# This file is the result of combining several RDB files, specifically # T0468.t06.str2.rdb (weight 1.54425) # T0468.t06.str4.rdb (weight 0.924988) # T0468.t06.pb.rdb (weight 0.789901) # T0468.t06.bys.rdb (weight 0.748322) # T0468.t06.alpha.rdb (weight 0.678173) # T0468.t04.str2.rdb (weight 1.54425) # T0468.t04.str4.rdb (weight 0.924988) # T0468.t04.pb.rdb (weight 0.789901) # T0468.t04.bys.rdb (weight 0.748322) # T0468.t04.alpha.rdb (weight 0.678173) # T0468.t2k.str2.rdb (weight 1.54425) # T0468.t2k.str4.rdb (weight 0.924988) # T0468.t2k.pb.rdb (weight 0.789901) # T0468.t2k.bys.rdb (weight 0.748322) # T0468.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 T0468.t06.str2.rdb # ============================================ # TARGET T0468 # 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 T0468.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 47.4163 # # ============================================ # Comments from T0468.t06.str4.rdb # ============================================ # TARGET T0468 # 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 T0468.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 47.4163 # # ============================================ # Comments from T0468.t06.pb.rdb # ============================================ # TARGET T0468 # 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 T0468.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 47.4163 # # ============================================ # Comments from T0468.t06.bys.rdb # ============================================ # TARGET T0468 # 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 T0468.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 47.4163 # # ============================================ # Comments from T0468.t06.alpha.rdb # ============================================ # TARGET T0468 # 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 T0468.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 47.4163 # # ============================================ # Comments from T0468.t04.str2.rdb # ============================================ # TARGET T0468 # 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 T0468.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 42.6786 # # ============================================ # Comments from T0468.t04.str4.rdb # ============================================ # TARGET T0468 # 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 T0468.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 42.6786 # # ============================================ # Comments from T0468.t04.pb.rdb # ============================================ # TARGET T0468 # 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 T0468.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 42.6786 # # ============================================ # Comments from T0468.t04.bys.rdb # ============================================ # TARGET T0468 # 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 T0468.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 42.6786 # # ============================================ # Comments from T0468.t04.alpha.rdb # ============================================ # TARGET T0468 # 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 T0468.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 42.6786 # # ============================================ # Comments from T0468.t2k.str2.rdb # ============================================ # TARGET T0468 # 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 T0468.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 17.8848 # # ============================================ # Comments from T0468.t2k.str4.rdb # ============================================ # TARGET T0468 # 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 T0468.