# This file is the result of combining several RDB files, specifically # T0443.t04.str2.rdb (weight 1.54425) # T0443.t04.str4.rdb (weight 0.924988) # T0443.t04.pb.rdb (weight 0.789901) # T0443.t04.bys.rdb (weight 0.748322) # T0443.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 T0443.t04.str2.rdb # ============================================ # TARGET T0443 # 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 T0443.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 208 # # ============================================ # Comments from T0443.t04.str4.rdb # ============================================ # TARGET T0443 # 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 T0443.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 208 # # ============================================ # Comments from T0443.t04.pb.rdb # ============================================ # TARGET T0443 # 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 T0443.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 208 # # ============================================ # Comments from T0443.t04.bys.rdb # ============================================ # TARGET T0443 # 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 T0443.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 208 # # ============================================ # Comments from T0443.t04.alpha.rdb # ============================================ # TARGET T0443 # 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 T0443.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 208 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2238 0.0914 0.6848 2 Q 0.1830 0.0306 0.7864 3 P 0.1349 0.1682 0.6969 4 E 0.0252 0.6180 0.3568 5 T 0.0279 0.6508 0.3213 6 S 0.0156 0.8092 0.1751 7 A 0.0092 0.8861 0.1046 8 Q 0.0084 0.9121 0.0794 9 Y 0.0084 0.9180 0.0736 10 Q 0.0083 0.9236 0.0681 11 H 0.0083 0.9236 0.0681 12 R 0.0083 0.9228 0.0688 13 F 0.0084 0.9198 0.0719 14 S 0.0084 0.9149 0.0767 15 Q 0.0085 0.9103 0.0812 16 A 0.0097 0.8849 0.1054 17 I 0.0212 0.7654 0.2133 18 R 0.0426 0.5111 0.4463 19 G 0.0728 0.2023 0.7249 20 G 0.0933 0.1571 0.7496 21 E 0.1409 0.1742 0.6849 22 A 0.1665 0.2047 0.6288 23 A 0.1142 0.3524 0.5335 24 D 0.0826 0.2108 0.7066 25 G 0.0542 0.1173 0.8285 26 L 0.1718 0.0446 0.7837 27 P 0.1499 0.1182 0.7318 28 Q 0.0364 0.6348 0.3288 29 D 0.0279 0.7299 0.2422 30 R 0.0508 0.7518 0.1973 31 L 0.0619 0.8044 0.1336 32 N 0.0524 0.8492 0.0984 33 V 0.0453 0.8756 0.0791 34 Y 0.0244 0.8966 0.0789 35 I 0.0115 0.9159 0.0725 36 R 0.0092 0.9183 0.0725 37 L 0.0096 0.9137 0.0767 38 I 0.0101 0.9152 0.0747 39 R 0.0088 0.9164 0.0747 40 N 0.0095 0.9030 0.0875 41 N 0.0138 0.8728 0.1134 42 I 0.0088 0.8899 0.1013 43 H 0.0089 0.9071 0.0840 44 S 0.0087 0.9131 0.0782 