# This file is the result of combining several RDB files, specifically # T0639.t06.str2.rdb (weight 1.54425) # T0639.t06.str4.rdb (weight 0.924988) # T0639.t06.pb.rdb (weight 0.789901) # T0639.t06.bys.rdb (weight 0.748322) # T0639.t06.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 T0639.t06.str2.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t06.str4.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t06.pb.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t06.bys.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t06.alpha.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0736 0.5319 0.3944 2 N 0.0592 0.5944 0.3464 3 A 0.0472 0.7192 0.2337 4 M 0.0322 0.8108 0.1570 5 E 0.0228 0.8204 0.1568 6 T 0.0314 0.7731 0.1956 7 L 0.0212 0.8191 0.1597 8 N 0.0107 0.8819 0.1074 9 D 0.0109 0.8968 0.0924 10 I 0.0100 0.9092 0.0808 11 K 0.0088 0.9154 0.0757 12 K 0.0086 0.9175 0.0738 13 I 0.0096 0.9115 0.0789 14 L 0.0134 0.8877 0.0988 15 I 0.0255 0.8607 0.1137 16 N 0.0504 0.7339 0.2157 17 V 0.0908 0.4998 0.4094 18 G 0.1105 0.3340 0.5555 19 L 0.1765 0.4030 0.4204 20 Y 0.2174 0.3790 0.4036 21 Q 0.1775 0.2625 0.5600 22 G 0.1732 0.1685 0.6584 23 F 0.3073 0.0769 0.6158 24 D 0.2890 0.0745 0.6365 25 L 0.1709 0.2722 0.5570 26 T 0.1602 0.1787 0.6612 27 D 0.2134 0.0692 0.7174 28 P 0.0992 0.3438 0.5569 29 K 0.1436 0.3463 0.5101 30 V 0.2208 0.2579 0.5213 31 S 0.2199 0.3011 0.4790 32 E 0.1800 0.4683 0.3517 33 E 0.2092 0.4077 0.3830 34 V 0.2730 0.2489 0.4782 35 N 0.2031 0.1711 0.6258 36 H 0.1307 0.2857 0.5836 37 E 0.1171 0.3056 0.5773 38 T 0.1835 0.1911 0.6254 39 A 0.1240 0.3036 0.5725 40 N 0.1418 0.2070 0.6512 41 M 0.2309 0.3027 0.4664 42 K 0.2990 0.3582 0.3428 43 W 0.4111 0.3040 0.2849 44 I 0.3257 0.3370 0.3373 45 K 0.2237 0.3818 0.3944 46 D 0.2119 0.2681 0.5199 47 Y 0.2363 0.1813 0.5824 48 T 0.2394 0.1447 0.6159 49 S 0.1724 0.2168 0.6108 50 D 0.1213 0.1693 0.7094 51 G 0.0908 0.1696 0.7396 52 N 0.1581 0.1523 0.6896 53 W 0.1463 0.2742 0.5795 54 D 0.0970 0.4060 0.4970 55 N 0.0496 0.6144 0.3359 56 E 0.0527 0.6870 0.2602 57 F 0.0657 0.7226 0.2116 58 K 0.0329 0.8257 0.1414 59 E 0.0204 0.8528 0.1268 60 D 0.0292 0.8175 0.1532 61 L 0.0136 0.8649 0.1215 62 K 0.0092 0.8925 0.0983 63 N 0.0103 0.8752 0.1144 64 F 0.0130 0.8770 0.1100 65 L 0.0105 0.8920 0.0975 66 D 0.0100 0.8764 0.1135 67 Y 0.0123 0.8622 0.1256 68 M 0.0164 0.8695 0.1141 69 E 0.0158 0.8862 0.0980 70 V 0.0230 0.8778 0.0993 71 C 0.0272 0.8704 0.1024 72 Q 0.0467 0.8374 0.1159 73 L 0.0786 0.7658 0.1556 74 A 0.1070 0.6299 0.2631 75 L 0.1661 0.4306 0.4033 76 N 0.1391 0.2713 0.5896 77 D 0.1045 0.2561 0.6393 78 K 0.0471 0.4383 0.5147 79 N 0.0853 0.3429 0.5718 80 F 0.1788 0.3869 0.4343 81 K 0.1783 0.5070 0.3148 82 I 0.1962 0.5444 0.2594 83 A 0.1141 0.5978 0.2881 84 S 0.0717 0.6238 0.3046 85 N 0.0419 0.6762 0.2819 86 S 0.0317 0.7835 0.1848 87 L 0.0185 0.8671 0.1145 88 F 0.0145 0.8933 0.0922 89 M 0.0140 0.9047 0.0814 90 A 0.0251 0.8869 0.0880 91 M 0.0602 0.8290 0.1108 92 I 0.1349 0.7126 0.1525 93 Y 0.1705 0.5732 0.2563 94 A 0.1344 0.4665 0.3991 95 G 0.1025 0.3542 0.5433 96 N 0.1118 0.4137 0.4745 97 L 0.0488 0.7130 0.2382 98 S 0.0267 0.8229 0.1503 99 L 0.0361 0.8372 0.1268 100 I 0.0426 0.8352 0.1222 101 F 0.0312 0.8524 0.1163 102 D 0.0215 0.8486 0.1300 103 S 0.0283 0.8060 0.1657 104 I 0.0460 0.7622 0.1918 105 K 0.0345 0.7757 0.1898 106 T 0.0382 0.7696 0.1922 107 D 0.0456 0.7530 0.2014 108 I 0.0234 0.8177 0.1589 109 S 0.0237 0.8503 0.1259 110 T 0.0318 0.8461 0.1220 111 L 0.0557 0.7854 0.1589 112 L 0.1025 0.6657 0.2318 113 S 0.1231 0.5648 0.3121 114 A 0.0785 0.6061 0.3154 115 E 0.0969 0.5604 0.3428 116 Y 0.1570 0.4677 0.3753 117 K 0.1871 0.3514 0.4615 118 K 0.1833 0.2679 0.5489 119 N 0.1652 0.1960 0.6388 120 S 0.2010 0.1667 0.6323 121 F 0.2905 0.1054 0.6040 122 S 0.2991 0.0708 0.6302 123 W 0.2878 0.0447 0.6675 124 P 0.1910 0.1788 0.6302 125 S 0.2366 0.1912 0.5721 126 L 0.2213 0.1909 0.5878 127 D 0.1816 0.1461 0.6723 128 E 0.1107 0.3336 0.5557