# This file is the result of combining several RDB files, specifically # T0370.t04.dssp-ebghstl.rdb (weight 1.53986) # T0370.t04.stride-ebghtl.rdb (weight 1.24869) # T0370.t04.str2.rdb (weight 1.54758) # T0370.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 T0370.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0370 # 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 T0370.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 320 # # ============================================ # Comments from T0370.t04.stride-ebghtl.rdb # ============================================ # TARGET T0370 # 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 T0370.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 320 # # ============================================ # Comments from T0370.t04.str2.rdb # ============================================ # TARGET T0370 # 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 T0370.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 320 # # ============================================ # Comments from T0370.t04.alpha.rdb # ============================================ # TARGET T0370 # 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 T0370.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 320 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0676 0.0317 0.9008 2 T 0.0711 0.0447 0.8842 3 T 0.0611 0.0478 0.8912 4 P 0.0573 0.0734 0.8693 5 P 0.0533 0.3735 0.5732 6 A 0.0596 0.4954 0.4450 7 R 0.0679 0.5711 0.3611 8 T 0.0730 0.5741 0.3529 9 A 0.0441 0.6793 0.2766 10 K 0.0350 0.7200 0.2450 11 Q 0.0484 0.6483 0.3034 12 R 0.0480 0.5828 0.3693 13 I 0.0128 0.8300 0.1572 14 Q 0.0058 0.9400 0.0543 15 D 0.0054 0.9437 0.0509 16 T 0.0051 0.9468 0.0481 17 L 0.0048 0.9473 0.0478 18 N 0.0050 0.9208 0.0742 19 R 0.0059 0.8730 0.1211 20 L 0.0106 0.7922 0.1972 21 E 0.0167 0.6085 0.3747 22 L 0.0408 0.2945 0.6647 23 D 0.0779 0.0586 0.8635 24 V 0.1151 0.0712 0.8137 25 D 0.5339 0.0395 0.4266 26 A 0.8991 0.0082 0.0926 27 W 0.9246 0.0052 0.0701 28 V 0.9189 0.0062 0.0749 29 S 0.8671 0.0095 0.1234 30 T 0.6709 0.0125 0.3165 31 A 0.4625 0.0304 0.5072 32 G 0.2121 0.0227 0.7651 33 A 0.0575 0.0999 0.8426 34 D 0.0488 0.0742 0.8770 35 G 0.0615 0.0625 0.8760 36 G 0.0701 0.0428 0.8871 37 A 0.1756 0.0334 0.7910 38 P 0.3576 0.0343 0.6080 39 Y 0.6510 0.0233 0.3256 40 L 0.7817 0.0106 0.2077 41 V 0.7859 0.0077 0.2064 42 P 0.8498 0.0051 0.1451 43 L 0.8302 0.0078 0.1620 44 S 0.8739 0.0057 0.1204 45 Y 0.8929 0.0044 0.1026 46 L 0.8744 0.0050 0.1206 47 W 0.8017 0.0145 0.1838 48 D 0.3629 0.0207 0.6164 49 G 0.0519 0.0452 0.9029 50 E 0.2002 0.0395 0.7603 51 T 0.8092 0.0067 0.1842 52 F 0.9143 0.0037 0.0820 53 L 0.9295 0.0034 0.0671 54 