# This file is the result of combining several RDB files, specifically # T0375.t06.dssp-ebghstl.rdb (weight 1.53986) # T0375.t06.stride-ebghtl.rdb (weight 1.24869) # T0375.t06.str2.rdb (weight 1.54758) # T0375.t06.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 T0375.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0375 # Using neural net t06-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 T0375.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 2429 # # ============================================ # Comments from T0375.t06.stride-ebghtl.rdb # ============================================ # TARGET T0375 # Using neural net t06-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 T0375.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 2429 # # ============================================ # Comments from T0375.t06.str2.rdb # ============================================ # TARGET T0375 # Using neural net 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 T0375.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 2429 # # ============================================ # Comments from T0375.t06.alpha.rdb # ============================================ # TARGET T0375 # Using neural net 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 T0375.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 2429 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.0460 0.0229 0.9311 2 S 0.1140 0.0233 0.8626 3 Q 0.4048 0.0190 0.5762 4 I 0.8911 0.0041 0.1048 5 L 0.9250 0.0036 0.0714 6 C 0.9186 0.0039 0.0775 7 V 0.7716 0.0289 0.1995 8 G 0.3286 0.0366 0.6348 9 L 0.2158 0.0875 0.6967 10 V 0.3252 0.1595 0.5153 11 V 0.4546 0.2335 0.3119 12 L 0.6213 0.1926 0.1862 13 D 0.5545 0.2315 0.2139 14 V 0.5910 0.2266 0.1824 15 I 0.5768 0.2438 0.1794 16 S 0.5491 0.2037 0.2472 17 L 0.5351 0.1328 0.3321 18 V 0.3629 0.1139 0.5232 19 D 0.1693 0.1201 0.7106 20 K 0.1226 0.0994 0.7780 21 Y 0.1459 0.0407 0.8133 22 P 0.1170 0.0384 0.8446 23 K 0.0840 0.0697 0.8463 24 E 0.0453 0.1318 0.8230 25 D 0.0502 0.0931 0.8567 26 S 0.2162 0.0598 0.7240 27 E 0.5396 0.0424 0.4180 28 I 0.6719 0.0386 0.2895 29 R 0.6109 0.0413 0.3478 30 C 0.5748 0.0694 0.3557 31 L 0.4372 0.1092 0.4536 32 S 0.3921 0.1210 0.4869 33 Q 0.5420 0.1113 0.3467 34 R 0.6650 0.1010 0.2339 35 W 0.6535 0.0994 0.2471 36 Q 0.4341 0.1022 0.4637 37 R 0.1964 0.1445 0.6590 38 G 0.0898 0.1001 0.8101 39 G 0.1002 0.1678 0.7320 40 N 0.0634 0.3892 0.5474 41 A 0.0174 0.8346 0.1480 42 S 0.0098 0.9144 0.0758 43 N 0.0078 0.9392 0.0530 44 S 0.0064 0.9551 0.0385 45 C 0.0050 0.9605 0.0345 46 T 0.0046 0.9613 0.0341 47 I 0.0046 0.9612 0.0342 48 L 0.0047 0.9599 0.0354 49 S 0.0048 0.9542 0.0410 50 L 0.0066 0.9119 0.0815 51 L 0.0443 0.4792 0.4765 52 G 0.0325 0.0283 0.9392 53 A 0.0566 0.0101 0.9334 54 P 0.2154 0.0123 0.7723 55 C 0.7837 0.0072 0.2092 56 A 0.8980 0.0066 0.0954 57 F 0.9258 0.0045 0.0697 58 M 0.9081 0.0092 0.0827 59 G 0.8498 0.0159 0.1343 60 S 0.7334 0.0267 0.2399 61 M 0.3684 0.0532 0.5784 62 A 0.1313 0.0397 0.8291 63 P 0.0541 0.1116 0.8342 64 G 0.0397 0.2127 0.7477 65 H 0.0171 0.6035 0.3793 66 V 0.0118 0.7979 