# This file is the result of combining several RDB files, specifically # T0440.t06.str2.rdb (weight 1.54425) # T0440.t06.str4.rdb (weight 0.924988) # T0440.t06.pb.rdb (weight 0.789901) # T0440.t06.bys.rdb (weight 0.748322) # T0440.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 T0440.t06.str2.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1611 # # ============================================ # Comments from T0440.t06.str4.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1611 # # ============================================ # Comments from T0440.t06.pb.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1611 # # ============================================ # Comments from T0440.t06.bys.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1611 # # ============================================ # Comments from T0440.t06.alpha.rdb # ============================================ # TARGET T0440 # 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 T0440.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 1611 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3262 0.0732 0.6006 2 K 0.3879 0.0597 0.5524 3 R 0.4575 0.0540 0.4885 4 D 0.3771 0.0669 0.5560 5 G 0.4071 0.1495 0.4434 6 H 0.4744 0.1195 0.4061 7 T 0.4965 0.0955 0.4080 8 H 0.4382 0.0778 0.4841 9 T 0.3506 0.0916 0.5578 10 E 0.2936 0.1361 0.5704 11 F 0.3146 0.1029 0.5824 12 C 0.2421 0.0504 0.7075 13 P 0.0604 0.3612 0.5784 14 H 0.0766 0.2479 0.6755 15 G 0.1113 0.1626 0.7261 16 T 0.1229 0.1738 0.7034 17 H 0.1252 0.1963 0.6785 18 D 0.1211 0.1585 0.7204 19 D 0.1616 0.0669 0.7715 20 V 0.0125 0.7546 0.2328 21 E 0.0091 0.8734 0.1175 22 E 0.0083 0.9245 0.0673 23 M 0.0083 0.9242 0.0676 24 V 0.0083 0.9216 0.0701 25 L 0.0083 0.9244 0.0673 26 K 0.0083 0.9243 0.0674 27 A 0.0083 0.9239 0.0678 28 I 0.0084 0.9168 0.0748 29 E 0.0111 0.8347 0.1543 30 L 0.0548 0.2954 0.6498 31 D 0.0500 0.0790 0.8710 32 F 0.1742 0.0512 0.7746 33 D 0.2458 0.1065 0.6477 34 E 0.7286 0.0385 0.2330 35 Y 0.7492 0.0167 0.2341 36 S 0.7947 0.0105 0.1948 37 I 0.7728 0.0114 0.2159 38 V 0.6363 0.0231 0.3406 39 E 0.2867 0.1334 0.5799 40 H 0.1578 0.1489 0.6932 41 A 0.1832 0.1409 0.6759 42 P 0.1109 0.2793 0.6099 43 L 0.1120 0.3299 0.5581 44 S 0.1298 0.4028 0.4674 45 S 0.0169 0.7696 0.2135 46 E 0.0120 0.8621 0.1260 47 F 0.0126 0.8951 0.0923 48 M 0.0123 0.8967 0.0910 49 K 0.0133 0.8713 0.1155 50 N 0.0202 0.7586 0.2211 51 T 0.0595 0.5526 0.3879 52 A 0.0558 0.3996 0.5446 53 G 0.0658 0.2514 0.6828 54 D 0.0970 0.1502 0.7528 55 K 0.2501 0.0872 0.6627 56 E 0.4594 0.0559 0.4847 57 A 0.5858 0.0356 0.3786 58 V 0.5509 0.0345 0.4146 59 T 0.4348 0.0620 0.5032 60 T 0.4226 0.0818 0.4956 61 A 0.5316 0.0755 0.3928 62 S 0.5927 0.0589 0.3484 63 M 0.6111 0.0491 0.3397 64 A 0.5268 0.0569 0.4164 65 M 0.4213 0.1404 0.4383 66 S 0.2685 0.2021 0.5293 67 D 0.1840 