# This file is the result of combining several RDB files, specifically # TR432.t06.str2.rdb (weight 1.54425) # TR432.t06.str4.rdb (weight 0.924988) # TR432.t06.pb.rdb (weight 0.789901) # TR432.t06.bys.rdb (weight 0.748322) # TR432.t06.alpha.rdb (weight 0.678173) # TR432.t04.str2.rdb (weight 1.54425) # TR432.t04.str4.rdb (weight 0.924988) # TR432.t04.pb.rdb (weight 0.789901) # TR432.t04.bys.rdb (weight 0.748322) # TR432.t04.alpha.rdb (weight 0.678173) # TR432.t2k.str2.rdb (weight 1.54425) # TR432.t2k.str4.rdb (weight 0.924988) # TR432.t2k.pb.rdb (weight 0.789901) # TR432.t2k.bys.rdb (weight 0.748322) # TR432.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 TR432.t06.str2.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1424 # # ============================================ # Comments from TR432.t06.str4.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1424 # # ============================================ # Comments from TR432.t06.pb.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1424 # # ============================================ # Comments from TR432.t06.bys.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1424 # # ============================================ # Comments from TR432.t06.alpha.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1424 # # ============================================ # Comments from TR432.t04.str2.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1442 # # ============================================ # Comments from TR432.t04.str4.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1442 # # ============================================ # Comments from TR432.t04.pb.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1442 # # ============================================ # Comments from TR432.t04.bys.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1442 # # ============================================ # Comments from TR432.t04.alpha.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1442 # # ============================================ # Comments from TR432.t2k.str2.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1174 # # ============================================ # Comments from TR432.t2k.str4.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1174 # # ============================================ # Comments from TR432.t2k.pb.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1174 # # ============================================ # Comments from TR432.t2k.bys.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1174 # # ============================================ # Comments from TR432.t2k.alpha.rdb # ============================================ # TARGET TR432 # 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 TR432.