# This file is the result of combining several RDB files, specifically # T0412.t04.str2.rdb (weight 1.54425) # T0412.t04.str4.rdb (weight 0.924988) # T0412.t04.pb.rdb (weight 0.789901) # T0412.t04.bys.rdb (weight 0.748322) # T0412.t04.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.t04.str2.rdb # ============================================ # TARGET T0412 # 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 T0412.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 1761 # # ============================================ # Comments from T0412.t04.str4.rdb # ============================================ # TARGET T0412 # 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 T0412.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 1761 # # ============================================ # Comments from T0412.t04.pb.rdb # ============================================ # TARGET T0412 # 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 T0412.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 1761 # # ============================================ # Comments from T0412.t04.bys.rdb # ============================================ # TARGET T0412 # 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 T0412.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 1761 # # ============================================ # Comments from T0412.t04.alpha.rdb # ============================================ # TARGET T0412 # 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 T0412.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 1761 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1626 0.2069 0.6305 2 N 0.1223 0.3351 0.5426 3 A 0.1239 0.3682 0.5079 4 L 0.1377 0.3015 0.5609 5 F 0.2018 0.1609 0.6372 6 S 0.1757 0.1467 0.6776 7 S 0.0538 0.5110 0.4352 8 R 0.0364 0.6470 0.3166 9 D 0.0397 0.6756 0.2847 10 I 0.0323 0.7308 0.2370 11 L 0.0285 0.7979 0.1736 12 E 0.0102 0.8946 0.0951 13 V 0.0103 0.9084 0.0813 14 L 0.0086 0.9147 0.0767 15 Q 0.0084 0.9186 0.0730 16 D 0.0083 0.9180 0.0737 17 I 0.0085 0.9134 0.0781 18 H 0.0086 0.9019 0.0896 19 M 0.0090 0.8750 0.1160 20 E 0.0152 0.7605 0.2243 21 T 0.0646 0.2136 0.7218 22 G 0.0510 0.1174 0.8316 23 E 0.2101 0.1438 0.6461 24 T 0.5171 0.0971 0.3858 25 V 0.6991 0.0606 0.2403 26 A 0.7538 0.0448 0.2013 27 I 0.7794 0.0333 0.1874 28 A 0.7739 0.0211 0.2050 29 T 0.7287 0.0212 0.2501 30 K 0.5975 0.0608 0.3418 31 N 0.2443 0.0947 0.6611 32 D 0.1362 0.0902 0.7735 33 I 0.2944 0.0573 0.6484 34 Y 0.5464 0.0458 0.4078 35 L 0.7672 0.0067 0.2261 36 Q 0.8058 0.0060 0.1882 37 Y 0.8043 0.0045 0.1912 38 I 0.8039 0.0105 0.1856 39 Q 0.7658 0.0230 0.2112 40 I 0.7327 0.0265 0.2408 41 I 0.5887 0.0565 0.3548 42 E 0.4189 0.0930 0.4882 43 S 0.2829 0.1055 0.6116 44 V 0.1770 0.2292 0.5938 45 H 0.2605 0.1580 0.5814 46 A 0.3465 0.1250 0.5285 47 L 0.4802 0.0711 0.4487 48 R 0.6055 0.0442 0.3503 49 F 0.6664 0.0280 0.3056 50 H 0.6042 0.0243 0.3716 51 V 0.4974 0.0374 0.4653 52 D 0.3037 0.0348 0.6615 53 E 0.1294 0.2430 0.6276 54 N 0.0987 0.1790 0.7223 55 A 0.3129 0.1118 0.5753 56 I 0.4887 0.0779 0.4334 57 R 0.5651 0.0486 0.3863 58 P 0.4650 0.0920 0.4430 59 L 0.4309 0.1886 0.3805 60 T 0.3796 0.2348 0.3857 