# This file is the result of combining several RDB files, specifically # T0409.t06.str2.rdb (weight 1.54425) # T0409.t06.str4.rdb (weight 0.924988) # T0409.t06.pb.rdb (weight 0.789901) # T0409.t06.bys.rdb (weight 0.748322) # T0409.t06.alpha.rdb (weight 0.678173) # T0409.t04.str2.rdb (weight 1.54425) # T0409.t04.str4.rdb (weight 0.924988) # T0409.t04.pb.rdb (weight 0.789901) # T0409.t04.bys.rdb (weight 0.748322) # T0409.t04.alpha.rdb (weight 0.678173) # T0409.t2k.str2.rdb (weight 1.54425) # T0409.t2k.str4.rdb (weight 0.924988) # T0409.t2k.pb.rdb (weight 0.789901) # T0409.t2k.bys.rdb (weight 0.748322) # T0409.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 T0409.t06.str2.rdb # ============================================ # TARGET T0409 # 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 T0409.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 26.3911 # # ============================================ # Comments from T0409.t06.str4.rdb # ============================================ # TARGET T0409 # 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 T0409.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 26.3911 # # ============================================ # Comments from T0409.t06.pb.rdb # ============================================ # TARGET T0409 # 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 T0409.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 26.3911 # # ============================================ # Comments from T0409.t06.bys.rdb # ============================================ # TARGET T0409 # 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 T0409.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 26.3911 # # ============================================ # Comments from T0409.t06.alpha.rdb # ============================================ # TARGET T0409 # 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 T0409.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 26.3911 # # ============================================ # Comments from T0409.t04.str2.rdb # ============================================ # TARGET T0409 # 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 T0409.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 24.6872 # # ============================================ # Comments from T0409.t04.str4.rdb # ============================================ # TARGET T0409 # 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 T0409.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 24.6872 # # ============================================ # Comments from T0409.t04.pb.rdb # ============================================ # TARGET T0409 # 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 T0409.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 24.6872 # # ============================================ # Comments from T0409.t04.bys.rdb # ============================================ # TARGET T0409 # 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 T0409.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 24.6872 # # ============================================ # Comments from T0409.t04.alpha.rdb # ============================================ # TARGET T0409 # 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 T0409.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 24.6872 # # ============================================ # Comments from T0409.t2k.str2.rdb # ============================================ # TARGET T0409 # 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 T0409.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 33.5932 # # ============================================ # Comments from T0409.t2k.str4.rdb # ============================================ # TARGET T0409 # 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 T0409.