# This file is the result of combining several RDB files, specifically # T0308.t06.dssp-ebghstl.rdb (weight 1.53986) # T0308.t06.stride-ebghtl.rdb (weight 1.24869) # T0308.t06.str2.rdb (weight 1.54758) # T0308.t06.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 T0308.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0308 # 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 T0308.t06-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 7493 # # ============================================ # Comments from T0308.t06.stride-ebghtl.rdb # ============================================ # TARGET T0308 # Using neural net t06-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 T0308.t06-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 7493 # # ============================================ # Comments from T0308.t06.str2.rdb # ============================================ # TARGET T0308 # Using neural net t06-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 T0308.t06-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 7493 # # ============================================ # Comments from T0308.t06.alpha.rdb # ============================================ # TARGET T0308 # Using neural net t06-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 T0308.t06-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 7493 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 E 0.1151 0.0122 0.8727 2 V 0.4244 0.0055 0.5701 3 H 0.8219 0.0054 0.1727 4 V 0.9291 0.0034 0.0675 5 L 0.9327 0.0032 0.0641 6 C 0.9308 0.0031 0.0661 7 L 0.8610 0.0201 0.1189 8 G 0.5767 0.0098 0.4135 9 L 0.1570 0.0389 0.8040 10 D 0.0293 0.1280 0.8427 11 N 0.0252 0.1120 0.8629 12 S 0.0699 0.1343 0.7957 13 G 0.0855 0.1181 0.7964 14 K 0.0831 0.7337 0.1832 15 T 0.0717 0.8207 0.1076 16 T 0.0556 0.8564 0.0880 17 I 0.0372 0.8946 0.0682 18 I 0.0289 0.9008 0.0703 19 N 0.0359 0.8351 0.1290 20 K 0.0488 0.7025 0.2487 21 L 0.1255 0.4477 0.4268 22 K 0.0860 0.1671 0.7470 23 P 0.0381 0.2984 0.6636 24 S 0.0422 0.2641 0.6937 25 N 0.0851 0.2151 0.6998 26 A 0.1513 0.1372 0.7115 27 Q 0.2456 0.1364 0.6181 28 S 0.2627 0.1992 0.5381 29 Q 0.2379 0.1569 0.6053 30 N 0.2848 0.0943 0.6209 31 I 0.3601 0.0509 0.5890 32 L 0.3569 0.0282 0.6149 33 P 0.3595 0.0388 0.6017 34 T 0.4671 0.0431 0.4898 35 I 0.4819 0.0805 0.4376 36 G 0.4299 0.0375 0.5327 37 F 0.5255 0.0215 0.4530 38 S 0.7089 0.0118 0.2793 39 I 0.8023 0.0119 0.1858 40 E 0.8428 0.0095 0.1477 41 K 0.9014 0.0059 0.0927 42 F 0.8997 0.0051 0.0952 43 K 0.8753 0.0061 0.1186 44 S 0.6953 0.0209 0.2838 45 S 0.0711 0.0643 0.8646 46 S 0.0776 0.0406 0.8818 47 L 0.6432 0.0074 0.3494 48 S 0.8602 0.0055 0.1343 49 F 0.9211 0.0033 0.0756 50 T 0.9282 0.0035 0.0684 51 V 0.9294 0.0032 0.0674 52 F 0.9029 0.0038 0.0933 53 D 0.6596 0.0066 0.3338 54 M 0.1608 0.0239 0.8153 55 S 0.0600 0.0782 0.8619 56 G 0.0457 0.0701 0.8842 57 Q 0.0546 0.3581 0.5873 58 