# This file is the result of combining several RDB files, specifically # T0393.t04.str2.rdb (weight 1.54425) # T0393.t04.str4.rdb (weight 0.924988) # T0393.t04.pb.rdb (weight 0.789901) # T0393.t04.bys.rdb (weight 0.748322) # T0393.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 T0393.t04.str2.rdb # ============================================ # TARGET T0393 # 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 T0393.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 2001 # # ============================================ # Comments from T0393.t04.str4.rdb # ============================================ # TARGET T0393 # 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 T0393.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 2001 # # ============================================ # Comments from T0393.t04.pb.rdb # ============================================ # TARGET T0393 # 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 T0393.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 2001 # # ============================================ # Comments from T0393.t04.bys.rdb # ============================================ # TARGET T0393 # 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 T0393.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 2001 # # ============================================ # Comments from T0393.t04.alpha.rdb # ============================================ # TARGET T0393 # 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 T0393.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 2001 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2409 0.1291 0.6300 2 K 0.2246 0.1233 0.6521 3 R 0.2445 0.2059 0.5496 4 S 0.2171 0.1591 0.6238 5 I 0.1433 0.3610 0.4958 6 E 0.1319 0.2718 0.5963 7 D 0.1791 0.1309 0.6900 8 T 0.3092 0.0414 0.6494 9 P 0.4509 0.0514 0.4977 10 I 0.7742 0.0173 0.2085 11 V 0.7837 0.0159 0.2004 12 L 0.7954 0.0097 0.1949 13 I 0.7096 0.0345 0.2559 14 G 0.5291 0.0529 0.4180 15 A 0.2517 0.1873 0.5610 16 G 0.1388 0.3152 0.5460 17 N 0.0779 0.5202 0.4019 18 L 0.0514 0.5786 0.3700 19 A 0.0278 0.7410 0.2312 20 T 0.0093 0.8677 0.1230 21 N 0.0085 0.9042 0.0874 22 L 0.0084 0.9171 0.0745 23 A 0.0085 0.9103 0.0812 24 K 0.0083 0.9149 0.0768 25 A 0.0084 0.9115 0.0801 26 L 0.0089 0.8976 0.0936 27 Y 0.0092 0.8879 0.1029 28 R 0.0114 0.8260 0.1626 29 K 0.0513 0.2806 0.6681 30 G 0.0462 0.0666 0.8871 31 F 0.2135 0.0198 0.7667 32 R 0.4209 0.0310 0.5480 33 I 0.6841 0.0170 0.2988 34 V 0.6981 0.0206 0.2813 35 Q 0.7626 0.0092 0.2282 36 V 0.7391 0.0178 0.2431 37 Y 0.6221 0.0323 0.3457 38 S 0.3255 0.0372 0.6373 39 R 0.1645 0.1660 0.6695 40 T 0.1628 0.0842 0.7530 41 E 0.0146 0.7243 0.2611 42 E 0.0101 0.8458 0.1441 43 S 0.0117 0.8885 0.0997 44 A 0.0086 0.9113 0.0801 45 R 0.0084 0.9152 0.0765 46 E 0.0083 0.9197 0.0720 47 L 0.0085 0.9157 0.0758 48 A 0.0085 0.9068 0.0847 49 Q 0.0091 0.8746 0.1163 