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 33.5932 # # ============================================ # Comments from T0409.t2k.pb.rdb # ============================================ # TARGET T0409 # 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 T0409.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 33.5932 # # ============================================ # Comments from T0409.t2k.bys.rdb # ============================================ # TARGET T0409 # 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 T0409.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 33.5932 # # ============================================ # Comments from T0409.t2k.alpha.rdb # ============================================ # TARGET T0409 # 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 T0409.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 33.5932 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Y 0.2095 0.1336 0.6569 2 R 0.1591 0.0654 0.7755 3 G 0.1550 0.0794 0.7657 4 P 0.0705 0.4850 0.4445 5 E 0.0887 0.5730 0.3383 6 A 0.1537 0.5571 0.2893 7 F 0.1993 0.5002 0.3005 8 L 0.2390 0.3617 0.3993 9 K 0.2465 0.1841 0.5693 10 L 0.1911 0.1091 0.6998 11 P 0.1137 0.2383 0.6479 12 K 0.0698 0.4176 0.5126 13 D 0.0963 0.4070 0.4967 14 L 0.0413 0.6494 0.3092 15 K 0.0381 0.6915 0.2704 16 D 0.0394 0.7337 0.2269 17 R 0.0107 0.8659 0.1235 18 E 0.0091 0.8925 0.0984 19 A 0.0085 0.9190 0.0725 20 L 0.0084 0.9180 0.0736 21 Q 0.0083 0.9222 0.0695 22 D 0.0083 0.9230 0.0687 23 I 0.0087 0.9121 0.0792 24 M 0.0091 0.8877 0.1032 25 Q 0.0102 0.8282 0.1616 26 D 0.0235 0.5384 0.4381 27 I 0.1010 0.2407 0.6583 28 G 0.0896 0.2177 0.6927 29 N 0.0975 0.2022 0.7002 30 S 0.0744 0.2929 0.6327 31 D 0.0678 0.3425 0.5897 32 D 0.1004 0.2768 0.6228 33 I 0.2392 0.1722 0.5886 34 L 0.3744 0.0921 0.5335 35 A 0.4584 0.1268 0.4148 36 A 0.6853 0.0420 0.2727 37 V 0.7776 0.0155 0.2069 38 V 0.7395 0.0179 0.2427 39 L 0.6970 0.0377 0.2653 40 S 0.6701 0.0352 0.2947 41 A 0.4894 0.0548 0.4559 42 T 0.2814 0.0239 0.6947 43 P 0.1145 0.2577 0.6277 44 G 0.0925 0.1802 0.7273 45 A 0.5257 0.0864 0.3879 46 V 0.7205 0.0185 0.2610 47 E 0.7865 0.0145 0.1990 48 A 0.7971 0.0098 0.1930 49 F 0.7780 0.0115 0.2106 50 R 0.6671 0.0186 0.3143 51 K 0.3429 0.1121 0.5450 52 N 0.1168 0.1077 0.7755 53 G 0.0879 0.0878 0.8243 54 E 0.4041 0.0168 0.5791 55 T 0.6993 0.0086 0.2920 56 I 0.7770 0.0086 0.2144 57 R 0.7959 0.0050 0.1991 58 I 0.7401 0.0088 0.2510 59 T 0.4617 0.0308 0.5075 60 G 0.2263 0.1845 0.5892 61 D 0.0944 0.3172 0.5883 62 G 0.1240 0.3453 0.5307 63 L 0.1155 0.5657 0.3187 64 K 0.0585 0.7656 0.1758 65 A 0.0405 0.8259 0.1336 66 A 0.0347 0.8404 0.1249 67 H 0.0278 0.8436 0.1286 68 R 0.0229 0.8219 0.1551 69 F 0.0426 0.6788 0.2786 70 L 0.0978 0.4344 0.4678 71 S 0.1084 0.2813 0.6103 72 N 0.0851 0.2646 0.6503 73 D 0.1569 0.1325 0.7106 74 P 0.0530 0.4209 0.5261 75 K 0.0875 0.3358 0.5767 76 I 0.1283 0.2016 0.6701 77 G 0.1146 0.2326 0.6528 78 E 0.1331 0.3008 0.5661 79 K 0.2330 0.2023 0.5646 80 R 0.4405 0.0825 0.4770 81 I 0.5222 0.0387 0.4392 82 R 0.3107 0.0217 0.6676 83 P 0.2114 0.1193 0.6693 84 G 0.1374 0.0712 0.7914 85 A 0.4379 0.0264 0.5357 86 L 0.7451 0.0097 0.2452 87 I 0.7991 0.0085 0.1924 88 R 0.8062 0.0055 0.1883 89 V 0.8007 0.0078 0.1915 90 K 0.7641 0.0131 0.2228 91 K 0.6708 0.0281 0.3010 92 T 0.3934 0.0551 0.5515 93 E 0.2096 0.2091 0.5812 94 K 0.1286 0.1482 0.7232 95 G 0.1846 0.0780 0.7375 96 S 0.4547 0.0346 0.5106 97 W 0.6847 0.0164 0.2989 98 Q 0.7528 0.0135 0.2337 99 I 0.7619 0.0204 0.2176 100 V 0.7349 0.0280 0.2371 101 Q 0.6559 0.0236 0.3204 102 L 0.3900 0.0185 0.5914 103 P 0.2154 0.0361 0.7485