# This file is the result of combining several RDB files, specifically # T0561.t2k.str2.rdb (weight 1.54425) # T0561.t2k.str4.rdb (weight 0.924988) # T0561.t2k.pb.rdb (weight 0.789901) # T0561.t2k.bys.rdb (weight 0.748322) # T0561.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 T0561.t2k.str2.rdb # ============================================ # TARGET T0561 # 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 T0561.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 2.81437 # # ============================================ # Comments from T0561.t2k.str4.rdb # ============================================ # TARGET T0561 # 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 T0561.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 2.81437 # # ============================================ # Comments from T0561.t2k.pb.rdb # ============================================ # TARGET T0561 # 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 T0561.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 2.81437 # # ============================================ # Comments from T0561.t2k.bys.rdb # ============================================ # TARGET T0561 # 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 T0561.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 2.81437 # # ============================================ # Comments from T0561.t2k.alpha.rdb # ============================================ # TARGET T0561 # 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 T0561.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 2.81437 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.3218 0.2483 0.4299 2 E 0.2376 0.3127 0.4497 3 K 0.1744 0.4803 0.3452 4 K 0.1256 0.5642 0.3102 5 K 0.1514 0.4985 0.3501 6 Y 0.1731 0.4235 0.4034 7 L 0.1825 0.4006 0.4169 8 D 0.1178 0.4637 0.4185 9 S 0.0185 0.7656 0.2159 10 E 0.0117 0.8382 0.1501 11 F 0.0134 0.8745 0.1121 12 L 0.0140 0.8834 0.1027 13 L 0.0132 0.8835 0.1033 14 H 0.0160 0.8543 0.1297 15 C 0.0347 0.7740 0.1913 16 I 0.0599 0.6799 0.2602 17 S 0.0602 0.6999 0.2399 18 A 0.0103 0.8430 0.1467 19 Q 0.0097 0.8834 0.1069 20 L 0.0100 0.9000 0.0900 21 L 0.0094 0.9131 0.0775 22 D 0.0087 0.9177 0.0736 23 M 0.0092 0.9129 0.0779 24 W 0.0092 0.9138 0.0770 25 K 0.0085 0.9117 0.0798 26 Q 0.0089 0.9043 0.0868 27 A 0.0104 0.8827 0.1069 28 R 0.0116 0.8795 0.1089 29 A 0.0137 0.8670 0.1193 30 R 0.0210 0.8521 0.1269 31 W 0.0326 0.8502 0.1172 32 L 0.0516 0.8305 0.1179 33 E 0.0550 0.8267 0.1183 34 L 0.0667 0.7519 0.1814 35 V 0.0793 0.6717 0.2490 36 G 0.0641 0.6644 0.2716 37 K 0.0281 0.7865 0.1854 38 E 0.0258 0.8185 0.1557 39 W 0.0236 0.8568 0.1196 40 A 0.0152 0.8838 0.1009 41 H 0.0196 0.8683 0.1120 42 M 0.0280 0.8346 0.1374 43 L 0.0424 0.7757 0.1819 44 A 0.0690 0.6076 0.3234 45 L 0.1447 0.3360 0.5193 46 N 0.1815 0.1069 0.7116 47 P 0.0531 0.4561 0.4909 48 E 0.0660 0.3944 0.5396 49 R 0.1715 0.3412 0.4873 50 K 0.1958 0.3155 0.4887 51 D 0.3304 0.2415 