# This file is the result of combining several RDB files, specifically # TR454.t04.str2.rdb (weight 1.54425) # TR454.t04.str4.rdb (weight 0.924988) # TR454.t04.pb.rdb (weight 0.789901) # TR454.t04.bys.rdb (weight 0.748322) # TR454.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 TR454.t04.str2.rdb # ============================================ # TARGET TR454 # 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 TR454.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 2159 # # ============================================ # Comments from TR454.t04.str4.rdb # ============================================ # TARGET TR454 # 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 TR454.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 2159 # # ============================================ # Comments from TR454.t04.pb.rdb # ============================================ # TARGET TR454 # 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 TR454.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 2159 # # ============================================ # Comments from TR454.t04.bys.rdb # ============================================ # TARGET TR454 # 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 TR454.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 2159 # # ============================================ # Comments from TR454.t04.alpha.rdb # ============================================ # TARGET TR454 # 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 TR454.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 2159 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.1199 0.1871 0.6930 2 C 0.0563 0.6037 0.3400 3 R 0.0159 0.7981 0.1859 4 S 0.0095 0.8884 0.1021 5 R 0.0089 0.9195 0.0716 6 L 0.0083 0.9213 0.0704 7 M 0.0083 0.9235 0.0682 8 E 0.0083 0.9250 0.0668 9 V 0.0083 0.9251 0.0666 10 A 0.0083 0.9243 0.0674 11 T 0.0083 0.9243 0.0675 12 E 0.0083 0.9241 0.0677 13 L 0.0083 0.9155 0.0762 14 F 0.0084 0.9094 0.0822 15 A 0.0088 0.8994 0.0919 16 Q 0.0121 0.8019 0.1860 17 K 0.0558 0.3610 0.5832 18 G 0.0586 0.1776 0.7639 19 F 0.1155 0.3000 0.5844 20 Y 0.1225 0.3148 0.5627 21 G 0.1431 0.2589 0.5980 22 V 0.2049 0.2221 0.5730 23 S 0.1985 0.1163 0.6852 24 I 0.0143 0.7470 0.2387 25 R 0.0092 0.8724 0.1184 26 E 0.0083 0.9219 0.0698 27 L 0.0084 0.9183 0.0733 28 A 0.0084 0.9115 0.0801 29 Q 0.0088 0.8977 0.0935 30 A 0.0131 0.8182 0.1686 31 A 0.0585 0.2907 0.6508 32 G 0.0392 0.0902 0.8706 33 A 0.1389 0.0904 0.7707 34 S 0.1780 0.0915 0.7305 35 I 0.1303 0.4745 0.3952 36 S 0.1577 0.5218 0.3205 37 M 0.2999 0.4742 0.2259 38 I 0.4438 0.3642 0.1920 39 S 0.4288 0.3854 0.1858 40 Y 0.4492 0.3302 0.2206 41 H 0.3327 0.2517 0.4156 42 F 0.1912 0.2001 0.6087 43 G 0.1161 0.1802 0.7037 44 G 0.1124 0.1705 0.7170 45 K 0.0181 0.6640 0.3179 46 E 0.0106 0.8352 0.1542 47 G 0.0086 0.9095 0.0819 48 L 0.0089 0.9190 0.0721 49 Y 0.0083 0.9218 0.0699 50 A 0.0083 0.9236 0.0681 51 A 0.0083 0.9237 0.0681 52 V 0.0083 0.9235 0.0682 53 L 0.0084 0.9182 0.0734 54 Q 0.0084 0.9210 0.0707 55 E 0.0086 0.9163 0.0751 56 Q 0.0092 0.9010 0.0898 57 F 0.0094 0.8865 0.1040 58 A 0.0094 0.8721 0.1185 59 C 0.0139 0.8217 0.1644 60 F 0.0210 0.7614 0.2176 61 G 0.0273 0.6996 0.2731 62 Q 0.0444 0.6602 0.2955 63 L 0.0517 0.6382 0.3101 64 D 0.0608 0.6037 0.3354 65 D 0.0609 0.6012 0.3379 66 I 0.0729 0.5899 0.3372 67 R 0.1004 0.4493 0.4503 68 