0.1597 0.6563 68 L 0.1707 0.1720 0.6573 69 P 0.0736 0.4840 0.4424 70 Y 0.0808 0.5872 0.3320 71 Y 0.0999 0.6729 0.2272 72 F 0.0667 0.7927 0.1406 73 K 0.0572 0.8290 0.1138 74 K 0.0540 0.8355 0.1105 75 M 0.0430 0.8367 0.1203 76 N 0.0298 0.8338 0.1364 77 H 0.0273 0.8132 0.1595 78 I 0.0467 0.7508 0.2025 79 K 0.0563 0.6896 0.2540 80 K 0.0515 0.6927 0.2557 81 K 0.0572 0.6074 0.3354 82 Y 0.0926 0.4360 0.4714 83 A 0.1140 0.3700 0.5160 84 S 0.0732 0.4665 0.4603 85 D 0.1315 0.3520 0.5165 86 L 0.3763 0.2139 0.4098 87 L 0.5122 0.1718 0.3161 88 I 0.6311 0.1266 0.2423 89 H 0.5169 0.1749 0.3081 90 I 0.3190 0.1878 0.4932 91 G 0.2349 0.1098 0.6553 92 F 0.3445 0.1160 0.5395 93 E 0.4279 0.1564 0.4157 94 V 0.3593 0.2478 0.3929 95 D 0.3016 0.2687 0.4297 96 Y 0.2874 0.3023 0.4103 97 L 0.2575 0.3065 0.4359 98 I 0.1279 0.3934 0.4787 99 G 0.0807 0.4248 0.4946 100 Y 0.0836 0.5356 0.3808 101 E 0.0379 0.7287 0.2334 102 D 0.0273 0.7738 0.1988 103 F 0.0281 0.7893 0.1825 104 T 0.0277 0.8280 0.1442 105 R 0.0129 0.8834 0.1037 106 D 0.0110 0.8909 0.0981 107 F 0.0138 0.8770 0.1092 108 L 0.0175 0.8487 0.1338 109 N 0.0178 0.7654 0.2168 110 E 0.0267 0.5737 0.3996 111 Y 0.0838 0.3059 0.6102 112 G 0.1030 0.1273 0.7697 113 P 0.1299 0.2128 0.6573 114 Q 0.1535 0.2266 0.6199 115 T 0.1553 0.2420 0.6026 116 D 0.1697 0.2035 0.6268 117 D 0.2044 0.1968 0.5988 118 G 0.3816 0.1712 0.4472 119 V 0.5152 0.1199 0.3648 120 L 0.5224 0.0868 0.3908 121 S 0.4704 0.0785 0.4511 122 L 0.3356 0.2277 0.4368 123 H 0.3805 0.2482 0.3713 124 F 0.3979 0.2470 0.3551 125 L 0.3197 0.2246 0.4557 126 E 0.2324 0.1992 0.5684 127 G 0.1451 0.2428 0.6121 128 Q 0.1498 0.2353 0.6150 129 G 0.1379 0.1954 0.6667 130 G 0.1537 0.1924 0.6539 131 F 0.2107 0.1856 0.6037 132 R 0.2280 0.1838 0.5882 133 S 0.2869 0.1756 0.5376 134 I 0.2804 0.1848 0.5348 135 D 0.2020 0.2396 0.5584 136 F 0.1806 0.2966 0.5228 137 S 0.1249 0.4262 0.4489 138 A 0.0514 0.6672 0.2814 139 E 0.0320 0.7597 0.2084 140 D 0.0324 0.7655 0.2021 141 Y 0.0434 0.7544 0.2022 142 N 0.0351 0.7724 0.1925 143 E 0.0284 0.7825 0.1891 144 G 0.0325 0.7757 0.1918 145 I 0.0556 0.7630 0.1814 146 V 0.0621 0.7550 0.1829 147 Q 0.0686 0.6957 0.2357 148 F 0.0830 0.5232 0.3938 149 Y 0.0851 0.3068 0.6081 150 G 0.0649 0.1755 0.7596 151 G 0.0973 0.1233 0.7794 152 F 0.1712 0.2349 0.5938 153 E 0.1449 0.4695 0.3856 154 Q 0.1940 0.5279 0.2781 155 A 0.2144 0.5384 0.2472 156 Q 0.1577 0.6290 0.2133 157 L 0.0826 0.7362 0.1812 158 A 0.0758 0.7000 0.2242 159 Y 0.0659 0.6532 0.2810 160 L 0.0464 0.7094 0.2442 161 E 0.0274 0.7239 0.2487 162 G 0.0300 0.7052 0.2648 163 V 0.0182 0.8249 0.1569 164 K 0.0106 0.8966 0.0927 165 Q 0.0100 0.9141 0.0759 166 S 0.0095 0.9179 0.0726 167 I 0.0093 0.9171 0.0736 168 E 0.0095 0.9164 0.0742 169 A 0.0099 0.9036 0.0865 170 D 0.0137 0.8662 0.1201 171 L 0.0252 0.7616 0.2132 172 G 