# This file is the result of combining several RDB files, specifically # T0615.t2k.str2.rdb (weight 1.54425) # T0615.t2k.str4.rdb (weight 0.924988) # T0615.t2k.pb.rdb (weight 0.789901) # T0615.t2k.bys.rdb (weight 0.748322) # T0615.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 T0615.t2k.str2.rdb # ============================================ # TARGET T0615 # 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 T0615.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 84.893 # # ============================================ # Comments from T0615.t2k.str4.rdb # ============================================ # TARGET T0615 # 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 T0615.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 84.893 # # ============================================ # Comments from T0615.t2k.pb.rdb # ============================================ # TARGET T0615 # 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 T0615.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 84.893 # # ============================================ # Comments from T0615.t2k.bys.rdb # ============================================ # TARGET T0615 # 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 T0615.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 84.893 # # ============================================ # Comments from T0615.t2k.alpha.rdb # ============================================ # TARGET T0615 # 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 T0615.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 84.893 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2409 0.0593 0.6997 2 A 0.1834 0.1017 0.7149 3 T 0.1638 0.1529 0.6833 4 Y 0.2283 0.0739 0.6977 5 P 0.1435 0.1304 0.7261 6 S 0.0173 0.7204 0.2623 7 A 0.0100 0.8522 0.1379 8 K 0.0093 0.9037 0.0870 9 F 0.0084 0.9178 0.0738 10 M 0.0083 0.9218 0.0699 11 E 0.0083 0.9242 0.0676 12 C 0.0083 0.9236 0.0681 13 L 0.0083 0.9237 0.0681 14 Q 0.0083 0.9239 0.0678 15 Y 0.0083 0.9224 0.0693 16 A 0.0084 0.9172 0.0744 17 A 0.0085 0.9111 0.0804 18 F 0.0095 0.8829 0.1076 19 K 0.0158 0.7972 0.1870 20 H 0.0439 0.6226 0.3335 21 R 0.0485 0.5299 0.4217 22 Q 0.0478 0.4212 0.5310 23 Q 0.1642 0.3500 0.4858 24 R 0.3202 0.2057 0.4740 25 R 0.3301 0.1344 0.5355 26 K 0.2270 0.1761 0.5969 27 D 0.1912 0.0640 0.7448 28 P 0.0643 0.3338 0.6019 29 Q 0.0890 0.2041 0.7069 30 E 0.0976 0.1193 0.7831 31 T 0.2626 0.0359 0.7014 32 P 0.3489 0.0684 0.5827 33 Y 0.4164 0.1179 0.4657 34 V 0.3751 0.2411 0.3838 35 N 0.2700 0.3585 0.3714 36 H 0.1885 0.4856 0.3259 37 V 0.0245 0.8092 0.1663 38 I 0.0125 0.8717 0.1158 39 N 0.0090 0.9178 0.0732 40 V 0.0085 0.9193 0.0722 41 S 0.0083 0.9216 0.0701 42 T 0.0083 0.9230 0.0687 43 I 0.0083 0.9209 0.0707 44 L 0.0087 0.9115 0.0798 45 S 0.0103 0.8867 0.1030 46 V 0.0146 0.8286 0.1568 47 E 0.0281 0.6797 0.2922 48 A 0.0605 0.4759 0.4636 49 C 0.0974 0.3516 0.5509 50 I 0.1325 0.3192 0.5483 51 T 0.1361 0.2285 0.6354 52 D 0.1277 0.1698 0.7024 53 E 0.0181 0.5366 0.4454 54 G 0.0186 0.6590 0.3224 55 V 0.0526 0.8048 0.1427 56 L 0.0554 0.8562 0.0885 57 M 0.0402 0.8849 0.0750 58 A 0.0287 0.8938 0.0776 59 A 0.0326 0.8720 0.0954 60 L 0.0488 0.8150 0.1362 61 L 