# This file is the result of combining several RDB files, specifically # T0269.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0269.t2k.stride-ebghtl.rdb (weight 1.24869) # T0269.t2k.str2.rdb (weight 1.54758) # T0269.t2k.alpha.rdb (weight 0.659012) # 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 T0269.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0269 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0269.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 670 # # ============================================ # Comments from T0269.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0269 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0269.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 670 # # ============================================ # Comments from T0269.t2k.str2.rdb # ============================================ # TARGET T0269 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0269.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 670 # # ============================================ # Comments from T0269.t2k.alpha.rdb # ============================================ # TARGET T0269 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0269.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 670 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1011 0.0512 0.8477 2 P 0.1324 0.0506 0.8170 3 G 0.1339 0.0673 0.7988 4 S 0.1410 0.0865 0.7725 5 I 0.2023 0.1109 0.6868 6 P 0.1859 0.0923 0.7218 7 L 0.2262 0.0835 0.6903 8 I 0.1489 0.1523 0.6988 9 G 0.0897 0.0807 0.8297 10 E 0.1547 0.0687 0.7766 11 R 0.2931 0.0519 0.6550 12 F 0.1449 0.0383 0.8167 13 P 0.1203 0.0308 0.8490 14 E 0.2161 0.0426 0.7413 15 M 0.5471 0.0217 0.4312 16 E 0.7558 0.0127 0.2315 17 V 0.7419 0.0122 0.2460 18 T 0.6417 0.0289 0.3294 19 T 0.4262 0.0418 0.5320 20 D 0.2085 0.0825 0.7090 21 H 0.1426 0.0404 0.8170 22 G 0.1460 0.0455 0.8085 23 V 0.4334 0.0162 0.5503 24 I 0.7260 0.0086 0.2654 25 K 0.5133 0.0121 0.4746 26 L 0.1078 0.6025 0.2897 27 P 0.0161 0.7508 0.2331 28 D 0.0267 0.8087 0.1646 29 H 0.0788 0.7598 0.1614 30 Y 0.1824 0.6691 0.1485 31 V 0.1673 0.6432 0.1895 32 S 0.1204 0.5479 0.3317 33 Q 0.0588 0.2008 0.7404 34 G 0.0354 0.0274 0.9372 35 K 0.2070 0.0123 0.7808 36 W 0.6941 0.0040 0.3019 37 F 0.9130 0.0038 0.0832 38 V 0.9309 0.0032 0.0659 39 L 0.9244 0.0033 0.0722 40 F 0.8824 0.0104 0.1073 41 S 0.6868 0.0109 0.3022 42 H 0.3505 0.0110 0.6385 43 P 0.1379 0.1463 0.7158 44 A 0.0551 0.3311 0.6137 45 D 0.0622 0.3099 0.6280 46 F 0.0896 0.1826 0.7278 47 T 0.0921 0.0868 0.8210 48 P 0.0789 0.1586 0.7625 49 V 0.0906 0.2242 0.6851 50 C 0.0982 0.2402 0.6616 51 T 0.0537 0.5077 0.4386 52 T 0.0471 0.6476 0.3053 