# This file is the result of combining several RDB files, specifically # T0368.t06.dssp-ebghstl.rdb (weight 1.53986) # T0368.t06.stride-ebghtl.rdb (weight 1.24869) # T0368.t06.str2.rdb (weight 1.54758) # T0368.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 T0368.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0368 # 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 T0368.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 3.53726 # # ============================================ # Comments from T0368.t06.stride-ebghtl.rdb # ============================================ # TARGET T0368 # 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 T0368.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 3.53726 # # ============================================ # Comments from T0368.t06.str2.rdb # ============================================ # TARGET T0368 # 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 T0368.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 3.53726 # # ============================================ # Comments from T0368.t06.alpha.rdb # ============================================ # TARGET T0368 # 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 T0368.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 3.53726 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0596 0.0279 0.9124 2 K 0.1112 0.0641 0.8247 3 P 0.1239 0.1491 0.7271 4 L 0.0181 0.7946 0.1873 5 K 0.0079 0.9264 0.0657 6 E 0.0077 0.9340 0.0584 7 V 0.0058 0.9412 0.0530 8 V 0.0061 0.9462 0.0477 9 G 0.0053 0.9462 0.0485 10 A 0.0052 0.9471 0.0477 11 Y 0.0057 0.9436 0.0507 12 L 0.0066 0.9255 0.0679 13 A 0.0106 0.8658 0.1236 14 L 0.0105 0.8417 0.1478 15 S 0.0150 0.8263 0.1587 16 D 0.0072 0.8750 0.1179 17 A 0.0072 0.9011 0.0917 18 Q 0.0071 0.9129 0.0800 19 R 0.0090 0.9179 0.0731 20 Q 0.0089 0.9164 0.0746 21 L 0.0133 0.8801 0.1066 22 V 0.0159 0.7946 0.1895 23 A 0.0235 0.6297 0.3468 24 G 0.0239 0.4299 0.5462 25 E 0.0363 0.4760 0.4878 26 Y 0.0162 0.7974 0.1864 27 D 0.0066 0.9238 0.0697 28 E 0.0059 0.9363 0.0578 29 A 0.0052 0.9383 0.0565 30 A 0.0053 0.9364 0.0583 31 A 0.0055 0.9103 0.0842 32 N 0.0063 0.8556 0.1381 33 C 0.0063 0.8642 0.1295 34 R 0.0077 0.8863 0.1060 35 R 0.0101 0.8704 0.1194 36 A 0.0140 0.8683 0.1177 37 M 0.0377 0.8204 0.1418 38 E 0.0707 0.7699 0.1594 39 I 0.0673 0.7327 0.2000 40 S 0.0878 0.5722 0.3400 41 H 0.1069 0.2943 0.5988 42 T 0.1334 0.1275 0.7391 43 M 0.1107 0.0262 0.8631 44 P 0.0682 0.0129 0.9190 45 P 0.0144 0.5805 0.4051 46 E 0.0137 0.6848 0.3016 47 E 0.0313 0.7286 0.2401 48 A 0.1389 0.5253 0.3358 49 F 0.1916 0.3280 0.4804 50 D 0.1431 0.2337 0.6233 51 H 0.0449 0.3434 0.6117 52 A 0.0437 0.2717 0.6845 53 G 0.0405 0.3262 0.6333 54 F 0.0695 0.3986 0.5319 55 D 0.0486 0.5575 0.3940 56 A 0.0898 0.8086 0.1016 57 F 0.0712 0.8710 0.0577 58 C 0.0784 0.8581 0.0635 59 H 0.0763 0.8452 0.0786 60 A 0.0683 0.8039 0.1278 61 G 0.0411 0.7941 0.1647 62 L 0.0139 0.8621 0.1240 63 A 0.0070 0.9165 0.0765 64 E 