# This file is the result of combining several RDB files, specifically # T0393.t06.str2.rdb (weight 1.54425) # T0393.t06.str4.rdb (weight 0.924988) # T0393.t06.pb.rdb (weight 0.789901) # T0393.t06.bys.rdb (weight 0.748322) # T0393.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 T0393.t06.str2.rdb # ============================================ # TARGET T0393 # 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 T0393.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 3171 # # ============================================ # Comments from T0393.t06.str4.rdb # ============================================ # TARGET T0393 # 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 T0393.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 3171 # # ============================================ # Comments from T0393.t06.pb.rdb # ============================================ # TARGET T0393 # 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 T0393.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 3171 # # ============================================ # Comments from T0393.t06.bys.rdb # ============================================ # TARGET T0393 # 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 T0393.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 3171 # # ============================================ # Comments from T0393.t06.alpha.rdb # ============================================ # TARGET T0393 # 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 T0393.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 3171 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2919 0.0900 0.6181 2 K 0.2873 0.0811 0.6316 3 R 0.2967 0.0904 0.6129 4 S 0.2223 0.0802 0.6975 5 I 0.1015 0.3733 0.5252 6 E 0.1010 0.3038 0.5952 7 D 0.1465 0.1400 0.7135 8 T 0.2829 0.0309 0.6863 9 P 0.4135 0.0359 0.5506 10 I 0.7752 0.0138 0.2109 11 V 0.8013 0.0097 0.1889 12 L 0.7843 0.0081 0.2077 13 I 0.7229 0.0202 0.2569 14 G 0.5224 0.0535 0.4241 15 A 0.2373 0.2015 0.5612 16 G 0.1313 0.3267 0.5420 17 N 0.0477 0.6237 0.3286 18 L 0.0233 0.7978 0.1788 19 A 0.0112 0.8853 0.1035 20 T 0.0084 0.9153 0.0763 21 N 0.0083 0.9224 0.0693 22 L 0.0083 0.9237 0.0680 23 A 0.0083 0.9233 0.0684 24 K 0.0083 0.9235 0.0682 25 A 0.0083 0.9231 0.0686 26 L 0.0084 0.9206 0.0709 27 Y 0.0087 0.9080 0.0833 28 R 0.0127 0.8061 0.1812 29 K 0.0532 0.2882 0.6587 30 G 0.0522 0.0759 0.8719 31 F 0.2093 0.0291 0.7617 32 R 0.4861 0.0269 0.4870 33 I 0.7262 0.0182 0.2556 34 V 0.7437 0.0239 0.2324 35 Q 0.7842 0.0120 0.2038 36 V 0.7382 0.0206 0.2412 37 Y 0.6626 0.0333 0.3041 38 S 0.3677 0.0453 0.5871 39 R 0.1522 0.1519 0.6959 40 T 0.1782 0.0466 0.7752 41 E 0.0137 0.7248 0.2615 42 E 0.0099 0.8418 0.1483 43 S 0.0116 0.8917 0.0967 44 A 0.0087 0.9088 0.0826 45 R 0.0084 0.9176 0.0740 46 E 0.0083 0.9198 0.0719 47 L 0.0087 0.9139 0.0774 48 A 0.0089 0.9018 0.0893 49 Q 0.0106 0.8665 0.1229 