# This file is the result of combining several RDB files, specifically # T0220.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0220.t2k.stride-ebghtl.rdb (weight 1.24869) # T0220.t2k.str2.rdb (weight 1.54758) # T0220.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 T0220.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0220 # 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 T0220.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 134 # # ============================================ # Comments from T0220.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0220 # 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 T0220.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 134 # # ============================================ # Comments from T0220.t2k.str2.rdb # ============================================ # TARGET T0220 # 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 T0220.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 134 # # ============================================ # Comments from T0220.t2k.alpha.rdb # ============================================ # TARGET T0220 # 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 T0220.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 134 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0857 0.0254 0.8888 2 E 0.1844 0.0273 0.7883 3 T 0.3701 0.0529 0.5770 4 L 0.5653 0.0457 0.3890 5 I 0.7143 0.0242 0.2616 6 L 0.5138 0.0176 0.4686 7 T 0.1977 0.0149 0.7873 8 Q 0.0061 0.8825 0.1114 9 E 0.0052 0.8994 0.0955 10 E 0.0056 0.9153 0.0792 11 V 0.0051 0.9179 0.0770 12 E 0.0065 0.8460 0.1476 13 S 0.0068 0.6309 0.3623 14 L 0.0181 0.4363 0.5456 15 I 0.0953 0.0843 0.8204 16 S 0.0686 0.0287 0.9027 17 M 0.0141 0.7821 0.2038 18 D 0.0065 0.9070 0.0865 19 E 0.0059 0.9266 0.0675 20 A 0.0055 0.9432 0.0513 21 M 0.0047 0.9559 0.0394 22 N 0.0047 0.9568 0.0384 23 A 0.0048 0.9568 0.0384 24 V 0.0047 0.9572 0.0381 25 E 0.0047 0.9579 0.0374 26 E 0.0047 0.9550 0.0403 27 A 0.0048 0.9526 0.0426 28 F 0.0048 0.9454 0.0497 29 R 0.0049 0.9362 0.0589 30 L 0.0052 0.9009 0.0939 31 Y 0.0081 0.8090 0.1829 32 A 0.0125 0.6329 0.3546 33 L 0.0431 0.3759 0.5809 34 G 0.0382 0.1429 0.8188 35 K 0.0692 0.1289 0.8019 36 A 0.1566 0.1072 0.7361 37 Q 0.1494 0.0981 0.7525 38 M 0.1561 0.0508 0.7931 39 P 0.1386 0.0352 0.8263 40 P 0.2499 0.0477 0.7024 41 K 0.5759 0.0424 0.3817 42 V 0.7169 0.0236 0.2596 43 Y 0.7699 0.0167 0.2134 44 L 0.7487 0.0126 0.2386 45 E 0.6659 0.0120 0.3221 46 F 0.2424 0.0273 