# This file is the result of combining several RDB files, specifically # T0386.t04.dssp-ebghstl.rdb (weight 1.53986) # T0386.t04.stride-ebghtl.rdb (weight 1.24869) # T0386.t04.str2.rdb (weight 1.54758) # T0386.t04.alpha.rdb (weight 0.659012) # 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 T0386.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0386.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 515 # # ============================================ # Comments from T0386.t04.stride-ebghtl.rdb # ============================================ # TARGET T0386 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0386.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 515 # # ============================================ # Comments from T0386.t04.str2.rdb # ============================================ # TARGET T0386 # Using neural net t04-2621-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 T0386.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 515 # # ============================================ # Comments from T0386.t04.alpha.rdb # ============================================ # TARGET T0386 # Using neural net t04-2621-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 T0386.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 515 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0270 0.6621 0.3108 2 M 0.0272 0.8675 0.1052 3 I 0.0284 0.8900 0.0816 4 N 0.0287 0.8856 0.0857 5 L 0.0233 0.8882 0.0886 6 R 0.0208 0.8678 0.1114 7 E 0.0201 0.8692 0.1107 8 E 0.0204 0.7893 0.1902 9 S 0.0262 0.5846 0.3893 10 L 0.0657 0.1271 0.8072 11 P 0.0340 0.1471 0.8189 12 E 0.0464 0.1374 0.8162 13 Y 0.0807 0.1047 0.8146 14 F 0.1331 0.0276 0.8393 15 D 0.0767 0.0170 0.9063 16 T 0.0049 0.9466 0.0485 17 A 0.0047 0.9596 0.0357 18 Y 0.0047 0.9603 0.0350 19 L 0.0047 0.9611 0.0343 20 C 0.0046 0.9611 0.0343 21 H 0.0047 0.9610 0.0344 22 I 0.0047 0.9607 0.0347 23 H 0.0047 0.9593 0.0360 24 Q 0.0047 0.9566 0.0387 25 Q 0.0049 0.9401 0.0550 26 L 0.0054 0.9121 0.0825 27 F 0.0093 0.8339 0.1568 28 K 0.0180 0.6600 0.3220 29 N 0.0260 0.3838 0.5902 30 T 0.0663 0.2893 0.6443 31 F 0.1178 0.2171 0.6650 32 E 0.1113 0.2387 0.6500 33 W 0.1504 0.2020 0.6476 34 A 0.1475 0.1798 0.6727 35 G 0.2142 0.0955 0.6903 36 Y 0.5268 0.0669 0.4064 37 L 0.7249 0.0294 0.2457 38 R 0.7110 0.0175 0.2715 39 H 0.6183 0.0177 0.3640 40 I 0.5373 0.0153 0.4473 41 P 0.5243 0.0240 0.4516 42 F 0.6012 0.0265 0.3722 43 T 0.6927 0.0239 0.2834 44 F 0.5937 0.0369 0.3694 45 A 0.4707 0.0456 0.4837 46 D 0.1983 0.0599 0.7417 47 G 0.1524 0.0539 0.7937 48 T 0.2389 0.0617 0.6994 49 T 0.2713 0.1057 0.6230 50 A 0.2932 0.1055 0.6013 51 A 0.4075 0.0944 0.4981 52 M 0.3807 0.0855 0.5338 53 P 0.3778 0.1127 0.5094 54 E 0.3673 0.1489 0.4839 55 M 0.4161 0.1317 0.4522 56 K 0.3323 0.1466 0.5211 57 R 0.2051 0.1815 0.6134 58 T 0.1147 0.1223 0.7630 59 G 0.1293 0.0750 0.7957 60 W 0.2596 0.0736 0.6668 61 K 0.4312 0.0792 0.4896 62 N 0.5848 0.0588 0.3564 63 A 0.6434 0.0625 0.2941 64 F 0.5928 0.0642 0.3430 65 A 0.3669 0.0653 0.5678 66 I 0.1674 0.0696 0.7630 67 G 0.0336 0.3990 0.5674 68 D 0.0082 0.7305 0.2613 69 E 0.0094 0.7960 0.1947 70 I 0.0078 0.8559 0.1363 71 Q 0.0054 0.9166 0.0781 72 E 0.0048 0.9251 0.0701 73 G 0.0049 0.9172 0.0779 74 L 0.0048 0.9459 0.0493 75 Q 0.0047 0.9522 0.0431 76 R 0.0048 0.9497 0.0456 77 L 0.0048 0.9492 0.0461 78 D 