0.0055 0.9196 0.0750 65 A 0.0070 0.9168 0.0763 66 L 0.0093 0.8965 0.0943 67 A 0.0148 0.7637 0.2215 68 G 0.0152 0.5546 0.4303 69 L 0.0338 0.4876 0.4786 70 R 0.0242 0.4380 0.5379 71 S 0.0423 0.4693 0.4884 72 F 0.0114 0.8055 0.1832 73 D 0.0060 0.9106 0.0834 74 E 0.0067 0.9135 0.0798 75 A 0.0066 0.9154 0.0780 76 L 0.0094 0.9043 0.0863 77 H 0.0078 0.8778 0.1144 78 S 0.0097 0.8668 0.1235 79 A 0.0055 0.9245 0.0700 80 D 0.0051 0.9405 0.0544 81 K 0.0053 0.9257 0.0690 82 A 0.0051 0.9278 0.0671 83 L 0.0082 0.9127 0.0791 84 H 0.0103 0.8621 0.1276 85 Y 0.0144 0.8326 0.1529 86 F 0.0561 0.6145 0.3294 87 N 0.0586 0.3587 0.5827 88 R 0.0758 0.2989 0.6254 89 R 0.1088 0.2062 0.6850 90 G 0.1178 0.1324 0.7497 91 E 0.2657 0.1396 0.5947 92 L 0.3272 0.1540 0.5188 93 N 0.2621 0.1154 0.6225 94 Q 0.0806 0.2920 0.6274 95 D 0.0692 0.2964 0.6345 96 E 0.0486 0.1883 0.7631 97 G 0.0561 0.1336 0.8102 98 K 0.1883 0.2709 0.5408 99 L 0.5515 0.3104 0.1381 100 W 0.5930 0.3380 0.0691 101 I 0.5184 0.4221 0.0595 102 S 0.3760 0.5655 0.0584 103 A 0.3752 0.5589 0.0659 104 V 0.2318 0.6858 0.0825 105 Y 0.1076 0.7914 0.1010 106 S 0.0477 0.8374 0.1149 107 R 0.0230 0.8648 0.1121 108 A 0.0212 0.8725 0.1063 109 L 0.0317 0.8413 0.1270 110 A 0.0403 0.7946 0.1651 111 L 0.0445 0.7231 0.2324 112 D 0.0240 0.6080 0.3680 113 G 0.0241 0.4409 0.5351 114 L 0.0595 0.2384 0.7021 115 G 0.0591 0.0847 0.8562 116 R 0.0617 0.1158 0.8225 117 G 0.0514 0.2713 0.6773 118 A 0.0139 0.7260 0.2601 119 E 0.0148 0.7345 0.2508 120 A 0.0161 0.7492 0.2347 121 M 0.0196 0.7254 0.2550 122 P 0.0065 0.8891 0.1044 123 E 0.0070 0.8768 0.1162 124 F 0.0074 0.9121 0.0804 125 K 0.0055 0.9231 0.0714 126 K 0.0061 0.9189 0.0750 127 V 0.0061 0.9298 0.0641 128 V 0.0063 0.9406 0.0531 129 E 0.0079 0.9334 0.0587 130 M 0.0072 0.9312 0.0615 131 I 0.0101 0.9206 0.0692 132 E 0.0139 0.9001 0.0861 133 E 0.0170 0.8633 0.1198 134 R 0.0355 0.7489 0.2156 135 K 0.0408 0.4359 0.5233 136 G 0.0396 0.1027 0.8578 137 E 0.0654 0.0759 0.8587 138 T 0.0846 0.0615 0.8539 139 P 0.0332 0.1783 0.7884 140 G 0.0368 0.2472 0.7160 141 K 0.0221 0.7534 0.2245 142 E 0.0087 0.9054 0.0859 143 R 0.0097 0.9252 0.0651 144 M 0.0075 0.9384 0.0541 145 M 0.0055 0.9525 0.0420 146 E 0.0052 0.9569 0.0379 147 V 0.0050 0.9570 0.0380 148 A 0.0050 0.9545 0.0405 149 I 0.0047 0.9552 0.0401 150 D 0.0048 0.9515 0.0437 151 R 0.0049 0.9444 0.0507 152 I 0.0054 0.9407 0.0539 153 A 0.0067 0.9157 0.0776 154 Q 0.0085 0.8554 0.1361 155 L 0.0318 0.6746 0.2936 156 G 0.0381 0.4041 0.5578 157 A 0.0416 0.3631 0.5954 158 S 0.0568 0.3260 0.6172 159 N 0.0728 0.2320 0.6952 160 Q 0.0554 0.2968 0.6478 161 Q 0.0688 0.2427 0.6886 162 K 0.1037 0.1506 0.7457 163 K 0.0837 0.0373 0.8790 164 P 0.0521 0.0977 0.8502 165 G 0.0728 0.0632 0.8640 166 Y 0.3966 0.0391 0.5643 167 K 0.6248 0.0377 0.3375 168 A 0.8234 0.0247 0.1519 169 W 0.8616 0.0282 0.1102 170 W 0.8566 0.0382 0.1052 171 E 0.8253 0.0563 0.1184 172 F 0.7332 0.0655 0.2012 173 W 0.4965 0.0639 0.4396 174 S 0.1769 0.0337 0.7893