0.7303 47 E 0.0757 0.0550 0.8693 48 K 0.0468 0.0418 0.9114 49 G 0.1167 0.0445 0.8388 50 D 0.5433 0.0214 0.4353 51 L 0.8358 0.0118 0.1524 52 R 0.8348 0.0185 0.1467 53 A 0.8274 0.0162 0.1564 54 M 0.7429 0.0164 0.2407 55 P 0.6052 0.0333 0.3615 56 A 0.4649 0.0722 0.4629 57 H 0.3919 0.0791 0.5290 58 L 0.2102 0.0776 0.7123 59 M 0.0758 0.1501 0.7741 60 G 0.0773 0.1198 0.8029 61 Y 0.3451 0.0810 0.5739 62 A 0.5928 0.0346 0.3726 63 G 0.8011 0.0175 0.1815 64 L 0.8779 0.0105 0.1117 65 K 0.8897 0.0089 0.1013 66 W 0.8844 0.0082 0.1074 67 V 0.7912 0.0132 0.1956 68 N 0.6333 0.0179 0.3489 69 S 0.3559 0.0381 0.6059 70 H 0.1778 0.0405 0.7816 71 P 0.0602 0.1185 0.8212 72 G 0.0475 0.1001 0.8524 73 N 0.0864 0.0999 0.8137 74 P 0.0352 0.3223 0.6425 75 D 0.0403 0.3315 0.6282 76 K 0.0658 0.2107 0.7236 77 G 0.0691 0.0847 0.8462 78 L 0.1217 0.0432 0.8352 79 P 0.1905 0.0764 0.7331 80 T 0.3307 0.0604 0.6089 81 V 0.5233 0.0252 0.4514 82 M 0.7275 0.0241 0.2484 83 A 0.8971 0.0048 0.0982 84 L 0.9248 0.0032 0.0719 85 M 0.9253 0.0034 0.0712 86 I 0.9246 0.0033 0.0722 87 L 0.9120 0.0043 0.0837 88 N 0.8368 0.0057 0.1575 89 S 0.5630 0.0076 0.4295 90 P 0.0224 0.1426 0.8350 91 E 0.0194 0.0940 0.8866 92 T 0.0620 0.0452 0.8928 93 G 0.0887 0.0254 0.8859 94 F 0.4560 0.0157 0.5284 95 P 0.8382 0.0086 0.1531 96 L 0.8537 0.0224 0.1239 97 A 0.8678 0.0190 0.1132 98 V 0.8486 0.0300 0.1214 99 M 0.7374 0.0450 0.2176 100 D 0.4774 0.0717 0.4509 101 A 0.1351 0.2990 0.5659 102 T 0.0733 0.3622 0.5646 103 Y 0.1007 0.6612 0.2381 104 T 0.0824 0.7778 0.1398 105 T 0.0396 0.8578 0.1026 106 S 0.0193 0.9034 0.0773 107 L 0.0099 0.9162 0.0740 108 R 0.0079 0.9201 0.0721 109 T 0.0057 0.9246 0.0697 110 G 0.0048 0.9425 0.0527 111 A 0.0047 0.9554 0.0398 112 A 0.0047 0.9568 0.0385 113 G 0.0047 0.9573 0.0380 114 G 0.0047 0.9572 0.0380 115 I 0.0048 0.9583 0.0370 116 A 0.0048 0.9573 0.0379 117 A 0.0049 0.9503 0.0449 118 K 0.0056 0.9354 0.0590 119 Y 0.0076 0.8697 0.1227 120 L 0.0116 0.7362 0.2522 121 A 0.0440 0.5279 0.4281 122 R 0.0503 0.3179 0.6318 123 K 0.0190 0.2202 0.7608 124 N 0.0426 0.0817 0.8757 125 S 0.1366 0.0504 0.8130 126 S 0.2716 0.0800 0.6485 127 V 0.7995 0.0211 0.1794 128 F 0.9103 0.0096 0.0801 129 G 0.9241 0.0047 0.0712 130 F 0.9188 0.0061 0.0751 131 I 0.7526 0.0486 0.1988 132 G 0.2890 0.0737 0.6373 133 C 0.0742 0.2826 0.6432 134 G 0.0298 0.5871 0.3831 135 T 0.0055 0.9245 0.0700 136 Q 0.0049 0.9444 0.0507 137 A 0.0048 0.9553 0.0399 138 Y 0.0048 0.9584 0.0369 139 F 0.0047 0.9594 0.0359 140 