45 F 0.0085 0.9132 0.0784 46 I 0.0089 0.9007 0.0904 47 D 0.0093 0.8805 0.1102 48 R 0.0122 0.7955 0.1923 49 C 0.0273 0.6360 0.3367 50 Y 0.0366 0.6385 0.3250 51 T 0.0191 0.7983 0.1826 52 E 0.0149 0.8649 0.1202 53 T 0.0138 0.8886 0.0976 54 R 0.0141 0.8924 0.0935 55 Q 0.0197 0.8612 0.1191 56 Y 0.0372 0.7134 0.2494 57 F 0.0932 0.4262 0.4805 58 D 0.1038 0.3537 0.5425 59 S 0.0202 0.6973 0.2825 60 K 0.0112 0.8271 0.1617 61 E 0.0116 0.8794 0.1090 62 W 0.0089 0.9086 0.0825 63 S 0.0085 0.9169 0.0746 64 R 0.0083 0.9189 0.0727 65 L 0.0085 0.9149 0.0766 66 K 0.0087 0.8982 0.0930 67 E 0.0085 0.9071 0.0844 68 G 0.0086 0.8978 0.0936 69 F 0.0118 0.8723 0.1159 70 V 0.0116 0.8749 0.1135 71 R 0.0161 0.8281 0.1558 72 D 0.0369 0.6062 0.3568 73 A 0.0965 0.3235 0.5801 74 R 0.0988 0.3025 0.5987 75 A 0.0646 0.3883 0.5470 76 Q 0.0811 0.2907 0.6282 77 T 0.1520 0.1884 0.6596 78 P 0.0732 0.5270 0.3997 79 Y 0.0723 0.5418 0.3859 80 F 0.0560 0.6626 0.2814 81 Q 0.0466 0.7070 0.2464 82 E 0.0504 0.6873 0.2623 83 I 0.0943 0.5516 0.3541 84 P 0.0296 0.7368 0.2336 85 G 0.0119 0.8467 0.1414 86 E 0.0131 0.8582 0.1287 87 F 0.0111 0.8916 0.0973 88 L 0.0102 0.8925 0.0973 89 Q 0.0099 0.8823 0.1077 90 Y 0.0144 0.8174 0.1682 91 C 0.0298 0.6758 0.2944 92 Q 0.0497 0.3791 0.5712 93 S 0.1282 0.1505 0.7213 94 P 0.1550 0.1160 0.7290 95 P 0.1262 0.2063 0.6674 96 L 0.1459 0.2195 0.6347 97 S 0.1271 0.2152 0.6577 98 D 0.0247 0.6057 0.3696 99 G 0.0269 0.6316 0.3415 100 I 0.0169 0.8407 0.1424 101 L 0.0113 0.8914 0.0972 102 A 0.0105 0.8984 0.0911 103 L 0.0182 0.8771 0.1047 104 M 0.0180 0.8708 0.1112 105 D 0.0179 0.8756 0.1064 106 F 0.0189 0.8858 0.0952 107 E 0.0175 0.8956 0.0869 108 Y 0.0148 0.9039 0.0814 109 T 0.0138 0.9072 0.0790 110 Q 0.0134 0.9001 0.0865 111 L 0.0194 0.8624 0.1182 112 L 0.0260 0.8273 0.1468 113 A 0.0369 0.7743 0.1888 114 E 0.0561 0.6885 0.2554 115 V 0.0657 0.6577 0.2766 116 A 0.0604 0.5426 0.3969 117 Q 0.0833 0.3707 0.5460 118 I 0.1758 0.1447 0.6795 119 P 0.1437 0.1567 0.6996 120 D 0.1732 0.1503 0.6765 121 I 0.1948 0.0596 0.7455 122 P 0.1557 0.0960 0.7483 123 D 0.0965 0.4829 0.4206 124 I 0.0795 0.5700 0.3505 125 H 0.0913 0.5860 0.3227 126 Y 0.0923 0.5178 0.3900 127 S 0.1117 0.3583 0.5300 128 N 0.1056 0.2808 0.6136 129 D 0.1307 0.2219 0.6474 130 S 0.1782 0.1747 0.6472 131 K 0.2425 0.1448 0.6127 132 Y 0.3064 0.0786 0.6150 133 T 0.2885 0.0357 0.6758 134 P 0.2558 0.0846 0.6596 135 S 0.2301 0.0523 0.7177 136 P 0.1149 0.3779 0.5072 137 A 0.1562 0.4545 0.3893 138 A 0.3341 0.3930 0.2729 139 F 0.4831 0.2888 0.2281 140 I 0.4720 0.3050 0.2230 141 R 0.4520 0.2940 0.2539 142 Q 0.3954 0.2416 0.3630 143 Y 0.3041 0.2027 0.4932 144 R 0.2252 0.1922 0.5826 145 Y 0.2671 0.1245 0.6084 146 D 0.2075 0.1299 0.6626 147 V 0.1967 0.1757 0.6276 