# This file is the result of combining several RDB files, specifically # T0415.t06.str2.rdb (weight 1.54425) # T0415.t06.str4.rdb (weight 0.924988) # T0415.t06.pb.rdb (weight 0.789901) # T0415.t06.bys.rdb (weight 0.748322) # T0415.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 T0415.t06.str2.rdb # ============================================ # TARGET T0415 # 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 T0415.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 1090 # # ============================================ # Comments from T0415.t06.str4.rdb # ============================================ # TARGET T0415 # 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 T0415.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 1090 # # ============================================ # Comments from T0415.t06.pb.rdb # ============================================ # TARGET T0415 # 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 T0415.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 1090 # # ============================================ # Comments from T0415.t06.bys.rdb # ============================================ # TARGET T0415 # 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 T0415.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 1090 # # ============================================ # Comments from T0415.t06.alpha.rdb # ============================================ # TARGET T0415 # 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 T0415.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 1090 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.1410 0.0809 0.7781 2 K 0.2475 0.0461 0.7064 3 S 0.4370 0.0322 0.5308 4 V 0.7100 0.0090 0.2811 5 V 0.7779 0.0080 0.2142 6 T 0.7715 0.0058 0.2227 7 L 0.7641 0.0079 0.2280 8 K 0.6964 0.0112 0.2925 9 T 0.4585 0.0387 0.5028 10 T 0.2157 0.1559 0.6285 11 D 0.1522 0.1206 0.7272 12 G 0.2481 0.0684 0.6835 13 W 0.5097 0.0377 0.4525 14 I 0.6958 0.0144 0.2898 15 P 0.6536 0.0131 0.3334 16 V 0.6625 0.0144 0.3231 17 P 0.3621 0.0133 0.6245 18 F 0.1298 0.4380 0.4322 19 S 0.1161 0.4776 0.4064 20 K 0.3797 0.2100 0.4103 21 V 0.6906 0.0293 0.2801 22 M 0.7205 0.0367 0.2428 23 Y 0.8200 0.0077 0.1723 24 L 0.7983 0.0121 0.1896 25 E 0.7902 0.0152 0.1946 26 A 0.6836 0.0351 0.2812 27 K 0.4048 0.1218 0.4733 28 D 0.1868 0.0794 0.7338 29 K 0.2918 0.0666 0.6416 30 K 0.6241 0.0156 0.3603 31 T 0.7582 0.0069 0.2349 32 Y 0.8143 0.0053 0.1804 33 V 0.8171 0.0048 0.1780 34 N 0.7756 0.0077 0.2167 35 A 0.6476 0.0223 0.3301 36 E 0.3519 0.1615 0.4866 37 E 0.2341 0.1251 0.6408 38 L 0.2644 0.1195 0.6162 39 T 0.4582 0.1000 0.4418 40 G 0.5282 0.0993 0.3725 41 T 0.6160 0.0834 0.3005 42 H 0.5680 0.1148 0.3172 43 K 0.4408 0.1750 0.3842 44 Y 0.3965 0.1610 0.4424 45 S 0.2767 0.1272 0.5960 46 L 0.0271 0.7452 0.2277 47 Q 0.0108 0.8643 0.1249 48 E 0.0103 0.9041 0.0857 49 F 0.0129 0.8906 0.0964 50 E 0.0114 0.8576 0.1309 51 Y 0.0136 0.7980 0.1884 52 L 0.0360 0.5797 0.3843 53 L 0.1559 0.1460 0.6981 54 P 0.1279 0.1297 0.7423 55 K 0.0307 0.4029 0.5664 56 D 0.0619 0.3823 0.5558 57 S 0.1291 0.3575 0.5133 58 F 0.3671 0.2418 0.3910 59 I 0.4959 0.1773 0.3267 60 R 0.5550 0.1576 0.2874 61 C 0.4991 0.1333 0.3676 62 H 0.3186 0.1774 0.5039 63 R 0.2150 0.3127 0.4723 64 S 0.3271 0.2885 0.3843 65 F 0.4700 0.2740 0.2560 66 I 0.4885 0.2761 0.2355 67 V 0.5542 0.1720 0.2738 68 N 0.3161 0.1808 0.5030 69 V 0.0385 0.6826 0.2789 70 N 0.0321 0.7463 0.2216 71 H 0.0466 0.7449 0.2085 72 I 0.0811 0.7355 0.1834 73 K 0.0702 0.6715 0.2583 74 A 0.1538 0.4350 0.4113 75 I 0.3566 0.2004 0.4429 76 Y 0.3755 0.0511 0.5734 77 P 0.2737 0.1640 0.5623 78 D 0.1443 0.1711 0.6846 79 T 0.1107 0.2270 0.6623 80 H 0.1367 0.1256 0.7377 81 S 0.2327 0.0840 0.6832 82 T 0.5920 0.0236 0.3844 83 F 0.7669 0.0069 0.2261 84 L 0.8223 0.0044 0.1733 85 L 0.8285 0.0044 0.1671 86 S 0.8244 0.0046 0.1710 87 M 0.7320 0.0089 0.2591 88 D 0.5688 0.0699 0.3613 89 N 0.1980 0.0661 0.7360 90 G 0.1065 0.0617 0.8319 91 E 0.4296 0.0297 0.5406 92 R 0.5944 0.0199 0.3857 93 V 0.6423 0.0182 0.3395 94 P 0.5667 0.0209 0.4123 95 V 0.5250 0.0720 0.4031 96 S 0.3116 0.0890 0.5994 97 Q 0.0314 0.6778 0.2908 98 S 0.0174 0.8024 0.1802 99 Y 0.0189 0.8475 0.1336 100 A 0.0100 0.9013 0.0887 101 S 0.0084 0.9180 0.0736 102 Y 0.0084 0.9207 0.0710 103 F 0.0084 0.9201 0.0715 104 R 0.0085 0.9141 0.0775 105 K 0.0086 0.9090 0.0825 106 L 0.0133 0.8010 0.1857 107 L 0.0591 0.4870 0.4539 108 G 0.0475 0.1982 0.7543 109 F 0.1429 0.1274 0.7297