Q 0.0047 0.9593 0.0361 141 L 0.0047 0.9602 0.0351 142 E 0.0047 0.9597 0.0356 143 A 0.0047 0.9577 0.0376 144 L 0.0048 0.9488 0.0464 145 R 0.0052 0.9014 0.0934 146 R 0.0063 0.7409 0.2528 147 V 0.0182 0.4498 0.5321 148 F 0.0647 0.0786 0.8567 149 D 0.0907 0.0495 0.8599 150 I 0.2177 0.0619 0.7204 151 G 0.3636 0.0763 0.5601 152 E 0.8067 0.0105 0.1828 153 V 0.8764 0.0046 0.1190 154 K 0.9101 0.0036 0.0862 155 A 0.8785 0.0048 0.1166 156 Y 0.6957 0.0288 0.2755 157 D 0.3530 0.0130 0.6340 158 V 0.0675 0.0456 0.8869 159 R 0.0815 0.0149 0.9036 160 E 0.0061 0.8160 0.1779 161 K 0.0059 0.8838 0.1102 162 A 0.0057 0.9051 0.0892 163 A 0.0048 0.9446 0.0506 164 K 0.0050 0.9503 0.0447 165 K 0.0048 0.9523 0.0429 166 F 0.0048 0.9525 0.0427 167 V 0.0048 0.9517 0.0435 168 S 0.0049 0.9432 0.0519 169 Y 0.0053 0.9258 0.0689 170 C 0.0087 0.9001 0.0912 171 E 0.0075 0.8607 0.1318 172 D 0.0120 0.7273 0.2607 173 R 0.0460 0.3398 0.6142 174 G 0.0453 0.0573 0.8974 175 I 0.1327 0.0276 0.8396 176 S 0.3686 0.0290 0.6024 177 A 0.4990 0.0161 0.4849 178 S 0.5499 0.0110 0.4391 179 V 0.3018 0.0310 0.6672 180 Q 0.1483 0.0171 0.8346 181 P 0.0071 0.8681 0.1248 182 A 0.0051 0.9180 0.0769 183 E 0.0054 0.9300 0.0646 184 E 0.0059 0.9173 0.0769 185 A 0.0126 0.8481 0.1393 186 S 0.0153 0.6050 0.3797 187 R 0.0367 0.1896 0.7737 188 C 0.0947 0.0159 0.8893 189 D 0.0982 0.0420 0.8597 190 V 0.9103 0.0036 0.0861 191 L 0.9322 0.0031 0.0646 192 V 0.9285 0.0034 0.0681 193 T 0.8998 0.0048 0.0954 194 T 0.6146 0.0093 0.3762 195 T 0.2557 0.0119 0.7324 196 P 0.0876 0.0970 0.8154 197 S 0.0871 0.0426 0.8704 198 R 0.0612 0.0562 0.8826 199 K 0.1130 0.0207 0.8663 200 P 0.2475 0.0229 0.7296 201 V 0.5476 0.0316 0.4208 202 V 0.6265 0.0134 0.3601 203 K 0.3570 0.0290 0.6139 204 A 0.0284 0.7692 0.2024 205 E 0.0238 0.7586 0.2176 206 W 0.0415 0.6883 0.2702 207 V 0.1914 0.1162 0.6924 208 E 0.1123 0.0541 0.8336 209 E 0.0513 0.1488 0.7999 210 G 0.0857 0.0878 0.8264 211 T 0.5183 0.0495 0.4322 212 H 0.8362 0.0208 0.1430 213 I 0.8848 0.0131 0.1021 214 N 0.8377 0.0185 0.1438 215 A 0.7717 0.0259 0.2023 216 I 0.5752 0.0571 0.3678 217 G 0.3250 0.0540 0.6211 218 A 0.1469 0.0756 0.7775 219 D 0.0777 0.0738 0.8485 220 G 0.0806 0.0415 0.8780 221 P 0.0507 0.1514 0.7979 222 G 0.0658 0.1529 0.7813 223 K 0.0974 0.3577 0.5449 224 Q 0.2304 0.2848 0.4848 225 E 0.2550 0.2333 0.5117 226 L 0.2233 0.0955 0.6811 227 D 0.0939 0.0898 0.8163 228 V 0.0057 0.9051 0.0892 229 E 0.0053 0.9177 0.0770 230 I 0.0063 0.9067 0.0870 231 L 0.0102 