# This file is the result of combining several RDB files, specifically # T0419.t06.str2.rdb (weight 1.54425) # T0419.t06.str4.rdb (weight 0.924988) # T0419.t06.pb.rdb (weight 0.789901) # T0419.t06.bys.rdb (weight 0.748322) # T0419.t06.alpha.rdb (weight 0.678173) # T0419.t04.str2.rdb (weight 1.54425) # T0419.t04.str4.rdb (weight 0.924988) # T0419.t04.pb.rdb (weight 0.789901) # T0419.t04.bys.rdb (weight 0.748322) # T0419.t04.alpha.rdb (weight 0.678173) # T0419.t2k.str2.rdb (weight 1.54425) # T0419.t2k.str4.rdb (weight 0.924988) # T0419.t2k.pb.rdb (weight 0.789901) # T0419.t2k.bys.rdb (weight 0.748322) # T0419.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 T0419.t06.str2.rdb # ============================================ # TARGET T0419 # 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 T0419.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 1703 # # ============================================ # Comments from T0419.t06.str4.rdb # ============================================ # TARGET T0419 # 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 T0419.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 1703 # # ============================================ # Comments from T0419.t06.pb.rdb # ============================================ # TARGET T0419 # 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 T0419.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 1703 # # ============================================ # Comments from T0419.t06.bys.rdb # ============================================ # TARGET T0419 # 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 T0419.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 1703 # # ============================================ # Comments from T0419.t06.alpha.rdb # ============================================ # TARGET T0419 # 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 T0419.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 1703 # # ============================================ # Comments from T0419.t04.str2.rdb # ============================================ # TARGET T0419 # 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 T0419.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 2152 # # ============================================ # Comments from T0419.t04.str4.rdb # ============================================ # TARGET T0419 # 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 T0419.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 2152 # # ============================================ # Comments from T0419.t04.pb.rdb # ============================================ # TARGET T0419 # 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 T0419.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 2152 # # ============================================ # Comments from T0419.t04.bys.rdb # ============================================ # TARGET T0419 # 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 T0419.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 2152 # # ============================================ # Comments from T0419.t04.alpha.rdb # ============================================ # TARGET T0419 # 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 T0419.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 2152 # # ============================================ # Comments from T0419.t2k.str2.rdb # ============================================ # TARGET T0419 # 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 T0419.