# This file is the result of combining several RDB files, specifically # T0470.t06.str2.rdb (weight 1.54425) # T0470.t06.str4.rdb (weight 0.924988) # T0470.t06.pb.rdb (weight 0.789901) # T0470.t06.bys.rdb (weight 0.748322) # T0470.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 T0470.t06.str2.rdb # ============================================ # TARGET T0470 # 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 T0470.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 3026 # # ============================================ # Comments from T0470.t06.str4.rdb # ============================================ # TARGET T0470 # 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 T0470.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 3026 # # ============================================ # Comments from T0470.t06.pb.rdb # ============================================ # TARGET T0470 # 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 T0470.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 3026 # # ============================================ # Comments from T0470.t06.bys.rdb # ============================================ # TARGET T0470 # 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 T0470.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 3026 # # ============================================ # Comments from T0470.t06.alpha.rdb # ============================================ # TARGET T0470 # 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 T0470.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 3026 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1903 0.0948 0.7148 2 T 0.1544 0.0915 0.7542 3 K 0.0501 0.5740 0.3759 4 Q 0.0269 0.7748 0.1983 5 E 0.0167 0.8678 0.1155 6 K 0.0176 0.8678 0.1145 7 I 0.0125 0.8997 0.0878 8 E 0.0086 0.9100 0.0814 9 K 0.0085 0.9134 0.0781 10 T 0.0088 0.9138 0.0774 11 I 0.0085 0.9144 0.0771 12 T 0.0085 0.9159 0.0756 13 F 0.0090 0.9115 0.0795 14 V 0.0098 0.9071 0.0831 15 K 0.0110 0.8960 0.0930 16 H 0.0163 0.8629 0.1208 17 I 0.0381 0.7694 0.1925 18 L 0.0711 0.6624 0.2665 19 E 0.1029 0.5131 0.3840 20 K 0.1203 0.3790 0.5007 21 D 0.1147 0.2775 0.6078 22 A 0.0937 0.2961 0.6102 23 S 0.0873 0.2698 0.6429 24 G 0.0925 0.1755 0.7320 25 H 0.1797 0.1520 0.6683 26 D 0.2033 0.2155 0.5812 27 W 0.1626 0.4741 0.3632 28 Y 0.1024 0.6568 0.2408 29 H 0.0635 0.7886 0.1479 30 I 0.0182 0.8901 0.0917 31 R 0.0085 0.9169 0.0746 32 R 0.0083 0.9237 0.0680 33 V 0.0083 0.9245 0.0673 34 H 0.0083 0.9242 0.0676 35 K 0.0083 0.9245 0.0673 36 