V 0.9200 0.0040 0.0760 55 A 0.8570 0.0066 0.1364 56 T 0.4187 0.0104 0.5709 57 P 0.0984 0.0798 0.8218 58 A 0.0373 0.1021 0.8606 59 A 0.0387 0.0862 0.8750 60 S 0.0638 0.0461 0.8901 61 P 0.0641 0.3192 0.6167 62 T 0.1376 0.4611 0.4013 63 G 0.1392 0.5731 0.2877 64 R 0.1463 0.6207 0.2329 65 N 0.1936 0.5735 0.2328 66 L 0.0654 0.7418 0.1928 67 S 0.0526 0.6789 0.2685 68 E 0.0677 0.4760 0.4562 69 T 0.1225 0.0542 0.8233 70 G 0.1138 0.0769 0.8093 71 R 0.3833 0.0450 0.5716 72 V 0.8026 0.0110 0.1865 73 R 0.8876 0.0053 0.1072 74 L 0.9122 0.0042 0.0836 75 G 0.9093 0.0044 0.0863 76 I 0.8598 0.0114 0.1288 77 G 0.5083 0.0089 0.4828 78 P 0.2071 0.0535 0.7393 79 T 0.0908 0.0708 0.8384 80 R 0.0849 0.0691 0.8459 81 D 0.1838 0.0618 0.7544 82 L 0.7988 0.0079 0.1933 83 V 0.9119 0.0038 0.0844 84 L 0.9292 0.0032 0.0675 85 V 0.9187 0.0044 0.0769 86 E 0.8609 0.0238 0.1153 87 G 0.8562 0.0062 0.1375 88 T 0.8766 0.0042 0.1191 89 A 0.8599 0.0050 0.1351 90 L 0.8280 0.0066 0.1654 91 P 0.7744 0.0047 0.2209 92 L 0.3736 0.0302 0.5962 93 E 0.1713 0.0209 0.8078 94 P 0.0525 0.2046 0.7428 95 A 0.0300 0.2656 0.7044 96 G 0.0296 0.2409 0.7295 97 L 0.0591 0.1099 0.8310 98 P 0.0544 0.3384 0.6072 99 D 0.0221 0.5577 0.4202 100 G 0.0284 0.6205 0.3512 101 V 0.0364 0.7137 0.2499 102 G 0.0254 0.7780 0.1966 103 D 0.0175 0.8460 0.1365 104 T 0.0122 0.8945 0.0933 105 F 0.0100 0.9063 0.0837 106 A 0.0109 0.8939 0.0951 107 E 0.0101 0.8573 0.1326 108 K 0.0155 0.7491 0.2355 109 T 0.0568 0.4169 0.5263 110 G 0.0418 0.0719 0.8863 111 F 0.0710 0.0504 0.8786 112 D 0.0991 0.0362 0.8647 113 P 0.0622 0.2104 0.7275 114 R 0.0797 0.2214 0.6989 115 R 0.1190 0.1950 0.6860 116 L 0.1362 0.1060 0.7578 117 T 0.1382 0.0675 0.7942 118 T 0.0880 0.0995 0.8125 119 S 0.1524 0.0628 0.7848 120 Y 0.6825 0.0117 0.3058 121 L 0.8725 0.0039 0.1236 122 Y 0.9264 0.0032 0.0704 123 F 0.9226 0.0037 0.0737 124 R 0.9222 0.0035 0.0743 125 I 0.8929 0.0048 0.1023 126 S 0.7621 0.0068 0.2311 127 P 0.6131 0.0349 0.3520 128 R 0.5052 0.0922 0.4026 129 R 0.7692 0.0536 0.1773 130 V 0.8262 0.0418 0.1320 131 Q 0.8243 0.0511 0.1247 132 A 0.7673 0.0743 0.1584 133 W 0.5948 0.1153 0.2899 134 R 0.3876 0.1667 0.4457 135 E 0.2045 0.2362 0.5593 136 A 0.1062 0.2291 0.6647 137 N 0.0583 0.2488 0.6929 138 E 0.0809 0.2604 0.6587 139 L 0.1538 0.2649 0.5812 140 S 0.1594 0.2515 0.5891 141 G 0.1507 0.2950 0.5544 142 R 0.1856 0.4137 0.4007 143 E 0.2385 0.4433 0.3182 144 L 0.2986 0.4310 0.2704 145 M 0.2933 0.3433 0.3634 146 R 0.2309 0.3022 0.4669 147 D 0.0888 0.1499 0.7612 148 G 0.0683 0.0538 0.8779 149 E 0.2559 0.0388 0.7053 150 W 0.5505 0.0247 0.4248 151 L 0.6548 0.0244 0.3208 152 V 0.5867 0.0289 0.3844 153 T 0.3093 0.0301 0.6606 154 D 0.0896 0.0190 0.8914