53 E 0.0487 0.7248 0.2266 54 F 0.0185 0.8286 0.1530 55 V 0.0088 0.9194 0.0718 56 S 0.0086 0.9124 0.0790 57 F 0.0060 0.9215 0.0725 58 A 0.0060 0.9117 0.0823 59 R 0.0065 0.8451 0.1483 60 R 0.0111 0.8041 0.1849 61 Y 0.0104 0.8841 0.1055 62 E 0.0053 0.9271 0.0676 63 D 0.0050 0.9363 0.0587 64 F 0.0052 0.9443 0.0505 65 Q 0.0051 0.9328 0.0620 66 R 0.0068 0.8559 0.1373 67 L 0.0445 0.2710 0.6845 68 G 0.0460 0.0137 0.9403 69 V 0.1410 0.0070 0.8520 70 D 0.8012 0.0042 0.1946 71 L 0.9295 0.0029 0.0676 72 I 0.9139 0.0073 0.0788 73 G 0.9211 0.0037 0.0752 74 L 0.8777 0.0061 0.1163 75 S 0.6485 0.0075 0.3440 76 V 0.2331 0.0638 0.7031 77 D 0.1019 0.0334 0.8647 78 S 0.0683 0.0936 0.8381 79 V 0.0077 0.7899 0.2024 80 F 0.0069 0.8772 0.1159 81 S 0.0063 0.9104 0.0832 82 H 0.0065 0.9298 0.0637 83 I 0.0072 0.9408 0.0520 84 K 0.0068 0.9340 0.0591 85 W 0.0071 0.9240 0.0689 86 K 0.0087 0.9103 0.0811 87 E 0.0082 0.8751 0.1167 88 W 0.0135 0.8098 0.1767 89 I 0.0084 0.8840 0.1076 90 E 0.0087 0.8788 0.1125 91 R 0.0098 0.8490 0.1412 92 H 0.0293 0.7255 0.2453 93 I 0.0411 0.3906 0.5684 94 G 0.0378 0.1907 0.7714 95 V 0.0816 0.1730 0.7453 96 R 0.0997 0.0760 0.8242 97 I 0.1096 0.0253 0.8651 98 P 0.1393 0.0277 0.8331 99 F 0.3504 0.0169 0.6327 100 P 0.4541 0.0164 0.5296 101 I 0.6632 0.0170 0.3199 102 I 0.6362 0.0241 0.3397 103 A 0.4796 0.0233 0.4971 104 D 0.1269 0.0243 0.8489 105 P 0.0106 0.1756 0.8138 106 Q 0.0352 0.1695 0.7954 107 G 0.0359 0.4816 0.4825 108 T 0.0754 0.6867 0.2379 109 V 0.1180 0.7735 0.1085 110 A 0.1087 0.7829 0.1084 111 R 0.0835 0.7852 0.1313 112 R 0.0521 0.8008 0.1471 113 L 0.0675 0.4087 0.5238 114 G 0.0655 0.0464 0.8881 115 L 0.2266 0.0438 0.7295 116 L 0.4492 0.0485 0.5023 117 H 0.2381 0.0607 0.7012 118 A 0.0912 0.2471 0.6617 119 E 0.0562 0.2243 0.7195 120 S 0.0696 0.1724 0.7581 121 A 0.0956 0.0965 0.8079 122 T 0.2096 0.0654 0.7250 123 H 0.4493 0.0367 0.5141 124 T 0.6521 0.0191 0.3288 125 V 0.7770 0.0151 0.2078 126 R 0.8202 0.0127 0.1671 127 G 0.8720 0.0059 0.1220 128 V 0.9141 0.0040 0.0819 129 F 0.9248 0.0035 0.0716 130 I 0.9229 0.0035 0.0735 131 V 0.8957 0.0052 0.0991 132 D 0.3278 0.0095 0.6628 133 A 0.0207 0.1107 0.8687 134 R 0.0507 0.0173 0.9319 135 G 0.0963 0.0220 0.8817 136 V 0.4479 0.0066 0.5455 137 I 0.8950 0.0030 0.1021 138 R 0.8763 0.0118 0.1119 139 T 0.9190 0.0032 0.0778 140 M 0.8970 0.0049 0.0981 141 L 0.8938 0.0042 0.1020 142 Y 0.7776 0.0188 0.2035 143 Y 0.4837 0.0209 0.4954 144 P 0.2641 0.0483 0.6876 145 M 0.1296 0.0704 0.8000 146 E 0.0993 0.0786 0.8222 147 L 0.0513 0.1125 0.8362 148 G 0.0629 0.0718 0.8653 149 R 0.0891 0.0923 0.8185 150 L 0.1173 0.0742 0.8085 151 V 0.0052 0.9349 0.0599 152 D 0.0047 0.9556 