0.1903 67 A 0.0058 0.9221 0.0720 68 D 0.0048 0.9526 0.0426 69 F 0.0050 0.9524 0.0426 70 V 0.0051 0.9521 0.0428 71 L 0.0047 0.9577 0.0376 72 D 0.0047 0.9578 0.0374 73 D 0.0048 0.9554 0.0397 74 L 0.0048 0.9523 0.0429 75 R 0.0051 0.9356 0.0593 76 R 0.0063 0.8847 0.1090 77 Y 0.0476 0.4388 0.5136 78 S 0.0568 0.0234 0.9198 79 V 0.1098 0.0122 0.8780 80 D 0.3299 0.0102 0.6599 81 L 0.4911 0.0479 0.4610 82 R 0.4957 0.0649 0.4394 83 Y 0.7149 0.0312 0.2539 84 T 0.8347 0.0090 0.1563 85 V 0.8810 0.0062 0.1128 86 F 0.8208 0.0105 0.1686 87 Q 0.5123 0.0181 0.4696 88 T 0.1383 0.0822 0.7795 89 T 0.0720 0.0415 0.8865 90 G 0.1262 0.0342 0.8396 91 S 0.2162 0.0272 0.7566 92 V 0.4319 0.0149 0.5532 93 P 0.6418 0.0118 0.3463 94 I 0.8453 0.0103 0.1444 95 A 0.9105 0.0040 0.0855 96 T 0.9273 0.0035 0.0692 97 V 0.9289 0.0041 0.0670 98 I 0.9245 0.0046 0.0709 99 I 0.9024 0.0056 0.0920 100 N 0.8115 0.0087 0.1798 101 E 0.3544 0.0368 0.6087 102 A 0.0660 0.1291 0.8049 103 S 0.0570 0.0406 0.9024 104 G 0.0750 0.0321 0.8930 105 S 0.3530 0.0172 0.6298 106 R 0.7834 0.0069 0.2098 107 T 0.8795 0.0071 0.1133 108 I 0.9139 0.0062 0.0799 109 L 0.8872 0.0114 0.1014 110 Y 0.7860 0.0185 0.1954 111 Y 0.4249 0.0539 0.5213 112 D 0.1477 0.1717 0.6806 113 R 0.0623 0.2477 0.6900 114 S 0.0751 0.2108 0.7141 115 L 0.0691 0.1154 0.8155 116 P 0.0257 0.2646 0.7097 117 D 0.0404 0.1989 0.7608 118 V 0.1500 0.0799 0.7700 119 S 0.0994 0.0588 0.8418 120 A 0.0070 0.8289 0.1641 121 T 0.0069 0.8049 0.1882 122 D 0.0106 0.7956 0.1939 123 F 0.0327 0.6556 0.3117 124 E 0.0354 0.5705 0.3941 125 K 0.0333 0.6586 0.3081 126 V 0.0559 0.5441 0.4000 127 D 0.0612 0.4186 0.5202 128 L 0.0593 0.4218 0.5189 129 T 0.0323 0.3266 0.6411 130 Q 0.0583 0.2209 0.7208 131 F 0.2052 0.0197 0.7751 132 K 0.1996 0.0438 0.7565 133 W 0.9168 0.0036 0.0796 134 I 0.9306 0.0032 0.0662 135 H 0.9311 0.0032 0.0657 136 I 0.8748 0.0130 0.1122 137 E 0.5449 0.0256 0.4295 138 G 0.1751 0.0433 0.7816 139 R 0.1161 0.0701 0.8137 140 N 0.0930 0.0673 0.8398 141 A 0.0299 0.3976 0.5725 142 S 0.0056 0.8864 0.1080 143 E 0.0052 0.9296 0.0652 144 Q 0.0047 0.9540 0.0412 145 V 0.0047 0.9603 0.0350 146 K 0.0047 0.9606 0.0347 147 M 0.0047 0.9599 0.0354 148 L 0.0047 0.9597 0.0356 149 Q 0.0047 0.9591 0.0362 150 R 0.0048 0.9559 0.0393 151 I 0.0049 0.9526 0.0425 152 D 0.0049 0.9373 0.0577 153 A 0.0058 0.8624 0.1318 154 H 0.0461 0.3313 0.6227 155 N 0.0406 0.0217 0.9377 156 T 0.0759 0.0108 0.9133 157 R 0.3147 0.0120 0.6733 158 Q 0.5168 0.0101 0.4731 159 P 0.4144 0.0119 0.5737 160 P 0.3378 0.0230 0.6392 161 E 0.1888 0.0209 0.7902 162 Q 0.0358 0.2241 0.7401 163 K 0.0391 0.2130 0.7479 164 I 0.0967 0.2179 0.6854 165 R 0.1195 0.1790 0.7014 166 V 0.1623 0.2476 0.5902 167 S 0.1991 0.2799 0.5210 168 V 0.1789 0.3283 0.4929 169 E 0.1599 0.2573 0.5828 170 V 0.1017 0.2474 0.6508 171 E 0.0519 0.2051 0.7430 172 K 0.0604 0.1573 0.7823 173 P 0.0413 0.3778 0.5809 174 R 0.0170 0.8105 0.1725 175 E 0.0061 0.9285 0.0654 176 E 0.0061 0.9373 0.0566 177 L 0.0062 0.9330 0.0608 178 F 0.0066 0.9288 0.0645 179 Q 0.0078 0.8767 0.1155 180 L 0.0133 0.7518 0.2349 181 F 0.0551 0.4475 0.4973 182 G 0.0270 