# This file is the result of combining several RDB files, specifically # T0471.t06.str2.rdb (weight 1.54425) # T0471.t06.str4.rdb (weight 0.924988) # T0471.t06.pb.rdb (weight 0.789901) # T0471.t06.bys.rdb (weight 0.748322) # T0471.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 T0471.t06.str2.rdb # ============================================ # TARGET T0471 # 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 T0471.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 15.2811 # # ============================================ # Comments from T0471.t06.str4.rdb # ============================================ # TARGET T0471 # 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 T0471.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 15.2811 # # ============================================ # Comments from T0471.t06.pb.rdb # ============================================ # TARGET T0471 # 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 T0471.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 15.2811 # # ============================================ # Comments from T0471.t06.bys.rdb # ============================================ # TARGET T0471 # 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 T0471.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 15.2811 # # ============================================ # Comments from T0471.t06.alpha.rdb # ============================================ # TARGET T0471 # 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 T0471.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 15.2811 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1527 0.3958 0.4515 2 W 0.1013 0.5747 0.3239 3 N 0.0580 0.6941 0.2479 4 D 0.0426 0.7414 0.2160 5 L 0.0194 0.8424 0.1382 6 A 0.0134 0.8899 0.0967 7 V 0.0146 0.9079 0.0775 8 Y 0.0210 0.8988 0.0802 9 I 0.0361 0.8715 0.0925 10 I 0.0703 0.7860 0.1438 11 R 0.1217 0.5700 0.3083 12 C 0.1390 0.3347 0.5263 13 S 0.1601 0.1508 0.6891 14 G 0.1657 0.0835 0.7507 15 P 0.1026 0.1719 0.7254 16 G 0.0562 0.1133 0.8305 17 T 0.2504 0.0380 0.7116 18 R 0.5664 0.0202 0.4133 19 V 0.7414 0.0080 0.2505 20 V 0.7809 0.0090 0.2102 21 E 0.7741 0.0072 0.2187 22 V 0.7365 0.0152 0.2483 23 G 0.5424 0.0297 0.4279 24 A 0.3492 0.1147 0.5361 25 G 0.2634 0.1453 0.5913 26 R 0.2040 0.2852 0.5109 27 F 0.1415 0.4577 0.4008 28 L 0.0431 0.7344 0.2225 29 Y 0.0349 0.7922 0.1730 30 V 0.0149 0.8813 0.1039 31 S 0.0096 0.9064 0.0840 32 D 0.0089 0.9096 0.0815 33 Y 0.0092 0.9008 0.0900 34 I 0.0149 0.8699 0.1153 35 R 0.0125 0.7982 0.1893 36 K 0.0218 0.6982 0.2800 37 H 0.0744 0.3670 0.5587 38 S 0.0586 0.2784 0.6630 39 K 0.0636 0.1082 0.8282 40 V 0.3217 0.0173 0.6610 41 D 0.5607 0.0183 0.4209 42 L 0.8083 0.0049 0.1868 43 V 0.7831 0.0083 0.2085 44 L 0.7955 0.0070 0.1974 45 T 0.7649 0.0160 0.2191 46 D 0.6659 0.0201 0.3141 47 I 0.4222 0.0582 0.5196 48 K 0.2811 0.0375 0.6814 49 P 0.2153 0.1553 0.6294 50 S 0.1323 0.1995 0.6682 51 H 0.1342 0.1662 0.6996 52 G 0.1631 0.1185 0.7184 53 G 0.2454 0.0972 0.6574 54 I 0.5130 0.0592 0.4278 55 V 0.6114 0.0625 0.3262 56 R 0.5554 0.0957 0.3489 57 D 0.4118 0.1344 0.4538 58 D 0.2979 0.1859 0.5162 59 I 0.2330 0.2641 0.5028 60 T 0.2156 0.1821 0.6023 61 S 0.2280 0.0864 0.6856 62 P 0.1441 0.2397 0.6162 63 R 0.1583 0.2167 0.6250 64 M 0.3262 0.2013 0.4724 65 E 0.4643 0.1984 0.3373 66 I 0.5200 0.1974 0.2826 67 Y 0.4230 0.2140 0.3630 68 R 0.2454 0.2418 0.5128 69 G 0.1716 0.1526 0.6758 70 A 0.3489 0.0525 0.5986 71 A 0.4811 0.0651 0.4538 72 L 0.7750 0.0270 0.1980 73 I 0.7326 0.0343 0.2331 74 Y 0.7576 0.0401 0.2023 75 S 0.7320 0.0345 0.2336 76 I 0.5804 0.0491 0.3704 77 R 0.3905 0.0230 0.5866 78 P 0.1986 0.0216 0.7798 79 P 0.1114 0.2224 0.6661 80 A 0.0228 0.6150 0.3622 81 E 0.0285 0.6936 0.2779 82 I 0.0417 0.7188 0.2395 83 H 0.0281 0.7963 0.1756 84 S 0.0118 0.8748 0.1134 85 S 0.0094 0.8994 0.0912 86 L 0.0085 0.9178 0.0737 87 M 0.0084 0.9195 0.0721 88 R 0.0086 0.9182 0.0732 89 V 0.0089 0.9085 0.0826 90 A 0.0100 0.8848 0.1051 91 D 0.0110 0.8321 0.1569 92 A 0.0228 0.7035 0.2737 93 V 0.0854 0.2311 0.6835 94 G 0.0839 0.0885 0.8276 95 A 0.3416 0.0255 0.6328 96 R 0.5486 0.0282 0.4232 97 L 0.8003 0.0071 0.1926 98 I 0.7703 0.0086 0.2210 99 I 0.7681 0.0077 0.2242 100 K 0.6689 0.0145 0.3165 101 P 0.3890 0.0294 0.5816 102 L 0.2190 0.1281 0.6529 103 T 0.1393 0.1128 0.7480 104 G 0.0925 0.1014 0.8061 105 E 0.2053 0.1362 0.6585 106 D 0.3166 0.1450 0.5384 107 I 0.3897 0.1596 0.4506 108 V 0.4119 0.1436 0.4444 109 T 0.3586 0.1193 0.5221 110 E 0.2135 0.2276 0.5589 111 R 0.2252 0.1929 0.5819 112 K 0.3119 0.1159 0.5722 113 M 0.4996 0.0393 0.4610 114 K 0.6640 0.0263 0.3097 115 L 0.6994 0.0176 0.2830 116 V 0.6908 0.0304 0.2788 117 N 0.5940 0.0379 0.3681 118 Y 0.3192 0.1049 0.5760 119 G 0.1878 0.0815 0.7307 120 R 0.3680 0.0725 0.5595 121 T 0.6089 0.0442 0.3470 122 Y 0.7181 0.0403 0.2416 123 F 0.7628 0.0305 0.2067 124 Y 0.7707 0.0353 0.1940 125 E 0.7201 0.0653 0.2146 126 Y 0.6583 0.1026 0.2391 127 I 0.5237 0.1999 0.2764 128 A 0.3251 0.3894 0.2855 129 E 0.2549 0.4348 0.3103 130 V 0.2701 0.3609 0.3690 131 R 0.2490 0.2871 0.4639 132 S 0.2071 0.2356 0.5573 133 R 0.1765 0.2058 0.6177