# This file is the result of combining several RDB files, specifically # T0446.t06.str2.rdb (weight 1.54425) # T0446.t06.str4.rdb (weight 0.924988) # T0446.t06.pb.rdb (weight 0.789901) # T0446.t06.bys.rdb (weight 0.748322) # T0446.t06.alpha.rdb (weight 0.678173) # T0446.t04.str2.rdb (weight 1.54425) # T0446.t04.str4.rdb (weight 0.924988) # T0446.t04.pb.rdb (weight 0.789901) # T0446.t04.bys.rdb (weight 0.748322) # T0446.t04.alpha.rdb (weight 0.678173) # T0446.t2k.str2.rdb (weight 1.54425) # T0446.t2k.str4.rdb (weight 0.924988) # T0446.t2k.pb.rdb (weight 0.789901) # T0446.t2k.bys.rdb (weight 0.748322) # T0446.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 T0446.t06.str2.rdb # ============================================ # TARGET T0446 # 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 T0446.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 26.7682 # # ============================================ # Comments from T0446.t06.str4.rdb # ============================================ # TARGET T0446 # 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 T0446.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 26.7682 # # ============================================ # Comments from T0446.t06.pb.rdb # ============================================ # TARGET T0446 # 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 T0446.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 26.7682 # # ============================================ # Comments from T0446.t06.bys.rdb # ============================================ # TARGET T0446 # 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 T0446.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 26.7682 # # ============================================ # Comments from T0446.t06.alpha.rdb # ============================================ # TARGET T0446 # 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 T0446.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 26.7682 # # ============================================ # Comments from T0446.t04.str2.rdb # ============================================ # TARGET T0446 # 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 T0446.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 27.4382 # # ============================================ # Comments from T0446.t04.str4.rdb # ============================================ # TARGET T0446 # 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 T0446.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 27.4382 # # ============================================ # Comments from T0446.t04.pb.rdb # ============================================ # TARGET T0446 # 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 T0446.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 27.4382 # # ============================================ # Comments from T0446.t04.bys.rdb # ============================================ # TARGET T0446 # 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 T0446.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 27.4382 # # ============================================ # Comments from T0446.t04.alpha.rdb # ============================================ # TARGET T0446 # 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 T0446.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 27.4382 # # ============================================ # Comments from T0446.t2k.str2.rdb # ============================================ # TARGET T0446 # 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 T0446.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 19.26 # # ============================================ # Comments from T0446.t2k.str4.rdb # ============================================ # TARGET T0446 # 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 T0446.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 19.26 # # ============================================ # Comments from T0446.t2k.pb.rdb # ============================================ # TARGET T0446 # 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 T0446.