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 27.2135 # # ============================================ # Comments from T0419.t2k.str4.rdb # ============================================ # TARGET T0419 # 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 T0419.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 27.2135 # # ============================================ # Comments from T0419.t2k.pb.rdb # ============================================ # TARGET T0419 # 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 T0419.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 27.2135 # # ============================================ # Comments from T0419.t2k.bys.rdb # ============================================ # TARGET T0419 # 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 T0419.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 27.2135 # # ============================================ # Comments from T0419.t2k.alpha.rdb # ============================================ # TARGET T0419 # 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 T0419.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 27.2135 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 K 0.1866 0.4016 0.4118 2 R 0.1258 0.5034 0.3709 3 F 0.1443 0.3913 0.4644 4 R 0.1309 0.2501 0.6190 5 Q 0.1360 0.1137 0.7503 6 H 0.3292 0.0219 0.6489 7 S 0.5302 0.0139 0.4559 8 L 0.8037 0.0051 0.1912 9 V 0.8209 0.0042 0.1749 10 A 0.8122 0.0044 0.1834 11 V 0.8111 0.0056 0.1832 12 F 0.7675 0.0086 0.2240 13 E 0.5854 0.0281 0.3866 14 G 0.3473 0.0654 0.5873 15 N 0.2602 0.2170 0.5229 16 D 0.1844 0.3034 0.5122 17 A 0.1493 0.3690 0.4816 18 A 0.1313 0.2823 0.5864 19 G 0.1313 0.1560 0.7126 20 K 0.1144 0.2397 0.6458 21 G 0.0760 0.2453 0.6786 22 G 0.0781 0.4757 0.4462 23 A 0.1130 0.6617 0.2253 24 I 0.0487 0.8252 0.1261 25 R 0.0350 0.8696 0.0955 26 R 0.0372 0.8665 0.0963 27 V 0.0384 0.8424 0.1192 28 T 0.0480 0.7694 0.1826 29 D 0.0295 0.6804 0.2901 30 A 0.0488 0.4551 0.4961 31 L 0.1638 0.2060 0.6302 32 D 0.1858 0.0921 0.7221 33 P 0.0513 0.4073 0.5413 34 R 0.0666 0.3492 0.5842 35 Q 0.2242 0.2327 0.5431 36 Y 0.5150 0.0626 0.4224 37 H 0.6535 0.0303 0.3162 38 I 0.6857 0.0272 0.2871 39 V 0.5991 0.0229 0.3780 40 P 0.4511 0.0712 0.4777 41 I 0.2989 0.1260 0.5751 42 A 0.2285 0.1233 0.6481 43 A 0.2455 0.0368 0.7177 44 P 0.1834 0.0643 0.7523 45 T 0.1764 0.0599 0.7637 46 E 0.0374 0.6259 0.3367 47 E 0.0255 0.7400 0.2344 48 E 0.0394 0.7574 0.2032 49 R 0.0440 0.7174 0.2387 50 A 0.0555 0.5549 0.3896 51 Q 0.1018 0.4896 0.4086 52 P 0.0328 0.7368 0.2303 53 Y 0.0277 0.7931 0.1792 54 L 0.0259 0.8571 0.1169 55 W 0.0264 0.8756 0.0981 56 R 0.0332 0.8650 0.1018 57 F 0.0456 0.8273 0.1271 58 W 0.0574 0.7615 0.1811 59 R 0.0729 0.6213 0.3058 60 H 0.1225 0.3322 0.5453 61 I 0.2339 0.0973 0.6688 62 P 0.1769 0.1040 0.7192 63 A 0.0883 0.3466 0.5651 64 R 0.1076 0.2345 0.6579 65 R 0.1711 0.1189 0.7099 66 Q 0.5320 0.0230 0.4449 67 F 0.7319 0.0092 0.2589 68 T 0.7979 0.0071 0.1949 69 I 0.7926 0.0095 0.1979 70 F 0.7034 0.0219 0.2747 71 D 0.4908 0.0429 0.4663 72 R 0.3106 0.1883 0.5011 73 S 0.2426 0.2509 0.5065 74 W 0.1630 0.4015 0.4356 75 Y 0.1710 0.3601 0.4690 76 G 0.1769 0.3441 0.4791 77 R 0.2602 0.3103 0.4296 78 V 0.4225 0.1980 0.3795 79 L 0.5317 0.1590 0.3093 80 V 0.5890 0.1609 