# This file is the result of combining several RDB files, specifically # T0495.t06.str2.rdb (weight 1.54425) # T0495.t06.str4.rdb (weight 0.924988) # T0495.t06.pb.rdb (weight 0.789901) # T0495.t06.bys.rdb (weight 0.748322) # T0495.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 T0495.t06.str2.rdb # ============================================ # TARGET T0495 # 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 T0495.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 133 # # ============================================ # Comments from T0495.t06.str4.rdb # ============================================ # TARGET T0495 # 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 T0495.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 133 # # ============================================ # Comments from T0495.t06.pb.rdb # ============================================ # TARGET T0495 # 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 T0495.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 133 # # ============================================ # Comments from T0495.t06.bys.rdb # ============================================ # TARGET T0495 # 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 T0495.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 133 # # ============================================ # Comments from T0495.t06.alpha.rdb # ============================================ # TARGET T0495 # 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 T0495.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 133 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2409 0.0673 0.6918 2 P 0.1818 0.1759 0.6423 3 M 0.1532 0.2699 0.5769 4 T 0.1692 0.3266 0.5042 5 L 0.1596 0.3490 0.4914 6 D 0.1722 0.2872 0.5405 7 L 0.1651 0.2754 0.5595 8 Q 0.1624 0.1915 0.6461 9 P 0.0617 0.5993 0.3390 10 G 0.0169 0.8216 0.1615 11 Q 0.0107 0.8966 0.0926 12 R 0.0096 0.9161 0.0743 13 L 0.0090 0.9174 0.0736 14 A 0.0086 0.9115 0.0798 15 R 0.0090 0.8965 0.0945 16 G 0.0094 0.8880 0.1026 17 V 0.0093 0.9006 0.0901 18 A 0.0085 0.9109 0.0806 19 R 0.0086 0.9127 0.0787 20 H 0.0095 0.9013 0.0892 21 L 0.0125 0.8597 0.1278 22 R 0.0193 0.7999 0.1808 23 A 0.0281 0.6209 0.3510 24 H 0.0696 0.2156 0.7148 25 G 0.0597 0.0856 0.8547 26 F 0.3141 0.0301 0.6559 27 V 0.5697 0.0193 0.4110 28 S 0.6454 0.0175 0.3371 29 V 0.6059 0.0413 0.3528 30 E 0.5115 0.1084 0.3801 31 E 0.5579 0.0856 0.3566 32 F 0.5344 0.0596 0.4060 33 V 0.4502 0.0325 0.5173 34 P 0.2850 0.0747 0.6403 35 A 0.1181 0.2529 0.6291 36 R 0.0852 0.1840 0.7308 37 G 0.0984 0.0954 0.8061 38 L 0.2551 0.0642 0.6807 39 R 0.4641 0.0437 0.4922 40 V 0.5172 0.0235 0.4593 41 D 0.5664 0.0254 0.4082 42 V 0.7913 0.0122 0.1965 43 M 0.7332 0.0174 0.2494 44 G 0.7672 0.0125 0.2203 45 L 0.7106 0.0164 0.2730 46 G 0.3481 