# This file is the result of combining several RDB files, specifically # T0618.t2k.str2.rdb (weight 1.54425) # T0618.t2k.str4.rdb (weight 0.924988) # T0618.t2k.pb.rdb (weight 0.789901) # T0618.t2k.bys.rdb (weight 0.748322) # T0618.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 T0618.t2k.str2.rdb # ============================================ # TARGET T0618 # 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 T0618.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 27.2384 # # ============================================ # Comments from T0618.t2k.str4.rdb # ============================================ # TARGET T0618 # 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 T0618.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 27.2384 # # ============================================ # Comments from T0618.t2k.pb.rdb # ============================================ # TARGET T0618 # 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 T0618.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 27.2384 # # ============================================ # Comments from T0618.t2k.bys.rdb # ============================================ # TARGET T0618 # 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 T0618.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 27.2384 # # ============================================ # Comments from T0618.t2k.alpha.rdb # ============================================ # TARGET T0618 # 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 T0618.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 27.2384 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3040 0.1478 0.5483 2 K 0.2950 0.1601 0.5449 3 K 0.2420 0.2624 0.4955 4 E 0.2139 0.3005 0.4856 5 S 0.1927 0.2462 0.5610 6 Q 0.2362 0.1813 0.5825 7 V 0.3224 0.1632 0.5145 8 I 0.2868 0.1651 0.5482 9 F 0.2316 0.1965 0.5719 10 D 0.1496 0.2798 0.5706 11 K 0.0200 0.7314 0.2485 12 N 0.0230 0.8052 0.1718 13 V 0.0133 0.8848 0.1018 14 I 0.0096 0.9062 0.0842 15 E 0.0084 0.9225 0.0692 16 F 0.0084 0.9213 0.0703 17 V 0.0083 0.9204 0.0712 18 T 0.0083 0.9240 0.0677 19 V 0.0083 0.9235 0.0682 20 A 0.0084 0.9183 0.0733 21 A 0.0083 0.9201 0.0716 22 E 0.0084 0.9193 0.0723 23 F 0.0085 0.9120 0.0795 24 C 0.0085 0.9121 0.0794 25 A 0.0086 0.9118 0.0796 26 F 0.0102 0.9009 0.0889 27 L 0.0143 0.8795 0.1062 28 E 0.0211 0.8439 0.1350 29 R 0.0446 0.7336 0.2218 30 A 0.0503 0.6635 0.2862 31 E 0.0357 0.6181 0.3462 32 S 0.0504 0.4646 0.4850 33 M 0.1066 0.3903 0.5031 34 K 0.0813 0.4729 0.4459 35 R 0.0403 0.6603 0.2994 36 S 0.0259 0.7673 0.2068 37 T 0.0240 0.8253 0.1507 38 F 0.0216 0.8668 0.1115 39 V 0.0103 0.9105 0.0792 40 D 0.0087 0.9190 0.0723 41 T 0.0087 0.9196 0.0716 42 T 0.0088 0.9170 0.0742 43 L 0.0088 0.9138 0.0775 44 K 0.0090 0.8999 0.0911 45 I 0.0121 0.8600 0.1279 46 L 0.0158 0.8512 0.1330 47 P 0.0126 0.8741 0.1133 48 L 0.0178 0.8789 0.1034 49 L 0.0249 0.8701 0.1050 50 Y 0.0516 0.8164 0.1320 51 L 0.0708 0.7630 0.1662 52 K 0.0951 0.6145 0.2904 53 A 0.1189 0.5488 0.3323 54 S 0.1151 0.4424 0.4425 55 M 0.1742 0.2469 0.5790 56 L 0.2242 0.0934 0.6825 57 P 0.1633 0.2398 0.5969 58 K 0.1790 0.2741 0.5468 59 C 0.3102 0.2067 0.4831 60 E 0.3692 0.1692 0.4615 61 M 0.3896 0.1443 0.4662 62 I 0.2547 0.1115 