# This file is the result of combining several RDB files, specifically # T0413.t04.dssp-ebghstl.rdb (weight 1.53986) # T0413.t04.stride-ebghtl.rdb (weight 1.24869) # T0413.t04.str2.rdb (weight 1.54758) # T0413.t04.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 T0413.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0413 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0413.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 2021 # # ============================================ # Comments from T0413.t04.stride-ebghtl.rdb # ============================================ # TARGET T0413 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0413.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 2021 # # ============================================ # Comments from T0413.t04.str2.rdb # ============================================ # TARGET T0413 # Using neural net t04-2621-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 T0413.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 2021 # # ============================================ # Comments from T0413.t04.alpha.rdb # ============================================ # TARGET T0413 # Using neural net t04-2621-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 T0413.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 2021 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0740 0.1187 0.8073 2 N 0.0952 0.1797 0.7251 3 A 0.1575 0.1271 0.7153 4 M 0.2244 0.0682 0.7074 5 K 0.1824 0.0362 0.7815 6 P 0.1248 0.2502 0.6250 7 A 0.1080 0.3813 0.5107 8 D 0.1381 0.3752 0.4867 9 L 0.1271 0.3173 0.5556 10 T 0.1043 0.3054 0.5903 11 N 0.0961 0.3194 0.5845 12 A 0.0571 0.5281 0.4148 13 D 0.0391 0.5759 0.3850 14 R 0.0392 0.6999 0.2609 15 I 0.0566 0.7375 0.2059 16 A 0.0567 0.7448 0.1985 17 L 0.0376 0.8109 0.1515 18 E 0.0376 0.7859 0.1765 19 L 0.0552 0.6214 0.3234 20 G 0.0493 0.2928 0.6579 21 H 0.0924 0.1500 0.7576 22 A 0.0964 0.1348 0.7688 23 G 0.0877 0.0758 0.8365 24 R 0.1313 0.0618 0.8070 25 N 0.2323 0.0273 0.7404 26 A 0.3913 0.0174 0.5912 27 I 0.6393 0.0087 0.3520 28 P 0.7626 0.0052 0.2322 29 Y 0.7904 0.0064 0.2032 30 L 0.7726 0.0075 0.2199 31 D 0.5460 0.0143 0.4397 32 D 0.3486 0.0357 0.6158 33 D 0.2517 0.0472 0.7011 34 R 0.1385 0.1193 0.7422 35 N 0.1212 0.0815 0.7974 36 A 0.0923 0.0553 0.8525 37 D 0.0723 0.0382 0.8894 38 R 0.3586 0.0146 0.6268 39 P 0.5303 0.0079 0.4618 40 F 0.8037 0.0063 0.1900 41 T 0.8742 0.0059 0.1198 42 L 0.8963 0.0062 0.0975 43 N 0.9114 0.0057 0.0828 44 T 0.9038 0.0074 0.0889 45 Y 0.8751 0.0074 0.1175 46 R 0.7063 0.0087 0.2850 47 P 0.2744 0.0220 0.7036 48 Y 0.0735 0.0818 0.8447 49 G 0.0476 0.0563 0.8961 50 Y 0.1174 0.0433 0.8393 51 T 0.0796 0.0251 0.8953 52 P 0.0592 0.0520 0.8888 53 D 0.0595 0.0643 0.8762 54 R 0.1392 0.0138 0.8470 55 P 0.3308 0.0057 0.6635 56 V 0.9105 0.0036 0.0859 57 V 0.9334 0.0033 0.0634 58 V 0.9330 0.0033 0.0637 59 V 0.9232 0.0041 0.0728 60 Q 0.7886 0.0080 0.2033 61 H 0.3609 0.0187 0.6204 62 G 0.1355 0.0387 0.8258 63 V 0.1328 0.0780 0.7892 64 L 0.1172 0.1396 0.7433 65 R 0.1007 0.1358 0.7635 66 N 0.0818 0.0893 0.8289 67 G 0.0440 0.2613 0.6947 68 A 0.0402 0.3983 0.5615 69 D 0.0650 0.4621 0.4729 70 Y 0.0431 