# 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) # T0639.t04.str2.rdb (weight 1.54425) # T0639.t04.str4.rdb (weight 0.924988) # T0639.t04.pb.rdb (weight 0.789901) # T0639.t04.bys.rdb (weight 0.748322) # T0639.t04.alpha.rdb (weight 0.678173) # T0639.t2k.str2.rdb (weight 1.54425) # T0639.t2k.str4.rdb (weight 0.924988) # T0639.t2k.pb.rdb (weight 0.789901) # T0639.t2k.bys.rdb (weight 0.748322) # T0639.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 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 # # ============================================ # Comments from T0639.t04.str2.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t04.str4.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t04.pb.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t04.bys.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t04.alpha.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t2k.str2.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t2k.str4.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t2k.pb.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t2k.bys.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ # Comments from T0639.t2k.alpha.rdb # ============================================ # TARGET T0639 # 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 T0639.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 2 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1006 0.3974 0.5020 2 N 0.0694 0.5046 0.4259 3 A 0.0721 0.5991 0.3288 4 M 0.0789 0.6617 0.2593 5 E 0.0524 0.7075 0.2400 6 T 0.0520 0.6905 0.2575 7 L 0.0279 0.8042 0.1679 8 N 0.0138 0.8666 0.1196 9 D 0.0130 0.8789 0.1081 10 I 0.0127 0.8904 0.0969 11 K 0.0097 0.9136 0.0767 12 K 0.0091 0.9179 0.0729 13 I 0.0110 0.9125 0.0765 14 L 0.0136 0.8971 0.0893 15 I 0.0163 0.8735 0.1101 16 N 0.0402 0.7430 0.2168 17 V 0.0688 0.5057 0.4254 18 G 0.0932 0.2791 0.6277 19 L 0.1786 0.3043 0.5170 20 Y 0.2325 0.2675 0.5001 21 Q 0.2163 0.1799 0.6038 22 G 0.1991 0.1058 0.6951 23 F 0.3286 0.0795 0.5920 24 D 0.3469 0.0835 0.5697 25 L 0.1965 0.2963 0.5072 26 T 0.1587 0.2140 0.6273 27 D 0.1898 0.1016 0.7086 28 P 0.0730 0.4328 0.4942 29 K 0.1102 0.4111 0.4787 30 V 0.1894 0.3380 0.4726 31 S 0.1892 0.3504 0.4604 32 E 0.1085 0.5927 0.2987 33 E 0.1502 0.4659 0.3838 34 V 0.2431 0.2793 0.4776 35 N 0.1675 0.1776 0.6550 36 H 0.1425 0.2633 0.5943 37 E 0.1890 0.2371 0.5740 38 T 0.2540 0.2109 0.5351 39 A 0.2579 0.1948 0.5473 40 N 0.2410 0.1653 0.5937 41 M 0.2487 0.3510 0.4003 42 K 0.3067 0.3734 0.3199 43 W 0.3549 0.3745 0.2706 44 I 0.3266 0.3814 0.2919 45 K 0.2939 0.3706 0.3355 46 D 0.2423 0.2768 0.4809 47 Y 0.2275 0.2007 0.5718 48 T 0.2057 0.1532 0.6411 49 S 0.1381 0.2522 0.6097 50 D 0.1040 0.1819 0.7141 51 G 0.0852 0.1772 0.7375 52 N 0.1529 0.1620 0.6851 53 W 0.1537 0.2556 0.5907 54 D 0.1109 0.3415 0.5476 55 N 0.0508 0.6035 0.3458 56 E 0.0495 0.6827 0.2678 57 F 0.0626 0.7207 0.2167 58 K 0.0275 0.8366 0.1359 59 E 0.0137 0.8817 0.1046 60 D 0.0205 0.8369 0.1427 61 L 0.0135 0.8699 0.1166 62 K 0.0093 0.8978 0.0929 63 N 0.0102 0.8864 0.1034 64 F 0.0126 0.8748 0.1127 65 L 0.0118 0.8957 0.0925 66 D 0.0099 0.8917 0.0984 67 Y 0.0154 0.8535 0.1311 68 M 0.0289 0.8498 0.1213 69 E 0.0181 0.8792 0.1027 70 V 0.0237 0.8601 0.1162 71 C 0.0369 0.8473 0.1158 72 Q 0.0481 0.8293 0.1226 73 L 0.0810 0.7617 0.1573 74 A 0.1238 0.6169 0.2593 75 L 0.1691 0.4392 0.3917 76 N 0.1286 0.2624 0.6091 77 D 0.1111 0.2746 0.6143 78 K 0.0496 0.4470 0.5033 79 N 0.0944 0.3494 0.5563 80 F 0.1843 0.4034 0.4123 81 K 0.2049 0.4815 0.3136 82 I 0.1763 0.5678 0.2558 83 A 0.1089 0.6323 0.2588 84 S 0.0669 0.6696 0.2635 85 N 0.0381 0.7293 0.2326 86 S 0.0333 0.7898 0.1769 87 L 0.0215 0.8535 0.1249 88 F 0.0180 0.8856 0.0964 89 M 0.0201 0.8930 0.0870 90 A 0.0283 0.8793 0.0924 91 M 0.0612 0.8216 0.1172 92 I 0.0914 0.7522 0.1564 93 Y 0.1270 0.6007 0.2722 94 A 0.1061 0.4785 0.4154 95 G 0.0819 0.3547 0.5635 96 N 0.1088 0.4047 0.4865 97 L 0.0503 0.6773 0.2724 98 S 0.0327 0.7969 0.1704 99 L 0.0329 0.8381 0.1290 100 I 0.0301 0.8482 0.1216 101 F 0.0259 0.8605 0.1136 102 D 0.0185 0.8607 0.1208 103 S 0.0283 0.8019 0.1697 104 I 0.0476 0.7559 0.1965 105 K 0.0436 0.7409 0.2155 106 T 0.0468 0.7349 0.2184 107 D 0.0504 0.7169 0.2327 108 I 0.0402 0.7814 0.1784 109 S 0.0353 0.8221 0.1425 110 T 0.0487 0.8081 0.1432 111 L 0.0723 0.7427 0.1851 112 L 0.1343 0.5998 0.2660 113 S 0.1377 0.5377 0.3246 114 A 0.0944 0.6060 0.2996 115 E 0.1300 0.5063 0.3636 116 Y 0.2066 0.3648 0.4286 117 K 0.2081 0.3121 0.4798 118 K 0.1984 0.2862 0.5153 119 N 0.1748 0.1891 0.6361 120 S 0.2127 0.1451 0.6421 121 F 0.2887 0.1054 0.6059 122 S 0.3273 0.0832 0.5895 123 W 0.3064 0.0499 0.6437 124 P 0.2168 0.1551 0.6280 125 S 0.2269 0.1566 0.6165 126 L 0.2213 0.1626 0.6161 127 D 0.1682 0.1321 0.6996 128 E 0.1104 0.3708 0.5188