 L 0.0083 0.9221 0.0696 58 Q 0.0083 0.9216 0.0701 59 E 0.0085 0.9153 0.0763 60 Q 0.0090 0.9036 0.0875 61 F 0.0098 0.8863 0.1039 62 A 0.0111 0.8617 0.1272 63 C 0.0188 0.7672 0.2140 64 F 0.0369 0.6584 0.3047 65 G 0.0314 0.6692 0.2994 66 Q 0.0547 0.6490 0.2962 67 L 0.0513 0.7510 0.1978 68 D 0.0292 0.8199 0.1509 69 D 0.0320 0.8077 0.1602 70 I 0.0438 0.7358 0.2205 71 R 0.0564 0.6257 0.3179 72 G 0.0523 0.5260 0.4218 73 Q 0.0733 0.3723 0.5544 74 A 0.0886 0.2263 0.6851 75 G 0.0921 0.1491 0.7588 76 D 0.1488 0.0701 0.7811 77 P 0.0154 0.7426 0.2419 78 L 0.0092 0.8680 0.1228 79 A 0.0083 0.9222 0.0694 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 0.9230 0.0687 86 R 0.0083 0.9231 0.0686 87 W 0.0084 0.9223 0.0693 88 T 0.0084 0.9202 0.0713 89 I 0.0085 0.9130 0.0785 90 Q 0.0091 0.8975 0.0934 91 R 0.0124 0.8456 0.1419 92 H 0.0224 0.7637 0.2138 93 R 0.0261 0.6686 0.3053 94 N 0.0483 0.4209 0.5308 95 N 0.1371 0.2237 0.6392 96 P 0.0171 0.6921 0.2907 97 Q 0.0124 0.8168 0.1707 98 L 0.0147 0.8859 0.0993 99 L 0.0126 0.9041 0.0832 100 R 0.0134 0.9033 0.0832 101 F 0.0189 0.8857 0.0954 102 Y 0.0327 0.8459 0.1214 103 T 0.0452 0.7913 0.1635 104 S 0.0365 0.7412 0.2223 105 E 0.0410 0.6409 0.3181 106 L 0.0650 0.4733 0.4617 107 T 0.0899 0.3075 0.6026 108 N 0.1558 0.1298 0.7144 109 P 0.1165 0.1899 0.6935 110 T 0.1620 0.1405 0.6975 111 P 0.0243 0.6785 0.2972 112 C 0.0208 0.7843 0.1949 113 F 0.0263 0.8314 0.1423 114 A 0.0132 0.8789 0.1079 115 A 0.0128 0.8709 0.1163 116 I 0.0197 0.8317 0.1486 117 V 0.0323 0.7780 0.1897 118 S 0.0314 0.7930 0.1756 119 P 0.0106 0.8662 0.1232 120 A 0.0104 0.8893 0.1004 121 I 0.0088 0.9117 0.0795 122 A 0.0084 0.9186 0.0730 123 S 0.0083 0.9233 0.0684 124 V 0.0083 0.9232 0.0685 125 I 0.0083 0.9230 0.0687 126 R 0.0083 0.9241 0.0677 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 0.9224 0.0693 132 I 0.0083 0.9221 0.0696 133 E 0.0085 0.9148 0.0767 134 A 0.0089 0.8807 0.1104 135 G 0.0121 0.8509 0.1370 136 M 0.0158 0.8568 0.1274 137 T 0.0213 0.7281 0.2506 138 R 0.0545 0.2829 0.6626 139 G 0.0501 0.1318 0.8181 140 L 0.1887 0.1551 0.6562 141 F 0.2801 0.1323 0.5875 142 R 0.1987 0.1649 0.6364 143 R 0.0819 0.4624 0.4557 144 D 0.1003 0.4038 0.4958 145 L 0.1577 0.3649 0.4773 146 H 0.1383 0.2977 0.5640 147 A 0.0148 0.7724 0.2128 148 V 0.0092 0.8739 0.1169 149 N 0.0083 0.9218 0.0699 150 S 0.0083 0.9235 0.0682 151 A 0.0083 0.9246 0.0671 152 L 0.0083 0.9248 0.0669 153 A 0.0083 0.9245 0.0672 154 L 0.0083 0.9241 0.0676 155 A 0.0083 0.9241 0.0676 156 G 0.0083 0.9235 0.0682 157 M 0.0083 0.9217 0.0699 158 V 0.0084 0.9159 0.0757 159 N 0.0086 0.9089 0.0825 160 Y 0.0088 0.9083 0.0829 161 F 0.0099 0.9094 0.0807 162 F 0.0117 0.9012 0.0871 163 L 0.0152 0.8809 0.1039 164 S 0.0217 0.8495 0.1289 165 T 0.0333 0.8157 0.1511 166 L 0.0542 0.7366 0.2092 167 A 0.0759 0.5973 0.3268 168 T 0.0979 0.4314 0.4706 169 E 0.0783 0.3197 0.6021 170 G 0.0761 0.2077 0.7162 171 L 0.1538 0.1766 0.6696 172 T 0.1686 0.1818 0.6496 173 S 0.1467 0.1950 0.6583 174 H 0.1676 0.1253 0.7070 175 S 0.1917 0.0443 0.7639 176 P 0.0560 0.3717 0.5723 177 D 0.0606 0.3676 0.5718 178 Q 0.0963 0.3689 0.5348 179 D 0.0190 0.7891 0.1919 180 E 0.0087 0.8953 0.0960 181 E 0.0084 0.9197 0.0720 182 L 0.0083 0.9242 0.0675 183 I 0.0083 0.9229 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 0.9231 0.0686 188 A 0.0083 0.9239 0.0679 189 I 0.0084 0.9209 0.0707 190 F 0.0085 0.9152 0.0763 191 T 0.0097 0.8848 0.1056 192 R 0.0184 0.7447 0.2369 193 G 0.0402 0.5830 0.3768 194 I 0.0931 0.5119 0.3950 195 M 0.1446 0.3628 0.4927 196 A 0.1363 0.2897 0.5740 197 D 0.1037 0.2146 0.6817 198 G 0.0772 0.1834 0.7394 199 G 0.1148 0.1756 0.7096 200 A 0.1890 0.1153 0.6957 201 A 0.2276 0.0789 0.6935 202 P 0.1955 0.1583 0.6462 203 A 0.2182 0.1678 0.6140