# This file is the result of combining several RDB files, specifically # T0489.t06.str2.rdb (weight 1.54425) # T0489.t06.str4.rdb (weight 0.924988) # T0489.t06.pb.rdb (weight 0.789901) # T0489.t06.bys.rdb (weight 0.748322) # T0489.t06.alpha.rdb (weight 0.678173) # T0489.t04.str2.rdb (weight 1.54425) # T0489.t04.str4.rdb (weight 0.924988) # T0489.t04.pb.rdb (weight 0.789901) # T0489.t04.bys.rdb (weight 0.748322) # T0489.t04.alpha.rdb (weight 0.678173) # T0489.t2k.str2.rdb (weight 1.54425) # T0489.t2k.str4.rdb (weight 0.924988) # T0489.t2k.pb.rdb (weight 0.789901) # T0489.t2k.bys.rdb (weight 0.748322) # T0489.t2k.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 T0489.t06.str2.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.6898 # # ============================================ # Comments from T0489.t06.str4.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.6898 # # ============================================ # Comments from T0489.t06.pb.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.6898 # # ============================================ # Comments from T0489.t06.bys.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.6898 # # ============================================ # Comments from T0489.t06.alpha.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.6898 # # ============================================ # Comments from T0489.t04.str2.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.4163 # # ============================================ # Comments from T0489.t04.str4.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.4163 # # ============================================ # Comments from T0489.t04.pb.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.4163 # # ============================================ # Comments from T0489.t04.bys.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.4163 # # ============================================ # Comments from T0489.t04.alpha.rdb # ============================================ # TARGET T0489 # 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 T0489.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 53.4163 # # ============================================ # Comments from T0489.t2k.str2.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t2k-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 T0489.t2k-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 25.7041 # # ============================================ # Comments from T0489.t2k.str4.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t2k-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 T0489.t2k-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 25.7041 # # ============================================ # Comments from T0489.t2k.pb.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t2k-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 T0489.t2k-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 25.7041 # # ============================================ # Comments from T0489.t2k.bys.