# This file is the result of combining several RDB files, specifically # T0492.t06.str2.rdb (weight 1.54425) # T0492.t06.str4.rdb (weight 0.924988) # T0492.t06.pb.rdb (weight 0.789901) # T0492.t06.bys.rdb (weight 0.748322) # T0492.t06.alpha.rdb (weight 0.678173) # T0492.t04.str2.rdb (weight 1.54425) # T0492.t04.str4.rdb (weight 0.924988) # T0492.t04.pb.rdb (weight 0.789901) # T0492.t04.bys.rdb (weight 0.748322) # T0492.t04.alpha.rdb (weight 0.678173) # T0492.t2k.str2.rdb (weight 1.54425) # T0492.t2k.str4.rdb (weight 0.924988) # T0492.t2k.pb.rdb (weight 0.789901) # T0492.t2k.bys.rdb (weight 0.748322) # T0492.t2k.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 T0492.t06.str2.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.5359 # # ============================================ # Comments from T0492.t06.str4.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.5359 # # ============================================ # Comments from T0492.t06.pb.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.5359 # # ============================================ # Comments from T0492.t06.bys.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.5359 # # ============================================ # Comments from T0492.t06.alpha.rdb # ============================================ # TARGET T0492 # 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 T0492.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 61.5359 # # ============================================ # Comments from T0492.t04.str2.rdb # ============================================ # TARGET T0492 # Using neural net dunbrack-40pc-3157-t04-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 T0492.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 61.0248 # # ============================================ # Comments from T0492.t04.str4.rdb # ============================================ # TARGET T0492 # Using neural net dunbrack-40pc-3157-t04-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 T0492.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 61.0248 # # ============================================ # Comments from T0492.t04.pb.rdb # ============================================ # TARGET T0492 # Using neural net dunbrack-40pc-3157-t04-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 T0492.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 61.0248 # # ============================================ # Comments from T0492.t04.bys.rdb # ============================================ # TARGET T0492 # Using neural net dunbrack-40pc-3157-t04-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 T0492.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 61.0248 # # ============================================ # Comments from T0492.t04.alpha.rdb # ============================================ # TARGET T0492 # Using neural net dunbrack-40pc-3157-t04-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 T0492.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 61.0248 # # ============================================ # Comments from T0492.t2k.str2.rdb # ============================================ # TARGET T0492 # Using neural net dunbrack-40pc-3157-t2k-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 T0492.t2k-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 38.1747 # # ============================================ # Comments from T0492.t2k.str4.rdb # ============================================ # TARGET T0492 # Using neural net dunbrack-40pc-3157-t2k-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 T0492.t2k-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 38.1747 # # ============================================ # Comments from T0492.t2k.pb.rdb # ============================================ # TARGET T0492 # Using neural net dunbrack-40pc-3157-t2k-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 T0492.t2k-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 38.1747 # # ============================================ # Comments from T0492.t2k.bys.rdb # ============================================ # TARGET T0492 # Using neural net dunbrack-40pc-3157-t2k-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 T0492.t2k-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 38.1747 # # ============================================ # Comments from T0492.t2k.alpha.rdb # ============================================ # TARGET T0492 # Using neural net dunbrack-40pc-3157-t2k-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 T0492.t2k-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 38.1747 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3788 0.1211 0.5001 2 F 0.4451 0.0623 0.4926 3 S 0.3309 0.0526 0.6165 4 L 0.1764 0.4148 0.4089 5 R 0.1194 0.4710 0.4096 6 D 0.1753 0.2880 0.5367 7 A 0.2974 0.1268 0.5758 8 K 0.2795 0.1071 0.6134 9 C 0.1738 0.1333 0.6929 10 G 0.1132 0.0886 0.7982 11 Q 0.3701 0.0395 0.5903 12 T 0.6733 0.0167 0.3100 13 V 0.7686 0.0072 0.2242 14 K 0.8061 0.0052 0.1887 15 V 0.7548 0.0063 0.2389 16 V 0.7019 0.0169 0.2812 17 K 0.7367 0.0160 0.2473 18 L 0.6200 0.0403 0.3397 19 H 0.4036 0.0694 0.5269 20 G 0.2125 0.1067 0.6808 21 T 0.0982 0.2450 0.6568 22 G 0.0554 0.4241 0.5205 23 A 0.0437 0.7356 0.2207 24 L 0.0259 0.8502 0.1238 25 K 0.0161 0.8975 0.0865 26 R 0.0135 0.9089 0.0776 27 R 0.0144 0.9054 0.0801 28 I 0.0140 0.8929 0.0932 29 M 0.0141 0.8644 0.1214 30 D 0.0403 0.7202 0.2395 31 M 0.0648 0.3320 0.6033 32 G 0.1044 0.1089 0.7867 33 I 0.2782 0.0709 0.6509 34 T 0.2883 0.0427 0.6689 35 R 0.2063 0.1224 0.6713 36 G 0.1049 0.0901 0.8050 37 C 0.4016 0.0260 0.5724 38 E 0.6962 0.0120 0.2918 39 I 0.7889 0.0064 0.2047 40 Y 0.7954 0.0069 0.1977 41 I 0.7741 0.0072 0.2187 42 R 0.7237 0.0223 0.2540 43 K 0.7043 0.0275 0.2682 44 V 0.5699 0.0634 0.3667 45 A 0.5219 0.0384 0.4397 46 P 0.3887 0.1226 0.4888 47 L 0.1686 0.1509 0.6805 48 G 0.1234 0.1113 0.7653 49 D 0.2306 0.0311 0.7383 50 P 0.3343 0.0535 0.6122 51 I 0.5982 0.0271 0.3747 52 Q 0.7870 0.0077 0.2053 53 I 0.8067 0.0059 0.1874 54 N 0.7788 0.0059 0.2154 55 V 0.7057 0.0148 0.2795 56 R 0.4684 0.0479 0.4837 57 G 0.2916 0.0496 0.6588 58 Y 0.5477 0.0378 0.4146 59 E 0.6949 0.0311 0.2740 60 L 0.7456 0.0402 0.2141 61 S 0.7068 0.0576 0.2356 62 L 0.6371 0.0972 0.2657 63 R 0.4104 0.1530 0.4366 64 K 0.1483 0.5129 0.3388 65 S 0.0751 0.5924 0.3326 66 A 0.1218 0.5327 0.3455 67 A 0.2084 0.4767 0.3150 68 E 0.2804 0.3687 0.3509 69 M 0.4790 0.1579 0.3631 70 I 0.6627 0.0472 0.2900 71 E 0.6732 0.0288 0.2980 72 V 0.6829 0.0250 0.2921 73 E 0.4746 0.0355 0.4899