148 T 0.1659 0.1752 0.6589 149 H 0.1368 0.3556 0.5075 150 D 0.1673 0.2961 0.5365 151 L 0.1032 0.4875 0.4092 152 Q 0.0858 0.4803 0.4340 153 E 0.0970 0.5130 0.3899 154 A 0.1959 0.3304 0.4737 155 E 0.2159 0.3393 0.4448 156 T 0.3488 0.2186 0.4326 157 A 0.6609 0.0737 0.2655 158 L 0.7700 0.0145 0.2155 159 L 0.8145 0.0079 0.1777 160 I 0.8096 0.0100 0.1805 161 W 0.7564 0.0141 0.2296 162 R 0.6801 0.0289 0.2910 163 N 0.3680 0.0213 0.6108 164 A 0.0905 0.3574 0.5521 165 E 0.0869 0.2946 0.6185 166 D 0.1353 0.1807 0.6840 167 D 0.3159 0.0825 0.6016 168 V 0.5628 0.0385 0.3987 169 M 0.6333 0.0384 0.3283 170 Y 0.6829 0.0354 0.2817 171 Q 0.6435 0.0393 0.3172 172 T 0.5580 0.0359 0.4061 173 L 0.3150 0.0930 0.5920 174 D 0.1508 0.1122 0.7370 175 G 0.0210 0.7155 0.2635 176 F 0.0122 0.8418 0.1460 177 D 0.0097 0.9065 0.0838 178 M 0.0088 0.9213 0.0698 179 M 0.0087 0.9224 0.0688 180 L 0.0084 0.9236 0.0680 181 L 0.0083 0.9224 0.0693 182 E 0.0083 0.9211 0.0706 183 I 0.0085 0.9083 0.0832 184 M 0.0101 0.8650 0.1249 185 G 0.0152 0.7562 0.2286 186 S 0.0362 0.4589 0.5049 187 S 0.0513 0.2357 0.7130 188 A 0.0974 0.2064 0.6962 189 L 0.1868 0.1320 0.6812 190 S 0.1790 0.0604 0.7607 191 F 0.0198 0.7138 0.2664 192 D 0.0097 0.8595 0.1308 193 T 0.0085 0.9140 0.0775 194 L 0.0086 0.9117 0.0797 195 A 0.0084 0.9169 0.0748 196 Q 0.0083 0.9171 0.0746 197 T 0.0084 0.9137 0.0778 198 L 0.0092 0.8866 0.1042 199 V 0.0090 0.8717 0.1193 200 E 0.0108 0.7400 0.2493 201 F 0.0258 0.5048 0.4694 202 M 0.1099 0.2317 0.6584 203 P 0.0456 0.4249 0.5296 204 K 0.0521 0.5082 0.4396 205 A 0.0340 0.6808 0.2852 206 D 0.0218 0.7584 0.2198 207 N 0.0146 0.8361 0.1493 208 W 0.0107 0.8885 0.1008 209 K 0.0089 0.9103 0.0808 210 N 0.0086 0.9167 0.0747 211 I 0.0084 0.9184 0.0732 212 L 0.0086 0.9093 0.0821 213 L 0.0087 0.9098 0.0815 214 G 0.0094 0.8982 0.0924 215 K 0.0110 0.8884 0.1006 216 W 0.0111 0.8574 0.1315 217 S 0.0114 0.8693 0.1193 218 G 0.0109 0.8381 0.1510 219 W 0.0131 0.8705 0.1164 220 I 0.0205 0.8306 0.1489 221 E 0.0288 0.7460 0.2252 222 Q 0.0539 0.4668 0.4793 223 R 0.1250 0.2000 0.6750 224 I 0.3393 0.1316 0.5291 225 I 0.4342 0.1050 0.4608 226 I 0.4604 0.0686 0.4710 227 P 0.3098 0.1752 0.5150 228 S 0.2567 0.2580 0.4852 229 L 0.2452 0.2254 0.5294 230 S 0.2161 0.2718 0.5121 231 A 0.1990 0.3293 0.4717 232 I 0.1912 0.3466 0.4622 233 S 0.2004 0.3077 0.4920 234 E 0.1858 0.2601 0.5541 235 N 0.1557 0.1599 0.6845 236 M 0.1235 0.2874 0.5890 237 E 0.1124 0.2176 0.6700 238 G 0.0782 0.1722 0.7495 239 N 0.1353 0.1296 0.7351 240 S 0.1982 0.1159 0.6859 241 P 0.1475 0.3038 0.5487 242 S 0.1626 0.4167 0.4207 243 Q 0.1409 0.5464 0.3127 244 N 0.1322 0.5082 0.3595 245 H 0.1493 0.4647 0.3860 246 L 0.1602 0.3443 0.4956 247 S 0.1824 0.2113 0.6063 248 A 0.1069 0.3916 0.5014