# This file is the result of combining several RDB files, specifically # T0489.t06.str2.rdb (weight 1.54425) # T0489.t06.str4.rdb (weight 0.924988) # T0489.t06.pb.rdb (weight 0.789901) # T0489.t06.bys.rdb (weight 0.748322) # T0489.t06.alpha.rdb (weight 0.678173) # T0489.t04.str2.rdb (weight 1.54425) # T0489.t04.str4.rdb (weight 0.924988) # T0489.t04.pb.rdb (weight 0.789901) # T0489.t04.bys.rdb (weight 0.748322) # T0489.t04.alpha.rdb (weight 0.678173) # T0489.t2k.str2.rdb (weight 1.54425) # T0489.t2k.str4.rdb (weight 0.924988) # T0489.t2k.pb.rdb (weight 0.789901) # T0489.t2k.bys.rdb (weight 0.748322) # T0489.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 T0489.t06.str2.rdb # ============================================ # TARGET T0489 # 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 T0489.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 23.1837 # # ============================================ # Comments from T0489.t06.str4.rdb # ============================================ # TARGET T0489 # 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 T0489.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 23.1837 # # ============================================ # Comments from T0489.t06.pb.rdb # ============================================ # TARGET T0489 # 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 T0489.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 23.1837 # # ============================================ # Comments from T0489.t06.bys.rdb # ============================================ # TARGET T0489 # 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 T0489.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 23.1837 # # ============================================ # Comments from T0489.t06.alpha.rdb # ============================================ # TARGET T0489 # 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 T0489.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 23.1837 # # ============================================ # Comments from T0489.t04.str2.rdb # ============================================ # TARGET T0489 # 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 T0489.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 23.1154 # # ============================================ # Comments from T0489.t04.str4.rdb # ============================================ # TARGET T0489 # 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 T0489.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 23.1154 # # ============================================ # Comments from T0489.t04.pb.rdb # ============================================ # TARGET T0489 # 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 T0489.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 23.1154 # # ============================================ # Comments from T0489.t04.bys.rdb # ============================================ # TARGET T0489 # 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 T0489.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 23.1154 # # ============================================ # Comments from T0489.t04.alpha.rdb # ============================================ # TARGET T0489 # 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 T0489.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 23.1154 # # ============================================ # Comments from T0489.t2k.str2.rdb # ============================================ # TARGET T0489 # 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 T0489.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 28.1803 # # ============================================ # Comments from T0489.t2k.str4.rdb # ============================================ # TARGET T0489 # 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 T0489.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 28.1803 # # ============================================ # Comments from T0489.t2k.pb.rdb # ============================================ # TARGET T0489 # 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 T0489.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 28.1803 # # ============================================ # Comments from T0489.t2k.bys.rdb # ============================================ # TARGET T0489 # 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 T0489.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 28.1803 # # ============================================ # Comments from T0489.t2k.alpha.rdb # ============================================ # TARGET T0489 # 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 T0489.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 28.1803 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2807 0.2728 0.4464 2 M 0.2705 0.2534 0.4761 3 F 0.2829 0.2232 0.4938 4 K 0.2810 0.1505 0.5685 5 W 0.2678 0.0887 0.6435 6 P 0.1750 0.3067 0.5183 7 W 0.1898 0.4085 0.4018 8 K 0.1925 0.3809 0.4266 9 A 0.1838 0.3649 0.4513 10 D 0.1354 0.3181 0.5465 11 D 0.1176 0.2925 0.5899 12 E 0.1441 0.2302 0.6257 13 S 0.1380 0.2051 0.6569 14 G 0.1485 0.1169 0.7346 15 N 0.1235 0.1780 0.6985 16 A 0.0366 0.5222 0.4413 17 E 0.0482 0.5056 0.4462 18 M 0.1008 0.4509 0.4483 19 P 0.0351 0.7576 0.2073 20 W 0.0156 0.8727 0.1117 21 E 0.0093 0.9122 0.0785 22 Q 0.0098 0.9063 0.0838 23 A 0.0132 0.8658 0.1210 24 L 0.0139 0.7884 0.1977 25 A 0.0326 0.6170 0.3505 26 I 0.1011 0.4454 0.4535 27 P 0.0608 0.5921 0.3471 28 V 0.0605 0.6289 0.3106 29 L 0.0585 0.7022 0.2393 30 A 0.0573 0.6187 0.3240 31 H 0.0857 0.2925 0.6218 32 L 0.1857 0.0849 0.7294 33 S 0.1559 0.0522 0.7920 34 S 0.0199 0.6185 0.3616 35 T 0.0109 0.8104 0.1787 36 E 0.0097 0.8892 0.1010 37 Q 0.0087 0.9103 0.0810 38 H 0.0084 0.9168 0.0748 39 K 0.0084 0.9181 0.0736 40 L 0.0084 0.9197 0.0720 41 T 0.0083 0.9224 0.0693 42 Q 0.0083 0.9241 0.0676 43 M 0.0083 0.9237 0.0681 44 A 0.0083 0.9224 0.0693 45 A 0.0083 0.9237 0.0680 46 R 0.0083 0.9223 0.0693 47 F 0.0091 0.9140 0.0769 48 L 0.0092 0.8976 0.0932 49 Q 0.0100 0.8529 0.1371 50 Q 0.0231 0.7591 0.2178 51 K 0.0630 0.6131 0.3239 52 R 0.1275 0.4215 0.4510 53 L 0.2527 0.2797 0.4676 54 V 0.3137 0.2100 0.4762 55 A 0.3030 0.1781 0.5189 56 L 0.2393 0.1849 0.5758 57 Q 0.1547 0.1247 0.7206 58 G 0.1252 0.0818 0.7931 59 L 0.4213 0.0365 0.5422 60 E 0.5629 0.0311 0.4060 61 L 0.4649 0.0619 0.4732 62 T 0.1995 0.0461 0.7544 63 P 0.0273 0.6290 0.3437 64 L 0.0161 0.7697 0.2142 65 H 0.0157 0.8888 0.0955 66 Q 0.0107 0.9025 0.0867 67 A 0.0099 0.9204 0.0696 68 R 0.0088 0.9237 0.0675 69 I 0.0089 0.9214 0.0698 70 A 0.0086 0.9204 0.0710 71 M 0.0096 0.9097 0.0807 72 L 0.0115 0.8874 0.1011 73 F 0.0191 0.8130 0.1679 74 C 0.0288 0.7246 0.2466 75 L 0.0699 0.6664 0.2637 76 P 0.0406 0.7609 0.1985 77 V 0.0502 0.7603 0.1895 78 L 0.0857 0.6787 0.2357 79 E 0.0999 0.5177 0.3824 80 L 0.0941 0.2983 0.6076 81 G 0.0887 0.1562 0.7551 82 I 0.1149 0.3317 0.5534 83 E 0.1298 0.4583 0.4119 84 W 0.1470 0.4675 0.3856 85 L 0.2070 0.3024 0.4907 86 D 0.1301 0.1914 0.6784 87 G 0.0793 0.1192 0.8016 88 F 0.2881 0.0760 0.6359 89 H 0.4030 0.0592 0.5378 90 E 0.7286 0.0168 0.2546 91 V 0.7657 0.0072 0.2271 92 L 0.7898 0.0056 0.2046 93 I 0.7544 0.0112 0.2344 94 Y 0.5429 0.0132 0.4439 95 P 0.2410 0.0754 0.6836