# This file is the result of combining several RDB files, specifically # T0299.t04.dssp-ebghstl.rdb (weight 1.53986) # T0299.t04.stride-ebghtl.rdb (weight 1.24869) # T0299.t04.str2.rdb (weight 1.54758) # T0299.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 T0299.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0299 # 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 T0299.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 50.4462 # # ============================================ # Comments from T0299.t04.stride-ebghtl.rdb # ============================================ # TARGET T0299 # 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 T0299.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 50.4462 # # ============================================ # Comments from T0299.t04.str2.rdb # ============================================ # TARGET T0299 # 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 T0299.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 50.4462 # # ============================================ # Comments from T0299.t04.alpha.rdb # ============================================ # TARGET T0299 # 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 T0299.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 50.4462 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0631 0.0358 0.9011 2 T 0.1812 0.1257 0.6932 3 R 0.5751 0.1597 0.2652 4 Y 0.7818 0.1164 0.1018 5 A 0.8193 0.1166 0.0642 6 L 0.8548 0.0834 0.0618 7 L 0.8645 0.0678 0.0678 8 V 0.7929 0.0707 0.1364 9 R 0.6155 0.1185 0.2660 10 G 0.6009 0.0965 0.3026 11 I 0.6652 0.0773 0.2575 12 N 0.5605 0.0728 0.3667 13 V 0.2887 0.0855 0.6258 14 G 0.0949 0.0667 0.8383 15 G 0.0514 0.1161 0.8325 16 K 0.0647 0.1920 0.7433 17 N 0.1012 0.1751 0.7237 18 K 0.2169 0.1794 0.6037 19 V 0.3927 0.1141 0.4932 20 V 0.2026 0.1447 0.6527 21 M 0.0079 0.9008 0.0913 22 A 0.0050 0.9506 0.0444 23 E 0.0047 0.9560 0.0392 24 L 0.0048 0.9540 0.0412 25 R 0.0047 0.9596 0.0357 26 Q 0.0047 0.9596 0.0357 27 E 0.0047 0.9595 0.0358 28 L 0.0047 0.9566 0.0387 29 T 0.0049 0.9444 0.0508 30 N 0.0056 0.8896 0.1048 31 L 0.0406 0.5203 0.4391 32 G 0.0439 0.0610 0.8952 33 L 0.0795 0.1646 0.7560 34 E 0.0594 0.3351 0.6055 35 K 0.1636 0.2391 0.5972 36 V 0.4470 0.0642 0.4888 37 E 0.6403 0.0647 0.2950 38 S 0.8358 0.0435 0.1207 39 Y 0.8269 0.0484 0.1247 40 I 0.7881 0.0474 0.1645 41 N 0.6826 0.0402 0.2771 42 S 0.4758 0.0370 0.4872 43 G 0.3304 0.0370 0.6325 44 N 0.4105 0.0357 0.5538 45 I 0.7289 0.0228 0.2483 46 F 0.8435 0.0179 0.1387 47 F 0.7741 0.0227 0.2032 48 T 0.4805 0.0335 0.4860 49 S 0.2153 0.0347 0.7499 50 I 0.0476 0.1953 0.7570 51 D 0.0551 0.1624 0.7826 52 S 0.0634 0.2438 0.6929 53 K 0.0051 0.9289 0.0661 54 A 0.0048 0.9503 0.0449 55 Q 0.0047 0.9568 0.0385 56 L 0.0047 0.9586 0.0367 57 V 0.0047 0.9609 0.0344 58 E 0.0046 0.9612 0.0342 59 K 0.0047 0.9603 0.0350 60 L 0.0047 0.9601 0.0352 61 E 0.0047 0.9607 0.0347 62 T 0.0048 0.9600 0.0352 63 F 0.0049 0.9563 0.0388 64 F 0.0052 0.9487 0.0462 65 A 0.0060 0.9228 0.0713 66 V 0.0095 0.8595 0.1310 67 H 0.0200 