# This file is the result of combining several RDB files, specifically # T0440.t2k.str2.rdb (weight 1.54425) # T0440.t2k.str4.rdb (weight 0.924988) # T0440.t2k.pb.rdb (weight 0.789901) # T0440.t2k.bys.rdb (weight 0.748322) # T0440.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 T0440.t2k.str2.rdb # ============================================ # TARGET T0440 # 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 T0440.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 193 # # ============================================ # Comments from T0440.t2k.str4.rdb # ============================================ # TARGET T0440 # 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 T0440.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 193 # # ============================================ # Comments from T0440.t2k.pb.rdb # ============================================ # TARGET T0440 # 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 T0440.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 193 # # ============================================ # Comments from T0440.t2k.bys.rdb # ============================================ # TARGET T0440 # 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 T0440.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 193 # # ============================================ # Comments from T0440.t2k.alpha.rdb # ============================================ # TARGET T0440 # 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 T0440.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 193 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3215 0.0936 0.5849 2 K 0.3108 0.1016 0.5877 3 R 0.2891 0.1518 0.5591 4 D 0.2429 0.1488 0.6083 5 G 0.2327 0.1817 0.5855 6 H 0.3324 0.1380 0.5295 7 T 0.3595 0.1315 0.5090 8 H 0.2973 0.1106 0.5921 9 T 0.2219 0.1406 0.6374 10 E 0.1283 0.3027 0.5690 11 F 0.1738 0.2070 0.6192 12 C 0.1761 0.1194 0.7045 13 P 0.0996 0.3562 0.5441 14 H 0.0895 0.2347 0.6758 15 G 0.0886 0.1560 0.7554 16 T 0.1316 0.1648 0.7036 17 H 0.1106 0.2426 0.6467 18 D 0.0880 0.3038 0.6082 19 D 0.1057 0.3682 0.5261 20 V 0.0112 0.7815 0.2073 21 E 0.0089 0.8842 0.1068 22 E 0.0083 0.9251 0.0667 23 M 0.0083 0.9239 0.0678 24 V 0.0083 0.9240 0.0677 25 L 0.0083 0.9243 0.0674 26 K 0.0083 0.9242 0.0675 27 A 0.0086 0.9187 0.0727 28 I 0.0085 0.9058 0.0857 29 E 0.0113 0.8308 0.1578 30 L 0.0495 0.3496 0.6009 31 D 0.0513 0.0801 0.8686 32 F 0.1731 0.0847 0.7422 33 D 0.2930 0.1041 0.6029 34 E 0.6531 0.0583 0.2886 35 Y 0.7297 0.0208 0.2494 36 S 0.7616 0.0158 0.2227 37 I 0.7128 0.0298 0.2574 38 V 0.5924 0.0636 0.3440 39 E 0.3502 0.1743 0.4756 40 H 0.2222 0.1613 0.6165 41 A 0.2298 0.1008 0.6694 42 P 0.2098 0.1353 0.6548 43 L 0.2271 0.1044 0.6685 44 S 0.1552 0.1927 0.6521 45 S 0.0623 0.4672 0.4706 46 E 0.0562 0.5209 0.4229 47 F 0.0912 0.4545 0.4543 48 M 0.1447 0.3398 0.5155 49 K 0.1712 0.2292 0.5996 50 N 0.1744 0.1543 0.6713 51 T 0.1524 0.2254 0.6222 52 A 0.0620 0.4845 0.4535 53 G 0.0736 0.4068 0.5196 54 D 