# This file is the result of combining several RDB files, specifically # T0397.t06.str2.rdb (weight 1.54425) # T0397.t06.str4.rdb (weight 0.924988) # T0397.t06.pb.rdb (weight 0.789901) # T0397.t06.bys.rdb (weight 0.748322) # T0397.t06.alpha.rdb (weight 0.678173) # 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 T0397.t06.str2.rdb # ============================================ # TARGET T0397 # Using neural net dunbrack-40pc-3157-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 T0397.t06-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 9.36989 # # ============================================ # Comments from T0397.t06.str4.rdb # ============================================ # TARGET T0397 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0397.t06-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 9.36989 # # ============================================ # Comments from T0397.t06.pb.rdb # ============================================ # TARGET T0397 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0397.t06-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 9.36989 # # ============================================ # Comments from T0397.t06.bys.rdb # ============================================ # TARGET T0397 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0397.t06-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 9.36989 # # ============================================ # Comments from T0397.t06.alpha.rdb # ============================================ # TARGET T0397 # Using neural net dunbrack-40pc-3157-t06-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 T0397.t06-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 9.36989 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3097 0.0580 0.6323 2 K 0.3067 0.0427 0.6506 3 I 0.3302 0.0184 0.6515 4 P 0.4010 0.0385 0.5605 5 K 0.7122 0.0185 0.2694 6 I 0.7848 0.0068 0.2084 7 Y 0.7825 0.0079 0.2096 8 V 0.7288 0.0106 0.2606 9 E 0.5173 0.0469 0.4358 10 G 0.3400 0.0507 0.6094 11 E 0.4863 0.0560 0.4577 12 L 0.5605 0.0667 0.3728 13 N 0.4069 0.0904 0.5027 14 D 0.1880 0.1569 0.6551 15 G 0.1344 0.1073 0.7582 16 D 0.4093 0.0532 0.5374 17 R 0.6875 0.0150 0.2975 18 V 0.7662 0.0070 0.2268 19 A 0.8073 0.0054 0.1874 20 I 0.8147 0.0050 0.1803 21 E 0.7613 0.0067 0.2320 22 K 0.6921 0.0314 0.2765 23 D 0.4132 0.0596 0.5272 24 G 0.2035 0.0834 0.7131 25 N 0.4678 0.0527 0.4795 26 A 0.6999 0.0148 0.2852 27 I 0.7686 0.0095 0.2218 28 I 0.8014 0.0079 0.1907 29 F 0.7842 0.0103 0.2055 30 L 0.7483 0.0158 0.2359 31 E 0.6039 0.0300 0.3661 32 K 0.3633 0.1618 0.4748 33 D 0.2357 0.1945 0.5698 34 E 0.3052 0.2308 0.4640 35 E 0.3889 0.1872 0.4239 36 Y 0.4038 0.1284 0.4678 37 S 0.2396 0.1558 0.6045 38 G 0.1213 0.1677 0.7110 39 N 0.1484 0.1334 0.7182 40 G 0.1985 0.1068 0.6947 41 K 0.4449 0.0935 0.4616 42 L 0.5547 0.1044 0.3409 43 L 0.5117 0.1892 