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 17.8848 # # ============================================ # Comments from T0468.t2k.pb.rdb # ============================================ # TARGET T0468 # 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 T0468.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 17.8848 # # ============================================ # Comments from T0468.t2k.bys.rdb # ============================================ # TARGET T0468 # 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 T0468.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 17.8848 # # ============================================ # Comments from T0468.t2k.alpha.rdb # ============================================ # TARGET T0468 # 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 T0468.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 17.8848 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3730 0.0936 0.5334 2 E 0.3358 0.1174 0.5468 3 R 0.3959 0.1673 0.4367 4 A 0.3876 0.1500 0.4624 5 S 0.3267 0.1144 0.5588 6 L 0.1736 0.4502 0.3762 7 N 0.1544 0.4422 0.4034 8 R 0.2110 0.3274 0.4616 9 I 0.2265 0.1815 0.5920 10 G 0.2177 0.0835 0.6988 11 K 0.3132 0.0805 0.6063 12 D 0.4564 0.0402 0.5034 13 V 0.7087 0.0119 0.2794 14 Y 0.7815 0.0075 0.2110 15 Y 0.8279 0.0043 0.1678 16 M 0.8245 0.0045 0.1710 17 Q 0.8208 0.0044 0.1748 18 I 0.7525 0.0065 0.2410 19 K 0.5635 0.0225 0.4140 20 G 0.3271 0.0410 0.6318 21 E 0.2326 0.0778 0.6896 22 G 0.2921 0.0637 0.6442 23 T 0.5267 0.0357 0.4376 24 I 0.5656 0.0537 0.3807 25 E 0.4419 0.0930 0.4651 26 K 0.3248 0.1131 0.5622 27 V 0.2477 0.1617 0.5905 28 D 0.2318 0.1153 0.6529 29 G 0.2755 0.0928 0.6317 30 R 0.4254 0.0804 0.4942 31 N 0.5349 0.0542 0.4110 32 L 0.6261 0.0429 0.3311 33 R 0.6726 0.0308 0.2966 34 N 0.7017 0.0217 0.2766 35 Y 0.7238 0.0199 0.2562 36 T 0.6975 0.0183 0.2842 37 L 0.6198 0.0194 0.3608 38 P 0.5383 0.0773 0.3844 39 A 0.5220 0.0975 0.3805 40 Y 0.5637 0.0683 0.3680 41 D 0.3572 0.0455 0.5974 42 E 0.1144 0.3803 0.5054 43 D 0.0664 0.1851 0.7485 44 G 0.0943 0.0800 0.8257 45 V 0.4171 0.0236 0.5593 46 K 0.6504 0.0180 0.3316 47 K 0.6736 0.0216 0.3048 48 Q 0.7662 0.0086 0.2251 49 I 0.7814 0.0064 0.2122 50 T 0.7875 0.0055 0.2070 51 F 0.7568 0.0098 0.2334 52 R 0.6665 0.0270 0.3064 53 S 0.6044 0.0625 0.3331 54 T 0.4080 0.1140 0.4780 55 K 0.3259 0.1247 0.5495 56 K 0.2212 0.2866 0.4922 57 E 0.1360 0.3422 0.5218 58 N 0.1415 0.2620 0.5965 59 D 0.0952 0.3975 0.5072 60 H 0.1169 0.4677 0.4154 61 K 0.1934 0.3935 0.4131 62 L 0.2188 0.3160 0.4652 63 N 0.2570 0.2269 0.5161 64 K 0.2519 0.3239 0.4242 65 Y 0.3264 0.2020 0.4716 66 A 0.5505 0.0837 0.3658 67 F 0.6876 0.0433 0.2690 68 L 0.7889 0.0185 0.1927 69 R 0.7939 0.0095 0.1966 70 L 0.7911 0.0082 0.2007 71 Y 0.7798 0.0099 0.2103 72 V 0.7352 0.0179 0.2469 73 D 0.5186 0.0324 0.4491 74 Q 0.2372 0.1909 0.5719 75 D 0.1598 0.2259 0.6143 76 D 0.1420 0.2154 0.6426 77 N 0.1474 0.2722 0.5804 78 S 0.1637 0.2977 0.5386 79 K 0.1403 0.4047 0.4550 80 N 0.1339 0.3699 0.4962 81 E 0.1916 0.2445 0.5639 82 I 0.2657 0.1474 0.5869 83 S 0.2238 0.1791 0.5971 84 S 0.2051 0.1945 0.6005 85 I 0.2831 0.1256 0.5913 86 E 0.4364 0.0664 0.4972 87 V 0.4870 0.0522 0.4608 88 K 0.3933 0.0579 0.5488 89 S 0.3191 0.0699 0.6110 90 Y 0.1291 0.5356 0.3353 91 E 0.1428 0.6122 0.2450 92 E 0.2189 0.5062 0.2749 93 I 0.2573 0.4695 0.2732 94 Q 0.1842 0.3884 0.4273 95 K 0.0391 0.6693 0.2917 96 A 0.0231 0.5837 0.3932 97 D 0.0513 0.3329 0.6158 98 L 0.1399 0.1797 0.6804 99 P 0.1012 0.3068 0.5921 100 E 0.0124 0.7776 0.2099 101 K 0.0119 0.8638 0.1243 102 V 0.0151 0.8636 0.1212 103 K 0.0160 0.8687 0.1153 104 D 0.0229 0.8093 0.1678 105 K 0.0625 0.5856 0.3519 106 F 0.2128 0.2526 0.5346 107 T 0.2938 0.0922 0.6140 108 I 0.3565 0.0576 0.5860 109 K 0.2952 0.0588 0.6460