M 0.0083 0.9245 0.0672 37 A 0.0083 0.9231 0.0686 38 I 0.0083 0.9222 0.0695 39 S 0.0083 0.9224 0.0693 40 L 0.0084 0.9172 0.0744 41 S 0.0086 0.9061 0.0853 42 E 0.0092 0.8938 0.0970 43 Q 0.0161 0.7865 0.1974 44 E 0.0601 0.3102 0.6297 45 G 0.0423 0.0965 0.8612 46 G 0.1177 0.1035 0.7788 47 N 0.1173 0.1866 0.6961 48 R 0.0340 0.6676 0.2984 49 F 0.0198 0.8376 0.1425 50 I 0.0133 0.9083 0.0784 51 I 0.0095 0.9191 0.0714 52 E 0.0088 0.9230 0.0681 53 M 0.0083 0.9234 0.0683 54 A 0.0089 0.9194 0.0717 55 A 0.0103 0.9072 0.0825 56 L 0.0152 0.8769 0.1080 57 L 0.0244 0.7873 0.1883 58 H 0.0383 0.6855 0.2762 59 D 0.0562 0.5778 0.3660 60 V 0.0577 0.5799 0.3624 61 A 0.0969 0.4363 0.4668 62 D 0.1284 0.3312 0.5404 63 E 0.1346 0.2812 0.5843 64 K 0.1193 0.2775 0.6033 65 L 0.1159 0.2668 0.6173 66 N 0.1135 0.2828 0.6037 67 E 0.0886 0.4574 0.4540 68 S 0.0891 0.5917 0.3193 69 E 0.0424 0.7606 0.1970 70 E 0.0416 0.7753 0.1831 71 A 0.0447 0.7214 0.2339 72 G 0.0356 0.7772 0.1872 73 M 0.0128 0.8662 0.1210 74 K 0.0093 0.8884 0.1023 75 K 0.0088 0.9158 0.0754 76 V 0.0086 0.9175 0.0740 77 S 0.0084 0.9167 0.0749 78 D 0.0084 0.9201 0.0715 79 W 0.0085 0.9168 0.0747 80 L 0.0090 0.9082 0.0828 81 E 0.0092 0.8838 0.1070 82 E 0.0142 0.7534 0.2324 83 L 0.0669 0.3182 0.6149 84 H 0.0476 0.1172 0.8353 85 V 0.1629 0.0363 0.8008 86 E 0.1519 0.0543 0.7938 87 E 0.0168 0.7119 0.2714 88 E 0.0112 0.8388 0.1499 89 E 0.0132 0.8870 0.0998 90 S 0.0097 0.9110 0.0793 91 K 0.0085 0.9151 0.0764 92 H 0.0084 0.9210 0.0707 93 V 0.0083 0.9231 0.0685 94 L 0.0083 0.9227 0.0690 95 H 0.0083 0.9231 0.0686 96 I 0.0085 0.9216 0.0699 97 I 0.0098 0.9111 0.0791 98 A 0.0148 0.8418 0.1434 99 N 0.0308 0.6284 0.3408 100 M 0.0932 0.3336 0.5732 101 S 0.1194 0.2385 0.6421 102 Y 0.1741 0.1686 0.6573 103 K 0.1187 0.2578 0.6235 104 G 0.0987 0.2360 0.6653 105 G 0.1168 0.1649 0.7182 106 H 0.1511 0.1558 0.6931 107 G 0.1147 0.1115 0.7738 108 G 0.1330 0.0898 0.7773 109 K 0.2537 0.0618 0.6845 110 V 0.3488 0.0712 0.5800 111 E 0.3578 0.0784 0.5638 112 S 0.2815 0.0812 0.6373 113 I 0.0646 0.6110 0.3244 114 E 0.0509 0.7285 0.2206 115 G 0.0952 0.7242 0.1806 116 K 0.0999 0.7541 0.1460 117 L 0.1246 0.7136 0.1618 118 V 0.1076 0.7278 0.1646 119 Q 0.0909 0.7141 0.1950 120 D 0.0624 0.6763 0.2613 121 A 0.0436 0.7543 0.2021 122 D 0.0257 0.7692 0.2050 123 R 0.0220 0.8250 0.1530 124 L 0.0307 0.8309 0.1384 125 D 0.0234 0.8465 0.1301 126 A 0.0283 0.7909 0.1808 127 L 0.0538 0.5782 0.3679 128 G 0.0690 0.4399 0.4911 129 A 0.1078 0.4409 0.4512 130 I 0.1115 0.3725 0.5160 131 G 