0.2991 44 Y 0.5014 0.2607 0.2378 45 Q 0.4506 0.3358 0.2136 46 V 0.4217 0.3674 0.2109 47 I 0.2317 0.5153 0.2531 48 Y 0.0423 0.7966 0.1611 49 D 0.0115 0.8756 0.1129 50 D 0.0100 0.8986 0.0914 51 L 0.0105 0.8997 0.0898 52 A 0.0092 0.8963 0.0945 53 K 0.0104 0.8637 0.1259 54 Y 0.0212 0.7659 0.2129 55 M 0.0956 0.5686 0.3359 56 S 0.1262 0.4069 0.4669 57 L 0.0671 0.5295 0.4035 58 D 0.0704 0.4539 0.4757 59 T 0.1384 0.3903 0.4713 60 L 0.2595 0.2151 0.5253 61 K 0.3409 0.1025 0.5566 62 K 0.4583 0.0665 0.4752 63 D 0.5391 0.0325 0.4284 64 V 0.7908 0.0065 0.2026 65 L 0.7711 0.0071 0.2217 66 I 0.7929 0.0059 0.2012 67 Q 0.7524 0.0091 0.2385 68 Y 0.5273 0.0116 0.4611 69 P 0.2235 0.1060 0.6705 70 D 0.1415 0.1176 0.7409 71 K 0.1237 0.1908 0.6854 72 H 0.2798 0.1243 0.5959 73 T 0.5695 0.0575 0.3730 74 L 0.7123 0.0265 0.2612 75 T 0.7685 0.0189 0.2125 76 Y 0.7808 0.0132 0.2060 77 L 0.7105 0.0317 0.2578 78 K 0.5535 0.0786 0.3679 79 A 0.1816 0.1515 0.6668 80 G 0.0868 0.0817 0.8315 81 T 0.3115 0.0408 0.6476 82 K 0.5996 0.0325 0.3679 83 L 0.6918 0.0183 0.2899 84 I 0.7274 0.0172 0.2554 85 S 0.7248 0.0100 0.2652 86 V 0.7074 0.0126 0.2801 87 P 0.6359 0.0107 0.3534 88 A 0.4950 0.0600 0.4451 89 E 0.4262 0.0818 0.4920 90 G 0.3250 0.0624 0.6126 91 Y 0.5292 0.0287 0.4421 92 K 0.6856 0.0193 0.2951 93 V 0.6873 0.0194 0.2933 94 Y 0.6999 0.0155 0.2845 95 P 0.6394 0.0296 0.3309 96 I 0.5777 0.0569 0.3654 97 M 0.4663 0.0929 0.4407 98 D 0.3348 0.1042 0.5611 99 F 0.1636 0.2311 0.6053 100 G 0.1569 0.1704 0.6728 101 F 0.3679 0.1770 0.4551 102 R 0.5125 0.1873 0.3002 103 V 0.5018 0.2108 0.2874 104 L 0.4486 0.1794 0.3719 105 K 0.2165 0.1430 0.6405 106 G 0.1190 0.0944 0.7866 107 Y 0.4000 0.0466 0.5534 108 R 0.5915 0.0683 0.3402 109 L 0.7000 0.0647 0.2353 110 A 0.7562 0.0353 0.2086 111 T 0.8009 0.0173 0.1818 112 L 0.7632 0.0234 0.2134 113 E 0.7163 0.0315 0.2522 114 S 0.5360 0.0364 0.4276 115 K 0.2668 0.1873 0.5459 116 K 0.2363 0.0960 0.6677 117 G 0.3038 0.0517 0.6445 118 D 0.5496 0.0307 0.4197 119 L 0.7137 0.0132 0.2731 120 R 0.7313 0.0234 0.2454 121 Y 0.7674 0.0096 0.2230 122 V 0.7289 0.0198 0.2513 123 N 0.6196 0.0277 0.3527 124 S 0.4536 0.0206 0.5258 125 P 0.2869 0.0665 0.6465 126 V 0.2919 0.0960 0.6121 127 S 0.2645 0.0877 0.6478 128 G 0.4235 0.0382 0.5383 129 T 0.7263 0.0106 0.2630 130 V 0.7850 0.0058 0.2092 131 I 0.7970 0.0070 0.1960 132 F 0.7795 0.0075 0.2130 133 M 0.7104 0.0227 0.2669 134 N 0.5606 0.0523 0.3870 135 E 0.3827 0.0596 0.5577 136 I 0.2800 0.0314 0.6886 137 P 0.1645 0.1232 0.7123 138 S 0.1242 0.2183 0.6575 139 E 0.1473 0.1790 0.6737 140 R 0.2344 0.0687 0.6968 141 A 0.2053 0.1801 0.6146 142 N 0.2854 0.1035 0.6110 143 Y 0.7108 0.0136 0.2756 144 V 0.7607 0.0083 0.2310 145 F 0.8189 0.0045 0.1765 146 Y 0.8042 0.0063 0.1895 147 M 0.7518 0.0080 0.2402 148 L 0.6460 0.0138 0.3402 149 E 0.3426 0.0633 0.5941 150 E 0.2070 0.1483 0.6446