# This file is the result of combining several RDB files, specifically # TR461.t06.str2.rdb (weight 1.54425) # TR461.t06.str4.rdb (weight 0.924988) # TR461.t06.pb.rdb (weight 0.789901) # TR461.t06.bys.rdb (weight 0.748322) # TR461.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 TR461.t06.str2.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2293 # # ============================================ # Comments from TR461.t06.str4.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2293 # # ============================================ # Comments from TR461.t06.pb.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2293 # # ============================================ # Comments from TR461.t06.bys.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2293 # # ============================================ # Comments from TR461.t06.alpha.rdb # ============================================ # TARGET TR461 # 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 TR461.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 2293 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 F 0.2259 0.1139 0.6602 2 Q 0.2257 0.0917 0.6826 3 S 0.1996 0.0821 0.7182 4 M 0.0951 0.3558 0.5491 5 E 0.0545 0.6178 0.3276 6 E 0.0327 0.7502 0.2171 7 T 0.0197 0.8527 0.1276 8 E 0.0088 0.9059 0.0852 9 K 0.0084 0.9143 0.0772 10 W 0.0086 0.9143 0.0771 11 M 0.0084 0.9170 0.0746 12 E 0.0083 0.9233 0.0684 13 E 0.0083 0.9233 0.0684 14 A 0.0083 0.9235 0.0682 15 M 0.0083 0.9201 0.0715 16 H 0.0083 0.9241 0.0676 17 M 0.0084 0.9198 0.0717 18 A 0.0084 0.9186 0.0730 19 K 0.0085 0.9116 0.0799 20 E 0.0102 0.8476 0.1422 21 A 0.0247 0.6939 0.2814 22 L 0.0455 0.6036 0.3509 23 E 0.0583 0.4622 0.4796 24 N 0.0851 0.2892 0.6257 25 T 0.0988 0.1854 0.7158 26 E 0.1706 0.1046 0.7248 27 V 0.2988 0.0226 0.6786 28 P 0.3672 0.0247 0.6081 29 V 0.5796 0.0347 0.3857 30 G 0.7009 0.0232 0.2758 31 C 0.8024 0.0060 0.1916 32 L 0.8249 0.0047 0.1704 33 M 0.7946 0.0055 0.1999 34 V 0.7478 0.0087 0.2435 35 Y 0.6234 0.0448 0.3319 36 N 0.2265 0.0643 0.7092 37 N 0.1675 0.0702 0.7623 38 E 0.5721 0.0169 0.4110 39 V 0.6969 0.0093 0.2938 40 V 0.7016 0.0176 0.2808 41 G 0.7488 0.0181 0.2331 42 K 0.6651 0.0431 0.2918 43 G 0.5538 0.0510 0.3952 44 R 0.4111 0.1144 0.4744 45 N 0.2892 0.1287 0.5821 46 E 0.2361 0.2171 0.5468 47 V 0.2609 0.2191 0.5199 48 N 0.2124 0.2523 0.5353 49 Q 0.1371 0.3129 0.5500 50 T 0.1331 0.2565 0.6104 51 K 0.1263 0.2204 0.6533 52 N 0.1630 0.1729 0.6641 53 A 0.0816 0.4972 0.4213 54 T 0.0985 0.5824 0.3191 55 R 0.0542 0.7581 0.1877 56 H 0.0372 0.8450 0.1178 57 A 0.0218 0.8939 0.0843 58 E 0.0123 0.9159 0.0718 59 M 0.0086 0.9220 