# This file is the result of combining several RDB files, specifically # T0454.t04.str2.rdb (weight 1.54425) # T0454.t04.str4.rdb (weight 0.924988) # T0454.t04.pb.rdb (weight 0.789901) # T0454.t04.bys.rdb (weight 0.748322) # T0454.t04.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.t04.str2.rdb # ============================================ # TARGET T0454 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 2183 # # ============================================ # Comments from T0454.t04.str4.rdb # ============================================ # TARGET T0454 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 2183 # # ============================================ # Comments from T0454.t04.pb.rdb # ============================================ # TARGET T0454 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 2183 # # ============================================ # Comments from T0454.t04.bys.rdb # ============================================ # TARGET T0454 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 2183 # # ============================================ # Comments from T0454.t04.alpha.rdb # ============================================ # TARGET T0454 # Using neural net dunbrack-40pc-3157-t04-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.t04-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 2183 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2377 0.0527 0.7096 2 T 0.1674 0.0391 0.7935 3 R 0.0739 0.4202 0.5058 4 A 0.0149 0.7269 0.2582 5 D 0.0240 0.7850 0.1910 6 C 0.0179 0.8609 0.1213 7 R 0.0091 0.8917 0.0992 8 S 0.0085 0.9133 0.0782 9 R 0.0083 0.9235 0.0683 10 L 0.0083 0.9224 0.0693 11 M 0.0083 0.9239 0.0678 12 E 0.0083 0.9252 0.0666 13 V 0.0083 0.9252 0.0666 14 A 0.0083 0.9245 0.0673 15 T 0.0083 0.9244 0.0674 16 E 0.0083 0.9241 0.0676 17 L 0.0083 0.9145 0.0772 18 F 0.0085 0.9087 0.0828 19 A 0.0088 0.8994 0.0918 20 Q 0.0122 0.8020 0.1858 21 K 0.0555 0.3608 0.5837 22 G 0.0584 0.1774 0.7642 23 F 0.1140 0.3009 0.5851 24 Y 0.1196 0.3173 0.5631 25 G 0.1407 0.2583 0.6009 26 V 0.2040 0.2206 0.5754 27 S 0.1979 0.1141 0.6880 28 I 0.0143 0.7461 0.2396 29 R 0.0092 0.8727 0.1181 30 E 0.0083 0.9218 0.0698 31 L 0.0084 0.9181 0.0735 32 A 0.0084 0.9108 0.0808 33 Q 0.0088 0.8966 0.0946 34 A 0.0132 0.8183 0.1685 35 A 0.0585 0.2896 0.6519 36 G 0.0393 0.0901 0.8706 37 A 0.1394 0.0895 0.7710 38 S 0.1781 0.0910 0.7309 39 I 0.1309 0.4794 0.3897 40 S 0.1572 0.5336 0.3092 41 M 0.2915 0.4905 0.2180 42 I 0.4340 0.3771 0.1888 43 S 0.4156 0.3990 0.1854 44 Y 0.4364 0.3415 0.2220 45 H 0.3180 0.2590 0.4230 46 F 0.1846 0.2040 0.6114 47 G 0.1129 0.1838 0.7033 48 G 0.1111 0.1758 0.7131 49 K 0.0180 0.6675 0.3146 50 E 0.0106 0.8364 0.1530 51 G 0.0086 0.9101 0.0813 52 L 0.0089 0.9191 0.0720 53 Y 0.0083 0.9218 0.0699 54 A 0.0083 0.9237 0.0680 55 A 0.0083 0.9237 0.0681 56 V 0.0083 0.9235 0.0683 57 L 0.0084 0.9176 0.0740 58 Q 0.0084 0.9195 0.0721 59 E 0.0087 0.9113 0.0800 60 Q 0.0103 0.8843 0.1054 61 F 0.0113 0.8587 0.1300 62 A 0.0112 0.7891 0.1997 63 C 0.0227 0.6820 0.2953 64 F 0.0501 0.5545 0.3954 65 G 0.0514 0.5205 0.4281 66 Q 0.0733 0.6080 0.3187 67 L 0.0444 0.7331 0.2225 68 D 0.0308 0.7960 0.1732 69 D 0.0286 0.8159 0.1555 70 I 0.0351 0.7595 0.2054 71 R 0.0606 0.6008 0.3386 72 G 0.0631 0.4292 0.5077 73 Q 0.0839 0.3078 0.6083 74 A 0.0801 0.2383 0.6817 75 G 0.0776 0.1539 0.7685 76 D 0.1584 0.0667 0.7749 77 P 0.0176 0.6937 0.2887 