# This file is the result of combining several RDB files, specifically # TR461.t06.str2.rdb (weight 1.54425) # TR461.t06.str4.rdb (weight 0.924988) # TR461.t06.pb.rdb (weight 0.789901) # TR461.t06.bys.rdb (weight 0.748322) # TR461.t06.alpha.rdb (weight 0.678173) # TR461.t04.str2.rdb (weight 1.54425) # TR461.t04.str4.rdb (weight 0.924988) # TR461.t04.pb.rdb (weight 0.789901) # TR461.t04.bys.rdb (weight 0.748322) # TR461.t04.alpha.rdb (weight 0.678173) # TR461.t2k.str2.rdb (weight 1.54425) # TR461.t2k.str4.rdb (weight 0.924988) # TR461.t2k.pb.rdb (weight 0.789901) # TR461.t2k.bys.rdb (weight 0.748322) # TR461.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 TR461.t06.str2.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2293 # # ============================================ # Comments from TR461.t06.str4.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2293 # # ============================================ # Comments from TR461.t06.pb.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2293 # # ============================================ # Comments from TR461.t06.bys.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2293 # # ============================================ # Comments from TR461.t06.alpha.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2293 # # ============================================ # Comments from TR461.t04.str2.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2123 # # ============================================ # Comments from TR461.t04.str4.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2123 # # ============================================ # Comments from TR461.t04.pb.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2123 # # ============================================ # Comments from TR461.t04.bys.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2123 # # ============================================ # Comments from TR461.t04.alpha.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2123 # # ============================================ # Comments from TR461.t2k.str2.rdb # ============================================ # TARGET TR461 # 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 TR461.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 677.451 # # ============================================ # Comments from TR461.t2k.str4.rdb # ============================================ # TARGET TR461 # 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 TR461.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 677.451 # # ============================================ # Comments from TR461.t2k.pb.rdb # ============================================ # TARGET TR461 # 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 TR461.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 677.451 # # ============================================ # Comments from TR461.t2k.bys.rdb # ============================================ # TARGET TR461 # 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 TR461.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 677.451 # # ============================================ # Comments from TR461.t2k.alpha.rdb # ============================================ # TARGET TR461 # 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 TR461.