# This file is the result of combining several RDB files, specifically # T0421.t2k.str2.rdb (weight 1.54425) # T0421.t2k.str4.rdb (weight 0.924988) # T0421.t2k.pb.rdb (weight 0.789901) # T0421.t2k.bys.rdb (weight 0.748322) # T0421.t2k.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 T0421.t2k.str2.rdb # ============================================ # TARGET T0421 # Using neural net dunbrack-40pc-3157-t2k-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 T0421.t2k-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 45.5732 # # ============================================ # Comments from T0421.t2k.str4.rdb # ============================================ # TARGET T0421 # Using neural net dunbrack-40pc-3157-t2k-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 T0421.t2k-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 45.5732 # # ============================================ # Comments from T0421.t2k.pb.rdb # ============================================ # TARGET T0421 # Using neural net dunbrack-40pc-3157-t2k-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 T0421.t2k-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 45.5732 # # ============================================ # Comments from T0421.t2k.bys.rdb # ============================================ # TARGET T0421 # Using neural net dunbrack-40pc-3157-t2k-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 T0421.t2k-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 45.5732 # # ============================================ # Comments from T0421.t2k.alpha.rdb # ============================================ # TARGET T0421 # Using neural net dunbrack-40pc-3157-t2k-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 T0421.t2k-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 45.5732 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2363 0.3575 0.4062 2 A 0.1974 0.3613 0.4413 3 L 0.2021 0.3395 0.4584 4 D 0.1556 0.2855 0.5589 5 E 0.1519 0.2479 0.6003 6 A 0.2331 0.0950 0.6719 7 P 0.1903 0.2531 0.5565 8 A 0.1286 0.5334 0.3380 9 E 0.1506 0.4262 0.4233 10 A 0.1983 0.2399 0.5618 11 R 0.2000 0.0611 0.7389 12 P 0.1259 0.1838 0.6903 13 G 0.0926 0.1206 0.7868 14 S 0.1561 0.2097 0.6342 15 R 0.2071 0.3127 0.4802 16 A 0.3845 0.2999 0.3156 17 V 0.5503 0.1948 0.2549 18 E 0.6299 0.1262 0.2439 19 L 0.6628 0.1016 0.2356 20 E 0.6067 0.1055 0.2878 21 I 0.5154 0.1197 0.3649 22 D 0.2292 0.1217 0.6491 23 G 0.1387 0.1202 0.7412 24 R 0.2309 0.1453 0.6237 25 