# This file is the result of combining several RDB files, specifically # T0469.t06.str2.rdb (weight 1.54425) # T0469.t06.str4.rdb (weight 0.924988) # T0469.t06.pb.rdb (weight 0.789901) # T0469.t06.bys.rdb (weight 0.748322) # T0469.t06.alpha.rdb (weight 0.678173) # T0469.t04.str2.rdb (weight 1.54425) # T0469.t04.str4.rdb (weight 0.924988) # T0469.t04.pb.rdb (weight 0.789901) # T0469.t04.bys.rdb (weight 0.748322) # T0469.t04.alpha.rdb (weight 0.678173) # T0469.t2k.str2.rdb (weight 1.54425) # T0469.t2k.str4.rdb (weight 0.924988) # T0469.t2k.pb.rdb (weight 0.789901) # T0469.t2k.bys.rdb (weight 0.748322) # T0469.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 T0469.t06.str2.rdb # ============================================ # TARGET T0469 # 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 T0469.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 21.8853 # # ============================================ # Comments from T0469.t06.str4.rdb # ============================================ # TARGET T0469 # 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 T0469.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 21.8853 # # ============================================ # Comments from T0469.t06.pb.rdb # ============================================ # TARGET T0469 # 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 T0469.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 21.8853 # # ============================================ # Comments from T0469.t06.bys.rdb # ============================================ # TARGET T0469 # 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 T0469.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 21.8853 # # ============================================ # Comments from T0469.t06.alpha.rdb # ============================================ # TARGET T0469 # 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 T0469.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 21.8853 # # ============================================ # Comments from T0469.t04.str2.rdb # ============================================ # TARGET T0469 # 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 T0469.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 20.9914 # # ============================================ # Comments from T0469.t04.str4.rdb # ============================================ # TARGET T0469 # 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 T0469.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 20.9914 # # ============================================ # Comments from T0469.t04.pb.rdb # ============================================ # TARGET T0469 # 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 T0469.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 20.9914 # # ============================================ # Comments from T0469.t04.bys.rdb # ============================================ # TARGET T0469 # 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 T0469.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 20.9914 # # ============================================ # Comments from T0469.t04.alpha.rdb # ============================================ # TARGET T0469 # 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 T0469.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 20.9914 # # ============================================ # Comments from T0469.t2k.str2.rdb # ============================================ # TARGET T0469 # 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 T0469.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 14.2513 # # ============================================ # Comments from T0469.t2k.str4.rdb # ============================================ # TARGET T0469 # 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 T0469.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 14.2513 # # ============================================ # Comments from T0469.t2k.pb.rdb # ============================================ # TARGET T0469 # 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 T0469.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 14.2513 # # ============================================ # Comments from T0469.t2k.bys.rdb # ============================================ # TARGET T0469 # 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 T0469.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 14.2513 # # ============================================ # Comments from T0469.t2k.alpha.rdb # ============================================ # TARGET T0469 # 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 T0469.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 14.2513 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2549 0.2081 0.5370 2 T 0.2258 0.2444 0.5298 3 Q 0.1724 0.4149 0.4127 4 K 0.2693 0.3080 0.4227 5 F 0.3389 0.2174 0.4437 6 T 0.2116 0.1673 0.6211 7 K 0.0780 0.5051 0.4169 8 D 0.0726 0.4315 0.4960 9 M 0.1791 0.3407 0.4802 10 T 0.1633 0.3965 0.4402 11 F 0.0433 0.7611 0.1956 12 A 0.0165 0.8640 0.1195 13 Q 0.0129 0.9093 0.0779 14 A 0.0140 0.8920 0.0940 15 L 0.0183 0.8649 0.1168 16 Q 0.0216 0.7729 0.2055 17 T 0.0493 0.5778 0.3728 18 H 0.1359 0.2112 0.6529 19 P 0.0328 0.5844 0.3828 20 G 0.0245 0.5544 0.4211 21 V 0.0371 0.7441 0.2188 22 A 0.0253 0.8467 0.1280 23 G 0.0178 0.8844 0.0978 24 V 0.0187 0.8945 0.0868 25 L 0.0206 0.8806 0.0988 26 R 0.0217 0.8497 0.1286 27 S 0.0327 0.7368 0.2305 28 Y 0.0670 0.3721 0.5608 29 N 0.0794 0.1884 0.7322 30 L 0.1593 0.1838 0.6569 31 G 0.1752 0.1608 0.6639 32 C 0.2310 0.2111 0.5579 33 I 0.2057 0.2192 0.5751 34 G 0.1864 0.1536 0.6600 35 C 0.2146 0.1613 0.6241 36 M 0.1304 0.3803 0.4893 37 G 0.0990 0.4205 0.4804 38 A 0.1039 0.4587 0.4374 39 Q 0.0807 0.4439 0.4753 40 N 0.0764 0.5138 0.4098 41 E 0.0771 0.6300 0.2930 42 S 0.0815 0.6280 0.2904 43 L 0.0165 0.7941 0.1894 44 E 0.0100 0.8829 0.1071 45 Q 0.0120 0.9008 0.0872 46 G 0.0169 0.8889 0.0942 47 A 0.0189 0.8656 0.1155 48 N 0.0250 0.8050 0.1700 49 A 0.0311 0.6998 0.2691 50 H 0.0641 0.2471 0.6888 51 G 0.0564 0.1030 0.8406 52 L 0.1881 0.0733 0.7386 53 N 0.1761 0.0438 0.7802 54 V 0.0126 0.7403 0.2470 55 E 0.0092 0.8720 0.1188 56 D 0.0088 0.9188 0.0724 57 I 0.0086 0.9213 0.0701 58 L 0.0083 0.9186 0.0730 59 R 0.0083 0.9120 0.0797 60 D 0.0091 0.8667 0.1242 61 L 0.0138 0.8430 0.1432 62 N 0.0126 0.7447 0.2428 63 A 0.0164 0.6871 0.2965 64 L 0.0431 0.5443 0.4127 65 A 0.0800 0.4088 0.5111