# This file is the result of combining several RDB files, specifically # T0364.t04.dssp-ebghstl.rdb (weight 1.53986) # T0364.t04.stride-ebghtl.rdb (weight 1.24869) # T0364.t04.str2.rdb (weight 1.54758) # T0364.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 T0364.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0364 # 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 T0364.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 1328 # # ============================================ # Comments from T0364.t04.stride-ebghtl.rdb # ============================================ # TARGET T0364 # 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 T0364.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 1328 # # ============================================ # Comments from T0364.t04.str2.rdb # ============================================ # TARGET T0364 # 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 T0364.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 1328 # # ============================================ # Comments from T0364.t04.alpha.rdb # ============================================ # TARGET T0364 # 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 T0364.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 1328 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0662 0.0104 0.9234 2 P 0.1140 0.0317 0.8543 3 A 0.2078 0.0537 0.7385 4 L 0.4909 0.0417 0.4673 5 I 0.7531 0.0124 0.2346 6 T 0.8521 0.0098 0.1382 7 Y 0.8201 0.0073 0.1726 8 R 0.7624 0.0108 0.2268 9 T 0.7850 0.0071 0.2079 10 T 0.7932 0.0073 0.1995 11 V 0.6093 0.0084 0.3823 12 Q 0.3448 0.0108 0.6444 13 E 0.0383 0.5827 0.3790 14 D 0.0339 0.5713 0.3948 15 W 0.0789 0.5742 0.3469 16 V 0.3177 0.2169 0.4654 17 D 0.1592 0.1303 0.7105 18 Y 0.0351 0.3271 0.6378 19 N 0.0479 0.1919 0.7602 20 G 0.0781 0.1598 0.7621 21 H 0.2220 0.1624 0.6156 22 L 0.4366 0.1345 0.4289 23 R 0.2136 0.1858 0.6006 24 D 0.0880 0.4170 0.4950 25 A 0.0556 0.7969 0.1475 26 F 0.0584 0.8623 0.0793 27 Y 0.0276 0.9229 0.0495 28 L 0.0196 0.9322 0.0483 29 L 0.0109 0.9403 0.0487 30 I 0.0072 0.9413 0.0515 31 F 0.0053 0.9472 0.0475 32 S 0.0049 0.9528 0.0424 33 Y 0.0049 0.9524 0.0426 34 A 0.0050 0.9419 0.0531 35 T 0.0049 0.9485 0.0466 36 D 0.0047 0.9556 0.0397 37 A 0.0047 0.9571 0.0381 38 L 0.0047 0.9581 0.0372 39 M 0.0047 0.9571 0.0382 40 D 0.0049 0.9484 0.0467 41 R 0.0063 0.9029 0.0908 42 I 0.0443 0.4462 0.5095 43 G 0.0421 0.0292 0.9287 44 L 0.0753 0.0125 0.9122 45 D 0.1089 0.0131 0.8780 46 A 0.0131 0.7913 0.1956 47 D 0.0115 0.8224 0.1661 48 S 0.0180 0.8185 0.1634 49 R 0.0565 0.6922 0.2513 50 G 0.0523 0.5280 0.4198 51 Q 0.0562 0.4385 0.5053 52 S 0.0540 0.1702 0.7759 53 G 0.0647 0.0464 0.8889 54 N 0.2671 0.0275 0.7054 55 