61 M 0.3186 0.2710 0.4104 62 S 0.1894 0.3786 0.4320 63 S 0.0807 0.6111 0.3082 64 N 0.0663 0.6414 0.2923 65 G 0.0527 0.7540 0.1933 66 W 0.0563 0.8338 0.1099 67 M 0.1369 0.7657 0.0974 68 L 0.0802 0.8160 0.1038 69 M 0.0739 0.7830 0.1431 70 S 0.0807 0.6604 0.2589 71 T 0.1047 0.3212 0.5742 72 M 0.1501 0.1078 0.7421 73 N 0.1610 0.0517 0.7873 74 D 0.0121 0.7230 0.2649 75 K 0.0094 0.8515 0.1391 76 A 0.0090 0.9102 0.0808 77 I 0.0089 0.9064 0.0847 78 D 0.0083 0.9179 0.0737 79 N 0.0084 0.9144 0.0772 80 T 0.0086 0.9056 0.0858 81 V 0.0088 0.8981 0.0932 82 R 0.0100 0.8665 0.1235 83 R 0.0197 0.7184 0.2619 84 A 0.0711 0.4955 0.4334 85 N 0.0799 0.3424 0.5777 86 T 0.1267 0.3093 0.5640 87 I 0.1823 0.2669 0.5508 88 T 0.2154 0.2432 0.5414 89 Q 0.2175 0.1671 0.6154 90 K 0.1733 0.1190 0.7077 91 D 0.0979 0.2667 0.6353 92 G 0.0780 0.2082 0.7138 93 I 0.2130 0.1037 0.6833 94 R 0.2827 0.1213 0.5960 95 F 0.2815 0.0966 0.6218 96 E 0.1856 0.0310 0.7833 97 V 0.0144 0.7242 0.2614 98 D 0.0094 0.8648 0.1258 99 D 0.0085 0.9173 0.0743 100 M 0.0085 0.9182 0.0734 101 M 0.0083 0.9212 0.0705 102 A 0.0083 0.9212 0.0705 103 R 0.0083 0.9223 0.0694 104 I 0.0083 0.9228 0.0689 105 R 0.0083 0.9221 0.0696 106 Q 0.0084 0.9193 0.0724 107 V 0.0084 0.9169 0.0746 108 R 0.0091 0.9032 0.0878 109 E 0.0113 0.8015 0.1871 110 Q 0.0555 0.3256 0.6188 111 G 0.0741 0.1067 0.8192 112 Y 0.2396 0.1430 0.6174 113 A 0.4780 0.0995 0.4226 114 S 0.4992 0.0943 0.4065 115 A 0.3719 0.1196 0.5085 116 E 0.1853 0.2195 0.5952 117 H 0.1950 0.1398 0.6652 118 I 0.3843 0.0721 0.5436 119 P 0.3855 0.0924 0.5221 120 F 0.3638 0.0969 0.5393 121 V 0.2165 0.1531 0.6304 122 G 0.1700 0.1201 0.7099 123 G 0.3191 0.1167 0.5642 124 G 0.5430 0.1025 0.3545 125 T 0.6741 0.0820 0.2440 126 I 0.7273 0.0659 0.2068 127 C 0.7338 0.0544 0.2118 128 V 0.7037 0.0712 0.2251 129 L 0.6284 0.0756 0.2960 130 L 0.5605 0.0461 0.3934 131 P 0.4280 0.0780 0.4940 132 M 0.3661 0.1129 0.5210 133 T 0.3013 0.0761 0.6226 134 I 0.2033 0.1785 0.6183 135 Q 0.1072 0.1363 0.7565 136 G 0.0868 0.0890 0.8242 137 Q 0.2991 0.0254 0.6756 138 P 0.5104 0.0250 0.4646 139 V 0.6579 0.0284 0.3136 140 T 0.7599 0.0118 0.2282 141 M 0.7532 0.0158 0.2310 142 G 0.7375 0.0165 0.2459 143 L 0.6388 0.0543 0.3069 144 G 0.4827 0.0703 0.4470 145 G 0.3168 0.0678 0.6154 146 A 0.1813 0.2238 0.5948 147 L 0.1032 0.4999 0.3969 148 D 0.0909 0.5099 0.3992 149 R 0.1092 0.4872 0.4036 150 I 0.1859 0.3203 0.4938 151 K 0.1449 0.2769 0.5782 152 Q 0.0378 0.6079 0.3543 153 N 0.0419 0.5423 0.4159 154 Y 0.0325 0.7051 0.2625 155 D 0.0176 0.8148 0.1676 156 R 0.0116 0.8694 0.1190 157 Y 0.0113 0.8739 0.1148 158 L 0.0085 0.9126 0.0789 159 E 0.0083 0.9196 0.0721 160 L 0.0083 0.9221 0.0696 161 L 0.0083 0.9229 0.0688 162 L 0.0083 0.9205 0.0712 163 N 0.0083 0.9152 0.0765 164 G 0.0085 0.9174 0.0741 165 V 0.0084 0.9185 0.0731 166 Q 0.0083 0.9158 0.0758 167 Q 0.0085 0.9059 0.0855 168 L 0.0092 0.8894 0.1014 169 K 0.0106 0.8344 0.1551 170 K 0.0134 0.7756 0.2110 171 S 0.0371 0.5812 0.3818 172 D 0.0594 0.3636 0.5770 173 S 0.0732 0.2532 0.6736 174 F 0.1296 0.2056 0.6648 175 H 0.1993 0.1199 0.6808 176 Q 0.2118 0.0838 0.7044 177 P 0.1716 0.1535 0.6750 178 I 0.1790 0.1864 0.6347