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 19.26 # # ============================================ # Comments from T0446.t2k.bys.rdb # ============================================ # TARGET T0446 # 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 T0446.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 19.26 # # ============================================ # Comments from T0446.t2k.alpha.rdb # ============================================ # TARGET T0446 # 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 T0446.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 19.26 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1841 0.1993 0.6166 2 G 0.1587 0.1861 0.6553 3 L 0.1893 0.3240 0.4867 4 L 0.2027 0.3871 0.4102 5 D 0.1171 0.5240 0.3588 6 A 0.0721 0.6194 0.3086 7 L 0.0983 0.5686 0.3332 8 M 0.1386 0.4089 0.4524 9 G 0.1383 0.3122 0.5495 10 N 0.1680 0.2544 0.5776 11 A 0.1655 0.2983 0.5362 12 A 0.1639 0.3362 0.4999 13 E 0.1821 0.3412 0.4766 14 V 0.2391 0.2286 0.5323 15 N 0.1802 0.1286 0.6912 16 L 0.0244 0.7040 0.2716 17 D 0.0145 0.8237 0.1617 18 E 0.0149 0.8781 0.1070 19 L 0.0139 0.8934 0.0927 20 A 0.0124 0.8908 0.0967 21 Q 0.0108 0.8809 0.1084 22 E 0.0175 0.7764 0.2061 23 L 0.0455 0.6403 0.3143 24 G 0.0820 0.5100 0.4080 25 P 0.0651 0.6287 0.3063 26 I 0.1297 0.4752 0.3951 27 M 0.2028 0.3666 0.4306 28 G 0.1626 0.2111 0.6263 29 D 0.0851 0.2225 0.6924 30 N 0.0553 0.1699 0.7748 31 E 0.2055 0.2315 0.5630 32 Q 0.3501 0.2927 0.3572 33 L 0.3259 0.4620 0.2121 34 A 0.3211 0.5220 0.1569 35 L 0.3603 0.5201 0.1195 36 A 0.2801 0.5966 0.1233 37 Y 0.2838 0.5753 0.1409 38 R 0.2900 0.5212 0.1888 39 V 0.3546 0.4094 0.2360 40 I 0.3293 0.3293 0.3414 41 R 0.2643 0.2830 0.4527 42 D 0.2555 0.1986 0.5458 43 M 0.5243 0.1179 0.3578 44 F 0.6683 0.0504 0.2813 45 V 0.7477 0.0299 0.2224 46 F 0.6495 0.0407 0.3098 47 T 0.4662 0.0565 0.4773 48 N 0.3701 0.0645 0.5654 49 K 0.3503 0.1373 0.5124 50 R 0.5842 0.0655 0.3504 51 L 0.7377 0.0274 0.2349 52 I 0.7874 0.0130 0.1996 53 L 0.7701 0.0159 0.2140 54 I 0.7125 0.0342 0.2533 55 D 0.5034 0.0490 0.4475 56 K 0.2046 0.2763 0.5191 57 Q 0.1347 0.2239 0.6414 58 G 0.1782 0.1228 0.6989 59 V 0.3062 0.1256 0.5682 60 T 0.3342 0.1040 0.5618 61 G 0.3074 0.0970 0.5955 62 K 0.4766 0.0609 0.4625 63 K 0.5534 0.0454 0.4012 64 V 0.6421 0.0352 0.3227 65 S 0.6619 0.0322 0.3059 66 Y 0.6674 0.0385 0.2942 67 H 0.6534 0.0305 0.3161 68 S 0.6344 0.0292 0.3364 69 V 0.5179 0.0233 0.4589 70 P 0.3751 0.0487 0.5762 71 Y 0.2420 0.2284 0.5296 72 K 0.2290 0.2922 0.4787 73 A 0.3942 0.1532 0.4526 74 I 0.4995 0.0815 0.4190 75 T 0.5112 0.0742 0.4145 76 H 0.6817 0.0454 0.2729 77 F 0.6966 0.0237 0.2797 78 E 0.7281 0.0189 0.2530 79 V 0.7002 0.0378 0.2620 80 E 0.6199 0.0723 0.3078 81 T 0.4871 0.0738 0.4391 82 A 0.3067 0.1082 0.5850 83 G 0.2534 0.1118 0.6348 84 T 0.3983 0.1007 0.5010 85 F 0.4264 0.0904 0.4833 86 D 0.3380 0.0784 0.5837 87 M 0.1645 0.2936 0.5419 88 D 0.1976 0.2058 0.5966 89 A 0.1885 0.3077 0.5038 90 E 0.3655 0.2216 0.4129 91 L 0.7058 0.0613 0.2329 92 K 0.7421 0.0609 0.1970 93 L 0.7791 0.0322 0.1887 94 W 0.7636 0.0298 0.2066 95 I 0.6778 0.0493 0.2730 96 S 0.3757 0.0812 0.5431 97 G 0.1884 0.1156 0.6959 98 Q 0.1803 0.1343 0.6854 99 K 0.2273 0.1382 0.6345 100 D 0.2588 0.0835 0.6577 101 P 0.2898 0.1676 0.5426 102 L 0.3240 0.2509 0.4251 103 V 0.3595 0.3291 0.3115 104 K 0.3071 0.4350 0.2579 105 E 0.2664 0.4287 0.3049 106 L 0.2532 0.3925 0.3543 107 K 0.1741 0.3213 0.5046 108 K 0.1105 0.1971 0.6924 109 G 0.0780 0.1321 0.7899 110 T 0.1762 0.1715 0.6524 111 D 0.2112 0.2009 0.5878 112 V 0.1009 0.6160 0.2832 113 V 0.0516 0.7547 0.1937 114 G 0.0453 0.8085 0.1462 115 I 0.0157 0.8713 0.1129 116 Q 0.0093 0.9117 0.0791 117 K 0.0088 0.9175 0.0736 118 T 0.0091 0.9135 0.0774 119 I 0.0123 0.8910 0.0967 120 A 0.0145 0.8678 0.1178 121 N 0.0272 0.7856 0.1872 122 F 0.1047 0.6153 0.2800 123 S 0.2066 0.4298 0.3636 124 L 0.2232 0.2578 0.5191