# This file is the result of combining several RDB files, specifically # T0496.t06.str2.rdb (weight 1.54425) # T0496.t06.str4.rdb (weight 0.924988) # T0496.t06.pb.rdb (weight 0.789901) # T0496.t06.bys.rdb (weight 0.748322) # T0496.t06.alpha.rdb (weight 0.678173) # T0496.t04.str2.rdb (weight 1.54425) # T0496.t04.str4.rdb (weight 0.924988) # T0496.t04.pb.rdb (weight 0.789901) # T0496.t04.bys.rdb (weight 0.748322) # T0496.t04.alpha.rdb (weight 0.678173) # T0496.t2k.str2.rdb (weight 1.54425) # T0496.t2k.str4.rdb (weight 0.924988) # T0496.t2k.pb.rdb (weight 0.789901) # T0496.t2k.bys.rdb (weight 0.748322) # T0496.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 T0496.t06.str2.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.5976 # # ============================================ # Comments from T0496.t06.str4.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.5976 # # ============================================ # Comments from T0496.t06.pb.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.5976 # # ============================================ # Comments from T0496.t06.bys.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.5976 # # ============================================ # Comments from T0496.t06.alpha.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.5976 # # ============================================ # Comments from T0496.t04.str2.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.6928 # # ============================================ # Comments from T0496.t04.str4.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.6928 # # ============================================ # Comments from T0496.t04.pb.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.6928 # # ============================================ # Comments from T0496.t04.bys.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.6928 # # ============================================ # Comments from T0496.t04.alpha.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.6928 # # ============================================ # Comments from T0496.t2k.str2.rdb # ============================================ # TARGET T0496 # 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 T0496.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 26.6098 # # ============================================ # Comments from T0496.t2k.str4.rdb # ============================================ # TARGET T0496 # 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 T0496.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 26.6098 # # ============================================ # Comments from T0496.t2k.pb.rdb # ============================================ # TARGET T0496 # 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 T0496.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 26.6098 # # ============================================ # Comments from T0496.t2k.bys.rdb # ============================================ # TARGET T0496 # 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 T0496.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 26.6098 # # ============================================ # Comments from T0496.t2k.alpha.rdb # ============================================ # TARGET T0496 # 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 T0496.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 26.6098 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3240 0.0975 0.5785 2 N 0.2613 0.0792 0.6595 3 T 0.3710 0.0407 0.5883 4 P 0.4113 0.0456 0.5431 5 V 0.4110 0.0363 0.5527 6 S 0.2207 0.0343 0.7450 7 V 0.0934 0.4711 0.4354 8 N 0.0840 0.6145 0.3015 9 E 0.0776 0.6951 0.2273 10 K 0.0275 0.8356 0.1369 11 K 0.0113 0.8988 0.0899 12 D 0.0100 0.9095 0.0804 13 F 0.0095 0.9151 0.0754 14 V 0.0096 0.9194 0.0709 15 K 0.0097 0.9209 0.0694 16 W 0.0117 0.9168 0.0715 17 F 0.0148 0.9037 0.0814 18 L 0.0163 0.8624 0.1213 19 N 0.0240 0.7020 0.2740 20 N 0.0463 0.3901 0.5636 21 Y 0.1230 0.3360 0.5410 22 Q 0.1965 0.2670 0.5365 23 L 0.2412 0.2871 0.4717 24 K 0.2001 0.2778 0.5221 25 Q 0.1431 0.4511 0.4059 26 R 0.0603 