0.0553 0.7073 0.2374 62 H 0.0517 0.6580 0.2903 63 D 0.0600 0.6342 0.3058 64 V 0.1005 0.5547 0.3448 65 V 0.1574 0.4662 0.3765 66 E 0.1435 0.4092 0.4473 67 D 0.1392 0.2299 0.6309 68 T 0.1246 0.2101 0.6653 69 D 0.1100 0.2151 0.6749 70 A 0.1649 0.1506 0.6845 71 S 0.1638 0.0612 0.7750 72 F 0.0129 0.7508 0.2363 73 E 0.0098 0.8634 0.1268 74 D 0.0087 0.9154 0.0759 75 V 0.0088 0.9113 0.0799 76 E 0.0086 0.9093 0.0821 77 K 0.0090 0.8934 0.0976 78 L 0.0192 0.7701 0.2106 79 F 0.0602 0.4838 0.4560 80 G 0.0551 0.4418 0.5031 81 P 0.0177 0.7279 0.2544 82 D 0.0192 0.7858 0.1950 83 V 0.0220 0.8608 0.1172 84 C 0.0158 0.8876 0.0966 85 G 0.0187 0.8876 0.0937 86 L 0.0242 0.8729 0.1029 87 V 0.0366 0.8363 0.1271 88 R 0.0364 0.8073 0.1563 89 E 0.0601 0.6635 0.2765 90 V 0.1159 0.5266 0.3575 91 T 0.1665 0.3124 0.5211 92 D 0.0835 0.3989 0.5176 93 D 0.0665 0.4006 0.5329 94 K 0.0615 0.4218 0.5167 95 S 0.0932 0.3219 0.5849 96 L 0.0888 0.4479 0.4633 97 E 0.0551 0.5894 0.3554 98 K 0.0283 0.7759 0.1958 99 Q 0.0161 0.8698 0.1141 100 E 0.0106 0.9044 0.0850 101 R 0.0092 0.9128 0.0780 102 K 0.0091 0.9059 0.0850 103 R 0.0091 0.9104 0.0804 104 L 0.0087 0.9158 0.0755 105 Q 0.0090 0.9143 0.0767 106 I 0.0090 0.9144 0.0766 107 E 0.0090 0.9114 0.0796 108 N 0.0136 0.8860 0.1004 109 A 0.0207 0.8349 0.1445 110 A 0.0343 0.7247 0.2409 111 K 0.0561 0.5956 0.3483 112 S 0.0828 0.4261 0.4911 113 S 0.1307 0.2527 0.6167 114 C 0.1618 0.2692 0.5690 115 R 0.2948 0.2039 0.5013 116 A 0.5361 0.1474 0.3165 117 K 0.6813 0.1079 0.2109 118 L 0.6977 0.0945 0.2078 119 I 0.6943 0.1089 0.1968 120 K 0.5058 0.2341 0.2601 121 L 0.2266 0.4134 0.3600 122 A 0.0820 0.5567 0.3613 123 D 0.0429 0.5819 0.3751 124 K 0.0541 0.5584 0.3875 125 L 0.0621 0.5678 0.3700 126 D 0.0703 0.5162 0.4135 127 N 0.1093 0.3464 0.5443 128 L 0.1348 0.3770 0.4882 129 R 0.1826 0.3925 0.4249 130 D 0.2283 0.3558 0.4160 131 L 0.2081 0.4177 0.3742 132 Q 0.2322 0.3628 0.4049 133 V 0.2582 0.2453 0.4966 134 N 0.2427 0.1081 0.6492 135 T 0.1748 0.0491 0.7760 136 P 0.0623 0.3572 0.5805 137 T 0.0434 0.5121 0.4445 138 G 0.0389 0.5548 0.4064 139 W 0.0582 0.6959 0.2459 140 T 0.0579 0.7639 0.1782 141 Q 0.0300 0.8551 0.1149 142 E 0.0167 0.8886 0.0948 143 R 0.0159 0.8866 0.0975 144 R 0.0146 0.8892 0.0962 145 D 0.0114 0.8951 0.0935 146 Q 0.0132 0.8840 0.1028 147 Y 0.0176 0.8756 0.1069 148 F 0.0166 0.8877 0.0957 149 V 0.0116 0.9066 0.0818 150 W 0.0114 0.9018 0.0868 151 A 0.0135 0.8893 0.0972 152 K 0.0149 0.8890 0.0961 153 K 0.0108 0.9020 0.0873 154 V 0.0124 0.8823 0.1053 155 V 0.0139 0.8671 0.1189 156 D 0.0157 0.8088 0.1756 157 N 0.0330 0.6560 0.3110 158 L 0.0682 0.4446 0.4872 159 R 0.0733 0.2750 0.6517 160 G 0.1112 0.3478 0.5410 161 T 0.1266 0.4685 0.4049 162 N 0.1476 0.4953 0.3571 163 A 0.1385 0.6079 0.2536 164 N 0.1012 0.6959 0.2028 165 L 0.0841 0.7563 0.1596 166 E 0.0762 0.7706 0.1532 167 L 0.0692 0.7775 0.1533 168 K 0.0473 0.8005 0.1523 169 L 0.0304 0.8251 0.1445 170 D 0.0180 0.8412 0.1408 171 E 0.0238 0.8353 0.1409 172 I 0.0379 0.8289 0.1332 173 F 0.0445 0.8052 0.1503 174 R 0.0618 0.6864 0.2518 175 Q 0.0924 0.4807 0.4269 176 R 0.1309 0.2094 0.6596 177 G 0.0995 0.3261 0.5744 178 L 0.1149 0.2778 0.6073 179 L 0.1705 0.2291 0.6003