0.0047 0.9572 0.0381 79 Q 0.0047 0.9546 0.0408 80 T 0.0047 0.9505 0.0447 81 L 0.0047 0.9308 0.0644 82 A 0.0056 0.8621 0.1323 83 E 0.0063 0.7907 0.2030 84 K 0.0104 0.7244 0.2651 85 N 0.0275 0.5332 0.4393 86 N 0.0287 0.4465 0.5248 87 L 0.0462 0.4034 0.5505 88 Q 0.0335 0.3169 0.6496 89 G 0.0370 0.2090 0.7540 90 L 0.0714 0.1478 0.7808 91 T 0.0727 0.1285 0.7988 92 R 0.0400 0.5551 0.4049 93 E 0.0217 0.7229 0.2554 94 E 0.0061 0.8782 0.1156 95 F 0.0076 0.8909 0.1015 96 N 0.0068 0.9043 0.0889 97 S 0.0047 0.9544 0.0409 98 E 0.0047 0.9574 0.0379 99 A 0.0047 0.9595 0.0358 100 I 0.0047 0.9600 0.0354 101 E 0.0047 0.9602 0.0351 102 L 0.0049 0.9527 0.0423 103 F 0.0050 0.9490 0.0461 104 N 0.0067 0.9284 0.0650 105 S 0.0095 0.8859 0.1047 106 L 0.0206 0.8698 0.1096 107 N 0.0375 0.8159 0.1466 108 Q 0.1078 0.7198 0.1724 109 L 0.1415 0.5926 0.2659 110 H 0.1207 0.2224 0.6569 111 P 0.0797 0.1633 0.7570 112 F 0.1226 0.1296 0.7478 113 R 0.0943 0.1724 0.7334 114 E 0.0540 0.1978 0.7483 115 G 0.0364 0.2619 0.7017 116 N 0.0374 0.2960 0.6666 117 G 0.0179 0.5945 0.3875 118 R 0.0068 0.9282 0.0650 119 T 0.0053 0.9545 0.0401 120 Q 0.0047 0.9591 0.0362 121 R 0.0046 0.9615 0.0339 122 L 0.0046 0.9612 0.0341 123 F 0.0047 0.9604 0.0349 124 F 0.0047 0.9607 0.0347 125 E 0.0046 0.9605 0.0348 126 N 0.0047 0.9599 0.0355 127 L 0.0047 0.9596 0.0358 128 A 0.0047 0.9600 0.0353 129 K 0.0049 0.9549 0.0401 130 A 0.0069 0.9155 0.0776 131 A 0.0440 0.4041 0.5519 132 G 0.0329 0.0193 0.9479 133 H 0.0647 0.0088 0.9265 134 Q 0.2327 0.0103 0.7570 135 L 0.4575 0.0087 0.5338 136 N 0.4814 0.0094 0.5092 137 F 0.3802 0.0984 0.5213 138 S 0.2740 0.1208 0.6052 139 L 0.2489 0.2085 0.5426 140 I 0.1993 0.0867 0.7140 141 T 0.1071 0.0484 0.8445 142 K 0.0072 0.9423 0.0505 143 E 0.0053 0.9566 0.0382 144 R 0.0047 0.9591 0.0362 145 M 0.0047 0.9605 0.0349 146 M 0.0047 0.9605 0.0349 147 V 0.0047 0.9594 0.0359 148 A 0.0048 0.9556 0.0396 149 S 0.0051 0.9483 0.0466 150 V 0.0055 0.9391 0.0554 151 A 0.0075 0.9205 0.0720 152 V 0.0163 0.8702 0.1135 153 A 0.0236 0.7372 0.2392 154 E 0.0250 0.5695 0.4055 155 N 0.0495 0.2077 0.7427 156 G 0.0288 0.0718 0.8995 157 D 0.0793 0.0452 0.8756 158 L 0.0672 0.4477 0.4850 159 E 0.0146 0.8698 0.1156 160 P 0.0072 0.9356 0.0571 161 M 0.0049 0.9512 0.0439 162 Q 0.0052 0.9561 0.0388 163 H 0.0052 0.9518 0.0430 164 L 0.0055 0.9445 0.0500 165 F 0.0055 0.9414 0.0530 166 E 0.0061 0.9245 0.0694 167 D 0.0073 0.8713 0.1214 168 I 0.0123 0.7597 0.2279 169 S 0.0310 0.5374 0.4315 170 N 0.0442 0.3494 0.6064 171 P 0.0049 0.9114 0.0837 172 E 0.0049 0.9320 0.0630 173 K 0.0048 0.9502 0.0450 174 I 0.0048 0.9561 0.0392 175 R 0.0048 0.9493 0.0459 176 L 0.0048 0.9423 0.0529 177 L 0.0047 0.9538 0.0415 178 K 0.0047 0.9578 0.0375 179 E 0.0048 0.9562 0.0390 180 F 0.0048 0.9546 0.0407 181 M 0.0048 0.9555 0.0398 182 H 0.0049 0.9518 0.0434 183 T 0.0052 0.9485 0.0463 184 M 0.0068 0.9381 0.0551 185 K 0.0083 0.8966 0.0951 186 N 0.0107 0.8231 0.1662 187 T 0.0454 0.5608 0.3938 188 G 0.0339 0.2452 0.7210 189 R 0.0681 0.2514 0.6805 190 N 0.1124 0.2841 0.6036 191 V 0.1007 0.3407 0.5587 192 N 0.0843 0.2605 0.6552 193 D 0.0950 0.2629 0.6420 194 R 0.1495 0.2354 0.6151 195 P 0.1904 0.3124 0.4971 196 V 0.3028 0.3602 0.3370 197 M 0.3556 0.3329 0.3115 198 V 0.2959 0.2948 0.4093 199 A 0.1752 0.2241 0.6007 200 K 0.0991 0.1660 0.7349 201 E 0.0811 0.0848 0.8340