# This file is the result of combining several RDB files, specifically # T0391.t06.str2.rdb (weight 1.54425) # T0391.t06.str4.rdb (weight 0.924988) # T0391.t06.pb.rdb (weight 0.789901) # T0391.t06.bys.rdb (weight 0.748322) # T0391.t06.alpha.rdb (weight 0.678173) # T0391.t04.str2.rdb (weight 1.54425) # T0391.t04.str4.rdb (weight 0.924988) # T0391.t04.pb.rdb (weight 0.789901) # T0391.t04.bys.rdb (weight 0.748322) # T0391.t04.alpha.rdb (weight 0.678173) # T0391.t2k.str2.rdb (weight 1.54425) # T0391.t2k.str4.rdb (weight 0.924988) # T0391.t2k.pb.rdb (weight 0.789901) # T0391.t2k.bys.rdb (weight 0.748322) # T0391.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 T0391.t06.str2.rdb # ============================================ # TARGET T0391 # 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 T0391.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 2619 # # ============================================ # Comments from T0391.t06.str4.rdb # ============================================ # TARGET T0391 # 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 T0391.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 2619 # # ============================================ # Comments from T0391.t06.pb.rdb # ============================================ # TARGET T0391 # 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 T0391.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 2619 # # ============================================ # Comments from T0391.t06.bys.rdb # ============================================ # TARGET T0391 # 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 T0391.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 2619 # # ============================================ # Comments from T0391.t06.alpha.rdb # ============================================ # TARGET T0391 # 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 T0391.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 2619 # # ============================================ # Comments from T0391.t04.str2.rdb # ============================================ # TARGET T0391 # 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 T0391.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 1888 # # ============================================ # Comments from T0391.t04.str4.rdb # ============================================ # TARGET T0391 # 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 T0391.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 1888 # # ============================================ # Comments from T0391.t04.pb.rdb # ============================================ # TARGET T0391 # 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 T0391.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 1888 # # ============================================ # Comments from T0391.t04.bys.rdb # ============================================ # TARGET T0391 # 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 T0391.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 1888 # # ============================================ # Comments from T0391.t04.alpha.rdb # ============================================ # TARGET T0391 # 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 T0391.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 1888 # # ============================================ # Comments from T0391.t2k.str2.rdb # ============================================ # TARGET T0391 # 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 T0391.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 619 # # ============================================ # Comments from T0391.t2k.str4.rdb # ============================================ # TARGET T0391 # 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 T0391.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 619 # # ============================================ # Comments from T0391.t2k.pb.rdb # ============================================ # TARGET T0391 # 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 T0391.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 619 # # ============================================ # Comments from T0391.t2k.bys.rdb # ============================================ # TARGET T0391 # 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 T0391.