0.0317 0.4731 0.4952 173 L 0.0743 0.2564 0.6693 174 F 0.0853 0.1247 0.7899 175 K 0.2220 0.0496 0.7284 176 P 0.3427 0.0592 0.5981 177 R 0.5350 0.0513 0.4136 178 R 0.7244 0.0403 0.2353 179 M 0.6568 0.0582 0.2850 180 G 0.6177 0.0520 0.3302 181 H 0.3397 0.0452 0.6152 182 I 0.0688 0.5193 0.4118 183 S 0.0471 0.6203 0.3325 184 L 0.0446 0.7279 0.2275 185 C 0.0497 0.7588 0.1915 186 Q 0.0337 0.8075 0.1587 187 K 0.0445 0.7564 0.1991 188 F 0.0656 0.6637 0.2707 189 Q 0.0764 0.6251 0.2985 190 Q 0.1022 0.5361 0.3617 191 F 0.1363 0.3696 0.4941 192 F 0.1361 0.2134 0.6505 193 G 0.0984 0.1919 0.7097 194 E 0.1246 0.2577 0.6177 195 D 0.1454 0.2171 0.6375 196 T 0.0905 0.4337 0.4758 197 S 0.0522 0.5821 0.3658 198 D 0.0454 0.6250 0.3296 199 F 0.0544 0.6153 0.3302 200 S 0.0386 0.7626 0.1987 201 E 0.0123 0.8503 0.1375 202 E 0.0121 0.8698 0.1181 203 V 0.0182 0.8471 0.1346 204 M 0.0142 0.8875 0.0983 205 E 0.0095 0.8963 0.0942 206 K 0.0099 0.8904 0.0997 207 F 0.0099 0.9003 0.0898 208 R 0.0084 0.9190 0.0726 209 V 0.0083 0.9230 0.0687 210 I 0.0083 0.9212 0.0704 211 L 0.0084 0.9196 0.0721 212 A 0.0083 0.9229 0.0688 213 L 0.0083 0.9232 0.0685 214 V 0.0085 0.9201 0.0714 215 K 0.0088 0.9015 0.0897 216 K 0.0140 0.7740 0.2120 217 R 0.0575 0.3014 0.6411 218 D 0.0585 0.0928 0.8486 219 Y 0.2330 0.0488 0.7182 220 E 0.6051 0.0321 0.3628 221 L 0.7649 0.0123 0.2228 222 D 0.7793 0.0108 0.2099 223 F 0.7688 0.0138 0.2174 224 N 0.5685 0.0421 0.3893 225 T 0.3090 0.1132 0.5778 226 A 0.1535 0.2299 0.6166 227 G 0.1140 0.2794 0.6067 228 L 0.1633 0.2772 0.5595 229 F 0.2223 0.2077 0.5700 230 K 0.2216 0.1650 0.6134 231 P 0.1581 0.2976 0.5443 232 L 0.1280 0.3475 0.5245 233 C 0.1318 0.2308 0.6374 234 G 0.1176 0.1528 0.7297 235 E 0.2020 0.1323 0.6657 236 T 0.2201 0.1382 0.6417 237 Y 0.2463 0.0546 0.6991 238 P 0.1663 0.0885 0.7452 239 P 0.0606 0.5850 0.3544 240 K 0.0119 0.8238 0.1644 241 K 0.0095 0.9009 0.0896 242 I 0.0085 0.9195 0.0720 243 V 0.0084 0.9196 0.0721 244 T 0.0083 0.9222 0.0695 245 L 0.0084 0.9204 0.0713 246 A 0.0086 0.9163 0.0751 247 S 0.0089 0.9000 0.0911 248 E 0.0136 0.8019 0.1846 249 L 0.0624 0.3061 0.6315 250 Q 0.0542 0.0818 0.8640 251 I 0.2369 0.0146 0.7485 252 P 0.3769 0.0294 0.5936 253 F 0.7506 0.0176 0.2318 254 V 0.7634 0.0183 0.2183 255 Y 0.7064 0.0260 0.2676 256 G 0.5679 0.0501 0.3820 257 S 0.2983 0.1004 0.6013 258 D 0.1891 0.1989 0.6120 259 S 0.1148 0.3485 0.5367 260 H 0.1498 0.2230 0.6272 261 G 0.1605 0.1665 0.6729 262 V 0.1202 0.3756 0.5042 263 Q 0.1082 0.4488 0.4430 264 D 0.1328 0.3989 0.4683 265 I 0.1359 0.3361 0.5280 266 G 0.1178 0.2566 0.6257 267 R 0.1069 0.3453 0.5477 268 G 0.1039 0.3267 0.5694 269 Y 0.1166 0.4613 0.4221 270 S 0.1047 0.5725 0.3228 271 T 0.1146 0.6076 0.2778 272 Y 0.1480 0.4947 0.3573 273 C 0.1800 0.3947 0.4253 274 Q 0.1446 0.3690 0.4864 275 K 0.1335 0.2765 0.5900