# This file is the result of combining several RDB files, specifically # T0454.t2k.str2.rdb (weight 1.54425) # T0454.t2k.str4.rdb (weight 0.924988) # T0454.t2k.pb.rdb (weight 0.789901) # T0454.t2k.bys.rdb (weight 0.748322) # T0454.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 T0454.t2k.str2.rdb # ============================================ # TARGET T0454 # 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 T0454.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 4968 # # ============================================ # Comments from T0454.t2k.str4.rdb # ============================================ # TARGET T0454 # 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 T0454.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 4968 # # ============================================ # Comments from T0454.t2k.pb.rdb # ============================================ # TARGET T0454 # 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 T0454.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 4968 # # ============================================ # Comments from T0454.t2k.bys.rdb # ============================================ # TARGET T0454 # 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 T0454.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 4968 # # ============================================ # Comments from T0454.t2k.alpha.rdb # ============================================ # TARGET T0454 # 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 T0454.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 4968 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2897 0.0686 0.6418 2 T 0.1769 0.0559 0.7672 3 R 0.0693 0.5045 0.4262 4 A 0.0164 0.7697 0.2140 5 D 0.0193 0.8114 0.1693 6 C 0.0140 0.8751 0.1109 7 R 0.0089 0.9087 0.0824 8 S 0.0083 0.9223 0.0694 9 R 0.0084 0.9236 0.0680 10 L 0.0083 0.9226 0.0691 11 M 0.0083 0.9239 0.0678 12 E 0.0083 0.9248 0.0670 13 V 0.0083 0.9246 0.0671 14 A 0.0083 0.9224 0.0693 15 T 0.0083 0.9225 0.0692 16 E 0.0083 0.9242 0.0676 17 L 0.0083 0.9225 0.0692 18 F 0.0085 0.9141 0.0774 19 A 0.0091 0.8877 0.1032 20 Q 0.0150 0.7936 0.1914 21 K 0.0473 0.3279 0.6248 22 G 0.0488 0.1180 0.8333 23 F 0.1405 0.1822 0.6773 24 Y 0.1889 0.2689 0.5421 25 G 0.1866 0.3462 0.4671 26 V 0.2027 0.3807 0.4165 27 S 0.1560 0.3538 0.4902 28 I 0.0142 0.7851 0.2007 29 R 0.0093 0.8782 0.1125 30 E 0.0083 0.9235 0.0682 31 L 0.0083 0.9235 0.0682 32 A 0.0083 0.9217 0.0700 33 Q 0.0084 0.9149 0.0766 34 A 0.0143 0.8171 0.1685 35 A 0.0564 0.4116 0.5320 36 G 0.0466 0.0772 0.8762 37 A 0.1481 0.0872 0.7647 38 S 0.1973 0.0893 0.7134 39 I 0.0974 0.5176 0.3850 40 S 0.1006 0.5836 0.3158 41 M 0.2663 0.5387 0.1950 42 I 0.2849 0.5425 0.1726 43 S 0.2734 0.5441 0.1826 44 Y 0.2189 0.5318 0.2493 45 H 0.2008 0.3815 0.4177 46 F 0.1718 0.2494 0.5788 47 G 0.0967 0.2099 0.6934 48 G 0.1041 0.1873 0.7086 49 K 0.0216 0.7198 0.2586 50 E 0.0118 0.8420 0.1462 51 G 0.0090 0.9030 0.0880 52 L 0.0084 0.9205 0.0711 53 Y 0.0083 0.9217 0.0700 54 A 0.0083 0.9238 0.0679 55 A 0.0083 0.9247 0.0671 56 V 0.0083 0.9237 0.0680 57 L 0.0083 0.9219 0.0698 58 Q 0.0084 0.9193 0.0724 59 E 0.0084 0.9185 0.0731 60 Q 0.0087 0.9112 0.0802 61 F 0.0087 0.9064 0.0849 62 A 0.0088 0.9018 0.0894 63 C 0.0118 0.8598 0.1285 64 F 0.0231 0.7934 0.1835 65 G 0.0243 0.7457 0.2300 66 Q 0.0406 0.7010 0.2584 67 L 0.0544 0.6571 0.2885 68 D 0.0547 0.6487 0.2966 69 D 0.0700 0.6003 0.3297 70 I 0.0837 0.5313 0.3850 71 R 0.1025 0.3852 0.5123 72 G 0.0850 0.2875 0.6275 73 Q 0.0903 0.2891 0.6206 