0.2837 0.6893 183 Y 0.0728 0.2181 0.7091 184 G 0.1864 0.0323 0.7813 185 D 0.1989 0.0666 0.7345 186 V 0.8790 0.0114 0.1096 187 V 0.9031 0.0090 0.0879 188 F 0.8802 0.0081 0.1117 189 V 0.5446 0.0157 0.4397 190 S 0.0961 0.0106 0.8932 191 K 0.0052 0.9258 0.0689 192 D 0.0052 0.9470 0.0478 193 V 0.0048 0.9533 0.0419 194 A 0.0051 0.9548 0.0401 195 K 0.0050 0.9297 0.0653 196 H 0.0065 0.8485 0.1451 197 L 0.0493 0.3260 0.6247 198 G 0.0307 0.0281 0.9412 199 F 0.0720 0.0160 0.9120 200 Q 0.0870 0.0293 0.8836 201 S 0.0736 0.0113 0.9151 202 A 0.0048 0.9398 0.0554 203 E 0.0047 0.9577 0.0376 204 E 0.0047 0.9582 0.0371 205 A 0.0047 0.9604 0.0349 206 L 0.0047 0.9601 0.0353 207 R 0.0047 0.9569 0.0384 208 G 0.0047 0.9514 0.0439 209 L 0.0048 0.9454 0.0499 210 Y 0.0051 0.9403 0.0546 211 G 0.0049 0.9330 0.0621 212 R 0.0053 0.9380 0.0566 213 V 0.0068 0.9185 0.0746 214 R 0.0092 0.8456 0.1453 215 K 0.0399 0.2787 0.6815 216 G 0.0430 0.0173 0.9397 217 A 0.1096 0.0085 0.8819 218 V 0.7454 0.0072 0.2473 219 L 0.9222 0.0035 0.0744 220 V 0.9283 0.0038 0.0679 221 C 0.9187 0.0045 0.0767 222 A 0.8233 0.0078 0.1690 223 W 0.4488 0.0265 0.5246 224 A 0.1501 0.0759 0.7739 225 E 0.0807 0.2323 0.6870 226 E 0.0858 0.1399 0.7742 227 G 0.1605 0.0908 0.7487 228 A 0.4425 0.0575 0.5000 229 D 0.7933 0.0352 0.1716 230 A 0.8760 0.0190 0.1049 231 L 0.8497 0.0190 0.1313 232 G 0.2979 0.0137 0.6885 233 P 0.0219 0.0985 0.8796 234 D 0.0449 0.0234 0.9317 235 G 0.0768 0.0322 0.8910 236 K 0.3231 0.0118 0.6651 237 L 0.8769 0.0043 0.1189 238 L 0.8702 0.0111 0.1187 239 H 0.8910 0.0062 0.1028 240 S 0.7468 0.0100 0.2432 241 D 0.4415 0.0172 0.5412 242 A 0.2104 0.0288 0.7609 243 F 0.1309 0.0164 0.8527 244 P 0.0892 0.0148 0.8959 245 P 0.0795 0.0145 0.9059 246 P 0.1575 0.0217 0.8208 247 R 0.3465 0.0275 0.6259 248 V 0.5857 0.0287 0.3856 249 V 0.5679 0.0462 0.3859 250 D 0.4241 0.0343 0.5416 251 T 0.2217 0.0766 0.7017 252 L 0.1215 0.1185 0.7600 253 G 0.0866 0.1463 0.7671 254 A 0.0228 0.5937 0.3835 255 G 0.0111 0.8263 0.1626 256 D 0.0055 0.9338 0.0607 257 T 0.0048 0.9559 0.0392 258 F 0.0047 0.9577 0.0375 259 N 0.0047 0.9595 0.0358 260 A 0.0047 0.9606 0.0347 261 S 0.0046 0.9613 0.0341 262 V 0.0046 0.9610 0.0344 263 I 0.0047 0.9611 0.0342 264 F 0.0047 0.9598 0.0355 265 S 0.0047 0.9546 0.0407 266 L 0.0050 0.9455 0.0495 267 S 0.0076 0.8654 0.1271 268 Q 0.0449 0.3574 0.5977 269 G 0.0424 0.0279 0.9298 270 R 0.0624 0.0139 0.9237 271 S 0.0817 0.0123 0.9060 272 V 0.0048 0.9471 0.0481 273 Q 0.0047 0.9610 0.0343 274 E 0.0047 0.9609 0.0345 275 A 0.0046 0.9615 0.0339 276 L 0.0047 0.9603 0.0350 277 R 0.0046 0.9603 0.0351 278 F 0.0046 0.9599 0.0355 279 G 0.0047 0.9604 0.0349 280 C 0.0047 0.9597 0.0356 281 Q 0.0047 0.9589 0.0364 282 V 0.0048 0.9551 0.0401 283 A 0.0053 0.9510 0.0437 284 G 0.0066 0.9480 0.0454 285 K 0.0080 0.9398 0.0522 286 K 0.0120 0.9155 0.0725 287 C 0.0266 0.8118 0.1616 288 G 0.0641 0.4831 0.4528 289 L 0.1126 0.3165 0.5709 290 Q 0.1118 0.2496 0.6386 291 G 0.0990 0.1159 0.7851 292 F 0.1028 0.1501 0.7470 293 D 0.1061 0.1724 0.7215 294 G 0.0877 0.1681 0.7441 295 I 0.0980 0.1318 0.7702 296 V 0.0810 0.0602 0.8589