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 1174 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1640 0.1634 0.6726 2 M 0.1790 0.1485 0.6725 3 Q 0.2349 0.1079 0.6572 4 E 0.1810 0.3525 0.4665 5 E 0.1437 0.4465 0.4098 6 D 0.1143 0.4798 0.4058 7 T 0.0577 0.6388 0.3034 8 F 0.0368 0.7767 0.1865 9 R 0.0171 0.8712 0.1117 10 E 0.0092 0.9088 0.0820 11 L 0.0085 0.9198 0.0717 12 R 0.0083 0.9230 0.0687 13 I 0.0083 0.9224 0.0693 14 F 0.0083 0.9243 0.0674 15 L 0.0083 0.9226 0.0691 16 R 0.0083 0.9211 0.0706 17 N 0.0083 0.9225 0.0692 18 V 0.0084 0.9157 0.0759 19 T 0.0084 0.9130 0.0786 20 H 0.0086 0.9084 0.0830 21 R 0.0100 0.8832 0.1067 22 L 0.0153 0.8330 0.1517 23 A 0.0259 0.7554 0.2188 24 I 0.0586 0.5859 0.3554 25 D 0.1038 0.4264 0.4698 26 K 0.0427 0.5931 0.3642 27 R 0.0654 0.4730 0.4615 28 F 0.1612 0.3255 0.5132 29 R 0.1937 0.2536 0.5527 30 V 0.1969 0.3525 0.4505 31 F 0.2224 0.2665 0.5111 32 T 0.2447 0.1866 0.5687 33 K 0.3157 0.0714 0.6129 34 P 0.2916 0.0530 0.6554 35 V 0.3708 0.0461 0.5831 36 D 0.1961 0.0186 0.7853 37 P 0.0226 0.6252 0.3521 38 D 0.0291 0.5425 0.4284 39 E 0.0717 0.3301 0.5982 40 V 0.2031 0.1258 0.6712 41 P 0.1557 0.2550 0.5893 42 D 0.1325 0.3296 0.5379 43 Y 0.2521 0.3521 0.3958 44 V 0.3912 0.2930 0.3157 45 T 0.5048 0.2210 0.2741 46 V 0.5911 0.1486 0.2604 47 I 0.5460 0.1142 0.3398 48 K 0.4022 0.1103 0.4874 49 Q 0.3588 0.0525 0.5887 50 P 0.2318 0.1400 0.6282 51 M 0.2789 0.1412 0.5799 52 D 0.1670 0.1174 0.7156 53 L 0.0138 0.7406 0.2456 54 S 0.0107 0.8502 0.1391 55 S 0.0112 0.9065 0.0823 56 V 0.0096 0.9122 0.0782 57 I 0.0090 0.9132 0.0778 58 S 0.0105 0.9117 0.0778 59 K 0.0164 0.8745 0.1090 60 I 0.0210 0.8369 0.1421 61 D 0.0336 0.7046 0.2619 62 L 0.0456 0.4192 0.5352 63 H 0.0627 0.2380 0.6994 64 K 0.1597 0.1905 0.6499 65 Y 0.2666 0.1444 0.5891 66 L 0.2814 0.1085 0.6101 67 T 0.1977 0.0408 0.7615 68 V 0.0230 0.6943 0.2827 69 K 0.0111 0.8380 0.1509 70 D 0.0099 0.8949 0.0952 71 Y 0.0111 0.8948 0.0941 72 L 0.0090 0.8930 0.0980 73 R 0.0086 0.9018 0.0896 74 D 0.0096 0.8976 0.0928 75 I 0.0149 0.8776 0.1075 76 D 0.0098 0.9155 0.0747 77 L 0.0110 0.9136 0.0754 78 I 0.0147 0.9022 0.0831 79 C 0.0179 0.8886 0.0935 80 S 0.0177 0.8647 0.1176 81 N 0.0358 0.7728 0.1914 82 A 0.0492 0.7565 0.1943 83 L 0.0789 0.7172 0.2039 84 E 0.1312 0.5732 0.2956 85 Y 0.2136 0.3502 0.4362 86 N 0.1838 0.1262 0.6901 87 P 0.0477 0.4046 0.5477 88 D 0.0577 0.2591 0.6832 89 R 0.0645 0.1810 0.7546 90 D 0.1460 0.1181 0.7359 91 P 0.0288 0.5942 0.3770 92 G 0.0175 0.7884 0.1941 93 D 0.0110 0.8974 0.0915 94 R 0.0085 0.9173 0.0742 95 L 0.0084 0.9215 0.0701 96 I 0.0083 0.9220 0.0697 97 R 0.0083 0.9196 0.0720 98 H 0.0083 0.9213 0.0704 99 R 0.0084 0.9187 0.0729 100 A 0.0083 0.9221 0.0696 101 C 0.0083 0.9221 0.0696 102 A 0.0083 0.9209 0.0708 103 L 0.0084 0.9181 0.0735 104 R 0.0084 0.9172 0.0744 105 D 0.0085 0.9140 0.0775 106 T 0.0094 0.8995 0.0911 107 A 0.0101 0.8905 0.0994 108 Y 0.0103 0.8772 0.1126 109 A 0.0186 0.7963 0.1851 110 I 0.0708 0.6474 0.2818 111 I 0.0884 0.5114 0.4002 112 K 0.0654 0.5574 0.3772 113 E 0.0822 0.5810 0.3368 114 E 0.1003 0.5438 0.3558 115 L 0.1276 0.4539 0.4186 116 D 0.1303 0.4160 0.4537 117 E 0.0494 0.6022 0.3484 118 D 0.0848 0.5150 0.4002 119 F 0.0710 0.6563 0.2727 120 E 0.0697 0.6826 0.2477 121 Q 0.0901 0.6643 0.2457 122 L 0.0834 0.6382 0.2784 123 C 0.0907 0.5966 0.3128 124 E 0.0787 0.6113 0.3100 125 E 0.1222 0.5156 0.3622 126 I 0.1467 0.4570 0.3963 127 Q 0.1328 0.4097 0.4575 128 E 0.1272 0.3545 0.5183 129 S 0.1327 0.2557 0.6116 130 R 0.1467 0.1891 0.6641