# This file is the result of combining several RDB files, specifically # T0475.t06.str2.rdb (weight 1.54425) # T0475.t06.str4.rdb (weight 0.924988) # T0475.t06.pb.rdb (weight 0.789901) # T0475.t06.bys.rdb (weight 0.748322) # T0475.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 T0475.t06.str2.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1478 # # ============================================ # Comments from T0475.t06.str4.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1478 # # ============================================ # Comments from T0475.t06.pb.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1478 # # ============================================ # Comments from T0475.t06.bys.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1478 # # ============================================ # Comments from T0475.t06.alpha.rdb # ============================================ # TARGET T0475 # 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 T0475.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 1478 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.1954 0.1032 0.7014 2 N 0.1661 0.0893 0.7446 3 S 0.0575 0.4601 0.4824 4 E 0.0558 0.5660 0.3782 5 I 0.0423 0.6916 0.2660 6 E 0.0223 0.8127 0.1650 7 L 0.0255 0.8589 0.1156 8 P 0.0126 0.9057 0.0817 9 V 0.0088 0.9152 0.0760 10 Q 0.0083 0.9226 0.0691 11 K 0.0083 0.9217 0.0699 12 Q 0.0084 0.9202 0.0714 13 L 0.0085 0.9143 0.0773 14 E 0.0086 0.9011 0.0903 15 A 0.0097 0.8554 0.1349 16 Y 0.0237 0.7431 0.2332 17 N 0.0404 0.5277 0.4319 18 A 0.0382 0.4801 0.4817 19 R 0.0546 0.3861 0.5593 20 D 0.1011 0.3175 0.5814 21 I 0.0132 0.7843 0.2025 22 D 0.0093 0.8736 0.1171 23 A 0.0085 0.9181 0.0735 24 F 0.0086 0.9194 0.0720 25 M 0.0086 0.9053 0.0861 26 A 0.0112 0.8541 0.1346 27 W 0.0263 0.7168 0.2569 28 W 0.0719 0.4234 0.5047 29 A 0.1257 0.2566 0.6177 30 D 0.0640 0.3618 0.5741 31 D 0.1173 0.1966 0.6860 32 C 0.4348 0.0837 0.4815 33 Q 0.6424 0.0432 0.3145 34 Y 0.6888 0.0314 0.2798 35 Y 0.5872 0.0413 0.3715 36 A 0.3953 0.0476 0.5571 37 F 0.2729 0.0498 0.6773 38 P 0.1592 0.1795 0.6613 39 A 0.1661 0.1881 0.6458 40 T 0.2126 0.1669 0.6204 41 L 0.2797 0.1991 0.5212 42 L 0.3029 0.1845 0.5126 43 A 0.2241 0.2032 0.5727 44 G 0.1730 0.1408 0.6862 45 N 0.1728 0.1179 0.7093 46 A 0.0137 0.7497 0.2366 47 A 0.0092 0.8666 0.1241 48 E 0.0084 0.9211 0.0705 49 I 0.0083 0.9223 0.0694 50 R 0.0083 0.9208 0.0708 51 V 0.0083 0.9214 0.0703 52 R 0.0087 0.9148 0.0764 53 H 0.0095 0.9083 0.0823 54 I 0.0091 0.8994 0.0915 55 E 0.0119 0.8449 0.1432 56 R 0.0254 0.6673 0.3072 57 F 0.0620 0.4306 0.5074 58 K 0.0989 0.2780 0.6231 59 E 0.1783 0.0846 0.7371 60 P 0.1276 0.2205 0.6519 61 D 0.1610 0.1445 0.6945 62 L 0.3327 0.1140 0.5533 63 Y 0.5074 0.0691 0.4235 64 G 0.6337 0.0334 0.3329 65 E 0.6782 0.0277 0.2941 66 L 0.6590 0.0344 0.3066 67 L 0.5848 0.0657 0.3494 68 T 0.7119 0.0333 0.2548 69 R 0.6939 0.0363 0.2698 70 V 0.7137 0.0354 0.2510 71 I 0.6496 0.0390 0.3114 72 V 0.3812 0.0737 0.5451 73 G 0.1654 0.0629 0.7717 74 N 0.3129 0.0560 0.6311 75 V 0.6297 0.0334 0.3369 76 V 0.7321 0.0233 0.2446 77 I 0.7775 0.0145 0.2080 78 D 0.7573 0.0205 0.2222 79 H 0.7325 0.0322 0.2352 80 E 0.7209 0.0344 0.2447 81 T 0.7526 0.0221 0.2253 82 V 0.7121 0.0299 0.2580 83 T 0.6746 0.0349 0.2905 84 R 0.6568 0.0363 0.3068 85 N 0.5834 0.0449 0.3717 86 F 0.3664 0.0313 0.6023 87 P 0.1425 0.2368 0.6206 88 E 0.0901 0.1558 0.7541 89 G 0.0761 0.0938 0.8301 90 K 0.2384 0.0619 0.6997 91 G 0.3872 0.0643 0.5485 92 E 0.4741 0.0553 0.4706 93 V 0.6138 0.0246 0.3616 94 D 0.6428 0.0306 0.3266 95 V 0.7851 0.0119 0.2030 96 A 0.7836 0.0099 0.2066 97 C 0.8102 0.0069 0.1829 98 I 0.8205 0.0051 0.1744 99 Y 0.8138 0.0058 0.1804 100 E 0.8094 0.0058 0.1849 101 V 0.7148 0.0163 0.2688 102 E 0.4688 0.1232 0.4080 103 N 0.1844 0.0740 0.7416 104 G 0.1063 0.0732 0.8205 105 R 0.4789 0.0267 0.4944 106 I 0.6546 0.0217 0.3237 107 A 0.6185 0.0582 0.3233 108 K 0.7757 0.0255 0.1988 109 A 0.7309 0.0545 0.2146 110 W 0.7257 0.0701 0.2042 111 F 0.6468 0.1125 0.2408 112 K 0.4889 0.1692 0.3419 113 I 0.3376 0.1229 0.5395 114 G 0.1710 0.0908 0.7383 115 E 0.1868 0.1303 0.6830 116 P 0.1414 0.3656 0.4930 117 R 0.1501 0.4604 0.3895 118 I 0.1577 0.4929 0.3494 119 V 0.1801 0.4697 0.3501 120 S 0.1619 0.4057 0.4324 121 Q 0.1748 0.2867 0.5385 122 K 0.1533 0.1920 0.6547