0.0974 0.4761 0.4265 55 K 0.0645 0.6323 0.3033 56 E 0.0722 0.6346 0.2932 57 A 0.0923 0.5737 0.3340 58 V 0.1210 0.5297 0.3493 59 T 0.1126 0.4922 0.3952 60 T 0.0935 0.4993 0.4072 61 A 0.0475 0.6464 0.3061 62 S 0.0630 0.5970 0.3400 63 M 0.1093 0.5341 0.3566 64 A 0.1091 0.4463 0.4446 65 M 0.0416 0.6383 0.3201 66 S 0.0254 0.6164 0.3582 67 D 0.0383 0.4302 0.5315 68 L 0.0685 0.4606 0.4709 69 P 0.0129 0.8245 0.1626 70 Y 0.0093 0.8896 0.1011 71 Y 0.0093 0.9099 0.0808 72 F 0.0085 0.9142 0.0773 73 K 0.0083 0.9213 0.0704 74 K 0.0084 0.9186 0.0729 75 M 0.0084 0.9176 0.0740 76 N 0.0083 0.9208 0.0708 77 H 0.0083 0.9222 0.0695 78 I 0.0084 0.9177 0.0738 79 K 0.0084 0.9175 0.0741 80 K 0.0085 0.9143 0.0772 81 K 0.0124 0.8710 0.1166 82 Y 0.0337 0.7507 0.2156 83 A 0.0478 0.6543 0.2979 84 S 0.0459 0.3812 0.5729 85 D 0.0967 0.1697 0.7336 86 L 0.3477 0.0411 0.6112 87 L 0.5523 0.0283 0.4195 88 I 0.7311 0.0164 0.2525 89 H 0.7144 0.0154 0.2702 90 I 0.7165 0.0266 0.2570 91 G 0.6738 0.0278 0.2984 92 F 0.7196 0.0241 0.2563 93 E 0.7117 0.0262 0.2621 94 V 0.6393 0.0613 0.2994 95 D 0.5213 0.1084 0.3704 96 Y 0.4229 0.1314 0.4457 97 L 0.2544 0.1209 0.6247 98 I 0.1464 0.2106 0.6429 99 G 0.0870 0.1928 0.7202 100 Y 0.1182 0.3238 0.5580 101 E 0.0634 0.6463 0.2904 102 D 0.0364 0.7750 0.1886 103 F 0.0273 0.8339 0.1388 104 T 0.0259 0.8594 0.1147 105 R 0.0112 0.8927 0.0961 106 D 0.0098 0.9075 0.0827 107 F 0.0111 0.8856 0.1032 108 L 0.0123 0.8629 0.1248 109 N 0.0161 0.7740 0.2099 110 E 0.0261 0.6098 0.3641 111 Y 0.0580 0.2793 0.6626 112 G 0.0951 0.1034 0.8015 113 P 0.1485 0.0924 0.7591 114 Q 0.1753 0.1529 0.6718 115 T 0.2398 0.1719 0.5883 116 D 0.2987 0.1613 0.5400 117 D 0.5209 0.1297 0.3494 118 G 0.6652 0.0744 0.2605 119 V 0.6834 0.0638 0.2527 120 L 0.6622 0.0526 0.2852 121 S 0.6771 0.0432 0.2797 122 L 0.6012 0.0791 0.3197 123 H 0.6252 0.0675 0.3073 124 F 0.5685 0.0781 0.3534 125 L 0.4208 0.1016 0.4775 126 E 0.2405 0.1348 0.6247 127 G 0.1644 0.1191 0.7165 128 Q 0.1684 0.1295 0.7021 129 G 0.1395 0.1505 0.7100 130 G 0.1617 0.1865 0.6518 131 F 0.2570 0.1723 0.5707 132 R 0.3115 0.1531 0.5355 133 S 0.2487 0.1835 0.5677 134 I 0.1533 0.4513 0.3954 135 D 0.1370 0.4360 0.4270 136 F 0.1686 0.3658 0.4656 137 S 0.1592 0.2989 0.5420 138 A 0.0497 0.6206 0.3297 139 E 0.0278 0.7378 0.2345 140 D 0.0319 0.7399 0.2282 141 Y 0.0309 0.7286 0.2405 142 N 0.0345 0.7040 0.2615 143 E 0.0480 0.5932 0.3588 144 G 0.0536 0.5803 0.3661 145 I 0.1034 0.6766 0.2201 146 V 0.1182 0.6990 0.1828 147 Q 0.1263 0.6716 0.2020 148 F 0.1161 0.6160 0.2679 149 Y 0.1307 0.4296 0.4397 150 G 0.0928 0.2801 0.6271 151 G 0.1132 0.2436 0.6432 152 F 0.1261 0.3079 0.5661 153 E 0.0853 0.4928 0.4219 154 Q 0.0679 0.6353 0.2968 155 A 0.0481 0.7615 0.1904 156 Q 0.0184 0.8736 0.1080 157 L 0.0095 0.9136 0.0769 158 A 0.0086 0.9194 0.0720 159 Y 0.0088 0.9189 0.0723 160 L 0.0088 0.9185 0.0727 161 E 0.0084 0.9160 0.0756 162 G 0.0085 0.9091 0.0824 163 V 0.0084 0.9158 0.0757 164 K 0.0084 0.9189 0.0727 165 Q 0.0083 0.9230 0.0687 