# This file is the result of combining several RDB files, specifically # T0446.t04.str2.rdb (weight 1.54425) # T0446.t04.str4.rdb (weight 0.924988) # T0446.t04.pb.rdb (weight 0.789901) # T0446.t04.bys.rdb (weight 0.748322) # T0446.t04.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.t04.str2.rdb # ============================================ # TARGET T0446 # 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 T0446.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 27.4382 # # ============================================ # Comments from T0446.t04.str4.rdb # ============================================ # TARGET T0446 # 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 T0446.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 27.4382 # # ============================================ # Comments from T0446.t04.pb.rdb # ============================================ # TARGET T0446 # 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 T0446.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 27.4382 # # ============================================ # Comments from T0446.t04.bys.rdb # ============================================ # TARGET T0446 # 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 T0446.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 27.4382 # # ============================================ # Comments from T0446.t04.alpha.rdb # ============================================ # TARGET T0446 # 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 T0446.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 27.4382 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1534 0.3165 0.5302 2 G 0.1371 0.2807 0.5822 3 L 0.1435 0.4234 0.4330 4 L 0.1654 0.4245 0.4101 5 D 0.1257 0.4595 0.4148 6 A 0.1027 0.5384 0.3589 7 L 0.1375 0.4626 0.3999 8 M 0.1945 0.3275 0.4780 9 G 0.1891 0.2181 0.5928 10 N 0.1821 0.1649 0.6530 11 A 0.1024 0.3961 0.5015 12 A 0.1113 0.4253 0.4634 13 E 0.1383 0.4070 0.4547 14 V 0.2490 0.2333 0.5177 15 N 0.1860 0.0552 0.7588 16 L 0.0236 0.6814 0.2951 17 D 0.0131 0.8341 0.1529 18 E 0.0109 0.8968 0.0923 19 L 0.0119 0.8942 0.0939 20 A 0.0101 0.8949 0.0951 21 Q 0.0094 0.8945 0.0961 22 E 0.0141 0.8495 0.1364 23 L 0.0267 0.7628 0.2104 24 G 0.0476 0.6870 0.2654 25 P 0.0614 0.6650 0.2736 26 I 0.0788 0.5416 0.3796 27 M 0.1421 0.3367 0.5213 28 G 0.0991 0.2244 0.6766 29 D 0.0581 0.2953 0.6467 30 N 0.0489 0.2134 0.7377 31 E 0.1682 0.3483 0.4836 32 Q 0.2594 0.4722 0.2685 33 L 0.2976 0.5014 0.2011 34 A 0.2610 0.5875 0.1515 35 L 0.3207 0.5507 0.1286 36 A 0.2464 0.6281 0.1255 37 Y 0.3434 0.5159 0.1406 38 R 0.2600 0.5841 0.1560 39 V 0.2981 0.4760 0.2259 40 I 0.2572 0.4141 0.3287 41 R 0.1937 0.3382 0.4681 42 D 0.2352 0.2444 0.5203 43 M 0.4746 0.1389 0.3865 44 F 0.6630 0.0699 0.2671 45 V 0.7248 0.0552 0.2200 46 F 0.6756 0.0488 0.2756 47 T 0.5189 0.0812 0.3999 48 N 0.3583 0.1153 0.5264 49 K 0.3394 0.1834 0.4772 50 R 0.5415 0.1351 0.3234 51 L 0.6988 0.0619 0.2394 52 I 0.7394 0.0547 0.2060 53 L 0.7437 0.0466 0.2097 54 I 0.7059 0.0552 0.2389 55 D 0.4513 0.0714 0.4773 56 K 0.1716 0.3360 0.4924 57 Q 0.1289 0.2198 0.6513 58 G 0.1638 0.1482 0.6880 59 V 0.2737 0.1289 0.5974 60 T 0.2827 0.0901 0.6272 61 G 0.3098 0.0660 0.6242 62 K 0.4665 0.0556 0.4780 63 K 0.6668 0.0237 0.3095 64 V 0.7207 0.0195 0.2598 65 S 0.7112 0.0215 0.2674 66 Y 0.7235 0.0225 0.2541 67 H 0.6865 0.0279 0.2856 68 S 0.6764 0.0199 0.3037 69 V 0.6127 0.0199 0.3673 70 P 0.4553 0.0328 0.5119 71 Y 0.2883 0.2199 0.4918 72 K 0.2546 0.2945 0.4509 73 A 0.3782 0.2144 0.4075 74 I 0.4499 0.1105 0.4395 75 T 0.4727 0.1031 0.4242 76 H 0.6800 0.0487 0.2713 77 F 0.7015 0.0268 0.2717 78 E 0.7273 0.0213 0.2514 79 V 0.7140 0.0342 0.2518 80 E 0.6256 0.0679 0.3064 81 T 0.5068 0.0773 0.4159 82 A 0.3198 0.1093 0.5709 83 G 0.2968 0.0948 0.6084 84 T 0.3810 0.1153 0.5037 85 F 0.4215 0.1040 0.4746 86 D 0.3285 0.0725 0.5989 87 M 0.1647 0.3199 0.5154 88 D 0.1865 0.3042 0.5093 89 A 0.2588 0.3661 0.3750 90 E 0.4582 0.2589 0.2829 91 L 0.7083 0.0799 0.2119 92 K 0.7589 0.0454 0.1956 93 L 0.7753 0.0298 0.1948 94 W 0.7470 0.0390 0.2140 95 I 0.6809 0.0494 0.2697 96 S 0.4066 0.0815 0.5119 97 G 0.1675 0.0960 0.7365 98 Q 0.2256 0.1008 0.6736 99 K 0.2468 0.1158 0.6373 100 D 0.3015 0.0508 0.6477 101 P 0.3171 0.1962 0.4866 102 L 0.4187 0.2025 0.3788 103 V 0.5103 0.1964 0.2933 104 K 0.5771 0.1686 0.2543 105 E 0.5206 0.1739 0.3055 106 L 0.3776 0.2016 0.4208 107 K 0.2041 0.2405 0.5554 108 K 0.1087 0.2143 0.6770 109 G 0.0774 0.1561 0.7664 110 T 0.1682 0.1994 0.6324 111 D 0.1932 0.3074 0.4994 112 V 0.0575 0.6684 0.2741 113 V 0.0257 0.8139 0.1604 114 G 0.0256 0.8653 0.1090 115 I 0.0099 0.9095 0.0806 116 Q 0.0084 0.9195 0.0721 117 K 0.0083 0.9230 0.0687 118 T 0.0083 0.9217 0.0700 119 I 0.0084 0.9115 0.0801 120 A 0.0086 0.8981 0.0933 121 N 0.0118 0.8431 0.1451 122 F 0.0427 0.7207 0.2366 123 S 0.1038 0.4892 0.4070 124 L 0.1076 0.3764 0.5160