# This file is the result of combining several RDB files, specifically # TR454.t06.str2.rdb (weight 1.54425) # TR454.t06.str4.rdb (weight 0.924988) # TR454.t06.pb.rdb (weight 0.789901) # TR454.t06.bys.rdb (weight 0.748322) # TR454.t06.alpha.rdb (weight 0.678173) # 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) # TR454.t2k.str2.rdb (weight 1.54425) # TR454.t2k.str4.rdb (weight 0.924988) # TR454.t2k.pb.rdb (weight 0.789901) # TR454.t2k.bys.rdb (weight 0.748322) # TR454.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 TR454.t06.str2.rdb # ============================================ # TARGET TR454 # 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 TR454.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 10175 # # ============================================ # Comments from TR454.t06.str4.rdb # ============================================ # TARGET TR454 # 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 TR454.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 10175 # # ============================================ # Comments from TR454.t06.pb.rdb # ============================================ # TARGET TR454 # 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 TR454.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 10175 # # ============================================ # Comments from TR454.t06.bys.rdb # ============================================ # TARGET TR454 # 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 TR454.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 10175 # # ============================================ # Comments from TR454.t06.alpha.rdb # ============================================ # TARGET TR454 # 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 TR454.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 10175 # # ============================================ # 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 # # ============================================ # Comments from TR454.t2k.str2.rdb # ============================================ # TARGET TR454 # 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 TR454.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 5079 # # ============================================ # Comments from TR454.t2k.str4.rdb # ============================================ # TARGET TR454 # 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 TR454.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 5079 # # ============================================ # Comments from TR454.t2k.pb.rdb # ============================================ # TARGET TR454 # 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 TR454.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 5079 # # ============================================ # Comments from TR454.t2k.bys.rdb # ============================================ # TARGET TR454 # 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 TR454.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 5079 # # ============================================ # Comments from TR454.t2k.alpha.rdb # ============================================ # TARGET TR454 # 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 TR454.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 5079 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.0530 0.5683 0.3787 2 C 0.0287 0.7693 0.2019 3 R 0.0100 0.8922 0.0978 4 S 0.0083 0.9205 0.0711 5 R 0.0084 0.9233 0.0683 6 L 0.0083 0.9223 0.0694 7 M 0.0083 0.9236 0.0681 8 E 0.0083 0.9247 0.0670 9 V 0.0083 0.9246 0.0671 10 A 0.0083 0.9225 0.0693 11 T 0.0083 0.9227 0.0690 12 E 0.0083 0.9242 0.0676 13 L 0.0083 0.9223 0.0693 14 F 0.0085 0.9141 0.0775 15 A 0.0091 0.8878 0.1031 16 Q 0.0152 0.7928 0.1920 17 K 0.0476 0.3255 0.6269 18 G 0.0489 0.1187 0.8324 19 F 0.1412 0.1820 0.6768 20 Y 0.1906 0.2677 0.5417 21 G 0.1883 0.3455 0.4663 22 V 0.2019 0.3813 0.4168 23 S 0.1550 0.3569 0.4881 24 I 0.0141 0.7862 0.1997 25 R 0.0093 0.8785 0.1122 26 E 0.0083 0.9238 0.0679 27 L 0.0083 0.9237 0.0680 28 A 0.0083 0.9221 0.0696 29 Q 0.0084 0.9152 0.0764 30 A 0.0141 0.8189 0.1670 31 A 0.0563 0.4129 0.5308 32 G 0.0466 0.0764 0.8770 33 A 0.1484 0.0855 0.7661 34 S 0.1993 0.0859 0.7149 35 I 0.1030 0.5010 