50 K 0.0163 0.7721 0.2116 51 V 0.0622 0.3222 0.6156 52 E 0.0540 0.1231 0.8229 53 A 0.2430 0.0763 0.6807 54 E 0.3779 0.1201 0.5020 55 Y 0.5281 0.1042 0.3677 56 T 0.3950 0.1102 0.4947 57 T 0.3265 0.0784 0.5952 58 D 0.1941 0.0320 0.7738 59 L 0.0225 0.6860 0.2915 60 A 0.0133 0.7495 0.2371 61 E 0.0165 0.8285 0.1550 62 V 0.0367 0.6764 0.2868 63 N 0.0916 0.4784 0.4301 64 P 0.0380 0.5102 0.4518 65 Y 0.0785 0.2421 0.6793 66 A 0.2505 0.1269 0.6226 67 K 0.4558 0.0597 0.4845 68 L 0.7970 0.0047 0.1983 69 Y 0.7661 0.0066 0.2273 70 I 0.8063 0.0042 0.1895 71 V 0.8068 0.0069 0.1863 72 S 0.7504 0.0077 0.2420 73 L 0.4580 0.0270 0.5149 74 K 0.1970 0.0345 0.7685 75 D 0.0710 0.4214 0.5076 76 S 0.0220 0.6924 0.2856 77 A 0.0243 0.7654 0.2103 78 F 0.0133 0.8709 0.1158 79 A 0.0092 0.9041 0.0867 80 E 0.0086 0.9151 0.0763 81 L 0.0092 0.9086 0.0822 82 L 0.0114 0.8607 0.1279 83 Q 0.0210 0.8223 0.1567 84 G 0.0212 0.7146 0.2642 85 I 0.0363 0.7394 0.2243 86 V 0.0527 0.6331 0.3142 87 E 0.0606 0.4901 0.4493 88 G 0.0705 0.3104 0.6191 89 K 0.1637 0.1900 0.6463 90 R 0.1851 0.0814 0.7335 91 E 0.0930 0.3083 0.5987 92 E 0.1061 0.1372 0.7568 93 A 0.4381 0.0244 0.5375 94 L 0.7240 0.0110 0.2650 95 M 0.8011 0.0064 0.1925 96 V 0.7983 0.0076 0.1941 97 H 0.7006 0.0175 0.2818 98 T 0.5243 0.0807 0.3950 99 A 0.3464 0.1345 0.5192 100 G 0.2497 0.1489 0.6015 101 S 0.2173 0.1494 0.6333 102 I 0.2287 0.1039 0.6674 103 P 0.1503 0.2019 0.6478 104 M 0.0424 0.6362 0.3214 105 N 0.0259 0.7920 0.1821 106 V 0.0207 0.8602 0.1191 107 W 0.0201 0.8304 0.1495 108 E 0.0203 0.8199 0.1598 109 G 0.0210 0.7578 0.2212 110 H 0.0462 0.5950 0.3588 111 V 0.1274 0.3169 0.5558 112 P 0.0638 0.4302 0.5060 113 H 0.0692 0.4066 0.5242 114 Y 0.1059 0.2055 0.6887 115 G 0.1484 0.0958 0.7558 116 V 0.4068 0.0483 0.5449 117 F 0.5542 0.0342 0.4116 118 Y 0.4896 0.0256 0.4848 119 P 0.3622 0.1960 0.4418 120 M 0.2993 0.1266 0.5742 121 Q 0.3861 0.0423 0.5716 122 T 0.4120 0.0599 0.5280 123 F 0.3919 0.0786 0.5295 124 S 0.2075 0.0769 0.7156 125 K 0.1162 0.2060 0.6778 126 Q 0.1252 0.1450 0.7298 127 R 0.2019 0.1274 0.6706 128 E 0.1747 0.3676 0.4577 129 V 0.1464 0.5813 0.2723 130 D 0.1423 0.5834 0.2742 131 F 0.1780 0.4777 0.3443 132 K 0.1754 0.2979 0.5268 133 E 0.2009 0.1390 0.6601 134 I 0.3364 0.0412 0.6225 135 P 0.4669 0.0656 0.4675 136 F 0.7351 0.0261 0.2388 137 F 0.7655 0.0174 0.2171 138 I 0.7351 0.0268 0.2382 139 E 0.6222 0.0441 0.3337 140 A 0.3362 0.0748 0.5890 141 S 0.1796 0.0650 0.7554 142 S 0.1520 0.0897 0.7583 143 T 0.0149 0.7132 0.2719 144 E 0.0102 0.8374 0.1524 145 D 0.0098 0.8930 0.0972 146 A 0.0085 0.9116 0.0800 147 A 0.0084 0.9077 0.0839 148 F 0.0086 0.9056 0.0858 149 L 0.0088 0.9022 0.0890 150 K 0.0084 0.9181 0.0735 151 A 0.0084 0.9157 0.0759 152 I 0.0086 0.9119 0.0795 153 A 0.0085 0.9130 0.0785 154 S 0.0088 0.8969 0.0942 155 T 0.0114 0.8291 0.1595 156 L 0.0343 0.6404 0.3253 157 S 0.0572 0.4967 0.4461 