0.6338 63 G 0.1822 0.1255 0.6923 64 D 0.1213 0.2312 0.6476 65 E 0.1559 0.1694 0.6747 66 S 0.2143 0.0516 0.7341 67 P 0.1836 0.1951 0.6213 68 E 0.2676 0.2090 0.5234 69 T 0.2978 0.2026 0.4996 70 Y 0.2944 0.1392 0.5664 71 V 0.2399 0.1552 0.6050 72 T 0.1800 0.1359 0.6841 73 E 0.0497 0.6239 0.3264 74 E 0.0368 0.7222 0.2410 75 I 0.0388 0.7791 0.1821 76 Y 0.0239 0.8628 0.1133 77 E 0.0152 0.8944 0.0904 78 V 0.0135 0.9025 0.0840 79 L 0.0120 0.9101 0.0779 80 R 0.0108 0.9093 0.0798 81 I 0.0103 0.9082 0.0816 82 N 0.0116 0.9019 0.0866 83 L 0.0113 0.8944 0.0943 84 A 0.0100 0.8915 0.0985 85 S 0.0115 0.8700 0.1185 86 I 0.0246 0.7517 0.2237 87 L 0.0699 0.4948 0.4352 88 A 0.0966 0.3391 0.5643 89 E 0.1000 0.3654 0.5346 90 K 0.1156 0.3281 0.5563 91 D 0.1262 0.3503 0.5235 92 D 0.0883 0.4902 0.4215 93 Y 0.1662 0.4883 0.3455 94 L 0.2602 0.4295 0.3103 95 E 0.3570 0.3587 0.2844 96 V 0.4036 0.2602 0.3362 97 F 0.3948 0.1435 0.4617 98 L 0.2318 0.0937 0.6746 99 P 0.0840 0.4048 0.5113 100 D 0.0763 0.3400 0.5837 101 M 0.1415 0.3519 0.5065 102 A 0.2102 0.2282 0.5616 103 Y 0.2201 0.1646 0.6153 104 S 0.1759 0.1477 0.6763 105 D 0.1194 0.2365 0.6441 106 E 0.2490 0.1163 0.6347 107 P 0.3240 0.1379 0.5381 108 I 0.3102 0.1960 0.4938 109 K 0.2363 0.2856 0.4781 110 K 0.2166 0.2821 0.5013 111 N 0.2131 0.2319 0.5550 112 I 0.1666 0.3865 0.4469 113 S 0.1190 0.4909 0.3901 114 E 0.0263 0.7623 0.2114 115 D 0.0315 0.7707 0.1978 116 L 0.0137 0.8136 0.1726 117 A 0.0095 0.8830 0.1075 118 D 0.0093 0.9090 0.0817 119 I 0.0095 0.9020 0.0884 120 Y 0.0094 0.9050 0.0856 121 Q 0.0090 0.8967 0.0943 122 D 0.0101 0.8616 0.1283 123 I 0.0134 0.8050 0.1816 124 K 0.0145 0.7982 0.1873 125 D 0.0189 0.7379 0.2432 126 F 0.0356 0.7737 0.1907 127 I 0.0739 0.7772 0.1489 128 F 0.1211 0.7427 0.1362 129 V 0.1665 0.6819 0.1517 130 F 0.1971 0.6054 0.1975 131 Q 0.1554 0.5265 0.3181 132 L 0.1028 0.2837 0.6134 133 G 0.0783 0.1340 0.7877 134 L 0.0886 0.3297 0.5817 135 N 0.0660 0.5002 0.4338 136 E 0.0706 0.5978 0.3316 137 T 0.0988 0.6173 0.2839 138 M 0.0773 0.7078 0.2149 139 N 0.0387 0.8179 0.1434 140 D 0.0153 0.8757 0.1090 141 S 0.0175 0.8944 0.0881 142 L 0.0218 0.8974 0.0808 143 A 0.0163 0.9068 0.0769 144 I 0.0179 0.9004 0.0817 145 C 0.0238 0.8777 0.0985 146 Q 0.0185 0.8739 0.1076 147 E 0.0180 0.8608 0.1212 148 N 0.0327 0.7617 0.2056 149 F 0.0476 0.7151 0.2373 150 G 0.0444 0.7373 0.2183 151 L 0.0404 0.7901 0.1695 152 L 0.0443 0.7656 0.1901 153 W 0.0258 0.8078 0.1664 154 G 0.0116 0.8833 0.1051 155 Q 0.0087 0.9097 0.0816 156 K 0.0086 0.9182 0.0732 157 L 0.0083 0.9196 0.0720 158 V 0.0083 0.9227 0.0691 159 N 0.0083 0.9233 0.0684 160 T 0.0083 0.9212 0.0704 161 M 0.0083 0.9223 0.0694 162 R 0.0083 0.9215 0.0702 163 A 0.0084 0.9191 0.0725 164 L 0.0087 0.9047 0.0865 165 H 0.0087 0.8983 0.0929 166 D 0.0121 0.8499 0.1380 167 V 0.0399 0.7625 0.1977 168 K 0.0999 0.5884 0.3117 169 Y 0.1756 0.3369 0.4875 170 S 0.1718 0.1173 0.7109 171 P 0.0477 0.5114 0.4408 172 K 0.0510 0.5449 0.4042 173 A 0.0848 0.5301 0.3851 174 R 0.1155 0.3954 0.4891 175 L 0.1278 0.4917 0.3806 176 E 0.0859 0.5741 0.3400 177 H 0.0772 0.6343 0.2885 178 H 0.0734 0.5798 0.3468 179 H 0.0864 0.4871 0.4264 180 H 0.0967 0.3741 0.5292 181 H 0.1060 0.2224 0.6715 182 H 0.1036 0.1540 0.7424