50 K 0.0218 0.7148 0.2634 51 V 0.0781 0.2938 0.6281 52 E 0.0872 0.1504 0.7624 53 A 0.3111 0.0481 0.6407 54 E 0.4238 0.0518 0.5245 55 Y 0.5680 0.0581 0.3738 56 T 0.4058 0.0846 0.5096 57 T 0.3268 0.0872 0.5860 58 D 0.2143 0.0318 0.7539 59 L 0.0214 0.6805 0.2981 60 A 0.0134 0.7676 0.2190 61 E 0.0165 0.7856 0.1979 62 V 0.0532 0.6426 0.3041 63 N 0.0883 0.4435 0.4683 64 P 0.0402 0.5173 0.4424 65 Y 0.0667 0.2700 0.6632 66 A 0.2266 0.1303 0.6432 67 K 0.4045 0.0466 0.5490 68 L 0.8057 0.0052 0.1890 69 Y 0.7769 0.0062 0.2169 70 I 0.8202 0.0044 0.1753 71 V 0.7985 0.0086 0.1929 72 S 0.7183 0.0137 0.2680 73 L 0.4889 0.0203 0.4908 74 K 0.2343 0.0239 0.7417 75 D 0.0647 0.3630 0.5723 76 S 0.0216 0.6315 0.3468 77 A 0.0248 0.7587 0.2165 78 F 0.0124 0.8781 0.1095 79 A 0.0085 0.9143 0.0772 80 E 0.0084 0.9186 0.0730 81 L 0.0086 0.9150 0.0764 82 L 0.0095 0.9045 0.0861 83 Q 0.0095 0.8708 0.1197 84 G 0.0133 0.8313 0.1554 85 I 0.0272 0.7726 0.2002 86 V 0.0377 0.6822 0.2801 87 E 0.0363 0.5075 0.4562 88 G 0.0545 0.3390 0.6065 89 K 0.1525 0.1667 0.6808 90 R 0.1668 0.1012 0.7320 91 E 0.0623 0.3429 0.5947 92 E 0.0892 0.1828 0.7280 93 A 0.4363 0.0383 0.5253 94 L 0.7374 0.0114 0.2512 95 M 0.7968 0.0069 0.1963 96 V 0.8088 0.0064 0.1848 97 H 0.7106 0.0168 0.2726 98 T 0.5231 0.0884 0.3885 99 A 0.2770 0.1323 0.5907 100 G 0.1872 0.1428 0.6701 101 S 0.2104 0.1208 0.6687 102 I 0.2595 0.0690 0.6715 103 P 0.1777 0.1859 0.6365 104 M 0.0706 0.5795 0.3499 105 N 0.0448 0.7485 0.2067 106 V 0.0474 0.7854 0.1672 107 W 0.0393 0.7912 0.1695 108 E 0.0286 0.7707 0.2007 109 G 0.0283 0.6766 0.2951 110 H 0.0645 0.5544 0.3811 111 V 0.1647 0.1923 0.6430 112 P 0.0832 0.3535 0.5634 113 H 0.0738 0.3125 0.6138 114 Y 0.1170 0.1859 0.6971 115 G 0.1922 0.0837 0.7241 116 V 0.5584 0.0287 0.4128 117 F 0.6847 0.0216 0.2938 118 Y 0.6894 0.0167 0.2939 119 P 0.5793 0.0487 0.3719 120 M 0.4576 0.0670 0.4754 121 Q 0.4094 0.0524 0.5382 122 T 0.3089 0.1124 0.5786 123 F 0.2352 0.1599 0.6049 124 S 0.1948 0.1372 0.6681 125 K 0.1106 0.2282 0.6612 126 Q 0.1555 0.1748 0.6697 127 R 0.2631 0.1644 0.5725 128 E 0.2614 0.2780 0.4606 129 V 0.2665 0.3362 0.3973 130 D 0.2371 0.3343 0.4286 131 F 0.1991 0.3239 0.4770 132 K 0.2154 0.1876 0.5970 133 E 0.2276 0.1189 0.6534 134 I 0.3313 0.0410 0.6277 135 P 0.4186 0.0613 0.5201 136 F 0.7168 0.0314 0.2518 137 F 0.7642 0.0166 0.2191 138 I 0.7369 0.0204 0.2427 139 E 0.5782 0.0390 0.3827 140 A 0.2908 0.0680 0.6413 141 S 0.1832 0.0784 0.7384 142 S 0.1693 0.0658 0.7649 143 T 0.0169 0.7106 0.2725 144 E 0.0111 0.8327 0.1563 145 D 0.0127 0.8757 0.1115 146 A 0.0087 0.9050 0.0863 147 A 0.0084 0.9149 0.0767 148 F 0.0083 0.9206 0.0710 149 L 0.0084 0.9199 0.0717 150 K 0.0084 0.9157 0.0759 151 A 0.0083 0.9168 0.0749 152 I 0.0088 0.9077 0.0835 153 A 0.0097 0.8876 0.1027 154 S 0.0126 0.8105 0.1769 155 T 0.0284 0.6338 0.3378 156 L 0.0788 0.3700 0.5512 157 S 0.1008 0.2339 0.6653 