# This file is the result of combining several RDB files, specifically # T0288.t04.dssp-ebghstl.rdb (weight 1.53986) # T0288.t04.stride-ebghtl.rdb (weight 1.24869) # T0288.t04.str2.rdb (weight 1.54758) # T0288.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 T0288.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0288 # 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 T0288.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 1591 # # ============================================ # Comments from T0288.t04.stride-ebghtl.rdb # ============================================ # TARGET T0288 # 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 T0288.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 1591 # # ============================================ # Comments from T0288.t04.str2.rdb # ============================================ # TARGET T0288 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0288.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 1591 # # ============================================ # Comments from T0288.t04.alpha.rdb # ============================================ # TARGET T0288 # 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 T0288.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 1591 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0817 0.0332 0.8851 2 M 0.1557 0.0208 0.8235 3 V 0.2261 0.0109 0.7630 4 P 0.2946 0.0248 0.6806 5 G 0.5297 0.0159 0.4544 6 K 0.8874 0.0043 0.1082 7 V 0.9142 0.0035 0.0823 8 T 0.9252 0.0037 0.0710 9 L 0.9166 0.0039 0.0795 10 Q 0.8702 0.0052 0.1246 11 K 0.7138 0.0171 0.2691 12 D 0.2319 0.0235 0.7445 13 A 0.0588 0.0907 0.8505 14 Q 0.0607 0.0728 0.8665 15 N 0.1337 0.0627 0.8035 16 L 0.4111 0.0347 0.5542 17 I 0.6696 0.0193 0.3111 18 G 0.8006 0.0096 0.1898 19 I 0.8986 0.0043 0.0971 20 S 0.9143 0.0042 0.0815 21 I 0.8859 0.0094 0.1048 22 G 0.6941 0.0200 0.2859 23 G 0.3521 0.0299 0.6180 24 G 0.1581 0.0455 0.7964 25 A 0.1227 0.1526 0.7247 26 Q 0.1146 0.1605 0.7249 27 Y 0.1548 0.1185 0.7266 28 C 0.1543 0.0386 0.8071 29 P 0.1846 0.0408 0.7746 30 C 0.5076 0.0202 0.4721 31 L 0.8365 0.0045 0.1590 32 Y 0.8950 0.0051 0.0999 33 I 0.9125 0.0033 0.0841 34 V 0.8221 0.0298 0.1481 35 Q 0.8412 0.0077 0.1511 36 V 0.7111 0.0150 0.2739 37 F 0.4053 0.0227 0.5720 38 D 0.0768 0.0542 0.8690 39 N 0.0331 0.0421 0.9248 40 T 0.0965 0.0438 0.8597 41 P 0.0691 0.5621 0.3688 42 A 0.0947 0.6637 0.2416 43 A 0.1395 0.6483 0.2123 44 L 0.1581 0.5197 0.3222 45 D 0.1121 0.1637 0.7242 46 G 0.0769 0.0764 0.8467 47 T 0.2637 0.0543 0.6820 48 V 0.4639 0.0271 0.5090 49 A 0.2087 0.0271 0.7642 50 A 0.0952 0.1028 0.8020 51 G 0.0487 0.0798 0.8715 52 D 0.2628 0.0907 0.6466 53 E 0.7680 0.0392 0.1928 54 I 0.8729 0.0154 0.1117 55 T 0.8659 0.0241 0.1100 56 G 0.8750 0.0099 0.1151 57 V 0.7550 0.0214 0.2236 58 N 0.4682 0.0239 0.5079 59 G 0.2215 0.0325 0.7460 60 R 0.5311 0.0163 0.4526 61 S 0.6676 0.0186 0.3138 62 I 0.3907 0.0757 0.5336 63 K 0.1540 0.0841 0.7620 64 G 0.0597 0.0574 0.8829 65 K 0.1796 0.0322 0.7882 66 T 0.1557 0.0464 0.7979 67 K 0.0055 0.9320 0.0625 68 V 0.0047 0.9590 0.0364 69 E 0.0047 0.9605 0.0348 70 V 0.0047 0.9609 0.0344 71 A 0.0046 0.9612 0.0342 72 K 0.0046 0.9607 0.0346 73 M 0.0047 0.9577 0.0376 74 I 0.0049 0.9484 0.0467 75 Q 0.0058 0.9206 0.0736 76 E 0.0097 0.7333 0.2570 77 V 0.0666 0.3251 0.6083 78 K 0.0310 0.0811 0.8879 79 G 0.0790 0.0355 0.8855 80 E 0.5834 0.0131 0.4035 81 V 0.8494 0.0040 0.1465 82 T 0.9059 0.0040 0.0901 83 I 0.9227 0.0035 0.0738 84 H 0.9214 0.0035 0.0752 85 Y 0.8971 0.0050 0.0979 86 N 0.7744 0.0129 0.2127 87 K 0.6067 0.0197 0.3736 88 L 0.3318 0.0827 0.5855 89 Q 0.2332 0.1254 0.6413 90 Y 0.1818 0.1282 0.6900 91 Y 0.1529 0.0781 0.7690 92 K 0.1029 0.0432 0.8538 93 V 0.0652 0.0408 0.8940