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 677.451 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 F 0.2749 0.1058 0.6193 2 Q 0.2492 0.1237 0.6271 3 S 0.2177 0.2370 0.5453 4 M 0.1196 0.4983 0.3821 5 E 0.0555 0.7032 0.2412 6 E 0.0219 0.8259 0.1522 7 T 0.0136 0.8857 0.1007 8 E 0.0085 0.9170 0.0745 9 K 0.0083 0.9207 0.0709 10 W 0.0083 0.9237 0.0680 11 M 0.0083 0.9228 0.0689 12 E 0.0083 0.9238 0.0679 13 E 0.0083 0.9246 0.0672 14 A 0.0083 0.9239 0.0678 15 M 0.0083 0.9226 0.0691 16 H 0.0083 0.9225 0.0692 17 M 0.0084 0.9179 0.0737 18 A 0.0086 0.9081 0.0833 19 K 0.0086 0.9020 0.0893 20 E 0.0103 0.8664 0.1233 21 A 0.0161 0.7956 0.1882 22 L 0.0256 0.7113 0.2631 23 E 0.0471 0.4953 0.4576 24 N 0.0817 0.2492 0.6691 25 T 0.0856 0.1849 0.7295 26 E 0.1670 0.0914 0.7416 27 V 0.3060 0.0305 0.6635 28 P 0.4403 0.0311 0.5286 29 V 0.5824 0.0350 0.3826 30 G 0.6571 0.0186 0.3242 31 C 0.7821 0.0051 0.2128 32 L 0.8231 0.0047 0.1722 33 M 0.7784 0.0052 0.2164 34 V 0.7443 0.0078 0.2479 35 Y 0.5769 0.0313 0.3918 36 N 0.2492 0.0577 0.6931 37 N 0.1047 0.0875 0.8077 38 E 0.5326 0.0175 0.4500 39 V 0.6795 0.0084 0.3121 40 V 0.7348 0.0151 0.2501 41 G 0.7298 0.0172 0.2530 42 K 0.6319 0.0406 0.3275 43 G 0.4968 0.0527 0.4506 44 R 0.3888 0.1188 0.4924 45 N 0.3776 0.1208 0.5016 46 E 0.3707 0.1890 0.4403 47 V 0.3612 0.1910 0.4477 48 N 0.2463 0.2295 0.5242 49 Q 0.1829 0.2501 0.5671 50 T 0.1323 0.2000 0.6677 51 K 0.1357 0.1644 0.6999 52 N 0.1949 0.1027 0.7025 53 A 0.0954 0.4132 0.4914 54 T 0.0996 0.5051 0.3953 55 R 0.0600 0.6824 0.2577 56 H 0.0493 0.7741 0.1766 57 A 0.0342 0.8596 0.1063 58 E 0.0187 0.8977 0.0836 59 M 0.0120 0.9135 0.0746 60 V 0.0091 0.9215 0.0694 61 A 0.0083 0.9236 0.0681 62 I 0.0083 0.9220 0.0697 63 D 0.0083 0.9219 0.0698 64 Q 0.0083 0.9198 0.0719 65 V 0.0084 0.9178 0.0738 66 L 0.0085 0.9108 0.0807 67 D 0.0086 0.8985 0.0928 68 W 0.0118 0.8484 0.1398 69 C 0.0276 0.6990 0.2734 70 R 0.0308 0.5315 0.4377 71 Q 0.0475 0.4840 0.4685 72 S 0.0628 0.2813 0.6559 73 G 0.0767 0.2155 0.7078 74 K 0.1496 0.1446 0.7058 75 S 0.1979 0.0512 0.7509 76 P 0.1199 0.2958 0.5843 77 S 0.1356 0.3072 0.5572 78 E 0.1722 0.3548 0.4730 79 V 0.2625 0.2671 0.4704 80 F 0.3261 0.1696 0.5043 81 E 0.2637 0.1352 0.6011 82 H 0.2028 0.0831 0.7141 83 T 0.5017 0.0150 0.4833 84 V 0.7239 0.0091 0.2670 85 L 0.8041 0.0067 0.1892 86 Y 0.8010 0.0065 0.1925 87 V 0.7671 0.0099 0.2230 88 T 0.5897 0.0183 0.3919 89 V 0.3323 0.1200 0.5477 90 E 0.2600 0.1168 0.6232 91 P 0.1768 0.2007 0.6225 92 C 0.1371 0.3147 0.5482 93 I 0.0527 0.6665 0.2807 94 M 0.0414 0.7377 0.2209 95 C 0.0200 0.8277 0.1523 96 A 0.0105 0.8815 0.1080 97 A 0.0093 0.9137 0.0770 98 A 0.0100 0.9154 0.0747 99 L 0.0100 0.9150 0.0749 100 R 0.0097 0.9043 0.0860 101 L 0.0202 0.8097 0.1701 102 M 0.0499 0.4100 0.5401 103 K 0.0560 0.0963 0.8477 104 I 0.2144 0.0271 0.7585 105 P 0.2500 0.0629 0.6872 106 L 0.6432 0.0293 0.3275 107 V 0.7448 0.0104 0.2447 108 V 0.7896 0.0085 0.2020 109 Y 0.7654 0.0142 0.2204 110 G 0.6889 0.0239 0.2872 111 C 0.5002 0.0652 0.4346 112 Q 0.3407 0.0897 0.5696 113 N 0.2696 0.0588 0.6716 114 E 0.0798 0.3787 0.5414 115 R 0.1038 0.3096 0.5866 116 F 0.1407 0.2315 0.6278 117 G 0.1438 0.1760 0.6802 118 G 0.2181 0.2378 0.5441 119 C 0.2184 0.2535 0.5282 120 G 0.2067 0.2607 0.5326 121 S 0.2347 0.3520 0.4133 122 V 0.2120 0.4753 0.3127 123 L 0.1981 0.5478 0.2541 124 N 0.1980 0.5197 0.2823 125 I 0.1528 0.5306 0.3166 126 A 0.1393 0.4492 0.4115 127 S 0.1192 0.4291 0.4516 128 A 0.1074 0.3930 0.4996 129 D 0.1198 0.2870 0.5932 130 L 0.1826 0.1625 0.6548 131 P 0.1377 0.2707 0.5916 132 N 0.1513 0.2124 0.6363 133 T 0.1801 0.1517 0.6682 134 G 0.1800 0.0927 0.7273 135 R 0.2799 0.0564 0.6637 136 P 0.3341 0.0704 0.5956 137 F 0.4232 0.0834 0.4934 138 Q 0.4056 0.0895 0.5048 139 C 0.3659 0.1329 0.5012 140 I 0.2746 0.1351 0.5904 141 P 0.1357 0.4750 0.3892 142 G 0.0678 0.6782 0.2540 143 Y 0.0401 0.8021 0.1577 144 R 0.0250 0.8430 0.1320 145 A 0.0167 0.8547 0.1286 146 E 0.0148 0.8569 0.1283 147 E 0.0122 0.8626 0.1252 148 A 0.0141 0.8699 0.1160 149 V 0.0120 0.8907 0.0973 150 E 0.0107 0.8962 0.0931 151 M 0.0170 0.8705 0.1125 152 L 0.0271 0.8251 0.1478 153 K 0.0318 0.7923 0.1759 154 T 0.0431 0.7393 0.2176 155 F 0.0809 0.5052 0.4139 156 Y 0.1236 0.2977 0.5787 157 K 0.1034 0.2070 0.6896