# This file is the result of combining several RDB files, specifically # T0484.t06.str2.rdb (weight 1.54425) # T0484.t06.str4.rdb (weight 0.924988) # T0484.t06.pb.rdb (weight 0.789901) # T0484.t06.bys.rdb (weight 0.748322) # T0484.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 T0484.t06.str2.rdb # ============================================ # TARGET T0484 # 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 T0484.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 23.0267 # # ============================================ # Comments from T0484.t06.str4.rdb # ============================================ # TARGET T0484 # 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 T0484.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 23.0267 # # ============================================ # Comments from T0484.t06.pb.rdb # ============================================ # TARGET T0484 # 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 T0484.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 23.0267 # # ============================================ # Comments from T0484.t06.bys.rdb # ============================================ # TARGET T0484 # 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 T0484.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 23.0267 # # ============================================ # Comments from T0484.t06.alpha.rdb # ============================================ # TARGET T0484 # 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 T0484.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 23.0267 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2059 0.1360 0.6582 2 R 0.2043 0.1601 0.6356 3 D 0.2015 0.2210 0.5776 4 M 0.1856 0.2936 0.5207 5 T 0.1839 0.2668 0.5494 6 E 0.1750 0.2854 0.5396 7 E 0.1954 0.2469 0.5576 8 T 0.1711 0.2285 0.6004 9 R 0.1288 0.3208 0.5503 10 K 0.1104 0.3302 0.5595 11 D 0.1338 0.1997 0.6665 12 L 0.2255 0.0534 0.7211 13 P 0.1599 0.0292 0.8109 14 P 0.0232 0.6404 0.3364 15 E 0.0137 0.7454 0.2409 16 A 0.0224 0.8050 0.1726 17 L 0.0314 0.8072 0.1614 18 R 0.0245 0.8338 0.1417 19 A 0.0143 0.8711 0.1146 20 L 0.0145 0.8730 0.1126 21 A 0.0168 0.8697 0.1136 22 E 0.0210 0.8442 0.1348 23 A 0.0319 0.7919 0.1761 24 E 0.0379 0.7508 0.2114 25 E 0.0432 0.7146 0.2422 26 R 0.0506 0.6696 0.2798 27 R 0.0636 0.6065 0.3299 28 R 0.0795 0.5683 0.3522 29 R 0.0637 0.6222 0.3140 30 A 0.0537 0.6336 0.3127 31 K 0.0686 0.5563 0.3750 32 A 0.1085 0.3876 0.5039 33 L 0.1529 0.2169 0.6302 34 D 0.1440 0.1537 0.7023 35 L 0.2064 0.0654 0.7282 36 P 0.1737 0.1407 0.6856 37 K 0.1358 0.3511 0.5131 38 E 0.1917 0.3779 0.4304 39 I 0.2180 0.2110 0.5710 40 G 0.1836 0.1059 0.7105 41 G 0.1996 0.0685 0.7319 42 R 0.1907 0.1617 0.6475 43 N 0.1647 0.1190 0.7162 44 G 0.2000 0.0589 0.7411 45 P 0.2145 0.0805 0.7050 46 E 0.3182 0.0560 0.6258 47 P 0.3417 0.0742 0.5842 48 V 0.3595 0.0647 0.5758 49 R 0.3638 0.0739 0.5623 50 F 0.2440 0.1468 0.6092 51 G 0.1829 0.1019 0.7152 52 D 0.2417 0.1012 0.6570 53 W 0.1879 0.3548 0.4573 54 E 0.1969 0.3557 0.4474 55 K 0.2372 0.2443 0.5185 56 K 0.2133 0.1161 0.6706 57 G 0.2953 0.0567 0.6480 58 I 0.6131 0.0344 0.3525 59 A 0.6931 0.0287 0.2782 60 I 0.6692 0.0453 0.2856 61 D 0.5137 0.0497 0.4366 62 F 0.2965 0.1431 0.5604