0.0397 153 E 0.0047 0.9577 0.0376 154 I 0.0047 0.9599 0.0354 155 L 0.0047 0.9595 0.0358 156 R 0.0047 0.9583 0.0370 157 I 0.0048 0.9570 0.0382 158 V 0.0051 0.9537 0.0412 159 K 0.0051 0.9506 0.0443 160 A 0.0060 0.9262 0.0678 161 L 0.0295 0.8785 0.0920 162 K 0.0226 0.8560 0.1214 163 L 0.0446 0.7849 0.1706 164 G 0.0754 0.6247 0.2999 165 D 0.0539 0.5904 0.3557 166 S 0.0350 0.4835 0.4816 167 L 0.0549 0.2145 0.7306 168 K 0.0530 0.0425 0.9045 169 R 0.2572 0.0286 0.7142 170 A 0.6132 0.0170 0.3698 171 V 0.4375 0.0224 0.5401 172 P 0.2785 0.0441 0.6774 173 A 0.1248 0.0909 0.7843 174 D 0.0955 0.0577 0.8468 175 W 0.0720 0.0374 0.8906 176 P 0.0677 0.0589 0.8733 177 N 0.0587 0.1977 0.7435 178 N 0.0495 0.2261 0.7244 179 E 0.1243 0.2602 0.6156 180 I 0.2538 0.2292 0.5170 181 I 0.2051 0.1619 0.6331 182 G 0.1473 0.0807 0.7720 183 E 0.1389 0.1206 0.7405 184 G 0.1873 0.1438 0.6689 185 L 0.3879 0.0855 0.5266 186 I 0.5159 0.0363 0.4478 187 V 0.3962 0.0205 0.5833 188 P 0.1564 0.0167 0.8269 189 P 0.0888 0.0177 0.8936 190 P 0.0764 0.0830 0.8406 191 T 0.0627 0.1326 0.8047 192 T 0.0576 0.1814 0.7610 193 E 0.0068 0.9038 0.0894 194 D 0.0053 0.9337 0.0610 195 Q 0.0049 0.9466 0.0485 196 A 0.0051 0.9490 0.0459 197 R 0.0059 0.9402 0.0540 198 A 0.0075 0.9088 0.0837 199 R 0.0156 0.8041 0.1803 200 M 0.0449 0.4539 0.5012 201 E 0.0271 0.3313 0.6416 202 S 0.0353 0.1794 0.7853 203 G 0.0405 0.0911 0.8684 204 Q 0.2277 0.0775 0.6948 205 Y 0.4784 0.0723 0.4493 206 R 0.5111 0.0796 0.4093 207 C 0.3658 0.1921 0.4421 208 L 0.2837 0.2330 0.4834 209 D 0.2138 0.3998 0.3864 210 W 0.1568 0.5467 0.2964 211 W 0.2295 0.5080 0.2624 212 F 0.2683 0.4054 0.3263 213 C 0.1871 0.2379 0.5749 214 W 0.1183 0.0919 0.7898 215 D 0.0544 0.1016 0.8440 216 T 0.0584 0.0379 0.9037 217 P 0.0378 0.1863 0.7758 218 A 0.0311 0.3111 0.6578 219 S 0.0346 0.3420 0.6234 220 R 0.0347 0.6228 0.3424 221 D 0.0265 0.6760 0.2975 222 D 0.0189 0.8156 0.1655 223 V 0.0069 0.9094 0.0837 224 E 0.0069 0.9300 0.0632 225 E 0.0065 0.9385 0.0549 226 A 0.0058 0.9369 0.0573 227 R 0.0062 0.9398 0.0540 228 R 0.0061 0.9294 0.0645 229 Y 0.0064 0.9096 0.0840 230 L 0.0093 0.8228 0.1679 231 R 0.0081 0.8261 0.1657 232 R 0.0080 0.8695 0.1224 233 A 0.0101 0.6987 0.2912 234 A 0.0117 0.7161 0.2722 235 E 0.0158 0.6583 0.3259 236 K 0.0158 0.6338 0.3503 237 P 0.0073 0.7687 0.2240 238 A 0.0056 0.8774 0.1170 239 K 0.0054 0.8916 0.1030 240 L 0.0054 0.9168 0.0778 241 L 0.0054 0.9111 0.0835 242 Y 0.0057 0.9166 0.0776 243 E 0.0092 0.8972 0.0936 244 E 0.0097 0.8509 0.1393 245 A 0.0138 0.7994 0.1868 246 R 0.0154 0.7526 0.2320 247 T 0.0211 0.6824 0.2964 248 H 0.0440 0.4855 0.4706 249 L 0.0436 0.2021 0.7543 250 H 0.0422 0.0464 0.9114