# This file is the result of combining several RDB files, specifically # T0476.t04.str2.rdb (weight 1.54425) # T0476.t04.str4.rdb (weight 0.924988) # T0476.t04.pb.rdb (weight 0.789901) # T0476.t04.bys.rdb (weight 0.748322) # T0476.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 T0476.t04.str2.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t04.str4.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t04.pb.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t04.bys.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ # Comments from T0476.t04.alpha.rdb # ============================================ # TARGET T0476 # 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 T0476.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 2.33036 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2210 0.1955 0.5835 2 A 0.2633 0.1703 0.5664 3 K 0.2780 0.1260 0.5960 4 C 0.3118 0.0499 0.6382 5 P 0.2557 0.1490 0.5953 6 I 0.2847 0.1913 0.5240 7 C 0.1946 0.1367 0.6687 8 G 0.1275 0.1003 0.7722 9 S 0.1886 0.0592 0.7522 10 P 0.1847 0.1977 0.6176 11 L 0.2204 0.2422 0.5374 12 K 0.1624 0.1623 0.6753 13 W 0.0161 0.7468 0.2371 14 E 0.0092 0.8664 0.1244 15 E 0.0083 0.9199 0.0717 16 L 0.0083 0.9209 0.0708 17 I 0.0084 0.9163 0.0753 18 E 0.0083 0.9161 0.0756 19 E 0.0085 0.9114 0.0801 20 M 0.0103 0.8960 0.0937 21 L 0.0125 0.8666 0.1209 22 I 0.0244 0.8183 0.1573 23 I 0.0352 0.7772 0.1876 24 E 0.0507 0.6657 0.2836 25 N 0.0674 0.5473 0.3854 26 F 0.0215 0.7370 0.2415 27 E 0.0159 0.8315 0.1526 28 E 0.0176 0.8667 0.1157 29 I 0.0296 0.8134 0.1569 30 V 0.0387 0.7560 0.2053 31 K 0.0431 0.6966 0.2602 32 D 0.0831 0.5165 0.4004 33 R 0.0125 0.8257 0.1618 34 E 0.0094 0.8908 0.0998 35 R 0.0091 0.9090 0.0818 36 F 0.0102 0.8937 0.0961 37 L 0.0090 0.8955 0.0954 38 A 0.0097 0.8899 0.1004 39 Q 0.0164 0.8398 0.1438 40 V 0.0230 0.8174 0.1595 41 E 0.0239 0.7723 0.2038 42 E 0.0682 0.6618 0.2700 43 F 0.2262 0.3919 0.3819 44 V 0.3858 0.2275 0.3867 45 F 0.4731 0.1311 0.3959 46 K 0.3776 0.1041 0.5183 47 C 0.2564 0.0426 0.7011 48 P 0.1590 0.2024 0.6386 49 V 0.1694 0.2276 0.6030 50 C 0.1561 0.1878 0.6561 51 G 0.1275 0.2598 0.6127 52 E 0.2040 0.3892 0.4068 53 E 0.2873 0.3836 0.3292 54 F 0.2775 0.3417 0.3809 55 Y 0.1936 0.2998 0.5066 56 G 0.1552 0.2453 0.5994 57 K 0.2230 0.2320 0.5450 58 T 0.2638 0.1280 0.6082 59 L 0.2532 0.0440 0.7028 60 P 0.1659 0.0570 0.7771 61 R 0.0709 0.5023 0.4268 62 R 0.0279 0.7083 0.2638 63 E 0.0228 0.7919 0.1853 64 A 0.0193 0.8571 0.1236 65 E 0.0122 0.8983 0.0895 66 K 0.0168 0.8967 0.0864 67 V 0.0231 0.8910 0.0859 68 F 0.0178 0.9023 0.0799 69 E 0.0208 0.8951 0.0841 70 L 0.0284 0.8622 0.1094 71 L 0.0522 0.7283 0.2196 72 N 0.0526 0.5879 0.3595 73 D 0.0738 0.4146 0.5116 74 F 0.1073 0.3042 0.5885 75 K 0.1220 0.2142 0.6638 76 G 0.1540 0.1523 0.6937 77 G 0.2525 0.1126 0.6349 78 I 0.4059 0.0855 0.5086 79 D 0.3095 0.0536 0.6369 80 W 0.1538 0.3894 0.4569 81 E 0.1083 0.4327 0.4590 82 N 0.1567 0.2420 0.6013 83 K 0.2738 0.1632 0.5630 84 R 0.4996 0.0876 0.4128 85 V 0.6780 0.0355 0.2866 86 K 0.6969 0.0462 0.2569 87 L 0.7175 0.0583 0.2242 88 K 0.5577 0.1122 0.3302 89 L 0.2526 0.4106 0.3369 90 N 0.0705 0.6629 0.2665 91 D 0.0302 0.7792 0.1907 92 L 0.0178 0.8773 0.1048 93 L 0.0161 0.8938 0.0901 94 A 0.0182 0.8905 0.0913 95 L 0.0102 0.8986 0.0912 96 E 0.0090 0.9039 0.0872 97 T 0.0091 0.8929 0.0980 98 M 0.0116 0.8635 0.1249 99 L 0.0122 0.8261 0.1617 100 E 0.0105 0.8571 0.1324 101 E 0.0163 0.8117 0.1720 102 W 0.0327 0.7361 0.2312 103 D 0.0421 0.6823 0.2756 104 R 0.0309 0.7456 0.2235 105 R 0.0832 0.5775 0.3393 106 V 0.1600 0.4341 0.4059 107 K 0.1378 0.3369 0.5253 108 R 0.1554 0.2476 0.5970