# This file is the result of combining several RDB files, specifically # T0481.t04.str2.rdb (weight 1.54425) # T0481.t04.str4.rdb (weight 0.924988) # T0481.t04.pb.rdb (weight 0.789901) # T0481.t04.bys.rdb (weight 0.748322) # T0481.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 T0481.t04.str2.rdb # ============================================ # TARGET T0481 # 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 T0481.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 839 # # ============================================ # Comments from T0481.t04.str4.rdb # ============================================ # TARGET T0481 # 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 T0481.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 839 # # ============================================ # Comments from T0481.t04.pb.rdb # ============================================ # TARGET T0481 # 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 T0481.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 839 # # ============================================ # Comments from T0481.t04.bys.rdb # ============================================ # TARGET T0481 # 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 T0481.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 839 # # ============================================ # Comments from T0481.t04.alpha.rdb # ============================================ # TARGET T0481 # 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 T0481.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 839 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1951 0.1232 0.6817 2 C 0.1454 0.1342 0.7205 3 Q 0.0661 0.5313 0.4026 4 S 0.0183 0.7860 0.1957 5 N 0.0103 0.8924 0.0973 6 Q 0.0095 0.9164 0.0741 7 I 0.0084 0.9207 0.0709 8 V 0.0084 0.9197 0.0720 9 S 0.0084 0.9200 0.0716 10 H 0.0086 0.9111 0.0804 11 F 0.0090 0.8992 0.0918 12 L 0.0092 0.8773 0.1135 13 S 0.0104 0.8504 0.1393 14 H 0.0157 0.8259 0.1584 15 R 0.0111 0.8580 0.1309 16 N 0.0102 0.8885 0.1013 17 V 0.0123 0.8891 0.0986 18 T 0.0092 0.9069 0.0839 19 N 0.0086 0.9150 0.0764 20 E 0.0084 0.9179 0.0737 21 L 0.0086 0.9109 0.0805 22 A 0.0096 0.8645 0.1259 23 E 0.0115 0.7085 0.2800 24 K 0.0279 0.3817 0.5905 25 I 0.1524 0.1385 0.7090 26 S 0.1631 0.0582 0.7787 27 K 0.0146 0.6539 0.3315 28 D 0.0138 0.7561 0.2301 29 H 0.0333 0.6588 0.3079 30 Y 0.1171 0.4703 0.4126 31 S 0.1781 0.2551 0.5669 32 Y 0.2524 0.1187 0.6290 33 K 0.2380 0.0326 0.7294 34 P 0.2222 0.0691 0.7087 35 A 0.1649 0.1379 0.6972 36 E 0.0915 0.3233 0.5852 37 T 0.0882 0.2687 0.6431 38 S 0.1117 0.2866 0.6017 39 M 0.1411 0.3376 0.5212 40 S 0.1737 0.3193 0.5069 41 A 0.0146 0.7494 0.2360 42 E 0.0092 0.8703 0.1205 43 E 0.0084 0.9175 0.0741 44 L 0.0085 0.9207 0.0708 45 V 0.0085 0.9176 0.0738 46 K 0.0084 0.9205 0.0710 47 H 0.0091 0.9170 0.0739 48 I 0.0104 