G 0.0920 0.3580 0.5500 69 Q 0.1017 0.2675 0.6308 70 A 0.0896 0.2293 0.6811 71 G 0.0851 0.1454 0.7695 72 D 0.1606 0.0627 0.7768 73 P 0.0177 0.6903 0.2920 74 L 0.0094 0.8608 0.1298 75 A 0.0083 0.9214 0.0702 76 V 0.0083 0.9224 0.0692 77 M 0.0083 0.9226 0.0691 78 T 0.0083 0.9240 0.0677 79 A 0.0083 0.9247 0.0670 80 Y 0.0083 0.9249 0.0668 81 L 0.0083 0.9239 0.0679 82 R 0.0083 0.9245 0.0672 83 W 0.0083 0.9237 0.0680 84 T 0.0084 0.9214 0.0703 85 I 0.0085 0.9193 0.0722 86 Q 0.0087 0.9163 0.0750 87 R 0.0123 0.8815 0.1063 88 H 0.0219 0.7946 0.1834 89 R 0.0232 0.6448 0.3320 90 N 0.0399 0.4267 0.5334 91 N 0.1320 0.2657 0.6023 92 P 0.0141 0.7435 0.2423 93 Q 0.0127 0.8270 0.1602 94 L 0.0200 0.8708 0.1092 95 L 0.0177 0.8950 0.0873 96 R 0.0184 0.9022 0.0795 97 F 0.0270 0.8888 0.0842 98 Y 0.0396 0.8558 0.1046 99 T 0.0355 0.8404 0.1241 100 S 0.0327 0.8158 0.1515 101 E 0.0515 0.6735 0.2749 102 L 0.0879 0.4220 0.4902 103 T 0.1038 0.2503 0.6460 104 N 0.1522 0.1160 0.7317 105 P 0.1132 0.1966 0.6901 106 T 0.1437 0.1586 0.6978 107 P 0.0178 0.7134 0.2688 108 C 0.0173 0.7937 0.1889 109 F 0.0169 0.8564 0.1267 110 A 0.0142 0.8765 0.1094 111 A 0.0127 0.8794 0.1079 112 I 0.0198 0.8334 0.1467 113 V 0.0303 0.7552 0.2146 114 S 0.0425 0.7610 0.1965 115 P 0.0124 0.8680 0.1196 116 A 0.0148 0.8698 0.1155 117 I 0.0098 0.9006 0.0896 118 A 0.0084 0.9191 0.0725 119 S 0.0083 0.9206 0.0710 120 V 0.0083 0.9221 0.0695 121 I 0.0083 0.9240 0.0677 122 R 0.0083 0.9246 0.0671 123 L 0.0083 0.9242 0.0676 124 L 0.0083 0.9229 0.0688 125 A 0.0083 0.9243 0.0675 126 E 0.0083 0.9242 0.0676 127 S 0.0083 0.9235 0.0683 128 I 0.0083 0.9232 0.0685 129 E 0.0083 0.9205 0.0712 130 A 0.0088 0.9098 0.0814 131 G 0.0099 0.8844 0.1057 132 M 0.0106 0.8798 0.1095 133 T 0.0135 0.8137 0.1729 134 R 0.0568 0.2910 0.6521 135 G 0.0506 0.1096 0.8398 136 L 0.1673 0.1505 0.6822 137 F 0.2993 0.1446 0.5561 138 R 0.2341 0.1677 0.5983 139 R 0.1036 0.4522 0.4442 140 D 0.1099 0.2754 0.6147 141 L 0.1560 0.2478 0.5962 142 H 0.1717 0.1496 0.6788 143 A 0.0142 0.7508 0.2349 144 V 0.0092 0.8695 0.1212 145 N 0.0083 0.9211 0.0705 146 S 0.0083 0.9239 0.0678 147 A 0.0083 0.9241 0.0676 148 L 0.0083 0.9249 0.0669 149 A 0.0083 0.9247 0.0671 150 L 0.0083 0.9228 0.0689 151 A 0.0083 0.9221 0.0696 152 G 0.0083 0.9205 0.0712 153 M 0.0083 0.9174 0.0743 154 V 0.0085 0.9064 0.0852 155 N 0.0085 0.8952 0.0963 156 Y 0.0102 0.8880 0.1018 157 F 0.0139 0.8857 0.1004 158 F 0.0203 0.8715 0.1083 159 L 0.0293 0.8415 0.1292 160 S 0.0404 0.7918 0.1678 161 T 0.0520 0.7504 0.1976 162 L 0.0697 0.6976 0.2327 163 A 0.0956 0.5855 0.3190 164 T 0.1071 0.4756 0.4173 165 E 0.1039 0.3537 0.5424 166 G 0.1136 0.2554 0.6310 167 L 0.1600 0.2220 0.6180 168 T 0.1846 0.1806 0.6349 169 S 0.1738 0.1719 0.6542 170 H 0.1554 0.1310 0.7136 171 S 0.1794 0.0455 0.7750 172 P 0.0683 0.3764 0.5553 173 D 0.0791 0.3257 0.5952 174 Q 0.1205 0.2916 0.5879 175 D 0.0169 0.7435 0.2396 176 E 0.0091 0.8716 0.1193 177 E 0.0084 0.9183 0.0733 178 L 0.0083 0.9225 0.0692 179 I 0.0083 0.9218 0.0699 180 R 0.0083 0.9247 0.0670 181 Q 0.0083 0.9249 0.0668 182 Y 0.0083 0.9243 0.0675 183 V 0.0083 0.9242 0.0675 184 A 0.0083 0.9248 0.0670 185 I 0.0084 0.9168 0.0749 186 F 0.0085 0.9188 0.0728 187 T 0.0093 0.9014 0.0894 188 R 0.0150 0.8163 0.1687 189 G 0.0339 0.6302 0.3359 190 I 0.0678 0.4639 0.4683 191 M 0.1164 0.2952 0.5884 192 A 0.1091 0.2618 0.6291