0.7005 0.2565 71 R 0.0367 0.7211 0.2423 72 D 0.0287 0.7079 0.2634 73 F 0.0256 0.7173 0.2571 74 W 0.0273 0.7325 0.2403 75 I 0.0189 0.8229 0.1582 76 P 0.0128 0.8710 0.1162 77 A 0.0154 0.8846 0.1000 78 A 0.0148 0.8696 0.1155 79 D 0.0094 0.8257 0.1649 80 R 0.0153 0.5485 0.4363 81 H 0.0636 0.0932 0.8432 82 K 0.0980 0.0225 0.8794 83 L 0.6159 0.0060 0.3781 84 L 0.9181 0.0036 0.0783 85 I 0.9300 0.0032 0.0668 86 V 0.8961 0.0083 0.0955 87 A 0.7621 0.0058 0.2321 88 P 0.3432 0.0349 0.6219 89 T 0.1753 0.0223 0.8024 90 F 0.1006 0.0705 0.8288 91 S 0.0812 0.1117 0.8071 92 D 0.0682 0.1367 0.7951 93 E 0.1088 0.0958 0.7953 94 I 0.1601 0.0951 0.7448 95 W 0.1140 0.0589 0.8270 96 P 0.0754 0.1135 0.8112 97 G 0.0777 0.1025 0.8198 98 V 0.1063 0.2159 0.6778 99 E 0.1150 0.2679 0.6171 100 S 0.1407 0.2602 0.5991 101 Y 0.1140 0.2075 0.6785 102 N 0.0836 0.1730 0.7435 103 N 0.0798 0.1267 0.7935 104 G 0.0740 0.1259 0.8001 105 R 0.1557 0.2363 0.6080 106 A 0.2720 0.2710 0.4570 107 F 0.3071 0.2313 0.4616 108 T 0.2854 0.2126 0.5020 109 A 0.2238 0.2935 0.4828 110 A 0.1674 0.2126 0.6200 111 G 0.1615 0.1261 0.7124 112 N 0.1235 0.0422 0.8343 113 P 0.0706 0.1464 0.7830 114 R 0.0844 0.1578 0.7577 115 H 0.0892 0.1340 0.7768 116 V 0.0829 0.1407 0.7763 117 D 0.0615 0.1136 0.8249 118 G 0.0538 0.2962 0.6500 119 W 0.1189 0.3679 0.5132 120 T 0.1263 0.5306 0.3431 121 Y 0.0072 0.9361 0.0567 122 A 0.0050 0.9557 0.0392 123 L 0.0048 0.9561 0.0391 124 V 0.0047 0.9589 0.0363 125 A 0.0047 0.9602 0.0351 126 R 0.0047 0.9590 0.0363 127 V 0.0048 0.9540 0.0412 128 L 0.0047 0.9588 0.0366 129 A 0.0047 0.9605 0.0349 130 N 0.0047 0.9591 0.0362 131 I 0.0048 0.9540 0.0413 132 R 0.0049 0.9391 0.0560 133 A 0.0066 0.8280 0.1655 134 A 0.0252 0.5063 0.4685 135 E 0.0358 0.3047 0.6596 136 I 0.0595 0.1636 0.7769 137 A 0.0955 0.1085 0.7961 138 D 0.1249 0.0448 0.8303 139 C 0.0498 0.5010 0.4492 140 E 0.0849 0.4182 0.4969 141 Q 0.3722 0.2999 0.3279 142 V 0.8028 0.0461 0.1512 143 Y 0.8912 0.0193 0.0894 144 L 0.8719 0.0249 0.1031 145 F 0.6646 0.0617 0.2737 146 G 0.2825 0.0704 0.6471 147 H 0.1082 0.1359 0.7559 148 S 0.0795 0.2436 0.6769 149 A 0.0350 0.5813 0.3836 150 G 0.0109 0.8515 0.1376 151 G 0.0048 0.9518 0.0434 152 Q 0.0047 0.9587 0.0366 153 F 0.0047 0.9604 0.0350 154 V 0.0046 0.9614 0.0340 155 H 0.0047 0.9610 0.0344 156 R 0.0047 0.9593 0.0361 157 L 0.0048 0.9456 0.0495 158 M 0.0055 0.9029 0.0916 159 S 0.0121 0.7761 0.2118 160 S 0.0322 0.4817 0.4861 161 Q 0.0770 0.0401 0.8829 162 P 0.0219 0.1097 0.8683 163 H 0.0265 0.0889 0.8846 164 A 0.0844 0.0535 0.8620 165 P 0.1501 0.0544 0.7954 166 F 0.5173 0.0390 0.4437 167 H 0.7031 0.0543 0.2426 168 A 0.8909 0.0204 0.0887 169 V 0.8819 0.0347 0.0835 170 T 0.8792 0.0297 0.0911 171 A 0.7929 0.0395 0.1675 172 A 0.4439 0.0641 0.4919 173 N 0.1582 0.0350 0.8068 174 P 0.0688 0.1377 0.7935 175 G 0.1018 0.1652 0.7331 176 W 0.1141 0.2209 0.6650 177 Y 0.1399 0.1637 0.6964 178 T 0.1242 0.1449 0.7309 179 L 0.0687 0.2985 0.6328 180 P 0.0530 0.4504 0.4967 181 T 0.0556 0.5554 0.3891 182 F 0.0557 0.5513 0.3930 183 E 0.0581 0.5452 0.3967 184 H 0.0719 0.4184 0.5097 185 R 0.1000 0.2717 0.6283 186 F 0.0916 0.0786 0.8298 187 P 0.0510 0.2466 0.7025 188 E 