# This file is the result of combining several RDB files, specifically # T0419.t06.str2.rdb (weight 1.54425) # T0419.t06.str4.rdb (weight 0.924988) # T0419.t06.pb.rdb (weight 0.789901) # T0419.t06.bys.rdb (weight 0.748322) # T0419.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 T0419.t06.str2.rdb # ============================================ # TARGET T0419 # 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 T0419.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 1703 # # ============================================ # Comments from T0419.t06.str4.rdb # ============================================ # TARGET T0419 # 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 T0419.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 1703 # # ============================================ # Comments from T0419.t06.pb.rdb # ============================================ # TARGET T0419 # 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 T0419.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 1703 # # ============================================ # Comments from T0419.t06.bys.rdb # ============================================ # TARGET T0419 # 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 T0419.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 1703 # # ============================================ # Comments from T0419.t06.alpha.rdb # ============================================ # TARGET T0419 # 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 T0419.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 1703 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 K 0.2493 0.2430 0.5077 2 R 0.2275 0.2793 0.4932 3 F 0.1829 0.2900 0.5271 4 R 0.1551 0.2340 0.6110 5 Q 0.1443 0.1788 0.6768 6 H 0.2577 0.0687 0.6736 7 S 0.3654 0.0407 0.5938 8 L 0.7363 0.0119 0.2518 9 V 0.8026 0.0053 0.1922 10 A 0.8098 0.0050 0.1853 11 V 0.7987 0.0051 0.1963 12 F 0.7732 0.0076 0.2192 13 E 0.7030 0.0162 0.2809 14 G 0.4255 0.0277 0.5469 15 N 0.1914 0.1477 0.6609 16 D 0.1213 0.1760 0.7027 17 A 0.0835 0.2728 0.6437 18 A 0.0955 0.2678 0.6367 19 G 0.0863 0.2726 0.6410 20 K 0.0648 0.5624 0.3728 21 G 0.0275 0.8049 0.1675 22 G 0.0125 0.8897 0.0978 23 A 0.0097 0.9141 0.0762 24 I 0.0086 0.9195 0.0719 25 R 0.0083 0.9226 0.0691 26 R 0.0083 0.9218 0.0699 27 V 0.0086 0.9135 0.0779 28 T 0.0094 0.8789 0.1116 29 D 0.0119 0.7722 0.2160 30 A 0.0258 0.5376 0.4367 31 L 0.1190 0.2179 0.6631 32 D 0.1481 0.0991 0.7528 33 P 0.0324 0.5182 0.4494 34 R 0.0535 0.4011 0.5454 35 Q 0.1961 0.1964 0.6074 36 Y 0.5258 0.0285 0.4456 37 H 0.6494 0.0190 0.3316 38 I 0.7172 0.0112 0.2716 39 V 0.6551 0.0147 0.3302 40 P 0.5626 0.0210 0.4164 41 I 0.4262 0.0500 0.5237 42 A 0.3374 0.0558 0.6068 43 A 0.2644 0.0343 0.7014 44 P 0.2101 0.0601 0.7297 45 T 0.1891 0.0479 0.7630 46 E 0.0552 0.4073 0.5375 47 E 0.0960 0.4205 0.4834 48 E 0.1926 0.3988 0.4085 49 R 0.2448 0.2943 0.4609 50 A 0.2104 0.2498 0.5398 51 Q 0.2277 0.2595 0.5127 52 P 0.1641 0.4465 0.3895 53 Y 0.1921 0.5155 0.2924 54 L 0.1716 0.6210 0.2074 55 W 0.1575 0.6529 0.1895 56 R 0.1698 0.6375 0.1927 57 F 0.1244 0.6413 0.2343 58 W 0.0608 0.6901 0.2491 59 R 0.0550 0.6150 0.3300 60 H 0.0751 0.3706 0.5543 61 I 0.1988 0.0929 0.7083 62 P 0.1414 0.1277 0.7309 63 A 0.0397 0.5069 0.4534 64 R 0.0646 0.4895 0.4459 65 R 0.1797 0.3930 0.4274 66 Q 0.4062 0.2825 0.3113 67 F 0.5544 0.2085 0.2371 68 T 0.6313 0.1592 0.2095 69 I 0.6657 0.1204 0.2139 70 F 0.5852 0.1297 0.2851 71 D 0.3488 0.1431 0.5080 72 R 0.1265 0.3998 0.4736 73 S 0.1073 0.4179 0.4748 74 W 0.0752 0.5116 