# This file is the result of combining several RDB files, specifically # T0474.t06.str2.rdb (weight 1.54425) # T0474.t06.str4.rdb (weight 0.924988) # T0474.t06.pb.rdb (weight 0.789901) # T0474.t06.bys.rdb (weight 0.748322) # T0474.t06.alpha.rdb (weight 0.678173) # T0474.t04.str2.rdb (weight 1.54425) # T0474.t04.str4.rdb (weight 0.924988) # T0474.t04.pb.rdb (weight 0.789901) # T0474.t04.bys.rdb (weight 0.748322) # T0474.t04.alpha.rdb (weight 0.678173) # T0474.t2k.str2.rdb (weight 1.54425) # T0474.t2k.str4.rdb (weight 0.924988) # T0474.t2k.pb.rdb (weight 0.789901) # T0474.t2k.bys.rdb (weight 0.748322) # T0474.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 T0474.t06.str2.rdb # ============================================ # TARGET T0474 # 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 T0474.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 19.7804 # # ============================================ # Comments from T0474.t06.str4.rdb # ============================================ # TARGET T0474 # 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 T0474.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 19.7804 # # ============================================ # Comments from T0474.t06.pb.rdb # ============================================ # TARGET T0474 # 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 T0474.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 19.7804 # # ============================================ # Comments from T0474.t06.bys.rdb # ============================================ # TARGET T0474 # 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 T0474.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 19.7804 # # ============================================ # Comments from T0474.t06.alpha.rdb # ============================================ # TARGET T0474 # 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 T0474.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 19.7804 # # ============================================ # Comments from T0474.t04.str2.rdb # ============================================ # TARGET T0474 # 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 T0474.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 16.4906 # # ============================================ # Comments from T0474.t04.str4.rdb # ============================================ # TARGET T0474 # 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 T0474.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 16.4906 # # ============================================ # Comments from T0474.t04.pb.rdb # ============================================ # TARGET T0474 # 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 T0474.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 16.4906 # # ============================================ # Comments from T0474.t04.bys.rdb # ============================================ # TARGET T0474 # 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 T0474.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 16.4906 # # ============================================ # Comments from T0474.t04.alpha.rdb # ============================================ # TARGET T0474 # 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 T0474.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 16.4906 # # ============================================ # Comments from T0474.t2k.str2.rdb # ============================================ # TARGET T0474 # 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 T0474.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 12.8793 # # ============================================ # Comments from T0474.t2k.str4.rdb # ============================================ # TARGET T0474 # 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 T0474.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 12.8793 # # ============================================ # Comments from T0474.t2k.pb.rdb # ============================================ # TARGET T0474 # 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 T0474.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 12.8793 # # ============================================ # Comments from T0474.t2k.bys.rdb # ============================================ # TARGET T0474 # 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 T0474.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 12.8793 # # ============================================ # Comments from T0474.t2k.alpha.rdb # ============================================ # TARGET T0474 # 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 T0474.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 12.8793 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2835 0.2280 0.4885 2 N 0.2335 0.2931 0.4735 3 S 0.2332 0.3972 0.3696 4 L 0.2457 0.3990 0.3554 5 A 0.2207 0.3901 0.3892 6 G 0.1921 0.3551 0.4529 7 I 0.2142 0.4092 0.3766 8 D 0.2373 0.3223 0.4404 9 M 0.3004 0.2425 0.4572 10 G 0.3234 0.1790 0.4976 11 R 0.5442 0.1042 0.3517 12 I 0.7063 0.0449 0.2488 13 L 0.7179 0.0299 0.2522 14 L 0.7056 0.0330 0.2614 15 D 0.3906 0.0382 0.5713 16 L 0.1529 0.1486 0.6985 17 S 0.1170 0.2349 0.6481 18 N 0.0149 0.7011 0.2840 19 E 0.0119 0.8255 0.1626 20 V 0.0112 0.8963 0.0925 21 I 0.0094 0.9105 0.0800 22 K 0.0088 0.9097 0.0814 23 Q 0.0110 0.8824 0.1067 24 L 0.0123 0.8724 0.1152 25 D 0.0100 0.8786 0.1114 26 D 0.0124 0.8635 0.1241 27 L 0.0144 0.8743 0.1113 28 E 0.0143 0.8818 0.1039 29 V 0.0222 0.8286 0.1492 30 Q 0.0434 0.6891 0.2676 31 R 0.0588 0.4823 0.4589 32 N 0.0588 0.2176 0.7237 33 L 0.1683 0.0519 0.7799 34 P 0.1517 0.0712 0.7770 35 R 0.0176 0.7202 0.2622 36 A 0.0093 0.8677 0.1230 37 D 0.0084 0.9206 0.0710 38 L 0.0083 0.9225 0.0692 39 L 0.0083 0.9213 0.0703 40 R 0.0083 0.9230 0.0687 41 E 0.0083 0.9241 0.0676 42 A 0.0084 0.9218 0.0698 43 V 0.0083 0.9207 0.0709 44 D 0.0083 0.9214 0.0703 45 Q 0.0084 0.9162 0.0754 46 Y 0.0092 0.9101 0.0807 47 L 0.0100 0.8970 0.0930 48 I 0.0124 0.8493 0.1383 49 N 0.0270 0.6348 0.3383 50 Q 0.0644 0.4252 0.5104 51 S 0.1059 0.2957 0.5983 52 Q 0.1081 0.3708 0.5212 53 T 0.1082 0.4140 0.4778 54 A 0.1001 0.5004 0.3995 55 R 0.0969 0.5291 0.3740 56 T 0.0988 0.4675 0.4337 57 S 0.1379 0.2853 0.5768 58 V 0.2235 0.1890 0.5875 59 P 0.2029 0.2040 0.5932 60 G 0.2321 0.2498 0.5181 61 I 0.3104 0.2935 0.3961 62 W 0.3430 0.2417 0.4153 63 Q 0.2192 0.1556 0.6253 64 G 0.1300 0.0995 0.7705 65 C 0.2403 0.0845 0.6751 66 E 0.2757 0.1522 0.5722 67 E 0.1588 0.3102 0.5311 68 D 0.1206 0.3032 0.5762 69 G 0.1032 0.4864 0.4104 70 V 0.0547 0.7603 0.1850 71 E 0.0345 0.8587 0.1069 72 Y 0.0256 0.8809 0.0935 73 Q 0.0122 0.9091 0.0787 74 R 0.0089 0.9130 0.0781 75 K 0.0098 0.8962 0.0939 76 L 0.0132 0.8595 0.1274 77 R 0.0131 0.8456 0.1413 78 E 0.0142 0.8230 0.1628 79 E 0.0355 0.6897 0.2748 80 W 0.0913 0.5109 0.3978