# This file is the result of combining several RDB files, specifically # T0417.t06.str2.rdb (weight 1.54425) # T0417.t06.str4.rdb (weight 0.924988) # T0417.t06.pb.rdb (weight 0.789901) # T0417.t06.bys.rdb (weight 0.748322) # T0417.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 T0417.t06.str2.rdb # ============================================ # TARGET T0417 # 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 T0417.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 5114 # # ============================================ # Comments from T0417.t06.str4.rdb # ============================================ # TARGET T0417 # 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 T0417.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 5114 # # ============================================ # Comments from T0417.t06.pb.rdb # ============================================ # TARGET T0417 # 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 T0417.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 5114 # # ============================================ # Comments from T0417.t06.bys.rdb # ============================================ # TARGET T0417 # 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 T0417.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 5114 # # ============================================ # Comments from T0417.t06.alpha.rdb # ============================================ # TARGET T0417 # 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 T0417.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 5114 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1400 0.2059 0.6541 2 N 0.1226 0.2061 0.6713 3 A 0.1311 0.2797 0.5892 4 M 0.2100 0.1808 0.6093 5 R 0.2189 0.1091 0.6720 6 K 0.1807 0.1751 0.6442 7 D 0.1840 0.1658 0.6501 8 E 0.1186 0.3424 0.5390 9 T 0.1530 0.2830 0.5640 10 S 0.1613 0.2253 0.6134 11 N 0.1495 0.1611 0.6894 12 T 0.2043 0.0909 0.7048 13 S 0.2062 0.0603 0.7335 14 P 0.1340 0.2202 0.6458 15 D 0.1740 0.1879 0.6381 16 I 0.2083 0.1770 0.6146 17 S 0.2080 0.1652 0.6268 18 V 0.2297 0.1973 0.5729 19 A 0.2654 0.1103 0.6243 20 Q 0.2646 0.0517 0.6837 21 P 0.2191 0.1183 0.6627 22 A 0.1648 0.2667 0.5685 23 S 0.1723 0.2246 0.6031 24 A 0.2449 0.1292 0.6259 25 L 0.3182 0.1260 0.5559 26 R 0.5204 0.0483 0.4313 27 Y 0.7042 0.0145 0.2813 28 H 0.7283 0.0119 0.2598 29 L 0.6736 0.0123 0.3141 30 R 0.5005 0.0152 0.4843 31 P 0.3384 0.0233 0.6383 32 P 0.2523 0.0640 0.6837 33 R 0.2142 0.0421 0.7437 34 R 0.0608 0.4414 0.4978 35 N 0.0513 0.4556 0.4932 36 D 0.0871 0.4310 0.4818 37 G 0.0160 0.8023 0.1817 38 A 0.0088 0.9045 0.0867 39 A 0.0088 0.9169 0.0743 40 I 0.0083 0.9220 0.0696 41 H 0.0084 0.9169 0.0747 42 Q 0.0085 0.9154 0.0761 43 L 0.0107 0.8879 0.1014 44 V 0.0181 0.8188 0.1632 45 S 0.0229 0.6551 0.3219 46 E 0.0485 0.4096 0.5419 47 C 0.1678 0.0884 0.7438 48 P 0.1494 0.0828 0.7679 49 P 0.1568 0.1031 0.7400 50 L 0.1254 0.2480 0.6266 51 D 0.1318 0.2905 0.5777 52 L 0.1014 0.4212 0.4774 53 N 0.1049 0.4198 0.4753 54 S 0.0467 0.7079 0.2453 55 L 0.0179 0.8406 0.1416 56 Y 0.0146 0.8852 0.1003 57 A 0.0105 0.9115 0.0780 58 Y 0.0095 0.9164 0.0742 59 L 0.0109 0.9126 0.0765 60 L 0.0138 0.8989 0.0873 61 L 0.0207 0.8631 0.1162 62 C 0.0350 0.7821 0.1829 63 E 0.0489 0.6327 0.3184 64 H 0.0967 0.3979 0.5055 65 H 0.1252 0.2716 0.6033 66 A 0.1305 0.2324 