# This file is the result of combining several RDB files, specifically # TR488.t06.str2.rdb (weight 1.54425) # TR488.t06.str4.rdb (weight 0.924988) # TR488.t06.pb.rdb (weight 0.789901) # TR488.t06.bys.rdb (weight 0.748322) # TR488.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 TR488.t06.str2.rdb # ============================================ # TARGET TR488 # 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 TR488.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 2908 # # ============================================ # Comments from TR488.t06.str4.rdb # ============================================ # TARGET TR488 # 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 TR488.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 2908 # # ============================================ # Comments from TR488.t06.pb.rdb # ============================================ # TARGET TR488 # 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 TR488.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 2908 # # ============================================ # Comments from TR488.t06.bys.rdb # ============================================ # TARGET TR488 # 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 TR488.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 2908 # # ============================================ # Comments from TR488.t06.alpha.rdb # ============================================ # TARGET TR488 # 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 TR488.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 2908 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2317 0.0834 0.6850 2 M 0.2661 0.0737 0.6602 3 E 0.4718 0.0356 0.4926 4 I 0.6490 0.0139 0.3371 5 L 0.7021 0.0190 0.2788 6 Q 0.7754 0.0062 0.2184 7 V 0.8080 0.0059 0.1861 8 A 0.8018 0.0051 0.1931 9 L 0.7832 0.0066 0.2102 10 H 0.7454 0.0124 0.2422 11 K 0.6300 0.0227 0.3474 12 R 0.3564 0.0521 0.5916 13 D 0.1810 0.1641 0.6549 14 S 0.1040 0.1719 0.7240 15 G 0.1038 0.1016 0.7945 16 E 0.2573 0.1103 0.6324 17 Q 0.4098 0.0784 0.5118 18 L 0.5208 0.0555 0.4237 19 G 0.6235 0.0185 0.3580 20 I 0.7736 0.0057 0.2207 21 K 0.7918 0.0068 0.2014 22 L 0.7313 0.0074 0.2612 23 V 0.6455 0.0285 0.3260 24 R 0.4327 0.0431 0.5242 25 R 0.2855 0.0738 0.6408 26 T 0.2367 0.1291 0.6341 27 D 0.1735 0.1149 0.7115 28 E 0.2271 0.0560 0.7169 29 P 0.1891 0.1169 0.6939 30 G 0.2873 0.0709 0.6417 31 V 0.6501 0.0130 0.3370 32 F 0.7537 0.0099 0.2363 33 I 0.6922 0.0189 0.2889 34 L 0.6169 0.0552 0.3278 35 D 0.6844 0.0425 0.2731 36 L 0.5342 0.0516 0.4142 37 L 0.3600 0.0523 0.5876 38 E 0.1322 0.2127 0.6552 39 G 0.0599 0.1599 0.7803 40 G 0.1627 0.1458 0.6915 41 L 0.1481 0.4392 0.4127 42 A 0.1033 0.6011 0.2955 43 A 0.0946 0.6187 0.2867 44 Q 0.0780 0.5504 0.3716 45 D 0.0878 0.2005 0.7117 46 G 0.0793 0.0890 0.8317 47 R 0.2923 0.0464 0.6613 48 L 0.3947 0.0328 0.5725 49 S 0.2796 0.0222 0.6982 50 S 0.1166 0.2527 0.6307 51 N 0.0751 0.1437 0.7812 52 D 0.3203 0.0605 0.6192 53 R 0.6347 0.0432 0.3220 54 V 0.7062 0.0480 0.2458 55 L 0.7281 0.0350 0.2369 56 A 0.7393 0.0407 0.2200 57 I 0.6177 0.0598 0.3224 58 N 0.2968 0.0693 0.6339 59 G 0.1228 0.0580 0.8192 60 H 0.3543 0.0368 0.6090 61 D 0.4392 0.0420 0.5188 62 L 0.2905 0.1884 0.5211 63 K 0.1859 0.2678 0.5462 64 Y 0.1551 0.1651 0.6798 65 G 0.1775 0.0784 0.7442 66 T 0.1728 0.0300 0.7973 67 P 0.0133 0.7436 0.2431 68 E 0.0093 0.8702 0.1205 69 L 0.0084 0.9223 0.0693 70 A 0.0083 0.9242 0.0675 71 A 0.0083 0.9221 0.0696 72 Q 0.0083 0.9245 0.0672 73 I 0.0083 0.9231 0.0685 74 I 0.0085 0.9143 0.0772 75 Q 0.0095 0.8763 0.1142 76 A 0.0190 0.6891 0.2918 77 S 0.0649 0.2147 0.7204 78 G 0.0507 0.0816 0.8677 79 E 0.1948 0.0559 0.7493 80 R 0.5331 0.0244 0.4425 81 V 0.7503 0.0090 0.2407 82 N 0.7867 0.0065 0.2067 83 L 0.7975 0.0056 0.1969 84 T 0.8020 0.0065 0.1915 85 I 0.7693 0.0067 0.2240 86 A 0.7104 0.0177 0.2719 87 R 0.4379 0.0155 0.5466 88 P 0.1664 0.1151 0.7185 89 G 0.1028 0.1096 0.7876 90 K 0.2043 0.0347 0.7610 91 P 0.2188 0.0946 0.6866 92 E 0.2533 0.1513 0.5954 93 I 0.2674 0.1533 0.5793 94 E 0.2644 0.1393 0.5963 95 L 0.2441 0.1566 0.5993