0.4133 75 Y 0.1024 0.3003 0.5973 76 G 0.1114 0.2160 0.6726 77 R 0.2632 0.1952 0.5416 78 V 0.4097 0.2035 0.3868 79 L 0.4202 0.2827 0.2971 80 V 0.4301 0.3367 0.2332 81 E 0.3285 0.4708 0.2007 82 R 0.3079 0.4777 0.2143 83 I 0.2706 0.4362 0.2932 84 E 0.1554 0.4187 0.4260 85 G 0.0770 0.3504 0.5727 86 F 0.1047 0.3014 0.5940 87 C 0.1792 0.1322 0.6886 88 A 0.1975 0.0849 0.7176 89 P 0.1500 0.2659 0.5841 90 A 0.1091 0.5104 0.3805 91 D 0.1206 0.5578 0.3216 92 W 0.1055 0.6348 0.2597 93 L 0.0877 0.6742 0.2381 94 R 0.1034 0.6585 0.2381 95 A 0.0887 0.6123 0.2989 96 Y 0.0360 0.7392 0.2248 97 G 0.0201 0.7813 0.1986 98 E 0.0282 0.7756 0.1963 99 I 0.0227 0.8410 0.1363 100 N 0.0111 0.8784 0.1105 101 D 0.0112 0.8926 0.0962 102 F 0.0100 0.9064 0.0835 103 E 0.0086 0.9096 0.0818 104 E 0.0089 0.9034 0.0877 105 Q 0.0137 0.8213 0.1649 106 L 0.0449 0.6978 0.2574 107 S 0.0319 0.6828 0.2852 108 E 0.0245 0.5584 0.4171 109 Y 0.0676 0.1841 0.7482 110 G 0.0655 0.0898 0.8447 111 I 0.3146 0.0321 0.6533 112 I 0.5954 0.0198 0.3848 113 V 0.7080 0.0141 0.2779 114 V 0.8135 0.0056 0.1808 115 K 0.8105 0.0055 0.1840 116 F 0.8124 0.0057 0.1819 117 W 0.7694 0.0116 0.2190 118 L 0.6415 0.0201 0.3385 119 A 0.3474 0.0262 0.6264 120 I 0.2302 0.0856 0.6842 121 D 0.1751 0.0278 0.7971 122 K 0.0118 0.7461 0.2422 123 Q 0.0092 0.8668 0.1240 124 T 0.0083 0.9225 0.0691 125 Q 0.0083 0.9218 0.0699 126 M 0.0084 0.9191 0.0726 127 E 0.0084 0.9168 0.0748 128 R 0.0087 0.9120 0.0793 129 F 0.0103 0.8902 0.0995 130 K 0.0116 0.8650 0.1234 131 E 0.0214 0.7222 0.2565 132 R 0.0684 0.5128 0.4188 133 E 0.0760 0.3584 0.5656 134 K 0.1471 0.2074 0.6455 135 T 0.1885 0.0697 0.7418 136 P 0.0832 0.3821 0.5347 137 Y 0.0682 0.5219 0.4099 138 K 0.1402 0.4693 0.3905 139 R 0.2487 0.3398 0.4115 140 Y 0.3044 0.2346 0.4610 141 K 0.3193 0.1816 0.4991 142 I 0.3270 0.0925 0.5805 143 T 0.1924 0.0309 0.7768 144 E 0.0191 0.7077 0.2733 145 E 0.0157 0.7822 0.2021 146 D 0.0259 0.8195 0.1545 147 W 0.0138 0.8680 0.1182 148 R 0.0118 0.8347 0.1535 149 N 0.0172 0.8056 0.1771 150 R 0.0247 0.8290 0.1463 151 D 0.0161 0.7992 0.1847 152 K 0.0225 0.7448 0.2327 153 W 0.0275 0.8073 0.1652 154 D 0.0128 0.8513 0.1358 155 Q 0.0145 0.8376 0.1479 156 Y 0.0222 0.8379 0.1399 157 V 0.0189 0.8751 0.1060 158 D 0.0226 0.8750 0.1024 159 A 0.0271 0.8540 0.1189 160 V 0.0251 0.8393 0.1356 161 G 0.0167 0.8390 0.1443 162 D 0.0187 0.8407 0.1406 163 M 0.0235 0.8343 0.1422 164 V 0.0232 0.8533 0.1235 165 D 0.0205 0.8431 0.1364 166 R 0.0302 0.7639 0.2060 167 T 0.0783 0.5827 0.3391 168 S 0.0900 0.4358 0.4743 169 T 0.1497 0.2927 0.5577 170 E 0.1577 0.2274 0.6149 171 I 0.2172 0.1165 0.6663 172 A 0.2538 0.0356 0.7106 173 P 0.2878 0.0732 0.6390 174 W 0.5464 0.0290 0.4246 175 T 0.7573 0.0119 0.2307 176 L 0.7473 0.0074 0.2453 177 V 0.7600 0.0126 0.2274 178 E 0.5822 0.0202 0.3976 179 A 0.2882 0.1704 0.5414 180 N 0.1330 0.2054 0.6616 181 D 0.1254 0.2057 0.6689 182 K 0.0783 0.5289 0.3928 183 R 0.0514 0.7120 0.2365 184 F 0.0459 0.7962 0.1579 185 A 0.0330 0.8480 0.1190 186 R 0.0178 0.8892 0.0930 187 V 0.0124 0.9118 0.0758 188 K 0.0086 0.9211 0.0703 189 V 0.0084 0.9224 0.0693 190 L 0.0083 0.9233 0.0685 191 R 0.0083 0.9235 0.0682 192 T 0.0083 0.9233 0.0684 193 I 0.0083 0.9201 0.0715 194 N 0.0085 0.9141 0.0774 195 D 0.0084 0.9183 0.0733 196 A 0.0087 0.9086 0.0827 197 I 0.0090 0.9100 0.0809 198 E 0.0088 0.9043 0.0869 199 A 0.0096 0.8857 0.1046 200 A 0.0185 0.7785 0.2030 201 Y 0.0402 0.6051 0.3547 202 K 0.0759 0.4498 0.4743 203 K 0.1221 0.2562 0.6216 204 D 0.1284 0.1660 0.7056 205 K 0.1237 0.1811 0.6951