# This file is the result of combining several RDB files, specifically # T0362.t04.dssp-ebghstl.rdb (weight 1.53986) # T0362.t04.stride-ebghtl.rdb (weight 1.24869) # T0362.t04.str2.rdb (weight 1.54758) # T0362.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 T0362.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0362 # 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 T0362.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 1459 # # ============================================ # Comments from T0362.t04.stride-ebghtl.rdb # ============================================ # TARGET T0362 # 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 T0362.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 1459 # # ============================================ # Comments from T0362.t04.str2.rdb # ============================================ # TARGET T0362 # 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 T0362.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 1459 # # ============================================ # Comments from T0362.t04.alpha.rdb # ============================================ # TARGET T0362 # 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 T0362.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 1459 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0866 0.0153 0.8981 2 N 0.0656 0.0108 0.9236 3 P 0.0222 0.2601 0.7177 4 E 0.0252 0.2579 0.7169 5 N 0.1049 0.2204 0.6747 6 W 0.4216 0.0669 0.5116 7 L 0.7442 0.0214 0.2343 8 L 0.8507 0.0132 0.1361 9 L 0.8521 0.0071 0.1408 10 R 0.8031 0.0110 0.1859 11 R 0.8483 0.0063 0.1454 12 V 0.8642 0.0057 0.1300 13 V 0.7764 0.0082 0.2154 14 R 0.5168 0.0087 0.4746 15 F 0.0928 0.3382 0.5691 16 G 0.0561 0.3484 0.5956 17 D 0.1258 0.3505 0.5236 18 T 0.2542 0.1385 0.6073 19 D 0.1413 0.0876 0.7712 20 A 0.0406 0.3437 0.6156 21 A 0.0623 0.2306 0.7072 22 G 0.1000 0.1835 0.7165 23 V 0.2913 0.1933 0.5154 24 M 0.4726 0.1641 0.3632 25 H 0.2810 0.2299 0.4891 26 F 0.0582 0.6653 0.2765 27 H 0.0333 0.8592 0.1075 28 Q 0.0432 0.8801 0.0766 29 L 0.0204 0.9283 0.0513 30 F 0.0124 0.9379 0.0497 31 R 0.0058 0.9468 0.0474 32 W 0.0048 0.9471 0.0481 33 C 0.0048 0.9493 0.0459 34 H 0.0047 0.9538 0.0415 35 E 0.0048 0.9548 0.0405 36 S 0.0048 0.9477 0.0475 37 W 0.0047 0.9508 0.0445 38 E 0.0047 0.9566 0.0388 39 E 0.0048 0.9564 0.0388 40 S 0.0047 0.9561 0.0392 41 L 0.0047 0.9549 0.0404 42 E 0.0050 0.9434 0.0516 43 S 0.0066 0.8850 0.1084 44 Y 0.0433 0.4391 0.5175 45 G 0.0369 0.0280 0.9351 46 L 0.0809 0.0129 0.9062 47 N 0.1135 0.0135 0.8729 48 P 0.0089 0.7851 0.2060 49 A 0.0061 0.8296 0.1643 50 D 0.0109 0.8198 0.1694 51 I 0.0731 0.5232 0.4037 52 F 0.0776 