74 A 0.0968 0.2087 0.6945 75 G 0.1005 0.1558 0.7437 76 D 0.1504 0.0619 0.7877 77 P 0.0157 0.7340 0.2503 78 L 0.0093 0.8687 0.1220 79 A 0.0083 0.9209 0.0707 80 V 0.0083 0.9228 0.0689 81 M 0.0083 0.9236 0.0682 82 T 0.0083 0.9236 0.0681 83 A 0.0083 0.9242 0.0675 84 Y 0.0083 0.9237 0.0680 85 L 0.0083 0.9227 0.0690 86 R 0.0083 0.9223 0.0694 87 W 0.0083 0.9228 0.0689 88 T 0.0084 0.9184 0.0732 89 I 0.0085 0.9133 0.0783 90 Q 0.0087 0.9065 0.0848 91 R 0.0109 0.8555 0.1336 92 H 0.0215 0.7402 0.2382 93 R 0.0344 0.5919 0.3737 94 N 0.0551 0.3693 0.5756 95 N 0.1297 0.2068 0.6635 96 P 0.0209 0.6913 0.2878 97 Q 0.0209 0.7590 0.2202 98 L 0.0296 0.8342 0.1362 99 L 0.0264 0.8769 0.0968 100 R 0.0301 0.8773 0.0926 101 F 0.0358 0.8669 0.0972 102 Y 0.0500 0.8266 0.1234 103 T 0.0512 0.7974 0.1514 104 S 0.0420 0.7758 0.1822 105 E 0.0508 0.6749 0.2743 106 L 0.0742 0.5068 0.4190 107 T 0.0980 0.2818 0.6202 108 N 0.1546 0.1340 0.7114 109 P 0.1142 0.1920 0.6939 110 T 0.1318 0.1400 0.7282 111 P 0.0217 0.6536 0.3246 112 C 0.0240 0.7438 0.2321 113 F 0.0289 0.8261 0.1450 114 A 0.0190 0.8685 0.1125 115 A 0.0153 0.8671 0.1176 116 I 0.0215 0.8239 0.1547 117 V 0.0416 0.7537 0.2047 118 S 0.0356 0.7602 0.2042 119 P 0.0109 0.8600 0.1291 120 A 0.0112 0.8859 0.1029 121 I 0.0092 0.9115 0.0793 122 A 0.0084 0.9152 0.0764 123 S 0.0083 0.9221 0.0695 124 V 0.0083 0.9214 0.0702 125 I 0.0083 0.9230 0.0687 126 R 0.0083 0.9242 0.0675 127 L 0.0083 0.9245 0.0672 128 L 0.0083 0.9225 0.0692 129 A 0.0083 0.9210 0.0707 130 E 0.0083 0.9244 0.0673 131 S 0.0083 0.9225 0.0692 132 I 0.0084 0.9186 0.0731 133 E 0.0084 0.9183 0.0733 134 A 0.0088 0.9087 0.0825 135 G 0.0118 0.8686 0.1196 136 M 0.0136 0.8337 0.1527 137 T 0.0212 0.7236 0.2552 138 R 0.0587 0.2982 0.6431 139 G 0.0482 0.1216 0.8301 140 L 0.1781 0.1254 0.6965 141 F 0.2832 0.1062 0.6106 142 R 0.2010 0.1347 0.6644 143 R 0.0855 0.3929 0.5216 144 D 0.0951 0.2979 0.6070 145 L 0.1346 0.3081 0.5573 146 H 0.1310 0.2679 0.6011 147 A 0.0122 0.7654 0.2223 148 V 0.0091 0.8756 0.1153 149 N 0.0083 0.9224 0.0693 150 S 0.0083 0.9228 0.0690 151 A 0.0083 0.9240 0.0677 152 L 0.0083 0.9246 0.0671 153 A 0.0083 0.9244 0.0673 154 L 0.0083 0.9232 0.0685 155 A 0.0083 0.9232 0.0685 156 G 0.0083 0.9214 0.0703 157 M 0.0085 0.9141 0.0774 158 V 0.0091 0.8993 0.0916 159 N 0.0099 0.8891 0.1011 160 Y 0.0141 0.8793 0.1066 161 F 0.0198 0.8652 0.1150 162 F 0.0305 0.8361 0.1333 163 L 0.0467 0.7946 0.1587 164 S 0.0729 0.7116 0.2155 165 T 0.1021 0.6185 0.2795 166 L 0.1254 0.5023 0.3723 167 A 0.1363 0.3691 0.4945 168 T 0.1380 0.2564 0.6056 169 E 0.1006 0.2321 0.6673 170 G 0.1028 0.1522 0.7450 171 L 0.1675 0.1480 0.6845 172 T 0.1972 0.1236 0.6792 173 S 0.1723 0.1512 0.6765 174 H 0.1596 0.1309 0.7094 175 S 0.1656 0.0649 0.7696 176 P 0.0500 0.4410 0.5090 177 D 0.0532 0.4973 0.4495 178 Q 0.0433 0.6822 0.2744 179 D 0.0163 0.8493 0.1343 180 E 0.0089 0.9027 0.0884 181 E 0.0084 0.9209 0.0706 182 L 0.0083 0.9216 0.0701 183 I 0.0083 0.9234 0.0683 184 R 0.0083 0.9236 0.0681 185 Q 0.0083 0.9228 0.0689 186 Y 0.0084 0.9202 0.0714 187 V 0.0084 0.9183 0.0733 188 A 0.0088 0.9151 0.0761 189 I 0.0119 0.8920 0.0961 190 F 0.0269 0.8131 0.1600 191 T 0.0547 0.6479 0.2974 192 R 0.0651 0.4087 0.5263 193 G 0.0784 0.2342 0.6874 194 I 0.1962 0.1952 0.6086 195 M 0.2684 0.1257 0.6059 196 A 0.2419 0.1506 0.6075 197 D 0.1414 0.1478 0.7108 198 G 0.0845 0.1501 0.7654 199 G 0.1152 0.1418 0.7430 200 A 0.1875 0.1503 0.6622 201 A 0.2277 0.0616 0.7107 202 P 0.2101 0.1595 0.6304 203 A 0.2135 0.2226 0.5639