166 S 0.0083 0.9230 0.0687 167 I 0.0083 0.9221 0.0696 168 E 0.0084 0.9191 0.0725 169 A 0.0084 0.9144 0.0772 170 D 0.0119 0.8444 0.1437 171 L 0.0294 0.6945 0.2760 172 G 0.0356 0.5181 0.4462 173 L 0.0754 0.3743 0.5503 174 F 0.1111 0.1594 0.7294 175 K 0.2248 0.0644 0.7108 176 P 0.2767 0.0900 0.6332 177 R 0.4790 0.0871 0.4339 178 R 0.6667 0.0616 0.2717 179 M 0.6416 0.0663 0.2921 180 G 0.5896 0.0591 0.3513 181 H 0.3870 0.1176 0.4955 182 I 0.1610 0.3943 0.4446 183 S 0.0808 0.6047 0.3145 184 L 0.0485 0.7582 0.1933 185 C 0.0395 0.8224 0.1382 186 Q 0.0432 0.8209 0.1360 187 K 0.0491 0.7513 0.1996 188 F 0.0785 0.5960 0.3254 189 Q 0.1035 0.5188 0.3777 190 Q 0.0964 0.4688 0.4349 191 F 0.1367 0.3496 0.5138 192 F 0.1367 0.2406 0.6227 193 G 0.1113 0.1900 0.6988 194 E 0.1064 0.3271 0.5665 195 D 0.1326 0.2580 0.6094 196 T 0.1374 0.3442 0.5184 197 S 0.0958 0.4621 0.4421 198 D 0.0652 0.5508 0.3840 199 F 0.0810 0.4969 0.4222 200 S 0.0890 0.5888 0.3222 201 E 0.0125 0.8123 0.1752 202 E 0.0109 0.8715 0.1177 203 V 0.0095 0.9097 0.0808 204 M 0.0084 0.9194 0.0722 205 E 0.0083 0.9237 0.0680 206 K 0.0083 0.9243 0.0674 207 F 0.0083 0.9228 0.0689 208 R 0.0083 0.9238 0.0680 209 V 0.0082 0.9251 0.0666 210 I 0.0083 0.9231 0.0686 211 L 0.0083 0.9219 0.0697 212 A 0.0083 0.9247 0.0670 213 L 0.0083 0.9244 0.0673 214 V 0.0084 0.9191 0.0725 215 K 0.0089 0.8857 0.1054 216 K 0.0126 0.8162 0.1712 217 R 0.0533 0.2712 0.6756 218 D 0.0517 0.0716 0.8767 219 Y 0.2341 0.0327 0.7331 220 E 0.5639 0.0279 0.4082 221 L 0.7728 0.0136 0.2136 222 D 0.7723 0.0112 0.2165 223 F 0.7486 0.0218 0.2296 224 N 0.5214 0.0416 0.4370 225 T 0.3196 0.1754 0.5050 226 A 0.1527 0.3245 0.5228 227 G 0.1461 0.3327 0.5213 228 L 0.2011 0.3301 0.4689 229 F 0.2424 0.2307 0.5269 230 K 0.2259 0.2329 0.5412 231 P 0.0985 0.4158 0.4857 232 L 0.1064 0.3695 0.5240 233 C 0.1447 0.2238 0.6315 234 G 0.1258 0.1216 0.7526 235 E 0.2324 0.1063 0.6613 236 T 0.3077 0.1169 0.5755 237 Y 0.2883 0.0553 0.6564 238 P 0.1790 0.0807 0.7403 239 P 0.0799 0.4020 0.5181 240 K 0.0139 0.7767 0.2095 241 K 0.0109 0.8710 0.1181 242 I 0.0084 0.9155 0.0761 243 V 0.0083 0.9210 0.0707 244 T 0.0083 0.9244 0.0673 245 L 0.0083 0.9233 0.0684 246 A 0.0084 0.9177 0.0739 247 S 0.0087 0.9005 0.0908 248 E 0.0133 0.8203 0.1664 249 L 0.0578 0.3549 0.5873 250 Q 0.0509 0.0670 0.8821 251 I 0.2144 0.0180 0.7676 252 P 0.4710 0.0230 0.5061 253 F 0.7260 0.0139 0.2601 254 V 0.7495 0.0147 0.2358 255 Y 0.7236 0.0247 0.2517 256 G 0.5745 0.0299 0.3956 257 S 0.2864 0.1339 0.5796 258 D 0.1460 0.2300 0.6241 259 S 0.0913 0.3542 0.5545 260 H 0.1056 0.2690 0.6254 261 G 0.1172 0.2540 0.6288 262 V 0.0544 0.5883 0.3573 263 Q 0.0445 0.6702 0.2853 264 D 0.0572 0.7019 0.2409 265 I 0.0727 0.6455 0.2818 266 G 0.0797 0.5443 0.3761 267 R 0.0605 0.5050 0.4346 268 G 0.0660 0.3843 0.5497 269 Y 0.0653 0.6279 0.3068 270 S 0.0248 0.8314 0.1438 271 T 0.0211 0.8579 0.1211 272 Y 0.0290 0.8374 0.1337 273 C 0.0523 0.7680 0.1797 274 Q 0.0803 0.6353 0.2844 275 K 0.1050 0.4172 0.4778