# This file is the result of combining several RDB files, specifically # T0345.t04.dssp-ebghstl.rdb (weight 1.53986) # T0345.t04.stride-ebghtl.rdb (weight 1.24869) # T0345.t04.str2.rdb (weight 1.54758) # T0345.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 T0345.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0345 # 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 T0345.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 58.3006 # # ============================================ # Comments from T0345.t04.stride-ebghtl.rdb # ============================================ # TARGET T0345 # 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 T0345.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 58.3006 # # ============================================ # Comments from T0345.t04.str2.rdb # ============================================ # TARGET T0345 # 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 T0345.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 58.3006 # # ============================================ # Comments from T0345.t04.alpha.rdb # ============================================ # TARGET T0345 # 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 T0345.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 58.3006 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1041 0.1465 0.7494 2 I 0.1160 0.2048 0.6792 3 A 0.1145 0.1768 0.7087 4 K 0.1011 0.1819 0.7169 5 S 0.1455 0.1310 0.7235 6 F 0.1968 0.2070 0.5962 7 Y 0.3242 0.1136 0.5622 8 D 0.4505 0.0473 0.5022 9 L 0.5449 0.0203 0.4347 10 S 0.7255 0.0149 0.2596 11 A 0.8373 0.0150 0.1477 12 I 0.8092 0.0227 0.1681 13 N 0.5773 0.0180 0.4047 14 L 0.1729 0.0838 0.7433 15 D 0.0684 0.0259 0.9057 16 G 0.0442 0.0329 0.9229 17 E 0.2224 0.0204 0.7572 18 K 0.7499 0.0078 0.2423 19 V 0.7378 0.0075 0.2547 20 D 0.5836 0.0066 0.4097 21 F 0.0649 0.7238 0.2113 22 N 0.0446 0.7797 0.1758 23 T 0.0382 0.7710 0.1908 24 F 0.1531 0.4042 0.4428 25 R 0.1048 0.1328 0.7624 26 G 0.0501 0.0476 0.9023 27 R 0.3697 0.0175 0.6128 28 A 0.8702 0.0059 0.1238 29 V 0.9162 0.0060 0.0778 30 L 0.9258 0.0087 0.0655 31 I 0.9150 0.0151 0.0699 32 E 0.8767 0.0221 0.1012 33 N 0.6817 0.0431 0.2752 34 V 0.4181 0.1114 0.4704 35 A 0.3026 0.2147 0.4826 36 S 0.1799 0.3009 0.5192 37 L 0.1255 0.2654 0.6091 38 C 0.1166 0.1393 0.7441 39 G 0.0683 0.0994 0.8323 40 T 0.1022 0.1042 0.7936 41 T 0.1078 0.0957 0.7965 42 T 0.0441 0.3136 0.6423 43 R 0.0285 0.4444 0.5271 44 D 0.0407 0.4508 0.5085 45 F 0.0119 0.8160 0.1721 46 T 0.0074 0.8846 0.1079 47 Q 0.0072 0.9095 0.0833 48 L 0.0073 0.9342 0.0585 49 N 0.0061 0.9460 0.0479 50 E 0.0054 0.9441 0.0505 51 L 0.0052 0.9259 0.0688 52 Q 0.0073 0.8738 0.1189 53 C 0.0111 0.8125 0.1764 54 R 0.0243 0.6648 0.3109 55 F 0.0915 0.0993 0.8092 56 P 0.0320 0.1359 0.8321 57 R 0.0333 0.1211 0.8456 58 R 0.1528 0.0480 0.7992 59 L 0.7276 0.0080 0.2644 60 V 0.9124 0.0036 0.0840 61 V 0.9261 0.0031 0.0708 62 L 0.8941 0.0150 0.0909 63 G 0.8543 0.0044 0.1413 64 F 0.5328 0.0107 0.4564 65 P 0.2705 0.0192 0.7103 66 C 0.1029 0.2321 0.6651 67 N 0.0516 0.3189 0.6296 68 Q 0.0561 0.4348 0.5090 69 F 0.0786 0.3300 0.5914 