# This file is the result of combining several RDB files, specifically # T0412.t2k.str2.rdb (weight 1.54425) # T0412.t2k.str4.rdb (weight 0.924988) # T0412.t2k.pb.rdb (weight 0.789901) # T0412.t2k.bys.rdb (weight 0.748322) # T0412.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 T0412.t2k.str2.rdb # ============================================ # TARGET T0412 # 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 T0412.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 214.171 # # ============================================ # Comments from T0412.t2k.str4.rdb # ============================================ # TARGET T0412 # 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 T0412.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 214.171 # # ============================================ # Comments from T0412.t2k.pb.rdb # ============================================ # TARGET T0412 # 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 T0412.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 214.171 # # ============================================ # Comments from T0412.t2k.bys.rdb # ============================================ # TARGET T0412 # 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 T0412.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 214.171 # # ============================================ # Comments from T0412.t2k.alpha.rdb # ============================================ # TARGET T0412 # 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 T0412.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 214.171 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1809 0.1542 0.6649 2 N 0.0888 0.3345 0.5767 3 A 0.1070 0.3062 0.5869 4 L 0.1570 0.2903 0.5528 5 F 0.1390 0.3591 0.5019 6 S 0.1029 0.5444 0.3528 7 S 0.0363 0.7773 0.1865 8 R 0.0121 0.8701 0.1178 9 D 0.0124 0.8885 0.0991 10 I 0.0123 0.8994 0.0883 11 L 0.0086 0.9174 0.0740 12 E 0.0083 0.9219 0.0698 13 V 0.0083 0.9215 0.0702 14 L 0.0084 0.9194 0.0722 15 Q 0.0083 0.9202 0.0715 16 D 0.0083 0.9203 0.0714 17 I 0.0089 0.9128 0.0783 18 H 0.0088 0.9071 0.0841 19 M 0.0090 0.8886 0.1024 20 E 0.0187 0.7699 0.2114 21 T 0.0617 0.3382 0.6001 22 G 0.0540 0.1156 0.8304 23 E 0.2345 0.1045 0.6610 24 T 0.5529 0.1052 0.3420 25 V 0.6837 0.0679 0.2484 26 A 0.7496 0.0440 0.2064 27 I 0.7839 0.0212 0.1950 28 A 0.7614 0.0195 0.2191 29 T 0.6955 0.0225 0.2820 30 K 0.4969 0.0723 0.4308 31 N 0.2453 0.0920 0.6627 32 D 0.1335 0.0985 0.7680 33 I 0.3608 0.0540 0.5852 34 Y 0.6851 0.0185 0.2964 35 L 0.7934 0.0061 0.2006 36 Q 0.8062 0.0064 0.1874 37 Y 0.8125 0.0057 0.1819 38 I 0.7833 0.0125 0.2042 39 Q 0.7514 0.0273 0.2213 40 I 0.7177 0.0439 0.2384 41 I 0.6153 0.0607 0.3240 42 E 0.5006 0.0927 0.4067 43 S 0.3211 0.1156 0.5633 44 V 0.1800 0.2361 0.5838 45 H 0.2809 0.1521 0.5670 46 A 0.3763 0.1479 0.4758 47 L 0.5115 0.0921 0.3964 48 R 0.6153 0.0577 0.3270 49 F 0.6479 0.0472 0.3048 50 H 0.6373 0.0348 0.3279 51 V 0.5156 0.0479 0.4365 52 D 0.3350 0.0452 0.6198 53 E 0.1329 0.2241 0.6430 54 N 0.0937 0.1336 0.7727 55 A 0.2319 0.1052 0.6628 56 I 0.4120 0.0873 0.5008 57 R 0.4637 0.0469 0.4893 58 P 0.4200 0.0864 0.4936 59 L 0.4078 0.1571 0.4351 60 T 0.3985 0.1998 