0.9096 0.0800 49 L 0.0102 0.9087 0.0811 50 T 0.0100 0.9038 0.0862 51 S 0.0122 0.8855 0.1023 52 F 0.0113 0.8893 0.0994 53 H 0.0105 0.9006 0.0889 54 L 0.0134 0.9010 0.0855 55 F 0.0180 0.8852 0.0968 56 A 0.0203 0.8736 0.1061 57 N 0.0241 0.8640 0.1119 58 V 0.0475 0.8011 0.1514 59 I 0.1037 0.6152 0.2811 60 K 0.1001 0.4342 0.4657 61 E 0.0871 0.2158 0.6971 62 G 0.0851 0.1271 0.7878 63 N 0.1684 0.0793 0.7523 64 A 0.2203 0.0948 0.6850 65 S 0.2146 0.0500 0.7354 66 P 0.1828 0.2205 0.5967 67 F 0.1771 0.2603 0.5625 68 Q 0.1448 0.2921 0.5631 69 N 0.1344 0.2494 0.6162 70 K 0.1329 0.2357 0.6314 71 Q 0.1464 0.1834 0.6702 72 E 0.1488 0.2137 0.6375 73 E 0.1534 0.1836 0.6630 74 T 0.1575 0.0931 0.7495 75 E 0.0136 0.7390 0.2474 76 T 0.0095 0.8656 0.1250 77 D 0.0089 0.9143 0.0768 78 L 0.0085 0.9182 0.0734 79 N 0.0083 0.9217 0.0700 80 V 0.0083 0.9229 0.0689 81 L 0.0083 0.9209 0.0708 82 A 0.0085 0.9156 0.0759 83 K 0.0084 0.9150 0.0765 84 T 0.0089 0.9044 0.0867 85 Y 0.0111 0.8901 0.0988 86 T 0.0086 0.9129 0.0785 87 E 0.0083 0.9210 0.0706 88 K 0.0084 0.9211 0.0705 89 T 0.0083 0.9230 0.0687 90 V 0.0083 0.9229 0.0688 91 A 0.0083 0.9235 0.0682 92 I 0.0084 0.9201 0.0715 93 L 0.0088 0.9003 0.0909 94 E 0.0101 0.8322 0.1577 95 Q 0.0193 0.5508 0.4299 96 L 0.1150 0.2769 0.6081 97 T 0.1567 0.0836 0.7598 98 E 0.0142 0.6709 0.3149 99 E 0.0109 0.8061 0.1830 100 Q 0.0161 0.7971 0.1868 101 L 0.0427 0.7033 0.2540 102 D 0.0583 0.5274 0.4142 103 R 0.1339 0.3492 0.5169 104 E 0.2336 0.1941 0.5723 105 I 0.3446 0.0945 0.5610 106 D 0.3353 0.0898 0.5749 107 L 0.3390 0.1594 0.5015 108 T 0.2921 0.1229 0.5851 109 S 0.1989 0.2339 0.5672 110 A 0.1203 0.3273 0.5524 111 F 0.0994 0.1787 0.7220 112 G 0.1032 0.0986 0.7982 113 R 0.2646 0.0527 0.6828 114 K 0.3590 0.0890 0.5519 115 V 0.3242 0.1375 0.5383 116 T 0.1929 0.1769 0.6301 117 G 0.0242 0.7368 0.2389 118 R 0.0095 0.8661 0.1244 119 A 0.0084 0.9194 0.0722 120 L 0.0085 0.9231 0.0684 121 L 0.0086 0.9222 0.0691 122 Q 0.0083 0.9233 0.0684 123 L 0.0084 0.9223 0.0693 124 A 0.0091 0.9157 0.0752 125 M 0.0095 0.9063 0.0842 126 E 0.0114 0.8790 0.1096 127 H 0.0202 0.8172 0.1626 128 E 0.0279 0.7898 0.1822 129 I 0.0394 0.7379 0.2227 130 H 0.0543 0.6658 0.2799 131 H 0.0554 0.6780 0.2665 132 K 0.0273 0.7461 0.2265 133 G 0.0242 0.8052 0.1706 134 N 0.0201 0.8788 0.1011 135 L 0.0138 0.9087 0.0775 136 F 0.0108 0.9197 0.0695 137 V 0.0110 0.9208 0.0681 138 Y 0.0091 0.9219 0.0689 139 V 0.0093 0.9183 0.0724 140 R 0.0093 0.9044 0.0862 141 E 0.0147 0.8021 0.1833 142 M 0.0597 0.3674 0.5729 143 G 0.0469 0.0878 0.8653 144 H 0.1417 0.0640 0.7943 145 T 0.2119 0.0607 0.7274 146 E 0.2635 0.0786 0.6580 147 L 0.2424 0.0676 0.6901 148 P 0.1902 0.2120 0.5978 149 F 0.1935 0.2367 0.5698 150 Y 0.1772 0.2355 0.5873 151 Q 0.1405 0.3410 0.5185 152 Q 0.1631 0.3552 0.4817 153 R 0.2066 0.2676 0.5259 154 M 0.1986 0.2052 0.5962