# This file is the result of combining several RDB files, specifically # T0586.t04.str2.rdb (weight 1.54425) # T0586.t04.str4.rdb (weight 0.924988) # T0586.t04.pb.rdb (weight 0.789901) # T0586.t04.bys.rdb (weight 0.748322) # T0586.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 T0586.t04.str2.rdb # ============================================ # TARGET T0586 # 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 T0586.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 1767 # # ============================================ # Comments from T0586.t04.str4.rdb # ============================================ # TARGET T0586 # 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 T0586.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 1767 # # ============================================ # Comments from T0586.t04.pb.rdb # ============================================ # TARGET T0586 # 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 T0586.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 1767 # # ============================================ # Comments from T0586.t04.bys.rdb # ============================================ # TARGET T0586 # 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 T0586.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 1767 # # ============================================ # Comments from T0586.t04.alpha.rdb # ============================================ # TARGET T0586 # 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 T0586.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 1767 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2107 0.1526 0.6367 2 N 0.2423 0.1535 0.6042 3 A 0.3419 0.1095 0.5486 4 M 0.4195 0.0452 0.5353 5 N 0.3522 0.0200 0.6278 6 P 0.3239 0.1360 0.5401 7 T 0.2431 0.1566 0.6004 8 F 0.1540 0.3187 0.5273 9 H 0.1286 0.2092 0.6622 10 A 0.1027 0.2544 0.6429 11 D 0.0989 0.1835 0.7176 12 K 0.2152 0.1162 0.6686 13 P 0.1917 0.3268 0.4815 14 I 0.0721 0.7267 0.2012 15 Y 0.0166 0.8660 0.1174 16 S 0.0096 0.9158 0.0747 17 Q 0.0099 0.9183 0.0718 18 I 0.0085 0.9177 0.0738 19 S 0.0083 0.9197 0.0720 20 D 0.0083 0.9233 0.0685 21 W 0.0083 0.9243 0.0674 22 M 0.0083 0.9221 0.0696 23 K 0.0083 0.9207 0.0710 24 K 0.0083 0.9209 0.0707 25 Q 0.0084 0.9150 0.0766 26 M 0.0098 0.8862 0.1040 27 I 0.0138 0.7949 0.1913 28 T 0.0574 0.3327 0.6099 29 G 0.0752 0.1406 0.7842 30 E 0.2060 0.1259 0.6681 31 W 0.2797 0.0733 0.6470 32 K 0.1986 0.0506 0.7508 33 G 0.0880 0.3343 0.5777 34 E 0.0638 0.2979 0.6383 35 D 0.1236 0.2658 0.6107 36 K 0.2122 0.1472 0.6405 37 L 0.2367 0.0600 0.7033 38 P 0.1462 0.2284 0.6255 39 S 0.1292 0.3871 0.4837 40 V 0.0178 0.7604 0.2219 41 R 0.0102 0.8835 0.1063 42 E 0.0097 0.9113 0.0790 43 M 0.0098 0.9098 0.0804 44 G 0.0124 0.9045 0.0831 45 V 0.0114 0.8949 0.0937 46 K 0.0218 0.7611 0.2171 47 L 0.0795 0.4650 0.4555 48 A 0.1134 0.2489 0.6377 49 V 0.1774 0.1707 0.6519 50 N 0.1883 0.0525 0.7592 51 P 0.0133 0.7169 0.2698 52 N 0.0121 0.8361 0.1518 53 T 0.0194 0.8878 0.0928 54 V 0.0089 0.9115 0.0796 55 S 0.0085 0.9177 0.0738 56 R 0.0083 0.9235 0.0683 57 A 0.0083 0.9244 0.0673 58 Y 0.0083 0.9237 0.0680 59 Q 0.0083 0.9235 0.0682 60 E 0.0083 0.9212 0.0704 61 L 0.0084 0.9146 0.0769 62 E 0.0089 0.8922 0.0989 63 R 0.0143 0.7648 0.2209 64 A 0.0587 0.2708 0.6705 65 G 0.0820 0.0799 0.8380 66 Y 0.4376 0.0622 0.5002 67 I 0.6980 0.0304 0.2717 68 Y 0.7517 0.0305 0.2178 69 A 0.7345 0.0296 0.2359 70 K 0.6436 0.0468 0.3095 71 R 0.3860 0.0591 0.5549 72 G 0.2341 0.0558 0.7101 73 M 0.3259 0.0736 0.6004 74 G 0.4622 0.0380 0.4998 75 S 0.6779 0.0295 0.2926 76 F 0.7343 0.0191 0.2466 77 V 0.7204 0.0291 0.2505 78 T 0.5315 0.0450 0.4235 79 S 0.2622 0.1689 0.5689 80 D 0.1530 0.2142 0.6328 81 K 0.0940 0.4687 0.4373 82 A 0.0843 0.5868 0.3289 83 L 0.0647 0.6925 0.2427 84 F 0.0501 0.7604 0.1895 85 D 0.0295 0.8153 0.1552 86 Q 0.0263 0.8173 0.1564 87 L 0.0397 0.7746 0.1857 88 K 0.0395 0.7815 0.1789 89 K 0.0258 0.8340 0.1402 90 E 0.0214 0.8489 0.1297 91 L 0.0238 0.8379 0.1383 92 A 0.0144 0.8718 0.1138 93 D 0.0112 0.8971 0.0918 94 A 0.0096 0.9063 0.0841 95 I 0.0104 0.8946 0.0950 96 T 0.0099 0.8989 0.0912 97 E 0.0091 0.9098 0.0811 98 R 0.0089 0.9067 0.0843 99 F 0.0102 0.8990 0.0908 100 L 0.0092 0.8987 0.0921 101 E 0.0091 0.9042 0.0867 102 E 0.0121 0.8822 0.1057 103 A 0.0147 0.8610 0.1243 104 K 0.0171 0.8214 0.1615 105 S 0.0284 0.6847 0.2869 106 I 0.0704 0.2834 0.6462 107 G 0.0600 0.0977 0.8423 108 L 0.1750 0.0558 0.7692 109 D 0.1680 0.0263 0.8057 110 D 0.0188 0.6994 0.2819 111 Q 0.0108 0.8400 0.1492 112 T 0.0114 0.8974 0.0912 113 A 0.0098 0.9097 0.0805 114 I 0.0088 0.9166 0.0746 115 E 0.0088 0.9175 0.0737 116 L 0.0089 0.9099 0.0813 117 L 0.0115 0.8831 0.1054 118 I 0.0157 0.8317 0.1526 119 K 0.0363 0.6468 0.3169 120 R 0.0978 0.3779 0.5243 121 S 0.1137 0.2865 0.5997 122 R 0.1146 0.3145 0.5709 123 N 0.1282 0.2149 0.6569 124 H 0.1474 0.2039 0.6487 125 E 0.1552 0.2041 0.6407