# This file is the result of combining several RDB files, specifically # T0467.t06.str2.rdb (weight 1.54425) # T0467.t06.str4.rdb (weight 0.924988) # T0467.t06.pb.rdb (weight 0.789901) # T0467.t06.bys.rdb (weight 0.748322) # T0467.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 T0467.t06.str2.rdb # ============================================ # TARGET T0467 # 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 T0467.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 49.5286 # # ============================================ # Comments from T0467.t06.str4.rdb # ============================================ # TARGET T0467 # 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 T0467.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 49.5286 # # ============================================ # Comments from T0467.t06.pb.rdb # ============================================ # TARGET T0467 # 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 T0467.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 49.5286 # # ============================================ # Comments from T0467.t06.bys.rdb # ============================================ # TARGET T0467 # 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 T0467.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 49.5286 # # ============================================ # Comments from T0467.t06.alpha.rdb # ============================================ # TARGET T0467 # 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 T0467.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 49.5286 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2816 0.1189 0.5995 2 D 0.2654 0.1121 0.6225 3 L 0.2874 0.1426 0.5699 4 N 0.2587 0.1159 0.6254 5 R 0.2224 0.2689 0.5087 6 M 0.2514 0.1980 0.5507 7 G 0.2775 0.1047 0.6178 8 K 0.3105 0.0902 0.5993 9 D 0.4266 0.0720 0.5014 10 E 0.6281 0.0264 0.3455 11 Y 0.7729 0.0091 0.2180 12 Y 0.8022 0.0052 0.1926 13 V 0.8189 0.0050 0.1760 14 Q 0.8029 0.0053 0.1917 15 I 0.7886 0.0063 0.2050 16 T 0.6395 0.0158 0.3446 17 V 0.4703 0.0935 0.4362 18 D 0.2295 0.0894 0.6811 19 G 0.1692 0.0753 0.7555 20 K 0.4765 0.0586 0.4648 21 E 0.6172 0.0507 0.3320 22 V 0.6452 0.0641 0.2908 23 H 0.6360 0.0697 0.2943 24 S 0.5927 0.1043 0.3031 25 K 0.5346 0.1213 0.3441 26 A 0.3709 0.1598 0.4693 27 D 0.1824 0.2342 0.5834 28 N 0.0926 0.1496 0.7578 29 G 0.0783 0.0911 0.8306 30 Q 0.3418 0.0561 0.6021 31 K 0.5521 0.0520 0.3958 32 Y 0.5678 0.0547 0.3775 33 K 0.5876 0.0748 0.3375 34 D 0.6261 0.0424 0.3315 35 Y 0.7247 0.0213 0.2540 36 E 0.7547 0.0145 0.2308 37 Y 0.7953 0.0080 0.1966 38 K 0.7815 0.0080 0.2105 39 L 0.7678 0.0106 0.2216 40 T 0.7099 0.0241 0.2659 41 G 0.7132 0.0304 0.2564 42 F 0.7032 0.0301 0.2667 43 D 0.4760 0.0270 0.4970 44 K 0.0684 0.3817 0.5499 45 D 0.0658 0.1854 0.7488 46 G 0.0723 0.0691 0.8586 47 K 0.4288 0.0326 0.5386 48 E 0.6662 0.0151 0.3187 49 K 0.7320 0.0127 0.2553 50 E 0.7852 0.0052 0.2096 51 L 0.7961 0.0065 0.1974 52 E 0.8012 0.0060 0.1928 53 F 0.7598 0.0137 0.2266 54 T 0.5984 0.0537 0.3479 55 A 0.3709 0.1754 0.4537 56 Q 0.1948 0.2856 0.5197 57 K 0.1341 0.3789 0.4870 58 N 0.1237 0.3476 0.5286 59 L 0.2038 0.2353 0.5609 60 R 0.2065 0.1666 0.6269 61 K 0.1112 0.4153 0.4736 62 E 0.1716 0.2351 0.5932 63 A 0.4896 0.1106 0.3998 64 F 0.7087 0.0278 0.2635 65 L 0.7932 0.0121 0.1948 66 R 0.8137 0.0082 0.1782 67 V 0.8083 0.0075 0.1842 68 Y 0.7782 0.0137 0.2081 69 H 0.6963 0.0335 0.2702 70 S 0.4431 0.0969 0.4600 71 D 0.2137 0.1337 0.6526 72 K 0.2198 0.1653 0.6149 73 K 0.2214 0.1492 0.6294 74 G 0.2591 0.0916 0.6493 75 V 0.4652 0.0330 0.5018 76 S 0.4620 0.0401 0.4979 77 A 0.3495 0.0350 0.6155 78 W 0.2187 0.3711 0.4102 79 E 0.2308 0.4552 0.3140 80 E 0.3274 0.3322 0.3405 81 V 0.3593 0.1791 0.4616 82 K 0.2275 0.1394 0.6331 83 K 0.0438 0.6166 0.3396 84 D 0.0260 0.6178 0.3563 85 E 0.0426 0.5065 0.4509 86 L 0.1507 0.2376 0.6117 87 P 0.0772 0.4689 0.4538 88 A 0.0112 0.7797 0.2092 89 K 0.0093 0.8789 0.1118 90 V 0.0099 0.9070 0.0831 91 K 0.0086 0.9177 0.0737 92 E 0.0090 0.8998 0.0912 93 K 0.0151 0.8015 0.1834 94 L 0.0650 0.4581 0.4769 95 G 0.0512 0.2126 0.7362 96 V 0.1706 0.1100 0.7194 97 K 0.1655 0.1238 0.7107