0.3959 36 S 0.1072 0.5636 0.3292 37 M 0.2835 0.5156 0.2009 38 I 0.3084 0.5148 0.1768 39 S 0.2969 0.5182 0.1848 40 Y 0.2364 0.5146 0.2489 41 H 0.2115 0.3736 0.4149 42 F 0.1792 0.2456 0.5752 43 G 0.0976 0.2081 0.6943 44 G 0.1043 0.1870 0.7087 45 K 0.0223 0.7170 0.2608 46 E 0.0118 0.8412 0.1470 47 G 0.0090 0.9023 0.0887 48 L 0.0084 0.9205 0.0710 49 Y 0.0083 0.9217 0.0700 50 A 0.0083 0.9238 0.0679 51 A 0.0083 0.9247 0.0671 52 V 0.0083 0.9236 0.0681 53 L 0.0083 0.9219 0.0698 54 Q 0.0084 0.9194 0.0723 55 E 0.0084 0.9184 0.0732 56 Q 0.0087 0.9110 0.0803 57 F 0.0087 0.9059 0.0854 58 A 0.0088 0.9013 0.0899 59 C 0.0115 0.8600 0.1285 60 F 0.0209 0.8052 0.1739 61 G 0.0213 0.7696 0.2091 62 Q 0.0329 0.7469 0.2202 63 L 0.0397 0.7414 0.2189 64 D 0.0339 0.7712 0.1950 65 D 0.0344 0.7782 0.1874 66 I 0.0480 0.7246 0.2273 67 R 0.0714 0.5624 0.3663 68 G 0.0716 0.3800 0.5485 69 Q 0.0892 0.2879 0.6228 70 A 0.0976 0.1880 0.7144 71 G 0.0891 0.1388 0.7721 72 D 0.1487 0.0532 0.7981 73 P 0.0171 0.7314 0.2515 74 L 0.0094 0.8676 0.1230 75 A 0.0083 0.9199 0.0717 76 V 0.0083 0.9228 0.0689 77 M 0.0083 0.9236 0.0681 78 T 0.0083 0.9236 0.0682 79 A 0.0083 0.9241 0.0676 80 Y 0.0083 0.9237 0.0681 81 L 0.0083 0.9227 0.0690 82 R 0.0083 0.9220 0.0697 83 W 0.0083 0.9224 0.0693 84 T 0.0084 0.9174 0.0742 85 I 0.0085 0.9125 0.0789 86 Q 0.0087 0.9048 0.0865 87 R 0.0115 0.8499 0.1385 88 H 0.0234 0.7297 0.2470 89 R 0.0365 0.5851 0.3784 90 N 0.0576 0.3623 0.5801 91 N 0.1317 0.2004 0.6679 92 P 0.0224 0.6793 0.2983 93 Q 0.0228 0.7458 0.2314 94 L 0.0342 0.8221 0.1437 95 L 0.0323 0.8645 0.1033 96 R 0.0381 0.8637 0.0982 97 F 0.0457 0.8519 0.1024 98 Y 0.0622 0.8056 0.1322 99 T 0.0621 0.7753 0.1627 100 S 0.0496 0.7553 0.1950 101 E 0.0584 0.6547 0.2868 102 L 0.0794 0.4899 0.4308 103 T 0.1003 0.2779 0.6218 104 N 0.1559 0.1331 0.7110 105 P 0.1151 0.1915 0.6934 106 T 0.1338 0.1343 0.7318 107 P 0.0217 0.6515 0.3267 108 C 0.0242 0.7404 0.2353 109 F 0.0294 0.8237 0.1469 110 A 0.0190 0.8680 0.1130 111 A 0.0154 0.8673 0.1173 112 I 0.0209 0.8274 0.1517 113 V 0.0402 0.7610 0.1988 114 S 0.0332 0.7699 0.1968 115 P 0.0104 0.8646 0.1250 116 A 0.0108 0.8877 0.1015 117 I 0.0091 0.9119 0.0790 118 A 0.0084 0.9152 0.0764 119 S 0.0083 0.9223 0.0694 120 V 0.0083 0.9216 0.0701 121 I 0.0083 0.9231 0.0686 122 R 0.0083 0.9242 0.0675 123 L 0.0083 0.9245 0.0672 124 L 0.0083 0.9224 0.0693 125 A 0.0083 0.9210 0.0707 126 E 0.0083 0.9243 0.0674 127 S 0.0083 0.9225 0.0691 128 I 0.0084 0.9181 0.0735 129 E 0.0084 0.9181 0.0735 130 A 0.0089 0.9069 0.0842 131 G 0.0121 0.8649 0.1230 132 M 0.0138 0.8303 0.1560 133 T 0.0212 0.7202 0.2586 134 R 0.0593 0.2957 0.6450 135 G 0.0478 0.1215 0.8307 136 L 0.1765 0.1292 0.6943 137 F 0.2793 0.1062 0.6145 138 R 0.1967 0.1414 0.6618 139 R 0.0808 0.4010 0.5183 140 D 0.0883 0.3039 0.6077 141 L 0.1384 0.2987 0.5629 142 H 0.1329 0.2626 0.6046 143 A 0.0123 0.7657 0.2220 144 V 0.0091 0.8757 0.1152 145 N 0.0083 0.9223 0.0694 146 S 0.0083 0.9228 0.0690 147 A 0.0083 0.9241 0.0676 148 L 0.0083 0.9246 0.0671 149 A 0.0083 0.9244 0.0673 150 L 0.0083 0.9232 0.0685 151 A 0.0083 0.9231 0.0686 152 G 0.0083 0.9212 0.0705 153 M 0.0085 0.9145 0.0770 154 V 0.0090 0.9013 0.0897 155 N 0.0096 0.8924 0.0980 156 Y 0.0129 0.8846 0.1025 157 F 0.0178 0.8731 0.1091 158 F 0.0266 0.8495 0.1239 159 L 0.0392 0.8180 0.1428 160 S 0.0618 0.7454 0.1928 161 T 0.0939 0.6440 0.2622 162 L 0.1210 0.5152 0.3638 163 A 0.1370 0.3646 0.4984 164 T 0.1373 0.2510 0.6116 165 E 0.0988 0.2307 0.6705 166 G 0.1002 0.1489 0.7509 167 L 0.1539 0.1678 0.6783 168 T 0.1845 0.1382 0.6773 169 S 0.1705 0.1471 0.6824 170 H 0.1479 0.1678 0.6843 171 S 0.1511 0.1267 0.7222 172 P 0.0496 0.5022 0.4482 173 D 0.0451 0.5773 0.3776 174 Q 0.0237 0.7803 0.1960 175 D 0.0119 0.8808 0.1072 176 E 0.0092 0.9121 0.0788 177 E 0.0092 0.9190 0.0718 178 L 0.0097 0.9171 0.0732 179 I 0.0089 0.9195 0.0716 180 R 0.0112 0.9091 0.0797 181 Q 0.0239 0.8744 0.1017 182 Y 0.0475 0.8016 0.1509 183 V 0.0576 0.7129 0.2295 184 A 0.1089 0.5276 0.3635 185 I 0.1956 0.3890 0.4154 186 F 0.2410 0.2241 0.5348 187 T 0.2088 0.1849 0.6063 188 R 0.1351 0.1750 0.6899 189 G 0.1012 0.1651 0.7337 190 I 0.1574 0.2080 0.6346 191 M 0.1740 0.1885 0.6376 192 A 0.2032 0.2563 0.5405