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 619 # # ============================================ # Comments from T0391.t2k.alpha.rdb # ============================================ # TARGET T0391 # 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 T0391.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 619 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1756 0.1438 0.6806 2 D 0.1716 0.1412 0.6872 3 P 0.0208 0.7022 0.2769 4 E 0.0241 0.7163 0.2596 5 I 0.0446 0.7399 0.2155 6 S 0.0335 0.7509 0.2156 7 E 0.0336 0.7290 0.2375 8 Q 0.0592 0.6448 0.2960 9 D 0.1072 0.4702 0.4226 10 E 0.0338 0.6715 0.2946 11 E 0.0455 0.6152 0.3393 12 K 0.0833 0.5307 0.3861 13 K 0.1458 0.3992 0.4550 14 K 0.1563 0.3445 0.4992 15 Y 0.1670 0.2135 0.6194 16 T 0.3407 0.1098 0.5494 17 S 0.5525 0.0566 0.3910 18 V 0.6675 0.0344 0.2980 19 C 0.6505 0.0326 0.3170 20 V 0.6122 0.0485 0.3393 21 G 0.4607 0.0420 0.4972 22 R 0.2874 0.0690 0.6436 23 E 0.0847 0.5506 0.3647 24 E 0.0448 0.6728 0.2823 25 D 0.0914 0.4352 0.4734 26 I 0.1985 0.2400 0.5615 27 R 0.1591 0.1953 0.6456 28 K 0.0996 0.2565 0.6439 29 S 0.0887 0.1468 0.7645 30 E 0.2227 0.0821 0.6953 31 R 0.4093 0.0528 0.5378 32 M 0.6285 0.0261 0.3454 33 T 0.7439 0.0113 0.2448 34 A 0.7746 0.0089 0.2165 35 V 0.7401 0.0073 0.2526 36 V 0.6364 0.0230 0.3406 37 H 0.3135 0.0537 0.6328 38 D 0.1566 0.0708 0.7726 39 R 0.4224 0.0192 0.5583 40 E 0.6470 0.0104 0.3426 41 V 0.8090 0.0047 0.1862 42 V 0.8291 0.0042 0.1668 43 I 0.8306 0.0042 0.1652 44 F 0.8009 0.0051 0.1940 45 Y 0.7407 0.0091 0.2502 46 H 0.5353 0.0363 0.4284 47 K 0.2499 0.0585 0.6916 48 G 0.1148 0.0847 0.8005 49 E 0.5212 0.0200 0.4588 50 Y 0.7093 0.0101 0.2807 51 H 0.7643 0.0132 0.2225 52 A 0.7703 0.0141 0.2156 53 M 0.6989 0.0433 0.2578 54 D 0.5732 0.0955 0.3313 55 I 0.3452 0.2322 0.4226 56 R 0.2845 0.1989 0.5166 57 C 0.2895 0.1835 0.5270 58 Y 0.1831 0.2806 0.5363 59 H 0.1827 0.2337 0.5836 60 S 0.1329 0.2024 0.6647 61 G 0.1313 0.1179 0.7508 62 G 0.2466 0.0628 0.6906 63 P 0.3033 0.1181 0.5786 64 L 0.2767 0.1960 0.5272 65 H 0.3015 0.1961 0.5024 66 L 0.2731 0.1555 0.5714 67 G 0.3720 0.0799 0.5481 68 E 0.6049 0.0524 0.3427 69 I 0.6454 0.0612 0.2934 70 E 0.5862 0.0810 0.3328 71 D 0.3903 0.0637 0.5459 72 F 0.2371 0.1650 0.5979 73 N 0.1177 0.1327 0.7496 74 G 0.1049 0.1014 0.7936 75 Q 0.2780 0.0600 0.6620 76 S 0.4869 0.0361 0.4770 77 C 0.6829 0.0174 0.2997 78 I 0.7667 0.0098 0.2235 79 V 0.7389 0.0126 0.2485 80 C 0.5066 0.0118 0.4817 81 P 0.2914 0.2100 0.4986 82 W 0.2139 0.2319 0.5543 83 H 0.2820 0.1333 0.5847 84 K 0.3852 0.0986 0.5161 85 Y 0.6143 0.0430 0.3426 86 K 0.7112 0.0227 0.2661 87 I 0.7605 0.0178 0.2217 88 T 0.6216 0.0185 0.3599 89 L 0.3586 0.2383 0.4031 90 A 0.2021 0.2483 0.5496 91 T 0.1507 0.1424 0.7069 92 G 0.1460 0.0950 0.7590 93 E 0.2933 0.0679 0.6388 94 G 0.4002 0.0985 0.5014 95 L 0.4221 0.1236 0.4543 96 Y 0.4239 0.0974 0.4787 97 Q 0.3484 0.0965 0.5551 98 S 0.2724 0.1688 0.5588 99 I 0.2210 0.1657 0.6133 100 N 0.2120 0.0747 0.7133 101 P 0.1205 0.1977 0.6818 102 K 0.1171 0.2317 0.6511 103 D 0.1817 0.0993 0.7190 104 P 0.0773 0.3170 0.6057 105 S 0.0991 0.2715 0.6294 106 A 0.1378 0.2536 0.6086 107 K 0.1804 0.1566 0.6630 108 P 0.1419 0.2884 0.5698 109 K 0.1926 0.2473 0.5601 110 W 0.2739 0.1927 0.5334 111 C 0.2531 0.1281 0.6188 112 S 0.1654 0.2446 0.5900 113 K 0.1044 0.2452 0.6504 114 G 0.0838 0.1388 0.7774 115 V 0.2402 0.0763 0.6836 116 K 0.3489 0.0598 0.5913 117 Q 0.4405 0.0459 0.5136 118 R 0.5254 0.0339 0.4407 119 I 0.6323 0.0261 0.3416 120 H 0.6358 0.0160 0.3482 121 T 0.6518 0.0115 0.3366 122 V 0.7085 0.0107 0.2808 123 K 0.7179 0.0087 0.2733 124 V 0.6827 0.0173 0.3000 125 D 0.5063 0.0539 0.4398 126 N 0.3029 0.0623 0.6348 127 G 0.2234 0.0513 0.7253 128 N 0.5919 0.0101 0.3980 129 I 0.7562 0.0062 0.2376 130 Y 0.8020 0.0055 0.1925 131 V 0.8202 0.0047 0.1751 132 T 0.7329 0.0071 0.2600 133 L 0.5864 0.0364 0.3771 134 S 0.2820 0.0463 0.6718 135 K 0.1374 0.1896 0.6729 136 E 0.1875 0.1223 0.6902 137 P 0.1666 0.2104 0.6230 138 F 0.1988 0.1699 0.6314 139 K 0.2036 0.1531 0.6433 140 C 0.1936 0.1211 0.6854 141 D 0.1534 0.1705 0.6761 142 S 0.0882 0.3511 0.5607 143 D 0.1033 0.3280 0.5687 144 Y 0.1799 0.2174 0.6027 145 Y 0.2030 0.1793 0.6177 146 A 0.1918 0.1863 0.6219 147 T 0.1315 0.2523 0.6162 148 G 0.1143 0.2690 0.6167 149 E 0.1827 0.2486 0.5687 150 F 0.2735 0.2203 0.5062 151 K 0.3254 0.2216 0.4530 152 V 0.3804 0.2189 0.4006 153 I 0.2969 0.2522 0.4509 154 Q 0.2423 0.2251 0.5325 155 S 0.1849 0.1926 0.6225 156 S 0.1700 0.1481 0.6819 157 S 0.1479 0.1493 0.7029