# 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) # 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 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3018 0.1111 0.5871 2 E 0.3513 0.1438 0.5048 3 R 0.3707 0.2358 0.3935 4 A 0.2929 0.3123 0.3948 5 S 0.2884 0.2424 0.4692 6 L 0.2893 0.2035 0.5072 7 N 0.2582 0.1256 0.6162 8 R 0.1876 0.3138 0.4985 9 I 0.2339 0.2296 0.5364 10 G 0.3212 0.1147 0.5641 11 K 0.4170 0.0825 0.5005 12 D 0.5750 0.0450 0.3799 13 V 0.7168 0.0127 0.2706 14 Y 0.7966 0.0068 0.1966 15 Y 0.8166 0.0047 0.1787 16 M 0.8223 0.0049 0.1729 17 Q 0.8072 0.0054 0.1873 18 I 0.7496 0.0069 0.2435 19 K 0.5725 0.0313 0.3963 20 G 0.3523 0.0552 0.5924 21 E 0.2893 0.0872 0.6234 22 G 0.3582 0.0701 0.5717 23 T 0.5347 0.0427 0.4226 24 I 0.5815 0.0446 0.3739 25 E 0.4681 0.0851 0.4468 26 K 0.3686 0.0985 0.5329 27 V 0.2367 0.1825 0.5808 28 D 0.2226 0.1237 0.6537 29 G 0.3019 0.1006 0.5975 30 R 0.4819 0.0906 0.4274 31 N 0.6111 0.0574 0.3315 32 L 0.6931 0.0361 0.2708 33 R 0.7442 0.0268 0.2289 34 N 0.7397 0.0178 0.2424 35 Y 0.7705 0.0124 0.2171 36 T 0.7377 0.0117 0.2506 37 L 0.6902 0.0161 0.2936 38 P 0.6250 0.0392 0.3358 39 A 0.6603 0.0625 0.2772 40 Y 0.6645 0.0463 0.2891 41 D 0.4172 0.0330 0.5498 42 E 0.0588 0.4034 0.5378 43 D 0.0661 0.1956 0.7384 44 G 0.0846 0.0704 0.8449 45 V 0.4352 0.0370 0.5278 46 K 0.6519 0.0190 0.3291 47 K 0.7368 0.0142 0.2491 48 Q 0.7936 0.0050 0.2014 49 I 0.8094 0.0056 0.1850 50 T 0.8131 0.0047 0.1822 51 F 0.7921 0.0066 0.2013 52 R 0.6865 0.0251 0.2884 53 S 0.5537 0.0617 0.3846 54 T 0.3699 0.1019 0.5282 55 K 0.2615 0.1593 0.5792 56 K 0.2024 0.2365 0.5611 57 E 0.1463 0.3057 0.5480 58 N 0.1226 0.2844 0.5930 59 D 0.0964 0.3214 0.5822 60 H 0.1336 0.3367 0.5297 61 K 0.1754 0.3082 0.5164 62 L 0.2737 0.1480 0.5783 63 N 0.2215 0.0936 0.6848 64 K 0.1236 0.3150 0.5614 65 Y 0.2166 0.1531 0.6303 66 A 0.5608 0.0519 0.3872 67 F 0.7344 0.0176 0.2479 68 L 0.8064 0.0093 0.1843 69 R 0.8234 0.0061 0.1705 70 L 0.8142 0.0062 0.1796 71 Y 0.7963 0.0096 0.1941 72 V 0.7429 0.0206 0.2364 73 D 0.4890 0.0486 0.4623 74 Q 0.2410 0.1823 0.5767 75 D 0.1691 0.2314 0.5995 76 D 0.1420 0.2127 0.6453 77 N 0.1231 0.1936 0.6833 78 S 0.1650 0.1905 0.6444 79 K 0.1362 0.2981 0.5657 80 N 0.1625 0.2643 0.5732 81 E 0.2317 0.2034 0.5650 82 I 0.2771 0.1028 0.6201 83 S 0.2323 0.1547 0.6129 84 S 0.2411 0.1185 0.6404 85 I 0.3849 0.0680 0.5471 86 E 0.5783 0.0492 0.3725 87 V 0.5825 0.0321 0.3853 88 K 0.4841 0.0500 0.4659 89 S 0.3613 0.0292 0.6095 90 Y 0.1284 0.3876 0.4840 91 E 0.1282 0.5568 0.3151 92 E 0.2162 0.4263 0.3575 93 I 0.2630 0.2480 0.4890 94 Q 0.1994 0.1859 0.6147 95 K 0.0431 0.6212 0.3357 96 A 0.0235 0.6312 0.3452 97 D 0.0346 0.4974 0.4680 98 L 0.1301 0.2468 0.6231 99 P 0.0640 0.4914 0.4447 100 E 0.0114 0.7713 0.2174 101 K 0.0104 0.8676 0.1220 102 V 0.0130 0.8883 0.0987 103 K 0.0101 0.9071 0.0828 104 D 0.0114 0.8677 0.1209 105 K 0.0238 0.7785 0.1977 106 F 0.0658 0.5371 0.3971 107 T 0.1008 0.3511 0.5480 108 I 0.1791 0.2071 0.6138 109 K 0.1587 0.1606 0.6806