S 0.3094 0.1584 0.5322 26 R 0.3419 0.1738 0.4843 27 I 0.3804 0.1609 0.4587 28 F 0.3514 0.1272 0.5214 29 D 0.2647 0.1125 0.6228 30 I 0.1369 0.3010 0.5621 31 D 0.1337 0.1993 0.6670 32 D 0.1653 0.1431 0.6915 33 P 0.0568 0.3806 0.5627 34 D 0.1026 0.2570 0.6404 35 L 0.1820 0.1243 0.6938 36 P 0.1414 0.2270 0.6316 37 K 0.1435 0.3197 0.5367 38 W 0.1570 0.3447 0.4983 39 I 0.1911 0.3173 0.4917 40 D 0.1663 0.3251 0.5086 41 E 0.0672 0.6278 0.3051 42 E 0.0688 0.6639 0.2674 43 A 0.1080 0.5955 0.2964 44 F 0.1538 0.4586 0.3876 45 R 0.1694 0.3006 0.5300 46 S 0.1398 0.2444 0.6158 47 D 0.0666 0.3225 0.6109 48 D 0.0951 0.2008 0.7041 49 Y 0.1971 0.0926 0.7103 50 P 0.1709 0.1772 0.6520 51 Y 0.1364 0.3701 0.4935 52 K 0.1218 0.4199 0.4583 53 K 0.1496 0.4163 0.4340 54 K 0.1809 0.2806 0.5385 55 L 0.2254 0.1893 0.5853 56 D 0.1647 0.0976 0.7378 57 R 0.0163 0.7377 0.2460 58 E 0.0097 0.8653 0.1250 59 E 0.0098 0.9071 0.0831 60 Y 0.0100 0.9153 0.0747 61 E 0.0083 0.9207 0.0710 62 E 0.0083 0.9223 0.0694 63 T 0.0084 0.9184 0.0732 64 L 0.0085 0.9143 0.0771 65 T 0.0084 0.9188 0.0728 66 K 0.0085 0.9122 0.0793 67 L 0.0087 0.9142 0.0772 68 Q 0.0084 0.9185 0.0731 69 I 0.0084 0.9185 0.0731 70 E 0.0084 0.9199 0.0717 71 L 0.0087 0.9138 0.0775 72 V 0.0084 0.9153 0.0763 73 K 0.0084 0.9155 0.0760 74 V 0.0088 0.9139 0.0773 75 Q 0.0088 0.9186 0.0727 76 F 0.0092 0.9187 0.0721 77 W 0.0100 0.9174 0.0726 78 M 0.0111 0.9093 0.0796 79 Q 0.0129 0.8742 0.1129 80 A 0.0233 0.7564 0.2203 81 T 0.0573 0.1844 0.7583 82 G 0.0490 0.0660 0.8850 83 K 0.2471 0.0158 0.7372 84 R 0.5374 0.0126 0.4500 85 V 0.8098 0.0048 0.1855 86 M 0.8246 0.0041 0.1713 87 A 0.8150 0.0043 0.1807 88 V 0.8092 0.0061 0.1848 89 F 0.7724 0.0085 0.2191 90 E 0.5935 0.0297 0.3768 91 G 0.3674 0.0691 0.5635 92 R 0.2798 0.2376 0.4825 93 D 0.2029 0.3125 0.4846 94 A 0.1514 0.3864 0.4622 95 A 0.1270 0.2848 0.5883 96 G 0.1325 0.1511 0.7164 97 K 0.1227 0.2094 0.6678 98 G 0.0883 0.1959 0.7158 99 G 0.1133 0.3443 0.5424 100 A 0.1911 0.5216 0.2873 101 I 0.1261 0.6969 0.1770 102 H 0.1023 0.7645 0.1332 103 A 0.0883 0.7796 0.1321 104 T 0.0845 0.7532 0.1624 105 T 0.0955 0.6654 0.2391 106 A 0.0574 0.5902 0.3524 107 N 0.0790 0.3306 0.5903 108 M 0.1858 0.1613 0.6528 109 N 0.2000 0.0637 0.7363 110 P 0.0707 0.3866 0.5426 111 R 0.0907 0.3291 0.5802 112 S 0.2868 0.2094 0.5037 113 A 0.5713 0.0610 0.3677 114 R 0.6993 0.0306 0.2701 115 V 0.7324 0.0261 0.2414 116 V 0.6866 0.0386 0.2747 117 A 0.5592 0.0683 0.3725 118 L 0.3391 0.0983 0.5626 