0.1969 0.7256 53 P 0.0370 0.2369 0.7261 54 G 0.0421 0.1901 0.7678 55 S 0.0855 0.1419 0.7726 56 R 0.0852 0.1516 0.7632 57 K 0.0696 0.1599 0.7704 58 S 0.0979 0.1221 0.7800 59 E 0.1405 0.0860 0.7736 60 V 0.1534 0.0552 0.7914 61 T 0.1091 0.0324 0.8586 62 P 0.0521 0.1438 0.8042 63 E 0.0672 0.1117 0.8212 64 V 0.3636 0.0446 0.5918 65 A 0.5648 0.0169 0.4184 66 L 0.7687 0.0101 0.2213 67 P 0.8179 0.0103 0.1718 68 I 0.8996 0.0083 0.0922 69 I 0.8827 0.0164 0.1008 70 H 0.9120 0.0052 0.0828 71 C 0.8857 0.0066 0.1077 72 Q 0.8452 0.0121 0.1427 73 A 0.8087 0.0101 0.1811 74 D 0.8126 0.0094 0.1780 75 F 0.7643 0.0124 0.2233 76 R 0.5318 0.0447 0.4235 77 R 0.4031 0.0155 0.5814 78 P 0.4411 0.0179 0.5410 79 I 0.4066 0.0174 0.5760 80 H 0.2113 0.0199 0.7688 81 T 0.0626 0.0782 0.8593 82 G 0.0391 0.0452 0.9157 83 D 0.2878 0.0315 0.6807 84 A 0.7794 0.0048 0.2158 85 L 0.9005 0.0038 0.0958 86 A 0.9278 0.0032 0.0690 87 M 0.9175 0.0040 0.0785 88 E 0.9128 0.0039 0.0834 89 L 0.8946 0.0045 0.1009 90 R 0.8342 0.0062 0.1596 91 P 0.8109 0.0098 0.1793 92 E 0.6831 0.0443 0.2726 93 R 0.7650 0.0221 0.2128 94 L 0.6544 0.0244 0.3212 95 N 0.3285 0.0214 0.6500 96 P 0.0826 0.0788 0.8386 97 N 0.1782 0.0632 0.7585 98 S 0.7746 0.0132 0.2122 99 F 0.9061 0.0037 0.0902 100 Q 0.9272 0.0035 0.0693 101 V 0.9301 0.0031 0.0668 102 H 0.9223 0.0035 0.0742 103 F 0.9264 0.0033 0.0702 104 E 0.9288 0.0033 0.0679 105 F 0.9268 0.0033 0.0698 106 R 0.8785 0.0054 0.1161 107 C 0.6252 0.0189 0.3559 108 E 0.0565 0.0358 0.9077 109 E 0.0526 0.0391 0.9082 110 Q 0.7452 0.0115 0.2433 111 I 0.9035 0.0038 0.0927 112 A 0.9168 0.0042 0.0790 113 A 0.9205 0.0039 0.0757 114 H 0.9194 0.0044 0.0763 115 A 0.9185 0.0039 0.0776 116 L 0.9182 0.0041 0.0777 117 I 0.9231 0.0033 0.0736 118 R 0.9037 0.0120 0.0843 119 H 0.9273 0.0036 0.0691 120 L 0.9254 0.0038 0.0708 121 A 0.9241 0.0036 0.0723 122 I 0.8824 0.0072 0.1105 123 N 0.6222 0.0058 0.3720 124 A 0.0514 0.1722 0.7765 125 Q 0.0332 0.1782 0.7887 126 T 0.0743 0.1407 0.7850 127 R 0.1418 0.0622 0.7960 128 H 0.2873 0.0307 0.6820 129 R 0.4864 0.0307 0.4829 130 C 0.3610 0.0255 0.6135 131 A 0.2389 0.0246 0.7365 132 L 0.0781 0.0122 0.9097 133 P 0.0569 0.0380 0.9051 134 E 0.0090 0.6693 0.3217 135 G 0.0120 0.7458 0.2421 136 I 0.0136 0.8563 0.1301 137 D 0.0081 0.9121 0.0798 138 R 0.0065 0.9356 0.0579 139 W 0.0061 0.9377 0.0562 140 L 0.0070 0.9306 0.0624 141 E 0.0070 0.9124 0.0805 142 A 0.0097 0.8470 0.1433 143 S 0.0405 0.6289 0.3305 144 G 0.0385 0.2934 0.6681 145 V 0.0640 0.2093 0.7267 146 G 0.0737 0.2195 0.7068 147 K 0.0851 0.2161 0.6988 148 I 0.0869 0.1581 0.7550 149 G 0.0656 0.0869 0.8475 150 S 0.0637 0.0617 0.8746 151 I 0.0468 0.0482 0.9050