78 L 0.0093 0.8621 0.1285 79 A 0.0083 0.9218 0.0699 80 V 0.0083 0.9225 0.0691 81 M 0.0083 0.9227 0.0690 82 T 0.0083 0.9240 0.0677 83 A 0.0083 0.9247 0.0671 84 Y 0.0083 0.9249 0.0668 85 L 0.0083 0.9239 0.0679 86 R 0.0083 0.9245 0.0672 87 W 0.0083 0.9237 0.0680 88 T 0.0084 0.9211 0.0705 89 I 0.0085 0.9186 0.0729 90 Q 0.0087 0.9158 0.0755 91 R 0.0124 0.8785 0.1090 92 H 0.0238 0.7851 0.1911 93 R 0.0249 0.6355 0.3396 94 N 0.0422 0.4181 0.5397 95 N 0.1335 0.2575 0.6090 96 P 0.0147 0.7393 0.2460 97 Q 0.0134 0.8222 0.1643 98 L 0.0223 0.8633 0.1144 99 L 0.0198 0.8897 0.0904 100 R 0.0203 0.8981 0.0816 101 F 0.0312 0.8816 0.0872 102 Y 0.0468 0.8432 0.1099 103 T 0.0417 0.8266 0.1316 104 S 0.0378 0.8027 0.1595 105 E 0.0555 0.6627 0.2818 106 L 0.0906 0.4152 0.4942 107 T 0.1065 0.2467 0.6468 108 N 0.1524 0.1149 0.7327 109 P 0.1125 0.2017 0.6858 110 T 0.1426 0.1653 0.6921 111 P 0.0175 0.7179 0.2646 112 C 0.0164 0.8010 0.1826 113 F 0.0156 0.8620 0.1224 114 A 0.0134 0.8801 0.1065 115 A 0.0120 0.8823 0.1057 116 I 0.0186 0.8377 0.1438 117 V 0.0292 0.7583 0.2125 118 S 0.0413 0.7641 0.1946 119 P 0.0125 0.8671 0.1204 120 A 0.0149 0.8694 0.1157 121 I 0.0097 0.9004 0.0899 122 A 0.0085 0.9189 0.0726 123 S 0.0084 0.9207 0.0710 124 V 0.0083 0.9221 0.0696 125 I 0.0083 0.9240 0.0677 126 R 0.0083 0.9246 0.0672 127 L 0.0083 0.9242 0.0676 128 L 0.0083 0.9230 0.0687 129 A 0.0083 0.9243 0.0675 130 E 0.0083 0.9242 0.0676 131 S 0.0083 0.9236 0.0682 132 I 0.0083 0.9232 0.0685 133 E 0.0083 0.9210 0.0707 134 A 0.0087 0.9101 0.0811 135 G 0.0099 0.8835 0.1066 136 M 0.0109 0.8778 0.1114 137 T 0.0136 0.8126 0.1739 138 R 0.0566 0.2907 0.6528 139 G 0.0506 0.1102 0.8391 140 L 0.1665 0.1510 0.6825 141 F 0.2955 0.1460 0.5585 142 R 0.2308 0.1651 0.6041 143 R 0.1015 0.4518 0.4467 144 D 0.1081 0.2760 0.6159 145 L 0.1545 0.2515 0.5939 146 H 0.1703 0.1582 0.6715 147 A 0.0143 0.7528 0.2329 148 V 0.0092 0.8697 0.1210 149 N 0.0083 0.9213 0.0703 150 S 0.0083 0.9240 0.0677 151 A 0.0083 0.9241 0.0677 152 L 0.0083 0.9248 0.0669 153 A 0.0083 0.9242 0.0675 154 L 0.0083 0.9211 0.0706 155 A 0.0084 0.9185 0.0732 156 G 0.0084 0.9132 0.0784 157 M 0.0092 0.9021 0.0887 158 V 0.0123 0.8601 0.1275 159 N 0.0169 0.8097 0.1734 160 Y 0.0229 0.8009 0.1762 161 F 0.0278 0.8003 0.1718 162 F 0.0325 0.7878 0.1797 163 L 0.0386 0.7538 0.2075 164 S 0.0363 0.7524 0.2113 165 T 0.0388 0.7571 0.2042 166 L 0.0543 0.7487 0.1970 167 A 0.0835 0.6990 0.2175 168 T 0.1086 0.6241 0.2673 169 E 0.1159 0.5271 0.3570 170 G 0.1332 0.3692 0.4975 171 L 0.1658 0.2655 0.5687 172 T 0.1875 0.1739 0.6386 173 S 0.1567 0.1821 0.6612 174 H 0.1288 0.1518 0.7195 175 S 0.1733 0.0535 0.7733 176 P 0.0686 0.3705 0.5609 177 D 0.0793 0.3190 0.6017 178 Q 0.1220 0.2719 0.6060 179 D 0.0170 0.7396 0.2434 180 E 0.0091 0.8705 0.1204 181 E 0.0084 0.9188 0.0728 182 L 0.0083 0.9225 0.0691 183 I 0.0083 0.9221 0.0696 184 R 0.0083 0.9247 0.0670 185 Q 0.0083 0.9249 0.0668 186 Y 0.0083 0.9242 0.0676 187 V 0.0083 0.9242 0.0675 188 A 0.0083 0.9246 0.0671 189 I 0.0084 0.9175 0.0741 190 F 0.0087 0.9187 0.0726 191 T 0.0097 0.9002 0.0902 192 R 0.0162 0.8169 0.1670 193 G 0.0421 0.6276 0.3303 194 I 0.0943 0.4750 0.4307 195 M 0.1639 0.3040 0.5321 196 A 0.1547 0.2771 0.5682 197 D 0.1293 0.1839 0.6868 198 G 0.1018 0.1938 0.7044 199 G 0.1182 0.1927 0.6891 200 A 0.1941 0.1288 0.6771 201 A 0.2437 0.0485 0.7078 202 P 0.2034 0.0697 0.7269 203 A 0.1911 0.1349 0.6740