158 N 0.0929 0.3710 0.5361 159 R 0.2505 0.2167 0.5328 160 V 0.4527 0.0984 0.4490 161 Y 0.5540 0.0728 0.3732 162 D 0.5311 0.0549 0.4140 163 A 0.3444 0.1224 0.5332 164 D 0.1946 0.0826 0.7228 165 S 0.0383 0.4898 0.4718 166 E 0.0353 0.6044 0.3603 167 Q 0.0473 0.6258 0.3268 168 R 0.0302 0.7760 0.1938 169 K 0.0188 0.8369 0.1444 170 S 0.0239 0.8667 0.1094 171 L 0.0243 0.8780 0.0977 172 H 0.0231 0.8877 0.0891 173 L 0.0262 0.8833 0.0905 174 A 0.0369 0.8344 0.1286 175 A 0.0590 0.7494 0.1915 176 V 0.0502 0.6390 0.3108 177 F 0.0535 0.5247 0.4218 178 T 0.0509 0.5924 0.3568 179 C 0.0169 0.7725 0.2106 180 N 0.0110 0.8777 0.1114 181 F 0.0100 0.9133 0.0767 182 T 0.0085 0.9210 0.0705 183 N 0.0083 0.9243 0.0674 184 H 0.0083 0.9251 0.0666 185 M 0.0083 0.9251 0.0667 186 Y 0.0083 0.9249 0.0668 187 A 0.0083 0.9252 0.0666 188 L 0.0083 0.9249 0.0668 189 A 0.0083 0.9247 0.0670 190 A 0.0083 0.9236 0.0681 191 E 0.0083 0.9230 0.0688 192 L 0.0083 0.9158 0.0759 193 L 0.0085 0.9152 0.0762 194 K 0.0088 0.9108 0.0805 195 K 0.0129 0.8225 0.1646 196 Y 0.0564 0.2154 0.7282 197 N 0.0460 0.0676 0.8864 198 L 0.1556 0.0240 0.8204 199 P 0.1622 0.0200 0.8178 200 F 0.0160 0.7118 0.2722 201 D 0.0125 0.8228 0.1647 202 V 0.0117 0.8738 0.1145 203 M 0.0118 0.8725 0.1157 204 L 0.0100 0.9025 0.0874 205 P 0.0085 0.9171 0.0744 206 L 0.0086 0.9126 0.0789 207 I 0.0092 0.9056 0.0852 208 D 0.0103 0.8967 0.0930 209 E 0.0129 0.8529 0.1341 210 T 0.0301 0.7886 0.1813 211 A 0.0235 0.7359 0.2406 212 R 0.0337 0.6717 0.2945 213 K 0.0395 0.5291 0.4314 214 V 0.0875 0.5263 0.3861 215 H 0.0983 0.5717 0.3301 216 E 0.1423 0.5081 0.3496 217 L 0.1999 0.3218 0.4784 218 E 0.2495 0.1134 0.6371 219 P 0.1731 0.2057 0.6212 220 K 0.1507 0.2596 0.5898 221 T 0.1951 0.1579 0.6470 222 A 0.1900 0.2499 0.5600 223 Q 0.2188 0.1831 0.5982 224 T 0.2173 0.1026 0.6801 225 G 0.1729 0.0781 0.7490 226 P 0.1617 0.1986 0.6397 227 A 0.2294 0.2058 0.5647 228 I 0.2852 0.1298 0.5849 229 R 0.2531 0.1341 0.6128 230 Y 0.2179 0.1150 0.6671 231 D 0.1302 0.3123 0.5575 232 E 0.0474 0.6335 0.3191 233 N 0.0428 0.6797 0.2774 234 V 0.0571 0.7723 0.1706 235 I 0.0358 0.8247 0.1395 236 G 0.0163 0.8840 0.0997 237 N 0.0101 0.8936 0.0963 238 H 0.0118 0.8823 0.1058 239 L 0.0116 0.8945 0.0939 240 R 0.0096 0.8926 0.0978 241 M 0.0105 0.8729 0.1166 242 L 0.0174 0.8457 0.1369 243 A 0.0227 0.7252 0.2520 244 D 0.0304 0.5816 0.3880 245 D 0.0608 0.5015 0.4376 246 P 0.0167 0.7521 0.2312 247 A 0.0136 0.8025 0.1839 248 M 0.0140 0.8323 0.1536 249 Q 0.0136 0.8286 0.1578 250 R 0.0190 0.7791 0.2019 251 L 0.0222 0.8118 0.1660 252 Y 0.0132 0.8827 0.1041 253 E 0.0105 0.9092 0.0804 254 L 0.0097 0.9133 0.0771 255 L 0.0087 0.9142 0.0771 256 S 0.0087 0.9144 0.0769 257 R 0.0086 0.9073 0.0840 258 S 0.0091 0.8943 0.0966 259 I 0.0125 0.8448 0.1427 260 H 0.0161 0.8182 0.1657 261 E 0.0403 0.5936 0.3662 262 R 0.0687 0.3341 0.5972 263 Q 0.0977 0.2188 0.6836