S 0.6525 0.0174 0.3300 56 L 0.8376 0.0165 0.1460 57 F 0.8691 0.0145 0.1164 58 T 0.8887 0.0136 0.0978 59 L 0.8637 0.0174 0.1188 60 E 0.8743 0.0132 0.1125 61 A 0.8811 0.0107 0.1081 62 H 0.8589 0.0170 0.1241 63 I 0.8685 0.0105 0.1210 64 N 0.8640 0.0132 0.1228 65 Y 0.8346 0.0149 0.1505 66 L 0.6589 0.0429 0.2982 67 H 0.5483 0.0237 0.4280 68 E 0.5011 0.0266 0.4723 69 V 0.3841 0.0155 0.6004 70 K 0.2405 0.0178 0.7417 71 L 0.0756 0.0795 0.8449 72 G 0.0419 0.0456 0.9126 73 T 0.2434 0.0296 0.7270 74 E 0.7340 0.0052 0.2608 75 V 0.9078 0.0039 0.0883 76 W 0.9286 0.0033 0.0682 77 V 0.9262 0.0037 0.0701 78 Q 0.9189 0.0041 0.0770 79 T 0.9145 0.0038 0.0818 80 Q 0.9119 0.0045 0.0836 81 I 0.9113 0.0043 0.0843 82 L 0.8036 0.0299 0.1665 83 G 0.7157 0.0165 0.2678 84 F 0.6058 0.0330 0.3612 85 D 0.3518 0.0412 0.6070 86 R 0.2171 0.0627 0.7201 87 K 0.4673 0.0466 0.4861 88 R 0.8143 0.0151 0.1705 89 L 0.9105 0.0038 0.0856 90 H 0.9210 0.0051 0.0739 91 V 0.9274 0.0037 0.0689 92 Y 0.9221 0.0049 0.0730 93 H 0.9242 0.0039 0.0719 94 S 0.9213 0.0048 0.0739 95 L 0.9206 0.0057 0.0737 96 H 0.8972 0.0099 0.0929 97 R 0.7864 0.0135 0.2001 98 A 0.1481 0.0609 0.7910 99 G 0.0532 0.0535 0.8932 100 F 0.0863 0.0288 0.8849 101 D 0.1510 0.0331 0.8159 102 E 0.7300 0.0105 0.2595 103 V 0.9069 0.0047 0.0884 104 L 0.9162 0.0053 0.0785 105 A 0.9154 0.0051 0.0795 106 A 0.9100 0.0062 0.0838 107 S 0.8987 0.0057 0.0956 108 E 0.8794 0.0094 0.1113 109 Q 0.9169 0.0036 0.0795 110 M 0.9203 0.0045 0.0752 111 L 0.9296 0.0032 0.0671 112 L 0.9236 0.0039 0.0725 113 H 0.9172 0.0038 0.0789 114 V 0.8519 0.0084 0.1397 115 D 0.5243 0.0084 0.4673 116 L 0.0760 0.1045 0.8195 117 A 0.0445 0.0774 0.8781 118 G 0.0619 0.0322 0.9059 119 P 0.0959 0.0329 0.8712 120 Q 0.2255 0.0167 0.7578 121 S 0.2699 0.0209 0.7092 122 A 0.1885 0.0186 0.7928 123 P 0.1856 0.0236 0.7908 124 F 0.1081 0.0422 0.8497 125 G 0.0667 0.0838 0.8495 126 H 0.0133 0.8120 0.1747 127 T 0.0161 0.8775 0.1064 128 T 0.0112 0.9151 0.0737 129 V 0.0104 0.9341 0.0556 130 C 0.0100 0.9280 0.0620 131 R 0.0093 0.9169 0.0738 132 L 0.0090 0.9073 0.0837 133 N 0.0068 0.9211 0.0722 134 H 0.0068 0.9147 0.0785 135 L 0.0087 0.9012 0.0901 136 V 0.0131 0.8785 0.1085 137 E 0.0156 0.8323 0.1521 138 Q 0.0247 0.7417 0.2336 139 Q 0.0360 0.6103 0.3537 140 E 0.0310 0.4901 0.4789 141 G 0.0333 0.3415 0.6252 142 A 0.0602 0.1543 0.7855 143 Q 0.0739 0.1159 0.8102 144 A 0.0737 0.0543 0.8720 145 P 0.0746 0.2980 0.6273 146 Q 0.0388 0.5748 0.3865 147 Y 0.0590 0.5793 0.3617 148 M 0.0891 0.3736 0.5373 149 G 0.0620 0.1672 0.7708 150 R 0.1776 0.1181 0.7043 151 T 0.4367 0.1497 0.4136 152 I 0.3836 0.1089 0.5074 153 K 0.3173 0.0688 0.6139 154 L 0.1679 0.0330 0.7991 155 P 0.0924 0.0237 0.8838 156 A 0.0594 0.0405 0.9001