# This file is the result of combining several RDB files, specifically # T0446.t06.str2.rdb (weight 1.54425) # T0446.t06.str4.rdb (weight 0.924988) # T0446.t06.pb.rdb (weight 0.789901) # T0446.t06.bys.rdb (weight 0.748322) # T0446.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 T0446.t06.str2.rdb # ============================================ # TARGET T0446 # 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 T0446.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 26.7682 # # ============================================ # Comments from T0446.t06.str4.rdb # ============================================ # TARGET T0446 # 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 T0446.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 26.7682 # # ============================================ # Comments from T0446.t06.pb.rdb # ============================================ # TARGET T0446 # 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 T0446.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 26.7682 # # ============================================ # Comments from T0446.t06.bys.rdb # ============================================ # TARGET T0446 # 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 T0446.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 26.7682 # # ============================================ # Comments from T0446.t06.alpha.rdb # ============================================ # TARGET T0446 # 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 T0446.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 26.7682 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1713 0.2743 0.5544 2 G 0.1415 0.3016 0.5569 3 L 0.1299 0.4805 0.3896 4 L 0.1136 0.5279 0.3585 5 D 0.0937 0.5586 0.3477 6 A 0.0669 0.6409 0.2922 7 L 0.0796 0.5763 0.3441 8 M 0.1200 0.4336 0.4463 9 G 0.1262 0.2991 0.5747 10 N 0.1436 0.2167 0.6396 11 A 0.1640 0.2224 0.6136 12 A 0.1735 0.2307 0.5957 13 E 0.2214 0.2226 0.5560 14 V 0.2681 0.1174 0.6145 15 N 0.1861 0.0444 0.7695 16 L 0.0173 0.7183 0.2645 17 D 0.0116 0.8425 0.1459 18 E 0.0124 0.8955 0.0921 19 L 0.0157 0.8915 0.0928 20 A 0.0108 0.8954 0.0938 21 Q 0.0097 0.8869 0.1033 22 E 0.0149 0.8148 0.1702 23 L 0.0459 0.6528 0.3013 24 G 0.0459 0.5362 0.4179 25 P 0.0739 0.4913 0.4348 26 I 0.1143 0.4308 0.4549 27 M 0.1966 0.2396 0.5638 28 G 0.1530 0.1498 0.6973 29 D 0.0889 0.2229 0.6882 30 N 0.0588 0.1911 0.7501 31 E 0.1988 0.2518 0.5494 32 Q 0.3392 0.3621 0.2988 33 L 0.2397 0.5779 0.1824 34 A 0.2108 0.6464 0.1428 35 L 0.2587 0.6176 0.1236 36 A 0.2255 0.6526 0.1219 37 Y 0.2601 0.5970 0.1428 38 R 0.2049 0.6234 0.1718 39 V 0.2503 0.4864 0.2633 40 I 0.2352 0.3772 0.3876 41 R 0.1791 0.3546 0.4663 42 D 0.2184 0.2228 0.5588 43 M 0.4893 0.1241 0.3866 44 F 0.6933 0.0442 0.2625 45 V 0.7477 0.0306 0.2217 46 F 0.6966 0.0304 0.2729 47 T 0.5185 0.0700 0.4115 48 N 0.3703 0.0756 0.5540 49 K 0.3635 0.1577 0.4787 50 R 0.6030 0.0981 0.2989 51 L 0.7143 0.0612 0.2245 52 I 0.7170 0.0743 0.2087 53 L 0.7478 0.0469 0.2053 54 I 0.7282 0.0495 0.2223 55 D 0.5135 0.0674 0.4191 56 K 0.2174 0.3369 0.4457 57 Q 0.1449 0.3194 0.5357 58 G 0.1525 0.2134 0.6340 59 V 0.2887 0.1332 0.5781 60 T 0.2921 0.1049 0.6030 61 G 0.2684 0.0623 0.6693 62 K 0.4341 0.0475 0.5184 63 K 0.6117 0.0315 0.3568 64 V 0.6595 0.0225 0.3180 65 S 0.6931 0.0247 0.2823 66 Y 0.7046 0.0261 0.2692 67 H 0.6782 0.0339 0.2879 68 S 0.6529 0.0261 0.3210 69 V 0.5238 0.0252 0.4510 70 P 0.3337 0.0493 0.6171 71 Y 0.2148 0.2779 0.5073 72 K 0.1955 0.3224 0.4821 73 A 0.3140 0.2005 0.4855 74 I 0.4609 0.0932 0.4459 75 T 0.4661 0.1026 0.4312 76 H 0.6746 0.0396 0.2858 77 F 0.6818 0.0260 0.2922 78 E 0.7354 0.0197 0.2449 79 V 0.6920 0.0333 0.2746 80 E 0.5921 0.0777 0.3302 81 T 0.5255 0.0778 0.3967 82 A 0.3775 0.1069 0.5156 83 G 0.3751 0.0895 0.5354 84 T 0.4673 0.0870 0.4457 85 F 0.4895 0.0770 0.4335 86 D 0.3698 0.0500 0.5802 87 M 0.1495 0.3527 0.4978 88 D 0.2112 0.2401 0.5487 89 A 0.3782 0.1939 0.4279 90 E 0.6279 0.0717 0.3004 91 L 0.7679 0.0192 0.2130 92 K 0.8122 0.0082 0.1796 93 L 0.8232 0.0057 0.1712 94 W 0.7907 0.0103 0.1990 95 I 0.7251 0.0256 0.2493 96 S 0.4368 0.0646 0.4986 97 G 0.1864 0.0953 0.7183 98 Q 0.2383 0.1241 0.6376 99 K 0.2584 0.1153 0.6263 100 D 0.2681 0.0825 0.6493 101 P 0.3105 0.1952 0.4942 102 L 0.3592 0.2940 0.3468 103 V 0.4145 0.3030 0.2824 104 K 0.4620 0.2702 0.2678 105 E 0.3882 0.2948 0.3170 106 L 0.3115 0.2422 0.4463 107 K 0.2066 0.2375 0.5558 108 K 0.1102 0.1859 0.7038 109 G 0.0727 0.1383 0.7891 110 T 0.1735 0.1399 0.6866 111 D 0.1947 0.2040 0.6013 112 V 0.0828 0.6701 0.2471 113 V 0.0220 0.8378 0.1402 114 G 0.0125 0.9062 0.0812 115 I 0.0087 0.9190 0.0723 116 Q 0.0083 0.9213 0.0704 117 K 0.0083 0.9224 0.0693 118 T 0.0084 0.9220 0.0696 119 I 0.0084 0.9192 0.0724 120 A 0.0087 0.8944 0.0969 121 N 0.0126 0.8188 0.1686 122 F 0.0370 0.6961 0.2669 123 S 0.0837 0.5006 0.4157 124 L 0.1128 0.3186 0.5686