# This file is the result of combining several RDB files, specifically # T0467.t04.str2.rdb (weight 1.54425) # T0467.t04.str4.rdb (weight 0.924988) # T0467.t04.pb.rdb (weight 0.789901) # T0467.t04.bys.rdb (weight 0.748322) # T0467.t04.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 T0467.t04.str2.rdb # ============================================ # TARGET T0467 # 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 T0467.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 47.9873 # # ============================================ # Comments from T0467.t04.str4.rdb # ============================================ # TARGET T0467 # 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 T0467.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 47.9873 # # ============================================ # Comments from T0467.t04.pb.rdb # ============================================ # TARGET T0467 # 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 T0467.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 47.9873 # # ============================================ # Comments from T0467.t04.bys.rdb # ============================================ # TARGET T0467 # 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 T0467.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 47.9873 # # ============================================ # Comments from T0467.t04.alpha.rdb # ============================================ # TARGET T0467 # 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 T0467.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 47.9873 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3172 0.0918 0.5910 2 D 0.3032 0.0927 0.6042 3 L 0.3345 0.1692 0.4964 4 N 0.3196 0.1158 0.5646 5 R 0.2543 0.2196 0.5262 6 M 0.2604 0.1415 0.5981 7 G 0.2486 0.0799 0.6715 8 K 0.2864 0.0807 0.6329 9 D 0.3858 0.0659 0.5483 10 E 0.6226 0.0261 0.3513 11 Y 0.7574 0.0096 0.2330 12 Y 0.7999 0.0052 0.1949 13 V 0.8235 0.0046 0.1719 14 Q 0.8167 0.0047 0.1786 15 I 0.7975 0.0068 0.1957 16 T 0.6968 0.0145 0.2887 17 V 0.5200 0.0681 0.4119 18 D 0.2009 0.0888 0.7103 19 G 0.1226 0.1038 0.7736 20 K 0.4792 0.0420 0.4787 21 E 0.6299 0.0300 0.3402 22 V 0.6505 0.0413 0.3083 23 H 0.5993 0.0739 0.3269 24 S 0.5331 0.1141 0.3528 25 K 0.4602 0.1286 0.4112 26 A 0.3338 0.1565 0.5097 27 D 0.1815 0.2001 0.6184 28 N 0.0936 0.1397 0.7666 29 G 0.0840 0.0983 0.8177 30 Q 0.3577 0.0460 0.5963 31 K 0.5683 0.0425 0.3893 32 Y 0.5530 0.0462 0.4007 33 K 0.5508 0.0615 0.3877 34 D 0.5886 0.0464 0.3650 35 Y 0.6891 0.0233 0.2875 36 E 0.7570 0.0152 0.2278 37 Y 0.7830 0.0078 0.2093 38 K 0.7696 0.0104 0.2200 39 L 0.7307 0.0115 0.2578 40 T 0.7048 0.0299 0.2653 41 G 0.7314 0.0182 0.2505 42 F 0.7091 0.0241 0.2668 43 D 0.4485 0.0222 0.5293 44 K 0.0931 0.3382 0.5687 45 D 0.0806 0.1743 0.7451 46 G 0.1195 0.0918 0.7888 47 K 0.4851 0.0196 0.4953 48 E 0.6655 0.0123 0.3221 49 K 0.6876 0.0211 0.2914 50 E 0.7734 0.0061 0.2205 51 L 0.7764 0.0080 0.2156 52 E 0.7589 0.0105 0.2306 53 F 0.7452 0.0162 0.2387 54 T 0.5849 0.0554 0.3596 55 A 0.4004 0.1466 0.4530 56 Q 0.1883 0.2881 0.5236 57 K 0.1339 0.3547 0.5114 58 N 0.1600 0.2893 0.5506 59 L 0.2381 0.2371 0.5248 60 R 0.2197 0.1754 0.6050 61 K 0.0960 0.5009 0.4030 62 E 0.1381 0.3463 0.5156 63 A 0.3942 0.2077 0.3981 64 F 0.6620 0.0606 0.2774 65 L 0.7789 0.0191 0.2020 66 R 0.8078 0.0133 0.1789 67 V 0.8061 0.0095 0.1844 68 Y 0.7796 0.0158 0.2046 69 H 0.7188 0.0250 0.2561 70 S 0.5021 0.0989 0.3990 71 D 0.1800 0.1548 0.6652 72 K 0.1619 0.1984 0.6397 73 K 0.1808 0.1345 0.6847 74 G 0.2571 0.0838 0.6590 75 V 0.4718 0.0322 0.4960 76 S 0.5298 0.0381 0.4321 77 A 0.5071 0.0405 0.4524 78 W 0.3555 0.2254 0.4191 79 E 0.3670 0.3012 0.3317 80 E 0.5557 0.1294 0.3149 81 V 0.4977 0.0819 0.4204 82 K 0.2449 0.0567 0.6983 83 K 0.0674 0.5742 0.3585 84 D 0.0434 0.5891 0.3675 85 E 0.0702 0.4267 0.5031 86 L 0.1711 0.1696 0.6594 87 P 0.1332 0.2393 0.6275 88 A 0.0142 0.7745 0.2113 89 K 0.0109 0.8591 0.1300 90 V 0.0101 0.9016 0.0883 91 K 0.0107 0.9016 0.0877 92 E 0.0121 0.8831 0.1048 93 K 0.0234 0.7573 0.2193 94 L 0.0730 0.4353 0.4916 95 G 0.0724 0.1675 0.7601 96 V 0.1881 0.0987 0.7132 97 K 0.1874 0.1048 0.7078