0.0177 0.6342 47 P 0.1246 0.2524 0.6231 48 K 0.0811 0.1649 0.7540 49 G 0.1012 0.0674 0.8313 50 E 0.4502 0.0235 0.5263 51 I 0.7292 0.0073 0.2635 52 W 0.7909 0.0088 0.2003 53 V 0.8212 0.0047 0.1741 54 I 0.8148 0.0054 0.1799 55 E 0.7988 0.0057 0.1955 56 C 0.7454 0.0086 0.2460 57 K 0.6500 0.0241 0.3259 58 S 0.4821 0.0365 0.4814 59 S 0.2665 0.0351 0.6984 60 R 0.0523 0.5812 0.3665 61 A 0.0453 0.6624 0.2923 62 D 0.0575 0.6873 0.2552 63 F 0.0488 0.7017 0.2495 64 Q 0.0399 0.7424 0.2177 65 A 0.0444 0.7212 0.2344 66 D 0.0562 0.6602 0.2836 67 A 0.0264 0.7136 0.2600 68 K 0.0403 0.6769 0.2828 69 W 0.0622 0.6875 0.2503 70 Q 0.0384 0.7185 0.2431 71 G 0.0371 0.6555 0.3074 72 Y 0.0619 0.6747 0.2634 73 L 0.0650 0.7176 0.2174 74 E 0.0728 0.6190 0.3082 75 W 0.1017 0.4440 0.4543 76 C 0.1644 0.2950 0.5406 77 D 0.2303 0.2184 0.5514 78 R 0.4931 0.1129 0.3939 79 Y 0.6811 0.0369 0.2820 80 F 0.7538 0.0206 0.2256 81 W 0.7713 0.0162 0.2125 82 A 0.7114 0.0204 0.2682 83 V 0.5480 0.0250 0.4270 84 D 0.2462 0.0513 0.7025 85 M 0.0703 0.3241 0.6057 86 E 0.1247 0.2217 0.6536 87 F 0.2520 0.0372 0.7109 88 P 0.1906 0.0354 0.7740 89 A 0.0501 0.5882 0.3618 90 E 0.0433 0.6373 0.3193 91 L 0.1141 0.4376 0.4483 92 L 0.2447 0.0603 0.6951 93 P 0.1822 0.0925 0.7253 94 A 0.0646 0.4523 0.4831 95 E 0.1039 0.3366 0.5595 96 S 0.3171 0.1228 0.5602 97 G 0.5614 0.0421 0.3966 98 L 0.7767 0.0087 0.2146 99 L 0.7911 0.0078 0.2010 100 I 0.7794 0.0091 0.2115 101 A 0.7056 0.0185 0.2759 102 D 0.4439 0.0196 0.5365 103 A 0.1348 0.3066 0.5586 104 Y 0.0971 0.2638 0.6392 105 D 0.1575 0.1853 0.6572 106 A 0.3498 0.2057 0.4445 107 E 0.5024 0.1992 0.2985 108 I 0.6151 0.1341 0.2508 109 V 0.5488 0.1672 0.2840 110 R 0.4884 0.1665 0.3451 111 M 0.3599 0.1594 0.4807 112 A 0.2419 0.0844 0.6737 113 P 0.1335 0.2840 0.5825 114 E 0.1044 0.3916 0.5040 115 Q 0.1446 0.3357 0.5197 116 K 0.1350 0.2735 0.5916 117 L 0.1828 0.2134 0.6038 118 A 0.1671 0.1805 0.6524 119 P 0.0907 0.4546 0.4546 120 A 0.0550 0.6145 0.3305 121 R 0.0477 0.6917 0.2607 122 R 0.0246 0.8177 0.1577 123 K 0.0115 0.8884 0.1001 124 V 0.0098 0.9121 0.0780 125 L 0.0094 0.9184 0.0722 126 I 0.0087 0.9191 0.0722 127 Q 0.0084 0.9194 0.0722 128 K 0.0084 0.9172 0.0743 129 F 0.0085 0.9138 0.0777 130 A 0.0085 0.9112 0.0803 131 T 0.0084 0.9155 0.0760 132 H 0.0085 0.9157 0.0758 133 A 0.0085 0.9151 0.0765 134 A 0.0085 0.9116 0.0799 135 R 0.0085 0.9122 0.0793 136 R 0.0086 0.9124 0.0790 137 L 0.0109 0.8864 0.1027 138 Q 0.0133 0.8410 0.1457 139 A 0.0216 0.7544 0.2240 140 L 0.0522 0.5889 0.3589 141 R 0.1087 0.3430 0.5483 142 D 0.1619 0.1178 0.7203 143 P 0.0289 0.5319 0.4391 144 E 0.0433 0.4169 0.5399 145 G 0.0794 0.3498 0.5708 146 H 0.1730 0.2833 0.5437 147 G 0.2181 0.2646 0.5174 148 I 0.2727 0.2088 0.5185 149 F 0.2639 0.1615 0.5746 150 E 0.2023 0.1823 0.6154