119 T 0.2471 0.0921 0.6608 120 K 0.2551 0.0350 0.7099 121 P 0.1985 0.0633 0.7382 122 T 0.1809 0.0763 0.7428 123 E 0.0484 0.6043 0.3473 124 T 0.0473 0.6785 0.2742 125 E 0.0831 0.6378 0.2791 126 R 0.0877 0.5375 0.3748 127 G 0.0716 0.4376 0.4908 128 Q 0.0868 0.5867 0.3265 129 W 0.0507 0.7363 0.2131 130 Y 0.0351 0.7989 0.1660 131 F 0.0272 0.8581 0.1147 132 Q 0.0265 0.8759 0.0977 133 R 0.0327 0.8710 0.0963 134 Y 0.0484 0.8321 0.1195 135 V 0.0628 0.7672 0.1699 136 A 0.0931 0.6297 0.2772 137 T 0.1533 0.3589 0.4878 138 F 0.2530 0.1107 0.6363 139 P 0.1711 0.1306 0.6983 140 T 0.1120 0.2904 0.5976 141 A 0.1254 0.1843 0.6903 142 G 0.1620 0.1080 0.7300 143 E 0.5170 0.0251 0.4579 144 F 0.7459 0.0099 0.2442 145 V 0.7933 0.0090 0.1977 146 L 0.7854 0.0126 0.2019 147 F 0.6986 0.0268 0.2747 148 D 0.4649 0.0460 0.4891 149 R 0.2732 0.2347 0.4921 150 S 0.2308 0.3068 0.4624 151 W 0.1623 0.4688 0.3690 152 Y 0.1558 0.4837 0.3605 153 N 0.1612 0.4436 0.3952 154 R 0.1864 0.3438 0.4698 155 A 0.2135 0.1936 0.5929 156 G 0.2721 0.1060 0.6219 157 V 0.4849 0.0680 0.4471 158 E 0.5667 0.0440 0.3894 159 P 0.6057 0.0640 0.3303 160 V 0.5170 0.1040 0.3790 161 M 0.3298 0.1484 0.5218 162 G 0.2088 0.1490 0.6421 163 F 0.2343 0.1363 0.6294 164 C 0.2474 0.0635 0.6891 165 T 0.1599 0.0230 0.8171 166 P 0.0126 0.7308 0.2566 167 D 0.0099 0.8571 0.1330 168 Q 0.0097 0.9068 0.0835 169 Y 0.0092 0.9130 0.0778 170 E 0.0083 0.9221 0.0695 171 Q 0.0083 0.9226 0.0691 172 F 0.0087 0.9132 0.0781 173 L 0.0089 0.8886 0.1025 174 K 0.0094 0.8196 0.1710 175 E 0.0182 0.6256 0.3562 176 A 0.0533 0.5629 0.3838 177 P 0.0165 0.8006 0.1829 178 R 0.0114 0.8684 0.1202 179 F 0.0102 0.9023 0.0875 180 E 0.0084 0.9205 0.0711 181 E 0.0085 0.9213 0.0702 182 M 0.0097 0.9088 0.0815 183 I 0.0134 0.8633 0.1233 184 A 0.0200 0.7542 0.2259 185 N 0.0309 0.6041 0.3650 186 E 0.0617 0.1741 0.7643 187 G 0.0756 0.0778 0.8466 188 I 0.3763 0.0260 0.5977 189 H 0.6748 0.0258 0.2993 190 L 0.7644 0.0273 0.2083 191 F 0.7619 0.0289 0.2091 192 K 0.7626 0.0250 0.2125 193 F 0.7722 0.0269 0.2008 194 W 0.7202 0.0523 0.2275 195 I 0.6570 0.0797 0.2633 196 N 0.4686 0.0941 0.4373 197 I 0.2768 0.1513 0.5720 198 G 0.1572 0.0515 0.7913 199 R 0.0130 0.7295 0.2576 200 E 0.0095 0.8529 0.1376 201 M 0.0087 0.9160 0.0753 202 Q 0.0086 0.9195 0.0719 203 L 0.0085 0.9157 0.0758 204 K 0.0083 0.9166 0.0751 205 R 0.0088 0.9042 0.0870 206 F 0.0100 0.8801 0.1099 207 H 0.0096 0.8780 0.1124 208 D 0.0140 0.8145 0.1715 209 R 0.0361 0.7040 0.2600 