0.4016 61 M 0.3018 0.3149 0.3833 62 S 0.1902 0.4096 0.4001 63 S 0.0870 0.6091 0.3039 64 N 0.0547 0.6700 0.2754 65 G 0.0443 0.7711 0.1846 66 W 0.0353 0.8625 0.1021 67 M 0.0641 0.8396 0.0963 68 L 0.0624 0.8302 0.1074 69 M 0.0575 0.7950 0.1475 70 S 0.0421 0.6273 0.3306 71 T 0.0523 0.3169 0.6308 72 M 0.1467 0.1338 0.7195 73 N 0.1489 0.1016 0.7495 74 D 0.0126 0.7106 0.2768 75 K 0.0095 0.8624 0.1281 76 A 0.0088 0.9132 0.0780 77 I 0.0089 0.9147 0.0764 78 D 0.0083 0.9217 0.0700 79 N 0.0084 0.9198 0.0719 80 T 0.0089 0.9097 0.0814 81 V 0.0094 0.8883 0.1023 82 R 0.0102 0.8322 0.1577 83 R 0.0236 0.6492 0.3272 84 A 0.0672 0.4643 0.4686 85 N 0.0795 0.2981 0.6224 86 T 0.1532 0.2948 0.5520 87 I 0.1961 0.3299 0.4741 88 T 0.2446 0.2863 0.4691 89 Q 0.2389 0.1756 0.5855 90 K 0.1802 0.1040 0.7158 91 D 0.1077 0.2126 0.6798 92 G 0.0716 0.1400 0.7884 93 I 0.1953 0.1046 0.7001 94 R 0.2869 0.1264 0.5866 95 F 0.3176 0.1052 0.5772 96 E 0.1763 0.0503 0.7734 97 V 0.0145 0.7424 0.2431 98 D 0.0092 0.8697 0.1211 99 D 0.0084 0.9209 0.0707 100 M 0.0083 0.9227 0.0690 101 M 0.0083 0.9223 0.0694 102 A 0.0083 0.9240 0.0677 103 R 0.0083 0.9240 0.0677 104 I 0.0084 0.9147 0.0768 105 R 0.0083 0.9229 0.0688 106 Q 0.0083 0.9205 0.0711 107 V 0.0088 0.9121 0.0791 108 R 0.0091 0.8951 0.0958 109 E 0.0210 0.7613 0.2177 110 Q 0.0556 0.3243 0.6201 111 G 0.0867 0.1151 0.7983 112 Y 0.3131 0.0717 0.6152 113 A 0.5067 0.0574 0.4359 114 S 0.4676 0.0772 0.4552 115 A 0.3313 0.1387 0.5300 116 E 0.1904 0.2681 0.5415 117 H 0.1984 0.1842 0.6174 118 I 0.3740 0.0765 0.5496 119 P 0.4072 0.0926 0.5002 120 F 0.4138 0.0749 0.5113 121 V 0.3517 0.1372 0.5111 122 G 0.3207 0.1000 0.5793 123 G 0.4755 0.0843 0.4402 124 G 0.6191 0.0553 0.3257 125 T 0.7167 0.0341 0.2492 126 I 0.7390 0.0301 0.2310 127 C 0.7403 0.0268 0.2329 128 V 0.7267 0.0155 0.2578 129 L 0.6529 0.0137 0.3333 130 L 0.5225 0.0280 0.4495 131 P 0.3605 0.0938 0.5457 132 M 0.2164 0.1581 0.6255 133 T 0.1522 0.2691 0.5787 134 I 0.1139 0.2433 0.6429 135 Q 0.1121 0.1302 0.7577 136 G 0.1821 0.0798 0.7381 137 Q 0.3941 0.0333 0.5727 138 P 0.5882 0.0365 0.3753 139 V 0.7322 0.0432 0.2246 140 T 0.7643 0.0293 0.2064 141 M 0.7672 0.0276 0.2052 142 G 0.6977 0.0397 0.2626 143 L 0.5757 0.0836 0.3406 144 G 0.3546 0.1214 0.5240 145 G 0.2622 0.1557 0.5821 146 A 0.1535 0.3898 0.4567 147 L 0.0775 0.6124 0.3101 148 D 0.0568 0.6888 0.2545 149 R 0.0828 0.5998 0.3174 150 I 0.1229 0.5362 0.3409 151 K 0.0935 0.5325 0.3740 152 Q 0.0202 0.7639 0.2159 153 N 0.0203 0.7896 0.1901 154 Y 0.0221 0.8414 0.1365 155 D 0.0117 0.8915 0.0968 156 R 0.0089 0.9064 0.0847 157 Y 0.0089 0.9142 0.0770 158 L 0.0092 0.9147 0.0761 159 E 0.0083 0.9207 0.0709 160 L 0.0083 0.9238 0.0679 161 L 0.0083 0.9215 0.0702 162 L 0.0084 0.9173 0.0743 163 N 0.0084 0.9170 0.0746 164 G 0.0084 0.9165 0.0751 165 V 0.0085 0.9151 0.0765 166 Q 0.0084 0.9162 0.0754 167 Q 0.0084 0.9118 0.0798 168 L 0.0089 0.8959 0.0952 169 K 0.0127 0.8373 0.1499 170 K 0.0165 0.7142 0.2693 171 S 0.0213 0.6306 0.3481 172 D 0.0419 0.4360 0.5220 173 S 0.0728 0.2948 0.6324 174 F 0.1070 0.2149 0.6781 175 H 0.1845 0.1522 0.6632 176 Q 0.3010 0.0668 0.6322 177 P 0.2946 0.0685 0.6369 178 I 0.3022 0.0977 0.6001