0.6934 0.2866 68 Y 0.0820 0.1579 0.7601 69 P 0.0399 0.1224 0.8377 70 F 0.1212 0.1015 0.7773 71 I 0.2707 0.0571 0.6722 72 Q 0.3975 0.0316 0.5709 73 S 0.5299 0.0251 0.4449 74 F 0.8677 0.0084 0.1239 75 S 0.9145 0.0053 0.0802 76 L 0.9068 0.0044 0.0888 77 L 0.7550 0.0109 0.2341 78 S 0.2897 0.0075 0.7028 79 L 0.0072 0.9063 0.0865 80 E 0.0050 0.9432 0.0518 81 D 0.0047 0.9507 0.0446 82 F 0.0048 0.9556 0.0396 83 E 0.0047 0.9582 0.0371 84 A 0.0047 0.9576 0.0377 85 E 0.0049 0.9520 0.0432 86 L 0.0049 0.9388 0.0563 87 E 0.0056 0.8715 0.1229 88 N 0.0116 0.5971 0.3913 89 L 0.0805 0.0772 0.8423 90 P 0.0223 0.2232 0.7545 91 A 0.0426 0.2872 0.6702 92 W 0.0747 0.3834 0.5420 93 W 0.1032 0.3538 0.5430 94 S 0.1037 0.2779 0.6184 95 R 0.0787 0.2323 0.6890 96 D 0.1053 0.1562 0.7386 97 L 0.0707 0.3172 0.6121 98 A 0.0977 0.2204 0.6820 99 R 0.3042 0.1182 0.5776 100 K 0.5137 0.0261 0.4603 101 D 0.8064 0.0110 0.1826 102 F 0.9145 0.0043 0.0812 103 L 0.9230 0.0047 0.0723 104 F 0.9127 0.0053 0.0820 105 Y 0.8025 0.0125 0.1851 106 T 0.3784 0.0387 0.5828 107 E 0.1045 0.0727 0.8228 108 G 0.0674 0.0514 0.8811 109 L 0.1104 0.0166 0.8730 110 D 0.0848 0.0151 0.9001 111 V 0.0054 0.8993 0.0952 112 D 0.0047 0.9454 0.0499 113 Q 0.0047 0.9514 0.0439 114 V 0.0058 0.9489 0.0453 115 I 0.0067 0.9416 0.0517 116 A 0.0068 0.9066 0.0866 117 T 0.0077 0.8596 0.1327 118 V 0.0135 0.8158 0.1707 119 E 0.0134 0.7423 0.2443 120 S 0.0177 0.6702 0.3121 121 L 0.0401 0.5116 0.4483 122 E 0.0609 0.3019 0.6372 123 L 0.0722 0.1969 0.7308 124 K 0.0745 0.1402 0.7853 125 D 0.1540 0.0937 0.7523 126 E 0.4665 0.0634 0.4701 127 V 0.8328 0.0258 0.1414 128 L 0.8915 0.0148 0.0938 129 Y 0.8931 0.0122 0.0947 130 F 0.8099 0.0255 0.1646 131 G 0.4652 0.0253 0.5095 132 K 0.2257 0.0458 0.7285 133 L 0.4709 0.0408 0.4883 134 G 0.8601 0.0092 0.1307 135 I 0.9110 0.0052 0.0838 136 F 0.9087 0.0060 0.0853 137 W 0.7900 0.0251 0.1849 138 G 0.4942 0.0405 0.4653 139 K 0.4019 0.0698 0.5282 140 F 0.3493 0.0648 0.5859 141 S 0.1836 0.0473 0.7691 142 E 0.0405 0.2657 0.6939 143 E 0.0318 0.2223 0.7459 144 S 0.0505 0.2277 0.7218 145 Y 0.0946 0.2523 0.6531 146 S 0.0980 0.2672 0.6348 147 K 0.0935 0.2919 0.6145 148 T 0.0876 0.3647 0.5477 149 A 0.0361 0.7148 0.2490 150 Y 0.0314 0.7956 0.1730 151 H 0.0332 0.7964 0.1704 152 K 0.0251 0.8316 0.1432 153 Y 0.0360 0.8105 0.1534 154 L 0.0430 0.7367 0.2203 155 L 0.0934 0.5402 0.3663 156 K 0.1187 0.3767 0.5047 157 V 0.1267 0.1726 0.7007 158 P 0.1318 0.1852 0.6830 159 F 0.1085 0.1990 0.6925 160 Y 0.1300 0.1067 0.7632 161 R 0.2618 0.0844 0.6538 162 H 0.3746 0.1002 0.5252 163 I 0.4540 0.1547 0.3913 164 T 0.4926 0.1818 0.3256 165 I 0.3718 0.3915 0.2368 166 R 0.2649 0.4658 0.2693 167 N 0.1117 0.4673 0.4210 168 A 0.0170 0.7738 0.2091 169 K 0.0162 0.8053 0.1785 170 T 0.0085 0.9076 0.0839 171 F 0.0047 0.9548 0.0405 172 D 0.0047 0.9603 0.0350 173 K 0.0047 0.9597 0.0356 174 I 0.0047 0.9576 0.0377 175 G 0.0047 0.9551 0.0402 176 Q 0.0048 0.9422 0.0530 177 M 0.0052 0.9076 0.0872 178 L 0.0091 0.7786 0.2123 179 K 0.0111 0.4108 0.5781 180 K 0.0197 0.0999 0.8804