# This file is the result of combining several RDB files, specifically # T0391.t04.str2.rdb (weight 1.54425) # T0391.t04.str4.rdb (weight 0.924988) # T0391.t04.pb.rdb (weight 0.789901) # T0391.t04.bys.rdb (weight 0.748322) # T0391.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 T0391.t04.str2.rdb # ============================================ # TARGET T0391 # 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 T0391.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 1888 # # ============================================ # Comments from T0391.t04.str4.rdb # ============================================ # TARGET T0391 # 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 T0391.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 1888 # # ============================================ # Comments from T0391.t04.pb.rdb # ============================================ # TARGET T0391 # 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 T0391.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 1888 # # ============================================ # Comments from T0391.t04.bys.rdb # ============================================ # TARGET T0391 # 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 T0391.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 1888 # # ============================================ # Comments from T0391.t04.alpha.rdb # ============================================ # TARGET T0391 # 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 T0391.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 1888 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1895 0.0954 0.7151 2 D 0.1936 0.0666 0.7398 3 P 0.0243 0.6539 0.3218 4 E 0.0276 0.7564 0.2160 5 I 0.0410 0.7501 0.2089 6 S 0.0536 0.7100 0.2364 7 E 0.0526 0.6965 0.2509 8 Q 0.0766 0.6745 0.2488 9 D 0.0821 0.6834 0.2346 10 E 0.0295 0.7851 0.1854 11 E 0.0355 0.7524 0.2121 12 K 0.0769 0.6296 0.2935 13 K 0.1367 0.4442 0.4191 14 K 0.1610 0.2882 0.5508 15 Y 0.1912 0.1909 0.6179 16 T 0.2600 0.1058 0.6341 17 S 0.4243 0.0544 0.5214 18 V 0.6209 0.0279 0.3512 19 C 0.6723 0.0184 0.3094 20 V 0.6185 0.0310 0.3506 21 G 0.4315 0.0278 0.5407 22 R 0.2703 0.0509 0.6787 23 E 0.0776 0.5653 0.3571 24 E 0.0427 0.6522 0.3051 25 D 0.0659 0.5741 0.3599 26 I 0.1767 0.3674 0.4559 27 R 0.1584 0.2357 0.6059 28 K 0.0840 0.3013 0.6147 29 S 0.1003 0.1510 0.7487 30 E 0.2461 0.0744 0.6795 31 R 0.4362 0.0410 0.5229 32 M 0.6424 0.0239 0.3337 33 T 0.7441 0.0108 0.2450 34 A 0.7856 0.0086 0.2057 35 V 0.7720 0.0069 0.2211 36 V 0.6938 0.0213 0.2848 37 H 0.3650 0.0474 0.5876 38 D 0.1936 0.0421 0.7644 39 R 0.4842 0.0139 0.5019 40 E 0.6988 0.0121 0.2891 41 V 0.8220 0.0048 0.1732 42 V 0.8248 0.0044 0.1708 43 I 0.8254 0.0041 0.1704 44 F 0.8167 0.0049 0.1784 45 Y 0.7244 0.0120 0.2636 46 H 0.5141 0.0403 0.4457 47 K 0.1994 0.0786 0.7219 48 G 0.1112 0.0804 0.8084 49 E 0.4791 0.0263 0.4946 