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t2k-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 T0489.t2k-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 25.7041 # # ============================================ # Comments from T0489.t2k.alpha.rdb # ============================================ # TARGET T0489 # Using neural net dunbrack-40pc-3157-t2k-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 T0489.t2k-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 25.7041 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2844 0.2655 0.4501 2 M 0.2734 0.2514 0.4752 3 F 0.2826 0.2238 0.4936 4 K 0.2817 0.1505 0.5678 5 W 0.2755 0.0875 0.6370 6 P 0.1884 0.2904 0.5212 7 W 0.2001 0.3901 0.4099 8 K 0.1945 0.3710 0.4345 9 A 0.1740 0.3810 0.4450 10 D 0.1326 0.3301 0.5373 11 D 0.1154 0.3074 0.5773 12 E 0.1481 0.2318 0.6201 13 S 0.1473 0.2013 0.6514 14 G 0.1535 0.1116 0.7348 15 N 0.1267 0.1738 0.6994 16 A 0.0412 0.5126 0.4462 17 E 0.0552 0.4945 0.4502 18 M 0.1109 0.4320 0.4571 19 P 0.0386 0.7392 0.2222 20 W 0.0173 0.8624 0.1203 21 E 0.0101 0.9078 0.0821 22 Q 0.0109 0.9014 0.0877 23 A 0.0147 0.8587 0.1267 24 L 0.0155 0.7812 0.2033 25 A 0.0364 0.6039 0.3598 26 I 0.1059 0.4310 0.4631 27 P 0.0658 0.5816 0.3526 28 V 0.0617 0.6337 0.3046 29 L 0.0537 0.7137 0.2326 30 A 0.0545 0.6175 0.3280 31 H 0.0843 0.2844 0.6313 32 L 0.1889 0.0749 0.7362 33 S 0.1555 0.0468 0.7977 34 S 0.0193 0.6218 0.3589 35 T 0.0108 0.8150 0.1743 36 E 0.0097 0.8926 0.0977 37 Q 0.0085 0.9121 0.0794 38 H 0.0084 0.9167 0.0749 39 K 0.0084 0.9177 0.0740 40 L 0.0084 0.9186 0.0730 41 T 0.0083 0.9214 0.0703 42 Q 0.0083 0.9237 0.0680 43 M 0.0083 0.9232 0.0685 44 A 0.0083 0.9220 0.0697 45 A 0.0083 0.9236 0.0681 46 R 0.0084 0.9217 0.0699 47 F 0.0098 0.9120 0.0781 48 L 0.0095 0.8957 0.0948 49 Q 0.0103 0.8528 0.1369 50 Q 0.0248 0.7565 0.2187 51 K 0.0635 0.6172 0.3193 52 R 0.1299 0.4270 0.4431 53 L 0.2557 0.2782 0.4661 54 V 0.3110 0.2053 0.4838 55 A 0.2987 0.1722 0.5291 56 L 0.2344 0.1869 0.5787 57 Q 0.1563 0.1223 0.7214 58 G 0.1339 0.0804 0.7857 59 L 0.4481 0.0330 0.5189 60 E 0.5854 0.0286 0.3860 61 L 0.4944 0.0578 0.4478 62 T 0.2171 0.0471 0.7359 63 P 0.0369 0.5861 0.3770 64 L 0.0222 0.7222 0.2556 65 H 0.0251 0.8559 0.1190 66 Q 0.0155 0.8865 0.0980 67 A 0.0134 0.9143 0.0723 68 R 0.0105 0.9211 0.0684 69 I 0.0108 0.9181 0.0712 70 A 0.0097 0.9173 0.0731 71 M 0.0107 0.9030 0.0863 72 L 0.0129 0.8774 0.1097 73 F 0.0218 0.8013 0.1769 74 C 0.0321 0.7164 0.2516 75 L 0.0777 0.6559 0.2665 76 P 0.0467 0.7491 0.2042 77 V 0.0587 0.7368 0.2045 78 L 0.0956 0.6439 0.2605 79 E 0.1048 0.4875 0.4077 80 L 0.1008 0.2843 0.6149 81 G 0.0914 0.1610 0.7476 82 I 0.1102 0.3540 0.5358 83 E 0.1237 0.4750 0.4013 84 W 0.1446 0.4747 0.3807 85 L 0.2029 0.3128 0.4843 86 D 0.1292 0.1998 0.6710 87 G 0.0811 0.1205 0.7984 88 F 0.2715 0.0754 0.6531 89 H 0.3517 0.0628 0.5854 90 E 0.7083 0.0174 0.2743 91 V 0.7663 0.0070 0.2267 92 L 0.7864 0.0058 0.2078 93 I 0.7498 0.0130 0.2372 94 Y 0.5340 0.0138 0.4522 95 P 0.2555 0.0672 0.6773 96 A 0.2254 0.0670 0.7076 97 P 0.2057 0.2152 0.5791 98 F 0.3409 0.1446 0.5145 99 I 0.4537 0.0879 0.4584 100 V 0.3932 0.0667 0.5401 101 D 0.2938 0.1134 0.5928 102 D 0.2273 0.2313 0.5414 103 E 0.2764 0.2533 0.4703 104 W 0.3630 0.2022 0.4348 105 E 0.3287 0.2235 0.4478 106 D 0.2468 0.2394 0.5138 107 D 0.1795 0.3229 0.4976 108 I 0.1738 0.1964 0.6298 109 G 0.2690 0.0932 0.6379 110 L 0.4995 0.0536 0.4469 111 V 0.5837 0.0592 0.3571 112 H 0.5037 0.0834 0.4129 113 N 0.3977 0.1586 0.4437 114 Q 0.3321 0.2242 0.4437 115 R 0.3780 0.2200 0.4020 116 V 0.4409 0.2265 0.3326 117 V 0.3906 0.2838 0.3257 118 Q 0.3988 0.2318 0.3694 119 S 0.2757 0.2196 0.5046 120 G 0.1963 0.1714 0.6323 121 Q 0.2780 0.2133 0.5087 122 S 0.2906 0.2570 0.4523 123 W 0.2234 0.2923 0.4843 124 Q 0.1991 0.2906 0.5104 125 Q 0.2200 0.1478 0.6321 126 G 0.3586 0.0542 0.5872 127 P 0.5129 0.0320 0.4551 128 V 0.7533 0.0120 0.2347 129 V 0.7613 0.0117 0.2270 130 L 0.7031 0.0208 0.2761 131 N 0.3697 0.0214 0.6088