0.4281 52 F 0.4262 0.1919 0.3819 53 L 0.4811 0.1698 0.3491 54 W 0.4094 0.2050 0.3856 55 K 0.2798 0.2028 0.5174 56 N 0.2198 0.1470 0.6332 57 Q 0.1120 0.3360 0.5520 58 S 0.0999 0.3703 0.5297 59 E 0.0763 0.4886 0.4351 60 M 0.1083 0.4957 0.3960 61 N 0.1117 0.5444 0.3439 62 S 0.0633 0.7035 0.2332 63 A 0.0630 0.7299 0.2071 64 F 0.0779 0.7281 0.1940 65 F 0.0961 0.7191 0.1848 66 D 0.0581 0.7330 0.2089 67 L 0.0186 0.8242 0.1572 68 C 0.0158 0.8782 0.1060 69 E 0.0112 0.8906 0.0982 70 V 0.0100 0.8922 0.0979 71 G 0.0092 0.9091 0.0818 72 K 0.0089 0.9140 0.0770 73 Q 0.0106 0.9107 0.0787 74 V 0.0148 0.8948 0.0904 75 M 0.0293 0.8326 0.1380 76 L 0.0480 0.7225 0.2295 77 G 0.0602 0.5939 0.3460 78 L 0.0818 0.5400 0.3781 79 L 0.0994 0.2822 0.6184 80 G 0.0965 0.1596 0.7439 81 K 0.1586 0.2409 0.6006 82 E 0.2331 0.2470 0.5199 83 V 0.3041 0.1723 0.5236 84 A 0.3127 0.0994 0.5879 85 L 0.2351 0.0363 0.7286 86 P 0.1462 0.1765 0.6774 87 K 0.0590 0.5249 0.4161 88 E 0.0512 0.6401 0.3088 89 E 0.0621 0.6398 0.2982 90 Q 0.0691 0.6900 0.2410 91 A 0.0703 0.7045 0.2252 92 F 0.0807 0.7694 0.1499 93 W 0.0923 0.7842 0.1235 94 I 0.1004 0.7976 0.1019 95 M 0.0931 0.8054 0.1014 96 Y 0.0679 0.8341 0.0981 97 A 0.0472 0.8474 0.1054 98 V 0.0512 0.8149 0.1339 99 H 0.0658 0.7093 0.2249 100 L 0.0456 0.7368 0.2176 101 S 0.0277 0.7470 0.2252 102 A 0.0197 0.7754 0.2048 103 A 0.0252 0.8010 0.1738 104 C 0.0411 0.7695 0.1894 105 A 0.0180 0.8457 0.1362 106 E 0.0146 0.8531 0.1323 107 E 0.0234 0.8009 0.1756 108 L 0.0452 0.7026 0.2522 109 H 0.0712 0.5047 0.4241 110 M 0.1326 0.4457 0.4217 111 E 0.1042 0.5438 0.3520 112 V 0.1001 0.5872 0.3127 113 A 0.1367 0.5209 0.3424 114 M 0.1715 0.4551 0.3733 115 S 0.1926 0.3991 0.4082 116 L 0.1704 0.4823 0.3473 117 R 0.1842 0.4320 0.3838 118 K 0.2575 0.3199 0.4225 119 L 0.3467 0.1805 0.4729 120 N 0.3582 0.0792 0.5626 121 V 0.4497 0.0527 0.4976 122 K 0.4771 0.0453 0.4776 123 L 0.4587 0.0924 0.4489 124 K 0.3187 0.1732 0.5082 125 D 0.3423 0.1179 0.5398 126 F 0.2737 0.1717 0.5546 127 N 0.2469 0.1814 0.5717 128 F 0.1917 0.1856 0.6226 129 G 0.1493 0.1714 0.6793 130 G 0.1811 0.2116 0.6073 131 T 0.2090 0.3688 0.4221 132 R 0.2001 0.4928 0.3071 133 Y 0.2299 0.4187 0.3514 134 F 0.1659 0.4529 0.3812 135 K 0.1157 0.4339 0.4505 136 D 0.1205 0.1961 0.6834 137 M 0.2027 0.0339 0.7634 138 P 0.1540 0.0272 0.8187 139 P 0.0367 0.6525 0.3108 140 E 0.0179 0.7929 0.1892 141 E 0.0332 0.8239 0.1430 142 K 0.0316 0.8513 0.1172 143 K 0.0401 0.8307 0.1292 144 R 0.0552 0.7982 0.1466 145 R 0.0461 0.7919 0.1620 146 M 0.0355 0.8059 0.1586 147 E 0.0382 0.7974 0.1644 148 R 0.0489 0.7782 0.1729 149 K 0.0326 0.8062 0.1612 150 Q 0.0395 0.7950 0.1655 151 R 0.0405 0.7852 0.1743 152 I 0.0237 0.8514 0.1248 153 E 0.0151 0.8918 0.0931 154 E 0.0179 0.8820 0.1002 155 A 0.0221 0.8664 0.1115 156 R 0.0299 0.8170 0.1531 157 R 0.0496 0.6886 0.2617 158 H 0.0680 0.3357 0.5963 159 G 0.0843 0.1273 0.7885 160 M 0.1845 0.0448 0.7707 161 P 0.1635 0.0836 0.7529