G 0.0277 0.6573 0.3150 59 R 0.0355 0.7209 0.2435 60 Y 0.0189 0.8430 0.1380 61 R 0.0118 0.8806 0.1076 62 N 0.0147 0.8819 0.1034 63 L 0.0121 0.8949 0.0930 64 W 0.0140 0.8988 0.0873 65 E 0.0068 0.9242 0.0690 66 H 0.0081 0.9004 0.0915 67 Y 0.0115 0.8598 0.1288 68 Y 0.0343 0.7773 0.1884 69 K 0.0209 0.5971 0.3820 70 E 0.0428 0.2674 0.6898 71 G 0.1502 0.0213 0.8285 72 Q 0.1053 0.0448 0.8499 73 A 0.9008 0.0037 0.0956 74 I 0.9314 0.0032 0.0654 75 I 0.9343 0.0031 0.0625 76 F 0.9319 0.0033 0.0647 77 V 0.9236 0.0035 0.0729 78 I 0.8691 0.0066 0.1243 79 D 0.5249 0.0061 0.4690 80 S 0.0731 0.1165 0.8103 81 S 0.0376 0.1239 0.8385 82 D 0.0686 0.1113 0.8201 83 R 0.0369 0.2867 0.6763 84 L 0.0903 0.3959 0.5138 85 R 0.1303 0.5079 0.3618 86 M 0.0468 0.8114 0.1418 87 V 0.0340 0.8861 0.0799 88 V 0.0328 0.8984 0.0688 89 A 0.0162 0.9163 0.0675 90 K 0.0084 0.9429 0.0488 91 E 0.0064 0.9452 0.0485 92 E 0.0050 0.9463 0.0488 93 L 0.0048 0.9535 0.0417 94 D 0.0047 0.9554 0.0399 95 T 0.0049 0.9516 0.0435 96 L 0.0054 0.9338 0.0608 97 L 0.0075 0.8620 0.1305 98 N 0.0143 0.5175 0.4682 99 H 0.0649 0.0939 0.8413 100 P 0.0225 0.2729 0.7045 101 D 0.0397 0.2832 0.6771 102 I 0.0797 0.4289 0.4914 103 K 0.0898 0.3605 0.5497 104 H 0.0722 0.2830 0.6448 105 R 0.0585 0.1387 0.8028 106 R 0.0929 0.0540 0.8532 107 I 0.2077 0.0097 0.7827 108 P 0.4298 0.0053 0.5649 109 I 0.9164 0.0035 0.0801 110 L 0.9327 0.0033 0.0640 111 F 0.9333 0.0032 0.0635 112 F 0.9212 0.0046 0.0743 113 A 0.8432 0.0089 0.1479 114 N 0.5489 0.0245 0.4266 115 K 0.2188 0.1379 0.6432 116 M 0.1472 0.2406 0.6122 117 D 0.1226 0.2416 0.6358 118 L 0.0639 0.4495 0.4866 119 R 0.0298 0.6047 0.3654 120 D 0.0399 0.5469 0.4132 121 A 0.0456 0.5243 0.4301 122 V 0.1029 0.3869 0.5102 123 T 0.1136 0.3842 0.5022 124 S 0.0864 0.5357 0.3779 125 V 0.1222 0.5640 0.3138 126 K 0.1433 0.5727 0.2840 127 V 0.1198 0.6483 0.2320 128 S 0.0793 0.6603 0.2603 129 Q 0.0155 0.9110 0.0736 130 L 0.0107 0.9251 0.0642 131 L 0.0090 0.9282 0.0628 132 C 0.0095 0.9277 0.0627 133 L 0.0068 0.9322 0.0610 134 E 0.0069 0.9093 0.0837 135 N 0.0080 0.8696 0.1224 136 I 0.0241 0.7753 0.2006 137 K 0.0180 0.6005 0.3815 138 D 0.0262 0.2890 0.6849 139 K 0.0628 0.0507 0.8865 140 P 0.0701 0.0439 0.8860 141 W 0.2431 0.0145 0.7424 142 H 0.6094 0.0148 0.3758 143 I 0.8697 0.0050 0.1253 144 C 0.8673 0.0065 0.1262 145 A 0.8318 0.0069 0.1613 146 S 0.6484 0.0213 0.3303 147 D 0.4463 0.0372 0.5165 148 A 0.1208 0.2209 0.6583 149 I 0.0734 0.2437 0.6829 150 K 0.0621 0.1713 0.7667 151 G 0.0354 0.1062 0.8583 152 E 0.0719 0.1402 0.7879 153 G 0.1430 0.2041 0.6529 154 L 0.0168 0.7978 0.1854 155 Q 0.0066 0.9247 0.0687 156 E 0.0068 0.9372 0.0560 157 G 0.0050 0.9483 0.0467 158 V 0.0047 0.9577 0.0376 159 D 0.0047 0.9589 0.0364 160 W 0.0047 0.9557 0.0396 161 L 0.0048 0.9499 0.0453 162 Q 0.0049 0.9418 0.0533 163 D 0.0058 0.8690 0.1252 164 Q 0.0082 0.7112 0.2805 165 I 0.0284 0.1475 0.8242