210 R 0.0550 0.5994 0.3456 211 H 0.0951 0.3453 0.5596 212 D 0.1558 0.1460 0.6981 213 P 0.0530 0.4297 0.5173 214 L 0.0695 0.4635 0.4670 215 K 0.1675 0.4301 0.4024 216 I 0.2988 0.2819 0.4192 217 W 0.4811 0.1469 0.3720 218 K 0.4834 0.0936 0.4230 219 L 0.3592 0.0576 0.5832 220 S 0.1814 0.0199 0.7986 221 P 0.0296 0.5811 0.3893 222 M 0.0297 0.6792 0.2911 223 D 0.0599 0.6982 0.2419 224 I 0.0122 0.8613 0.1265 225 A 0.0092 0.8796 0.1112 226 A 0.0105 0.8758 0.1137 227 L 0.0134 0.8592 0.1274 228 S 0.0151 0.8233 0.1616 229 K 0.0236 0.7240 0.2525 230 W 0.0352 0.7561 0.2087 231 D 0.0144 0.8429 0.1427 232 D 0.0113 0.8432 0.1456 233 Y 0.0156 0.8342 0.1503 234 T 0.0148 0.8486 0.1366 235 G 0.0118 0.8589 0.1294 236 K 0.0109 0.8856 0.1036 237 R 0.0097 0.9059 0.0844 238 D 0.0086 0.9152 0.0762 239 R 0.0088 0.9131 0.0781 240 M 0.0119 0.8923 0.0958 241 L 0.0147 0.8740 0.1113 242 K 0.0228 0.7856 0.1915 243 E 0.0501 0.5524 0.3975 244 T 0.1179 0.3020 0.5801 245 H 0.1258 0.1980 0.6761 246 T 0.1435 0.2013 0.6552 247 E 0.0630 0.3727 0.5644 248 H 0.1158 0.1978 0.6864 249 G 0.2374 0.0568 0.7057 250 P 0.2931 0.0687 0.6382 251 W 0.5370 0.0462 0.4168 252 A 0.7376 0.0190 0.2435 253 V 0.7547 0.0115 0.2337 254 I 0.6873 0.0167 0.2960 255 R 0.5516 0.0318 0.4166 256 G 0.3005 0.1262 0.5733 257 N 0.1793 0.1696 0.6510 258 D 0.1557 0.2076 0.6367 259 K 0.0723 0.5616 0.3661 260 R 0.0656 0.6630 0.2714 261 R 0.0759 0.6910 0.2332 262 S 0.0610 0.7791 0.1598 263 R 0.0461 0.8283 0.1255 264 I 0.0352 0.8707 0.0942 265 N 0.0198 0.9009 0.0793 266 V 0.0108 0.9149 0.0743 267 I 0.0086 0.9206 0.0709 268 R 0.0088 0.9232 0.0681 269 H 0.0083 0.9235 0.0682 270 M 0.0084 0.9188 0.0728 271 L 0.0088 0.9042 0.0871 272 T 0.0095 0.8767 0.1138 273 K 0.0222 0.7451 0.2328 274 L 0.0878 0.6117 0.3005 275 D 0.0788 0.5394 0.3818 276 Y 0.0747 0.5450 0.3803 277 D 0.0653 0.2772 0.6575 278 G 0.0580 0.1399 0.8021 279 K 0.1549 0.1396 0.7056 280 D 0.1795 0.1300 0.6905 281 E 0.1839 0.3181 0.4980 282 A 0.1513 0.3894 0.4593 283 A 0.1752 0.3602 0.4645 284 I 0.1841 0.2803 0.5356 285 G 0.1601 0.2097 0.6301 286 E 0.1950 0.2277 0.5773 287 V 0.2175 0.2132 0.5693 288 D 0.1934 0.1981 0.6085 289 E 0.0702 0.6291 0.3008 290 K 0.0869 0.6414 0.2717 291 I 0.1462 0.5225 0.3313 292 L 0.1537 0.3415 0.5048 293 G 0.1196 0.2306 0.6498 294 S 0.1290 0.1787 0.6923 295 G 0.1511 0.1074 0.7415 296 P 0.1006 0.3153 0.5841 297 G 0.0903 0.3119 0.5978 298 F 0.2027 0.3303 0.4669 299 L 0.3209 0.2281 0.4510 300 R 0.2455 0.1804 0.5741