# This file is the result of combining several RDB files, specifically # T0476.t06.str2.rdb (weight 1.54425) # T0476.t06.str4.rdb (weight 0.924988) # T0476.t06.pb.rdb (weight 0.789901) # T0476.t06.bys.rdb (weight 0.748322) # T0476.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 T0476.t06.str2.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t06.str4.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t06.pb.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t06.bys.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t06.alpha.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2223 0.2155 0.5622 2 A 0.2379 0.1945 0.5676 3 K 0.2558 0.1287 0.6155 4 C 0.2755 0.0410 0.6835 5 P 0.2146 0.1545 0.6309 6 I 0.2540 0.2058 0.5403 7 C 0.1922 0.1353 0.6725 8 G 0.1259 0.0915 0.7826 9 S 0.2074 0.0660 0.7266 10 P 0.2068 0.1771 0.6161 11 L 0.2327 0.2100 0.5573 12 K 0.1843 0.1643 0.6513 13 W 0.0209 0.7392 0.2399 14 E 0.0092 0.8685 0.1223 15 E 0.0084 0.9192 0.0724 16 L 0.0085 0.9189 0.0726 17 I 0.0084 0.9175 0.0741 18 E 0.0083 0.9194 0.0723 19 E 0.0085 0.9147 0.0768 20 M 0.0106 0.8966 0.0929 21 L 0.0164 0.8576 0.1260 22 I 0.0378 0.7655 0.1967 23 I 0.0437 0.7377 0.2186 24 E 0.0481 0.5885 0.3633 25 N 0.0630 0.4892 0.4478 26 F 0.0285 0.7527 0.2189 27 E 0.0133 0.8566 0.1301 28 E 0.0183 0.8677 0.1140 29 I 0.0325 0.8255 0.1420 30 V 0.0513 0.7869 0.1618 31 K 0.0442 0.7519 0.2039 32 D 0.0679 0.6815 0.2506 33 R 0.0118 0.8467 0.1415 34 E 0.0096 0.8940 0.0964 35 R 0.0100 0.9066 0.0833 36 F 0.0125 0.8970 0.0905 37 L 0.0113 0.8946 0.0942 38 A 0.0104 0.8662 0.1234 39 Q 0.0167 0.8164 0.1669 40 V 0.0422 0.7475 0.2103 41 E 0.0403 0.7211 0.2386 42 E 0.1012 0.5559 0.3429 43 F 0.2536 0.3643 0.3821 44 V 0.4045 0.2357 0.3598 45 F 0.4919 0.1274 0.3808 46 K 0.4072 0.0868 0.5060 47 C 0.2823 0.0373 0.6804 48 P 0.1683 0.1754 0.6563 49 V 0.1900 0.1991 0.6109 50 C 0.1623 0.1690 0.6686 51 G 0.1251 0.2124 0.6625 52 E 0.2088 0.3574 0.4338 53 E 0.2904 0.3929 0.3167 54 F 0.3111 0.3147 0.3741 55 Y 0.2561 0.2147 0.5292 56 G 0.1669 0.1976 0.6355 57 K 0.2475 0.2333 0.5192 58 T 0.2584 0.1700 0.5716 59 L 0.2535 0.0690 0.6775 60 P 0.1720 0.0895 0.7385 61 R 0.0533 0.5818 0.3649 62 R 0.0296 0.7389 0.2315 63 E 0.0288 0.7856 0.1856 64 A 0.0176 0.8663 0.1161 65 E 0.0112 0.8997 0.0891 66 K 0.0114 0.9063 0.0823 67 V 0.0134 0.9058 0.0809 68 F 0.0147 0.9053 0.0801 69 E 0.0202 0.8949 0.0850 70 L 0.0273 0.8627 0.1100 71 L 0.0463 0.7563 0.1974 72 N 0.0611 0.5780 0.3610 73 D 0.0787 0.4308 0.4905 74 F 0.1085 0.2959 0.5956 75 K 0.1259 0.2129 0.6612 76 G 0.1510 0.1241 0.7249 77 G 0.2842 0.0909 0.6249 78 I 0.4370 0.0605 0.5025 79 D 0.3267 0.0466 0.6267 80 W 0.1346 0.3751 0.4902 81 E 0.0894 0.3573 0.5533 82 N 0.1542 0.1898 0.6560 83 K 0.3082 0.1264 0.5654 84 R 0.5099 0.0625 0.4276 85 V 0.6657 0.0382 0.2961 86 K 0.6834 0.0475 0.2691 87 L 0.6997 0.0596 0.2407 88 K 0.5616 0.1255 0.3129 89 L 0.2456 0.4400 0.3144 90 N 0.0780 0.6547 0.2674 91 D 0.0391 0.8012 0.1596 92 L 0.0207 0.8778 0.1014 93 L 0.0125 0.9015 0.0860 94 A 0.0136 0.9051 0.0812 95 L 0.0095 0.9138 0.0767 96 E 0.0086 0.9122 0.0793 97 T 0.0088 0.9042 0.0870 98 M 0.0114 0.8909 0.0978 99 L 0.0102 0.9010 0.0888 100 E 0.0091 0.8973 0.0936 101 E 0.0105 0.8745 0.1150 102 W 0.0179 0.8250 0.1570 103 D 0.0233 0.7761 0.2007 104 R 0.0271 0.7554 0.2175 105 R 0.0529 0.6496 0.2975 106 V 0.1432 0.4361 0.4208 107 K 0.1547 0.3468 0.4985 108 R 0.1718 0.2374 0.5907