0.0509 0.3093 0.6398 189 G 0.0628 0.2860 0.6512 190 L 0.1111 0.2359 0.6530 191 D 0.0887 0.1732 0.7380 192 G 0.0668 0.1540 0.7792 193 V 0.0903 0.1421 0.7676 194 G 0.0749 0.1842 0.7409 195 L 0.0932 0.2296 0.6773 196 T 0.0847 0.2310 0.6843 197 E 0.0636 0.2875 0.6490 198 D 0.0471 0.4680 0.4849 199 H 0.0273 0.6519 0.3208 200 L 0.0293 0.7434 0.2273 201 A 0.0348 0.7786 0.1866 202 R 0.0311 0.7362 0.2328 203 L 0.0423 0.5549 0.4028 204 L 0.1117 0.2141 0.6742 205 A 0.0905 0.0748 0.8346 206 Y 0.1465 0.0163 0.8372 207 P 0.2845 0.0154 0.7001 208 M 0.8691 0.0075 0.1233 209 T 0.9230 0.0041 0.0729 210 I 0.9248 0.0052 0.0699 211 L 0.8882 0.0095 0.1023 212 A 0.6176 0.0197 0.3628 213 G 0.2089 0.0364 0.7547 214 D 0.1359 0.1225 0.7416 215 Q 0.1076 0.1866 0.7058 216 D 0.1054 0.1656 0.7290 217 I 0.0680 0.2607 0.6713 218 A 0.0965 0.1376 0.7660 219 T 0.1506 0.0498 0.7996 220 D 0.1136 0.0296 0.8568 221 D 0.0422 0.2099 0.7479 222 P 0.0142 0.3100 0.6758 223 N 0.0245 0.2996 0.6759 224 L 0.0515 0.1708 0.7776 225 P 0.0247 0.3932 0.5821 226 S 0.0482 0.4585 0.4933 227 E 0.0244 0.6501 0.3254 228 P 0.0070 0.9123 0.0808 229 A 0.0054 0.9385 0.0561 230 A 0.0064 0.9377 0.0559 231 L 0.0147 0.8854 0.0999 232 R 0.0153 0.7337 0.2509 233 Q 0.0362 0.4186 0.5452 234 G 0.0509 0.0936 0.8555 235 P 0.0521 0.1148 0.8330 236 H 0.1007 0.1402 0.7591 237 R 0.1332 0.1701 0.6967 238 Y 0.1432 0.2189 0.6379 239 A 0.1560 0.2228 0.6212 240 R 0.1832 0.2622 0.5547 241 A 0.2351 0.2148 0.5501 242 R 0.2769 0.2039 0.5191 243 H 0.2909 0.2060 0.5032 244 Y 0.2791 0.2106 0.5103 245 Y 0.2259 0.2173 0.5567 246 E 0.1680 0.2564 0.5756 247 A 0.1434 0.3191 0.5376 248 G 0.1691 0.3583 0.4727 249 Q 0.2615 0.4047 0.3338 250 R 0.3878 0.4168 0.1953 251 A 0.3867 0.4558 0.1575 252 A 0.3866 0.4408 0.1727 253 A 0.2707 0.4294 0.2998 254 Q 0.2114 0.3706 0.4180 255 R 0.1788 0.2049 0.6163 256 G 0.1004 0.0789 0.8207 257 L 0.1331 0.0470 0.8198 258 P 0.1593 0.0520 0.7887 259 F 0.2302 0.0298 0.7400 260 G 0.3705 0.0135 0.6160 261 W 0.7702 0.0051 0.2247 262 Q 0.8822 0.0044 0.1134 263 L 0.9152 0.0032 0.0816 264 Q 0.9156 0.0037 0.0807 265 V 0.8913 0.0042 0.1045 266 V 0.5089 0.0076 0.4835 267 P 0.0988 0.0467 0.8545 268 G 0.0478 0.0342 0.9180 269 I 0.1046 0.0610 0.8344 270 G 0.1344 0.0587 0.8069 271 H 0.1605 0.0751 0.7645 272 D 0.1145 0.1070 0.7785 273 G 0.0946 0.2036 0.7018 274 Q 0.1108 0.2654 0.6238 275 A 0.0989 0.3734 0.5277 276 M 0.0577 0.5484 0.3938 277 S 0.0453 0.6457 0.3090 278 Q 0.0262 0.7537 0.2201 279 V 0.0311 0.8187 0.1502 280 C 0.0402 0.8363 0.1235 281 A 0.0378 0.8385 0.1237 282 S 0.0479 0.8235 0.1286 283 L 0.0585 0.7684 0.1731 284 W 0.0705 0.7037 0.2258 285 F 0.0892 0.6228 0.2880 286 D 0.0752 0.5509 0.3739 287 G 0.0429 0.4330 0.5241 288 R 0.0586 0.3151 0.6263 289 M 0.0703 0.0760 0.8537 290 P 0.0332 0.2560 0.7107 291 D 0.0318 0.3410 0.6272 292 A 0.0614 0.5323 0.4063 293 A 0.0382 0.6863 0.2754 294 E 0.0486 0.7314 0.2200 295 L 0.0528 0.7460 0.2012 296 A 0.0553 0.7156 0.2291 297 R 0.0663 0.6360 0.2977 298 L 0.0722 0.5437 0.3841 299 A 0.0791 0.3736 0.5472 300 G 0.0534 0.2108 0.7358 301 S 0.0666 0.2226 0.7108 302 Q 0.0808 0.2091 0.7101 303 S 0.0880 0.0955 0.8165 304 A 0.0620 0.0608 0.8771