0.6371 67 H 0.2446 0.1024 0.6530 68 T 0.5342 0.0324 0.4333 69 C 0.7408 0.0074 0.2519 70 V 0.8097 0.0055 0.1849 71 V 0.8213 0.0044 0.1743 72 A 0.8144 0.0056 0.1800 73 E 0.7925 0.0073 0.2002 74 S 0.5926 0.0097 0.3977 75 P 0.1710 0.1993 0.6297 76 G 0.0669 0.1309 0.8022 77 G 0.0882 0.0541 0.8577 78 R 0.4314 0.0177 0.5509 79 I 0.6800 0.0127 0.3073 80 D 0.6668 0.0233 0.3099 81 G 0.7568 0.0168 0.2264 82 F 0.7722 0.0131 0.2147 83 V 0.8108 0.0094 0.1798 84 S 0.7818 0.0157 0.2025 85 A 0.7475 0.0253 0.2272 86 Y 0.6799 0.0305 0.2896 87 L 0.5773 0.0405 0.3822 88 L 0.3634 0.0355 0.6011 89 P 0.2121 0.1149 0.6730 90 T 0.1528 0.1433 0.7039 91 R 0.1974 0.0683 0.7343 92 P 0.1376 0.2208 0.6416 93 D 0.1777 0.1929 0.6294 94 V 0.5398 0.0839 0.3763 95 L 0.6756 0.0333 0.2910 96 F 0.7420 0.0290 0.2290 97 V 0.7322 0.0428 0.2250 98 W 0.6475 0.0884 0.2641 99 Q 0.7265 0.0595 0.2140 100 V 0.7104 0.0701 0.2195 101 A 0.6633 0.0822 0.2544 102 V 0.5887 0.0764 0.3350 103 H 0.3442 0.0589 0.5969 104 S 0.0651 0.5190 0.4159 105 R 0.0328 0.5921 0.3751 106 A 0.0583 0.5237 0.4180 107 R 0.0893 0.3432 0.5674 108 G 0.0530 0.2530 0.6939 109 H 0.0977 0.4347 0.4676 110 R 0.0639 0.5991 0.3370 111 L 0.0323 0.7711 0.1966 112 G 0.0111 0.8979 0.0909 113 R 0.0083 0.9206 0.0710 114 A 0.0083 0.9223 0.0694 115 M 0.0083 0.9232 0.0685 116 L 0.0083 0.9219 0.0698 117 G 0.0083 0.9237 0.0681 118 H 0.0083 0.9242 0.0675 119 I 0.0083 0.9230 0.0687 120 L 0.0084 0.9188 0.0728 121 E 0.0084 0.9178 0.0738 122 R 0.0088 0.9051 0.0861 123 Q 0.0108 0.8895 0.0997 124 E 0.0125 0.8618 0.1257 125 C 0.0249 0.7270 0.2480 126 R 0.0559 0.3657 0.5784 127 H 0.0600 0.1444 0.7957 128 V 0.2314 0.0684 0.7002 129 R 0.3090 0.1011 0.5899 130 H 0.6823 0.0298 0.2879 131 L 0.7207 0.0191 0.2601 132 E 0.7670 0.0176 0.2154 133 T 0.7637 0.0155 0.2208 134 T 0.7019 0.0263 0.2718 135 V 0.5822 0.0280 0.3898 136 G 0.2802 0.0327 0.6871 137 P 0.0917 0.3261 0.5823 138 D 0.0631 0.3382 0.5987 139 N 0.0879 0.3814 0.5307 140 Q 0.0271 0.7273 0.2457 141 A 0.0147 0.8475 0.1378 142 S 0.0132 0.8958 0.0910 143 R 0.0088 0.9128 0.0784 144 R 0.0088 0.9164 0.0748 145 T 0.0096 0.9110 0.0794 146 F 0.0131 0.8944 0.0925 147 A 0.0157 0.8290 0.1553 148 G 0.0252 0.6668 0.3081 149 L 0.0738 0.4171 0.5090 150 A 0.0668 0.2325 0.7006 151 G 0.1131 0.1721 0.7148 152 E 0.2415 0.1373 0.6213 153 R 0.2696 0.1667 0.5637 154 G 0.2844 0.1416 0.5740 155 A 0.4130 0.1295 0.4576 156 H 0.5175 0.0997 0.3828 157 V 0.5204 0.1129 0.3668 158 S 0.3963 0.1358 0.4679 159 E 0.2922 0.1272 0.5806 160 Q 0.2755 0.0732 0.6513 161 P 0.2117 0.1984 0.5899 162 F 0.2153 0.2405 0.5442 163 F 0.2082 0.2666 0.5252 164 D 0.1762 0.3159 0.5079 165 R 0.1587 0.4679 0.3734 166 Q 0.2117 0.4580 0.3303 167 A 0.2488 0.3890 0.3622 168 F 0.2550 0.2702 0.4748 169 G 0.2025 0.2163 0.5812 170 G 0.1863 0.1755 0.6381 171 A 0.2142 0.1648 0.6210 172 D 0.1657 0.1826 0.6517 173 H 0.1392 0.2218 0.6390 174 D 0.1199 0.2795 0.6006 175 D 0.1140 0.3701 0.5159 176 E 0.1863 0.3880 0.4257 177 M 0.2793 0.2933 0.4273 178 L 0.3907 0.1874 0.4219 179 L 0.5329 0.0935 0.3735 180 R 0.5410 0.0591 0.3999 181 I 0.4870 0.0501 0.4629 182 G 0.2558 0.0376 0.7066 183 P 0.2035 0.1713 0.6252 184 F 0.1706 0.1886 0.6408 185 T 0.2059 0.1335 0.6605 186 H 0.2445 0.0425 0.7130 187 P 0.2009 0.0484 0.7508 188 P 0.1675 0.1488 0.6836 189 H 0.1742 0.1666 0.6592