70 G 0.0631 0.2433 0.6936 71 H 0.0831 0.1747 0.7422 72 Q 0.1424 0.1581 0.6995 73 E 0.1062 0.1071 0.7867 74 N 0.0746 0.0906 0.8348 75 C 0.0697 0.0636 0.8668 76 Q 0.0606 0.0818 0.8576 77 N 0.0237 0.7949 0.1814 78 E 0.0053 0.9473 0.0473 79 E 0.0060 0.9464 0.0476 80 I 0.0079 0.9451 0.0470 81 L 0.0159 0.9236 0.0604 82 N 0.0312 0.8614 0.1073 83 S 0.0501 0.7725 0.1774 84 L 0.1505 0.6439 0.2057 85 K 0.2174 0.5793 0.2033 86 Y 0.2959 0.4419 0.2623 87 V 0.3447 0.2676 0.3877 88 R 0.2049 0.0468 0.7483 89 P 0.0780 0.0905 0.8316 90 G 0.0551 0.0537 0.8912 91 G 0.0614 0.0569 0.8816 92 G 0.0953 0.0514 0.8533 93 Y 0.2870 0.0389 0.6741 94 Q 0.2852 0.0283 0.6865 95 P 0.2998 0.0302 0.6700 96 T 0.4845 0.0343 0.4812 97 F 0.5314 0.0343 0.4343 98 T 0.5121 0.0599 0.4281 99 L 0.6216 0.0771 0.3013 100 V 0.6464 0.0739 0.2797 101 Q 0.6487 0.0649 0.2864 102 K 0.7264 0.0530 0.2206 103 C 0.7446 0.0331 0.2223 104 E 0.7544 0.0271 0.2185 105 V 0.5696 0.0417 0.3887 106 N 0.2567 0.0552 0.6882 107 G 0.0871 0.0441 0.8688 108 Q 0.0439 0.1622 0.7939 109 N 0.0629 0.1553 0.7818 110 E 0.0667 0.2388 0.6945 111 H 0.0534 0.3598 0.5868 112 P 0.0164 0.8489 0.1347 113 V 0.0121 0.9233 0.0646 114 F 0.0124 0.9397 0.0479 115 A 0.0091 0.9467 0.0441 116 Y 0.0062 0.9412 0.0526 117 L 0.0081 0.9185 0.0735 118 K 0.0115 0.8996 0.0890 119 D 0.0153 0.8024 0.1823 120 K 0.0350 0.5676 0.3975 121 L 0.0773 0.0486 0.8741 122 P 0.0640 0.0622 0.8738 123 Y 0.0926 0.0382 0.8692 124 P 0.1093 0.0713 0.8194 125 Y 0.1097 0.0773 0.8131 126 D 0.0761 0.0686 0.8553 127 D 0.0904 0.0535 0.8561 128 P 0.0857 0.2145 0.6998 129 F 0.1313 0.2708 0.5979 130 S 0.1814 0.2814 0.5372 131 L 0.2479 0.2595 0.4926 132 M 0.2609 0.1581 0.5810 133 T 0.2042 0.1034 0.6924 134 D 0.1399 0.0468 0.8133 135 P 0.0471 0.3613 0.5916 136 K 0.0741 0.4082 0.5177 137 L 0.1749 0.4195 0.4057 138 I 0.3245 0.2647 0.4108 139 I 0.3884 0.1637 0.4479 140 W 0.3043 0.1392 0.5565 141 S 0.1931 0.0874 0.7195 142 P 0.1373 0.1847 0.6779 143 V 0.2008 0.1879 0.6113 144 R 0.2294 0.1551 0.6155 145 R 0.1431 0.2343 0.6226 146 S 0.1042 0.1693 0.7265 147 D 0.1682 0.1429 0.6889 148 V 0.3560 0.0944 0.5496 149 A 0.4545 0.0987 0.4468 150 W 0.5981 0.1074 0.2946 151 N 0.5764 0.0693 0.3543 152 F 0.5658 0.1251 0.3091 153 E 0.5812 0.1205 0.2983 154 K 0.6999 0.1132 0.1869 155 F 0.7679 0.0698 0.1622 156 L 0.8149 0.0307 0.1544 157 I 0.7576 0.0207 0.2217 158 G 0.1806 0.0157 0.8037 159 P 0.0139 0.1051 0.8810 160 E 0.0427 0.0273 0.9300 161 G 0.0581 0.0363 0.9056 162 E 0.3294 0.0131 0.6576 163 P 0.8411 0.0056 0.1532 164 F 0.7804 0.0231 0.1966 165 R 0.7512 0.0259 0.2229 166 R 0.7031 0.0327 0.2642 167 Y 0.5346 0.0408 0.4246 168 S 0.2690 0.0443 0.6867 169 R 0.0909 0.1039 0.8052 170 T 0.1005 0.0740 0.8255 171 F 0.1325 0.0224 0.8451 172 P 0.1128 0.0205 0.8667 173 T 0.0535 0.5692 0.3774 174 I 0.0227 0.6638 0.3135 175 N 0.0339 0.6325 0.3336 176 I 0.0399 0.6485 0.3116 177 E 0.0191 0.7759 0.2050 178 P 0.0072 0.9234 0.0694 179 D 0.0070 0.9348 0.0582 180 I 0.0051 0.9500 0.0449 181 K 0.0048 0.9500 0.0453 182 R 0.0049 0.9316 0.0635 183 L 0.0058 0.8561 0.1381 184 L 0.0133 0.6599 0.3268 185 K 0.0128 0.1874 0.7998