0.0694 60 V 0.0083 0.9235 0.0682 61 A 0.0083 0.9229 0.0687 62 I 0.0083 0.9224 0.0693 63 D 0.0084 0.9185 0.0731 64 Q 0.0084 0.9156 0.0760 65 V 0.0087 0.9106 0.0807 66 L 0.0089 0.9007 0.0904 67 D 0.0096 0.8863 0.1041 68 W 0.0162 0.7686 0.2152 69 C 0.0480 0.5546 0.3973 70 R 0.0537 0.4668 0.4795 71 Q 0.0794 0.3939 0.5266 72 S 0.0805 0.2632 0.6563 73 G 0.0779 0.1953 0.7267 74 K 0.1499 0.1303 0.7198 75 S 0.2083 0.0615 0.7302 76 P 0.1567 0.1848 0.6585 77 S 0.1619 0.2720 0.5660 78 E 0.2260 0.2994 0.4746 79 V 0.3136 0.2572 0.4293 80 F 0.3111 0.1986 0.4903 81 E 0.1863 0.2181 0.5956 82 H 0.1736 0.1137 0.7127 83 T 0.5028 0.0271 0.4701 84 V 0.7034 0.0135 0.2830 85 L 0.7948 0.0081 0.1972 86 Y 0.7969 0.0090 0.1940 87 V 0.7634 0.0129 0.2237 88 T 0.6249 0.0229 0.3522 89 V 0.3919 0.1127 0.4954 90 E 0.3173 0.1183 0.5644 91 P 0.2312 0.1951 0.5737 92 C 0.1372 0.2751 0.5877 93 I 0.0277 0.6824 0.2899 94 M 0.0173 0.7996 0.1831 95 C 0.0117 0.8959 0.0924 96 A 0.0085 0.9138 0.0777 97 A 0.0083 0.9201 0.0716 98 A 0.0083 0.9229 0.0688 99 L 0.0083 0.9210 0.0707 100 R 0.0092 0.8928 0.0980 101 L 0.0184 0.7821 0.1994 102 M 0.0626 0.2947 0.6427 103 K 0.0617 0.0921 0.8462 104 I 0.2115 0.0153 0.7732 105 P 0.2828 0.0433 0.6739 106 L 0.7501 0.0152 0.2347 107 V 0.7614 0.0086 0.2300 108 V 0.8066 0.0063 0.1871 109 Y 0.7813 0.0101 0.2086 110 G 0.6745 0.0235 0.3020 111 C 0.5188 0.0404 0.4408 112 Q 0.3230 0.0819 0.5951 113 N 0.2418 0.0664 0.6917 114 E 0.0675 0.3501 0.5824 115 R 0.0972 0.2951 0.6078 116 F 0.1299 0.2347 0.6354 117 G 0.1492 0.1974 0.6534 118 G 0.2408 0.2125 0.5467 119 C 0.2195 0.2142 0.5663 120 G 0.1730 0.2079 0.6191 121 S 0.1788 0.3168 0.5044 122 V 0.1445 0.5193 0.3363 123 L 0.1002 0.6253 0.2745 124 N 0.0898 0.6561 0.2541 125 I 0.1030 0.5999 0.2972 126 A 0.1227 0.5099 0.3674 127 S 0.0748 0.5690 0.3561 128 A 0.0583 0.5231 0.4186 129 D 0.0943 0.3679 0.5377 130 L 0.1758 0.1750 0.6492 131 P 0.1054 0.3221 0.5725 132 N 0.0897 0.3111 0.5991 133 T 0.0909 0.2362 0.6729 134 G 0.0663 0.0971 0.8366 135 R 0.2409 0.0213 0.7378 136 P 0.3501 0.0282 0.6217 137 F 0.6287 0.0154 0.3558 138 Q 0.6972 0.0154 0.2874 139 C 0.6738 0.0139 0.3123 140 I 0.5119 0.0228 0.4652 141 P 0.2249 0.1159 0.6591 142 G 0.1141 0.1317 0.7542 143 Y 0.1665 0.1977 0.6357 144 R 0.1533 0.2646 0.5821 145 A 0.0243 0.7649 0.2107 146 E 0.0099 0.8834 0.1067 147 E 0.0090 0.9134 0.0776 148 A 0.0085 0.9189 0.0726 149 V 0.0084 0.9183 0.0733 150 E 0.0083 0.9189 0.0728 151 M 0.0087 0.9054 0.0858 152 L 0.0098 0.8892 0.1010 153 K 0.0095 0.8609 0.1296 154 T 0.0137 0.7434 0.2429 155 F 0.0371 0.5486 0.4143 156 Y 0.0860 0.4224 0.4916 157 K 0.1173 0.3036 0.5792