0.8782 0.1116 232 K 0.0134 0.7728 0.2138 233 K 0.0307 0.4335 0.5359 234 A 0.0987 0.0583 0.8429 235 K 0.0952 0.0627 0.8422 236 I 0.8118 0.0108 0.1774 237 V 0.8827 0.0056 0.1118 238 V 0.8733 0.0066 0.1201 239 D 0.6716 0.0152 0.3132 240 D 0.2540 0.0229 0.7231 241 L 0.0179 0.5095 0.4726 242 E 0.0118 0.7332 0.2550 243 Q 0.0142 0.7437 0.2421 244 A 0.0380 0.6673 0.2946 245 K 0.0391 0.6355 0.3254 246 H 0.0352 0.6505 0.3143 247 G 0.0443 0.6620 0.2937 248 G 0.0379 0.5218 0.4403 249 E 0.0486 0.7081 0.2434 250 I 0.0388 0.8191 0.1421 251 N 0.0248 0.8598 0.1153 252 V 0.0225 0.8910 0.0865 253 A 0.0176 0.8978 0.0846 254 V 0.0141 0.8915 0.0944 255 S 0.0106 0.8791 0.1103 256 K 0.0470 0.4410 0.5120 257 G 0.0356 0.0697 0.8948 258 V 0.0825 0.0476 0.8699 259 I 0.1853 0.0270 0.7877 260 G 0.0981 0.0317 0.8702 261 V 0.0135 0.7003 0.2862 262 E 0.0143 0.6817 0.3040 263 D 0.0396 0.6982 0.2621 264 V 0.1059 0.5573 0.3368 265 H 0.1299 0.5988 0.2713 266 A 0.1096 0.6869 0.2035 267 T 0.0821 0.7399 0.1780 268 I 0.0157 0.9042 0.0802 269 G 0.0102 0.9263 0.0634 270 E 0.0137 0.9203 0.0661 271 V 0.0131 0.9185 0.0684 272 I 0.0223 0.8657 0.1120 273 A 0.0322 0.6401 0.3277 274 G 0.0425 0.2153 0.7421 275 L 0.0746 0.0744 0.8510 276 K 0.1558 0.0643 0.7799 277 D 0.1148 0.1176 0.7675 278 G 0.1132 0.0991 0.7877 279 R 0.2070 0.0574 0.7355 280 E 0.2129 0.0449 0.7422 281 S 0.1077 0.0423 0.8500 282 D 0.0258 0.1640 0.8102 283 E 0.0353 0.1241 0.8405 284 E 0.1846 0.0723 0.7431 285 I 0.5356 0.0206 0.4437 286 T 0.8569 0.0178 0.1253 287 I 0.8765 0.0226 0.1009 288 F 0.8142 0.0367 0.1491 289 D 0.6705 0.0633 0.2662 290 S 0.4313 0.1179 0.4508 291 T 0.2257 0.2395 0.5349 292 G 0.1551 0.4022 0.4427 293 L 0.0834 0.6429 0.2737 294 A 0.0427 0.8369 0.1204 295 I 0.0071 0.9350 0.0579 296 Q 0.0057 0.9434 0.0509 297 D 0.0050 0.9403 0.0546 298 V 0.0047 0.9581 0.0372 299 A 0.0047 0.9583 0.0370 300 V 0.0047 0.9578 0.0375 301 A 0.0047 0.9587 0.0366 302 K 0.0047 0.9587 0.0366 303 V 0.0047 0.9598 0.0355 304 V 0.0047 0.9591 0.0362 305 Y 0.0047 0.9578 0.0375 306 E 0.0048 0.9550 0.0402 307 N 0.0048 0.9550 0.0402 308 A 0.0049 0.9522 0.0429 309 L 0.0050 0.9391 0.0559 310 S 0.0060 0.8823 0.1117 311 K 0.0414 0.3410 0.6176 312 N 0.0289 0.0347 0.9363 313 V 0.0775 0.0372 0.8853 314 G 0.2750 0.0374 0.6876 315 S 0.5257 0.0301 0.4441 316 K 0.6918 0.0342 0.2739 317 I 0.5819 0.0834 0.3347 318 K 0.4759 0.1292 0.3949 319 F 0.4107 0.2110 0.3783 320 F 0.4393 0.1216 0.4391 321 R 0.3491 0.0641 0.5868 322 I 0.0603 0.0233 0.9164