50 Y 0.7075 0.0166 0.2759 51 H 0.7579 0.0211 0.2209 52 A 0.7774 0.0157 0.2070 53 M 0.7140 0.0539 0.2321 54 D 0.5482 0.1415 0.3103 55 I 0.3486 0.1925 0.4588 56 R 0.2768 0.1916 0.5316 57 C 0.2545 0.1705 0.5750 58 Y 0.1434 0.3298 0.5268 59 H 0.1360 0.2920 0.5721 60 S 0.1141 0.2021 0.6838 61 G 0.1277 0.0987 0.7736 62 G 0.2517 0.0431 0.7052 63 P 0.3322 0.0907 0.5771 64 L 0.3848 0.1595 0.4557 65 H 0.3686 0.1435 0.4879 66 L 0.3005 0.1430 0.5564 67 G 0.3033 0.0939 0.6029 68 E 0.4836 0.0828 0.4337 69 I 0.5598 0.0982 0.3420 70 E 0.4640 0.1595 0.3766 71 D 0.3769 0.1803 0.4428 72 F 0.2141 0.1971 0.5887 73 N 0.0963 0.1181 0.7857 74 G 0.0819 0.0906 0.8275 75 Q 0.2754 0.0323 0.6923 76 S 0.4355 0.0445 0.5200 77 C 0.6571 0.0277 0.3152 78 I 0.7206 0.0153 0.2641 79 V 0.6950 0.0172 0.2877 80 C 0.4167 0.0198 0.5635 81 P 0.2178 0.2378 0.5444 82 W 0.1928 0.2030 0.6042 83 H 0.2301 0.1365 0.6335 84 K 0.3257 0.1154 0.5589 85 Y 0.6132 0.0593 0.3275 86 K 0.7231 0.0259 0.2510 87 I 0.7615 0.0145 0.2240 88 T 0.6215 0.0184 0.3601 89 L 0.4247 0.2121 0.3632 90 A 0.2313 0.2666 0.5021 91 T 0.1280 0.1543 0.7176 92 G 0.1455 0.0952 0.7593 93 E 0.3580 0.0849 0.5571 94 G 0.4780 0.0912 0.4308 95 L 0.4973 0.1063 0.3964 96 Y 0.4921 0.0940 0.4139 97 Q 0.4854 0.0629 0.4518 98 S 0.3655 0.0933 0.5412 99 I 0.2637 0.1392 0.5971 100 N 0.2239 0.0625 0.7136 101 P 0.0926 0.3265 0.5809 102 K 0.0962 0.2537 0.6501 103 D 0.1858 0.1196 0.6947 104 P 0.0868 0.3333 0.5799 105 S 0.0963 0.2849 0.6189 106 A 0.1470 0.2083 0.6447 107 K 0.1792 0.1330 0.6878 108 P 0.1122 0.3420 0.5458 109 K 0.1316 0.3052 0.5631 110 W 0.2049 0.2158 0.5793 111 C 0.1964 0.1558 0.6478 112 S 0.1310 0.3515 0.5175 113 K 0.0712 0.3449 0.5839 114 G 0.0682 0.1852 0.7466 115 V 0.2432 0.0811 0.6757 116 K 0.3729 0.0502 0.5769 117 Q 0.4928 0.0267 0.4806 118 R 0.5731 0.0219 0.4049 119 I 0.6594 0.0165 0.3241 120 H 0.6792 0.0152 0.3056 121 T 0.7015 0.0126 0.2859 122 V 0.7513 0.0111 0.2376 123 K 0.7381 0.0136 0.2483 124 V 0.6992 0.0196 0.2812 125 D 0.5169 0.0662 0.4169 126 N 0.2247 0.0447 0.7306 127 G 0.2668 0.0386 0.6946 128 N 0.6624 0.0083 0.3292 129 I 0.7674 0.0063 0.2264 130 Y 0.8149 0.0047 0.1804 131 V 0.8187 0.0048 0.1766 132 T 0.7614 0.0061 0.2325 133 L 0.6460 0.0308 0.3233 134 S 0.3221 0.0394 0.6385 135 K 0.1512 0.2174 0.6314 136 E 0.1795 0.1342 0.6863 137 P 0.1663 0.2626 0.5712 138 F 0.1956 0.1681 0.6364 139 K 0.1959 0.1723 0.6318 140 C 0.1982 0.1457 0.6561 141 D 0.1848 0.1704 0.6448 142 S 0.1627 0.2603 0.5770 143 D 0.1536 0.3077 0.5387 144 Y 0.1521 0.4019 0.4459 145 Y 0.1822 0.3328 0.4850 146 A 0.1911 0.2589 0.5499 147 T 0.1685 0.1894 0.6421 148 G 0.1069 0.2206 0.6725 149 E 0.1652 0.2398 0.5950 150 F 0.2359 0.2509 0.5133 151 K 0.2822 0.2763 0.4415 152 V 0.4252 0.2162 0.3585 153 I 0.4486 0.1649 0.3866 154 Q 0.4581 0.1252 0.4167 155 S 0.3295 0.1212 0.5493 156 S 0.2190 0.1852 0.5958 157 S 0.1958 0.1579 0.6463