0.2501 81 E 0.5767 0.1713 0.2520 82 R 0.5643 0.1717 0.2640 83 I 0.4488 0.2082 0.3429 84 E 0.2608 0.2142 0.5251 85 G 0.1381 0.1807 0.6813 86 F 0.1849 0.1508 0.6643 87 C 0.2356 0.0775 0.6869 88 A 0.1623 0.0300 0.8077 89 P 0.0219 0.6798 0.2983 90 A 0.0111 0.8409 0.1479 91 D 0.0119 0.8923 0.0958 92 W 0.0117 0.9056 0.0828 93 L 0.0089 0.9154 0.0757 94 R 0.0085 0.9140 0.0775 95 A 0.0113 0.8837 0.1051 96 Y 0.0163 0.8373 0.1463 97 G 0.0133 0.8149 0.1719 98 E 0.0216 0.7132 0.2652 99 I 0.0275 0.7641 0.2084 100 N 0.0137 0.8502 0.1360 101 D 0.0111 0.8886 0.1004 102 F 0.0107 0.9039 0.0855 103 E 0.0085 0.9173 0.0742 104 E 0.0084 0.9187 0.0729 105 Q 0.0109 0.8959 0.0932 106 L 0.0174 0.8437 0.1389 107 S 0.0227 0.7628 0.2145 108 E 0.0306 0.6251 0.3443 109 Y 0.0622 0.1816 0.7562 110 G 0.0805 0.0823 0.8371 111 I 0.4029 0.0353 0.5619 112 I 0.6971 0.0247 0.2782 113 V 0.7809 0.0165 0.2026 114 V 0.7815 0.0197 0.1988 115 K 0.7746 0.0180 0.2075 116 F 0.7817 0.0208 0.1975 117 W 0.7371 0.0318 0.2311 118 L 0.7027 0.0424 0.2550 119 A 0.5520 0.0555 0.3925 120 I 0.3734 0.0858 0.5408 121 D 0.1690 0.0262 0.8048 122 K 0.0140 0.7282 0.2578 123 Q 0.0096 0.8470 0.1434 124 T 0.0090 0.9121 0.0789 125 Q 0.0091 0.9191 0.0718 126 M 0.0085 0.9193 0.0722 127 E 0.0083 0.9216 0.0701 128 R 0.0086 0.9150 0.0764 129 F 0.0096 0.9007 0.0898 130 K 0.0090 0.9067 0.0843 131 E 0.0119 0.8700 0.1181 132 R 0.0313 0.7732 0.1955 133 E 0.0465 0.6909 0.2626 134 K 0.0835 0.3892 0.5273 135 T 0.1452 0.1475 0.7073 136 P 0.0664 0.3527 0.5809 137 Y 0.0892 0.3878 0.5229 138 K 0.1710 0.3534 0.4756 139 R 0.2744 0.2315 0.4940 140 Y 0.4449 0.1055 0.4496 141 K 0.4606 0.0641 0.4752 142 I 0.3796 0.0415 0.5789 143 T 0.1892 0.0182 0.7926 144 E 0.0314 0.6409 0.3277 145 E 0.0245 0.7509 0.2247 146 D 0.0526 0.7415 0.2059 147 W 0.0183 0.8394 0.1423 148 R 0.0147 0.8307 0.1547 149 N 0.0186 0.7852 0.1962 150 R 0.0216 0.7918 0.1866 151 D 0.0198 0.8043 0.1759 152 K 0.0240 0.7767 0.1993 153 W 0.0206 0.8636 0.1158 154 D 0.0093 0.9109 0.0799 155 Q 0.0087 0.9152 0.0761 156 Y 0.0091 0.9161 0.0748 157 V 0.0084 0.9188 0.0728 158 D 0.0084 0.9203 0.0713 159 A 0.0086 0.9160 0.0754 160 V 0.0086 0.9110 0.0805 161 G 0.0086 0.9092 0.0822 162 D 0.0088 0.9011 0.0902 163 M 0.0125 0.8659 0.1216 164 V 0.0165 0.8483 0.1352 165 D 0.0281 0.7475 0.2244 166 R 0.0602 0.5262 0.4136 167 T 0.1247 0.2868 0.5884 168 S 0.1224 0.2266 0.6510 169 T 0.1212 0.2598 0.6190 170 E 0.0825 0.3878 0.5296 171 I 0.1584 0.2124 0.6292 172 A 0.2954 0.0541 0.6505 173 P 0.3202 0.0668 0.6130 174 W 0.5497 0.0459 0.4043 175 T 0.7323 0.0175 0.2502 176 L 0.7464 0.0101 0.2436 177 V 0.6939 0.0171 0.2890 178 E 0.5981 0.0295 0.3724 179 A 0.3123 0.1455 0.5422 180 N 0.1674 0.1722 0.6604 181 D 0.1471 0.1964 0.6565 182 K 0.0703 0.5532 0.3765 183 R 0.0763 0.6559 0.2677 184 F 0.0800 0.7052 0.2148 185 A 0.0573 0.7968 0.1459 186 R 0.0351 0.8593 0.1056 187 V 0.0218 0.8935 0.0848 188 K 0.0106 0.9172 0.0722 189 V 0.0085 0.9204 0.0711 190 L 0.0083 0.9220 0.0697 191 R 0.0083 0.9225 0.0692 192 T 0.0083 0.9235 0.0682 193 I 0.0084 0.9186 0.0730 194 N 0.0084 0.9174 0.0742 195 D 0.0084 0.9165 0.0751 196 A 0.0088 0.9095 0.0818 197 I 0.0097 0.9035 0.0868 198 E 0.0091 0.8973 0.0936 199 A 0.0116 0.8779 0.1105 200 A 0.0213 0.7954 0.1833 201 Y 0.0397 0.6368 0.3235 202 K 0.0637 0.5056 0.4306 203 K 0.1076 0.2849 0.6075 204 D 0.1648 0.1169 0.7183 205 K 0.0920 0.2579 0.6501