0.1114 0.3572 0.5314 132 I 0.1172 0.5657 0.3171 133 A 0.1146 0.6519 0.2335 134 R 0.0906 0.7165 0.1928 135 T 0.1124 0.6819 0.2057 136 F 0.1193 0.6772 0.2035 137 A 0.1360 0.6437 0.2203 138 Y 0.1711 0.5183 0.3106 139 G 0.1293 0.3731 0.4976 140 G 0.1180 0.2997 0.5823 141 A 0.1820 0.3454 0.4726 142 K 0.1596 0.3279 0.5125 143 G 0.1384 0.2338 0.6278 144 R 0.1856 0.2520 0.5624 145 L 0.2340 0.2633 0.5027 146 M 0.2845 0.1911 0.5244 147 Y 0.3082 0.1137 0.5781 148 D 0.2041 0.0399 0.7560 149 P 0.0272 0.4823 0.4905 150 T 0.0546 0.3265 0.6188 151 I 0.2003 0.0943 0.7055 152 P 0.1814 0.0653 0.7533 153 P 0.1136 0.3480 0.5384 154 R 0.0770 0.5698 0.3531 155 E 0.1072 0.6185 0.2743 156 V 0.1602 0.5344 0.3055 157 M 0.1845 0.4157 0.3998 158 T 0.1960 0.3231 0.4809 159 K 0.0987 0.5372 0.3641 160 D 0.0588 0.6908 0.2504 161 E 0.0468 0.7473 0.2059 162 Y 0.0755 0.6768 0.2477 163 R 0.0787 0.5873 0.3340 164 K 0.0858 0.4723 0.4419 165 N 0.0984 0.3124 0.5893 166 N 0.1120 0.2241 0.6639 167 D 0.1645 0.1865 0.6490 168 P 0.0577 0.5431 0.3992 169 S 0.0550 0.6574 0.2876 170 L 0.0322 0.7871 0.1807 171 N 0.0153 0.8600 0.1247 172 H 0.0122 0.8908 0.0970 173 F 0.0114 0.9027 0.0858 174 Y 0.0088 0.9143 0.0769 175 E 0.0085 0.9154 0.0762 176 K 0.0088 0.9118 0.0794 177 L 0.0107 0.8937 0.0957 178 L 0.0120 0.8696 0.1184 179 K 0.0202 0.7983 0.1815 180 L 0.0358 0.7756 0.1886 181 K 0.0179 0.7947 0.1874 182 D 0.0183 0.7975 0.1842 183 L 0.0285 0.7451 0.2263 184 M 0.0606 0.6260 0.3134 185 N 0.0773 0.5091 0.4136 186 T 0.0884 0.5250 0.3866 187 N 0.0453 0.6727 0.2820 188 A 0.0258 0.8074 0.1668 189 A 0.0146 0.8861 0.0993 190 K 0.0107 0.9095 0.0798 191 Q 0.0102 0.9119 0.0779 192 E 0.0091 0.9133 0.0776 193 A 0.0090 0.9062 0.0848 194 E 0.0091 0.9055 0.0853 195 V 0.0109 0.8871 0.1020 196 R 0.0129 0.8691 0.1181 197 H 0.0096 0.8930 0.0974 198 R 0.0087 0.9025 0.0888 199 Y 0.0091 0.9057 0.0852 200 M 0.0088 0.9135 0.0777 201 E 0.0083 0.9206 0.0710 202 Q 0.0083 0.9223 0.0694 203 F 0.0083 0.9234 0.0683 204 I 0.0083 0.9206 0.0711 205 E 0.0083 0.9219 0.0698 206 Q 0.0085 0.9143 0.0772 207 F 0.0090 0.9060 0.0850 208 M 0.0089 0.8959 0.0951 209 K 0.0100 0.8865 0.1036 210 E 0.0172 0.7834 0.1994 211 W 0.0658 0.5809 0.3533 212 N 0.0570 0.5166 0.4264 213 A 0.0355 0.6616 0.3029 214 Q 0.0424 0.6882 0.2694 215 I 0.0617 0.6895 0.2488 216 L 0.0393 0.7745 0.1862 217 E 0.0326 0.7799 0.1875 218 H 0.0534 0.7137 0.2329 219 H 0.0975 0.5968 0.3058 220 H 0.1182 0.4634 0.4184 221 H 0.1390 0.3108 0.5502 222 H 0.1428 0.2092 0.6480 223 H 0.1702 0.1489 0.6808