158 N 0.1735 0.1557 0.6708 159 R 0.3557 0.0852 0.5591 160 V 0.5439 0.0536 0.4025 161 Y 0.6067 0.0474 0.3459 162 D 0.5464 0.0447 0.4089 163 A 0.3463 0.0997 0.5541 164 D 0.2154 0.0733 0.7113 165 S 0.0449 0.5057 0.4494 166 E 0.0383 0.6140 0.3477 167 Q 0.0511 0.6194 0.3295 168 R 0.0468 0.7069 0.2463 169 K 0.0322 0.7348 0.2330 170 S 0.0549 0.7168 0.2283 171 L 0.0877 0.7226 0.1897 172 H 0.0825 0.7644 0.1532 173 L 0.1317 0.7355 0.1328 174 A 0.1285 0.7325 0.1390 175 A 0.0926 0.7493 0.1581 176 V 0.0635 0.7379 0.1986 177 F 0.0466 0.7530 0.2004 178 T 0.0251 0.8353 0.1397 179 C 0.0109 0.8867 0.1023 180 N 0.0092 0.9055 0.0852 181 F 0.0085 0.9190 0.0725 182 T 0.0083 0.9209 0.0708 183 N 0.0083 0.9230 0.0687 184 H 0.0083 0.9238 0.0679 185 M 0.0083 0.9243 0.0674 186 Y 0.0083 0.9240 0.0678 187 A 0.0083 0.9247 0.0670 188 L 0.0083 0.9240 0.0677 189 A 0.0083 0.9234 0.0683 190 A 0.0083 0.9200 0.0717 191 E 0.0083 0.9247 0.0670 192 L 0.0083 0.9242 0.0676 193 L 0.0084 0.9213 0.0703 194 K 0.0086 0.9111 0.0804 195 K 0.0121 0.8178 0.1701 196 Y 0.0577 0.3123 0.6300 197 N 0.0375 0.0871 0.8753 198 L 0.1607 0.0169 0.8224 199 P 0.1562 0.0228 0.8210 200 F 0.0174 0.7009 0.2818 201 D 0.0117 0.8113 0.1770 202 V 0.0146 0.8710 0.1143 203 M 0.0178 0.8786 0.1036 204 L 0.0111 0.8933 0.0956 205 P 0.0097 0.8938 0.0965 206 L 0.0117 0.8817 0.1066 207 I 0.0179 0.8593 0.1229 208 D 0.0151 0.8446 0.1403 209 E 0.0138 0.7982 0.1880 210 T 0.0204 0.7880 0.1916 211 A 0.0190 0.8093 0.1718 212 R 0.0190 0.7810 0.1999 213 K 0.0280 0.6859 0.2860 214 V 0.0624 0.6538 0.2838 215 H 0.0673 0.6483 0.2844 216 E 0.1026 0.5035 0.3938 217 L 0.1678 0.3234 0.5088 218 E 0.1939 0.1932 0.6128 219 P 0.1203 0.3521 0.5275 220 K 0.1105 0.3299 0.5596 221 T 0.1446 0.2486 0.6068 222 A 0.1157 0.2915 0.5928 223 Q 0.1581 0.2214 0.6205 224 T 0.1740 0.1052 0.7207 225 G 0.1728 0.1321 0.6951 226 P 0.1576 0.2529 0.5895 227 A 0.2449 0.2581 0.4970 228 I 0.3477 0.1717 0.4806 229 R 0.3312 0.1373 0.5314 230 Y 0.2616 0.1407 0.5977 231 D 0.1679 0.1723 0.6597 232 E 0.0252 0.5763 0.3984 233 N 0.0289 0.6875 0.2836 234 V 0.0357 0.8000 0.1644 235 I 0.0155 0.8856 0.0989 236 G 0.0090 0.9119 0.0792 237 N 0.0085 0.9175 0.0739 238 H 0.0085 0.9190 0.0725 239 L 0.0087 0.9154 0.0759 240 R 0.0087 0.9095 0.0818 241 M 0.0109 0.8587 0.1304 242 L 0.0308 0.7219 0.2472 243 A 0.0300 0.5777 0.3923 244 D 0.0582 0.4400 0.5019 245 D 0.1325 0.3071 0.5604 246 P 0.0191 0.6913 0.2896 247 A 0.0157 0.7899 0.1944 248 M 0.0116 0.8848 0.1037 249 Q 0.0086 0.9140 0.0775 250 R 0.0084 0.9214 0.0703 251 L 0.0083 0.9221 0.0695 252 Y 0.0083 0.9222 0.0695 253 E 0.0083 0.9240 0.0677 254 L 0.0083 0.9235 0.0682 255 L 0.0083 0.9220 0.0696 256 S 0.0084 0.9177 0.0739 257 R 0.0084 0.9161 0.0755 258 S 0.0090 0.9020 0.0890 259 I 0.0113 0.8768 0.1119 260 H 0.0152 0.8030 0.1818 261 E 0.0342 0.5888 0.3770 262 R 0.0821 0.3312 0.5867 263 Q 0.1432 0.1690 0.6878