0.6525 0.2872 27 E 0.0544 0.7440 0.2016 28 C 0.0474 0.8282 0.1244 29 V 0.0390 0.8674 0.0936 30 W 0.0337 0.8828 0.0835 31 I 0.0167 0.9058 0.0775 32 L 0.0136 0.9077 0.0787 33 N 0.0112 0.9074 0.0814 34 Y 0.0157 0.8810 0.1034 35 L 0.0171 0.8175 0.1654 36 M 0.0282 0.7057 0.2661 37 S 0.0449 0.5644 0.3907 38 H 0.0753 0.5024 0.4223 39 D 0.0155 0.7803 0.2042 40 Q 0.0142 0.8452 0.1406 41 L 0.0180 0.8381 0.1439 42 M 0.0352 0.7985 0.1664 43 H 0.0460 0.6799 0.2740 44 K 0.0965 0.3950 0.5086 45 V 0.3324 0.2049 0.4627 46 H 0.4793 0.1707 0.3500 47 F 0.5286 0.1814 0.2901 48 V 0.4073 0.2910 0.3017 49 E 0.2507 0.4392 0.3101 50 H 0.1712 0.4157 0.4131 51 A 0.1406 0.4418 0.4175 52 K 0.1397 0.4008 0.4595 53 Y 0.1649 0.2325 0.6026 54 C 0.2227 0.0757 0.7017 55 P 0.1603 0.2347 0.6050 56 R 0.1783 0.1984 0.6233 57 G 0.5493 0.0839 0.3668 58 L 0.7143 0.0227 0.2631 59 V 0.7818 0.0134 0.2047 60 M 0.7754 0.0166 0.2080 61 S 0.6470 0.0320 0.3209 62 A 0.4127 0.2161 0.3712 63 N 0.2907 0.2169 0.4924 64 C 0.2698 0.1543 0.5759 65 V 0.2336 0.2146 0.5518 66 K 0.1598 0.2286 0.6116 67 D 0.1922 0.1664 0.6414 68 T 0.2690 0.0686 0.6625 69 P 0.2949 0.1447 0.5604 70 F 0.4302 0.1438 0.4259 71 H 0.5524 0.1341 0.3135 72 F 0.5849 0.1233 0.2918 73 F 0.5324 0.1162 0.3514 74 K 0.4014 0.1548 0.4438 75 Q 0.2262 0.1833 0.5906 76 N 0.1939 0.1424 0.6637 77 V 0.3369 0.1007 0.5624 78 M 0.4475 0.0901 0.4624 79 T 0.4620 0.0915 0.4465 80 T 0.3504 0.0971 0.5525 81 D 0.2219 0.0531 0.7250 82 A 0.0229 0.7029 0.2741 83 E 0.0157 0.8061 0.1782 84 K 0.0254 0.8307 0.1439 85 S 0.0310 0.8318 0.1372 86 F 0.0431 0.7874 0.1696 87 H 0.0364 0.8056 0.1580 88 D 0.0842 0.6929 0.2229 89 I 0.1797 0.5582 0.2621 90 R 0.3125 0.3614 0.3261 91 L 0.3317 0.2229 0.4454 92 N 0.2157 0.0916 0.6927 93 R 0.0841 0.3260 0.5899 94 D 0.1098 0.2106 0.6796 95 E 0.2087 0.1652 0.6261 96 D 0.3658 0.0888 0.5454 97 I 0.6739 0.0303 0.2958 98 Y 0.7613 0.0137 0.2250 99 I 0.8151 0.0070 0.1779 100 Q 0.7936 0.0075 0.1989 101 L 0.7817 0.0103 0.2080 102 N 0.6444 0.0205 0.3351 103 F 0.3892 0.0523 0.5585 104 K 0.1741 0.2355 0.5903 105 S 0.1342 0.2638 0.6019 106 S 0.1055 0.3711 0.5234 107 F 0.1184 0.4003 0.4813 108 Q 0.1204 0.3989 0.4808 109 N 0.1209 0.3651 0.5140 110 A 0.0187 0.7323 0.2490 111 N 0.0165 0.8217 0.1618 112 Y 0.0201 0.8690 0.1109 113 V 0.0150 0.8967 0.0883 114 A 0.0137 0.9058 0.0806 115 V 0.0169 0.8839 0.0992 116 L 0.0273 0.8284 0.1443 117 E 0.0434 0.7370 0.2196 118 E 0.0845 0.3806 0.5349 119 N 0.1582 0.1351 0.7068 120 P 0.0511 0.3474 0.6015 121 Y 0.0999 0.2272 0.6728 122 L 0.2081 0.0670 0.7249 123 P 0.1922 0.1288 0.6790 124 K 0.1992 0.2701 0.5307 125 H 0.1909 0.3094 0.4997 126 I 0.2360 0.3799 0.3842 127 E 0.2097 0.4349 0.3555 128 V 0.1601 0.5145 0.3254 129 N 0.1111 0.5829 0.3060 130 E 0.0499 0.7355 0.2146 131 K 0.0257 0.8135 0.1607 132 D 0.0180 0.8755 0.1066 133 R 0.0099 0.9059 0.0842 134 L 0.0086 0.9162 0.0751 135 L 0.0085 0.9178 0.0737 136 A 0.0085 0.9164 0.0751 137 E 0.0085 0.9138 0.0776 138 R 0.0087 0.9111 0.0802 139 F 0.0095 0.9025 0.0879 140 L 0.0091 0.9028 0.0881 141 E 0.0088 0.9078 0.0834 142 E 0.0093 0.9016 0.0890 143 S 0.0107 0.9020 0.0873 144 V 0.0097 0.9060 0.0843 145 F 0.0089 0.9084 0.0828 146 S 0.0088 0.9082 0.0830 147 F 0.0091 0.9106 0.0803 148 R 0.0089 0.9155 0.0756 149 R 0.0084 0.9191 0.0726 150 E 0.0083 0.9214 0.0703 151 R 0.0083 0.9208 0.0709 152 L 0.0084 0.9167 0.0748 153 L 0.0085 0.9120 0.0795 154 K 0.0084 0.9121 0.0795 155 Q 0.0099 0.8795 0.1106 156 I 0.0208 0.8685 0.1107 157 D 0.0126 0.8936 0.0938 158 E 0.0093 0.8882 0.1025 159 A 0.0117 0.8634 0.1249 160 L 0.0157 0.8212 0.1631 161 D 0.0236 0.6930 0.2834 162 K 0.0366 0.5929 0.3705 163 Q 0.0572 0.4698 0.4730 164 D 0.1040 0.4556 0.4404 165 K 0.0115 0.7954 0.1931 166 E 0.0092 0.8756 0.1152 167 A 0.0092 0.9127 0.0781 168 F 0.0101 0.9132 0.0767 169 H 0.0097 0.9172 0.0731 170 R 0.0105 0.9102 0.0793 171 L 0.0157 0.8824 0.1019 172 T 0.0131 0.8958 0.0911 173 A 0.0086 0.9084 0.0830 174 E 0.0091 0.8992 0.0917 175 L 0.0108 0.8864 0.1029 176 K 0.0110 0.8428 0.1462 177 M 0.0239 0.6956 0.2805 178 L 0.0761 0.4502 0.4737