# This file is the result of combining several RDB files, specifically # T0136.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0136.t2k.stride-ebghtl.rdb (weight 1.24869) # T0136.t2k.str.rdb (weight 1.53983) # T0136.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 T0136.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0136 # 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 T0136.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 294 # # ============================================ # Comments from T0136.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0136 # 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 T0136.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 294 # # ============================================ # Comments from T0136.t2k.str.rdb # ============================================ # TARGET T0136 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0136.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 294 # # ============================================ # Comments from T0136.t2k.alpha.rdb # ============================================ # TARGET T0136 # 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 T0136.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 294 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0428 0.0678 0.8894 2 E 0.0592 0.2617 0.6791 3 N 0.0394 0.4176 0.5431 4 N 0.0448 0.4426 0.5126 5 N 0.0272 0.5968 0.3760 6 L 0.0202 0.6750 0.3049 7 K 0.0173 0.6978 0.2849 8 L 0.0260 0.7176 0.2564 9 A 0.0109 0.8558 0.1332 10 S 0.0080 0.8814 0.1106 11 T 0.0080 0.8925 0.0995 12 M 0.0071 0.9163 0.0766 13 E 0.0062 0.9268 0.0670 14 G 0.0066 0.9117 0.0817 15 R 0.0080 0.8824 0.1097 16 V 0.0101 0.8922 0.0977 17 E 0.0052 0.9294 0.0654 18 Q 0.0061 0.9215 0.0725 19 L 0.0050 0.9367 0.0583 20 A 0.0049 0.9391 0.0560 21 E 0.0045 0.9431 0.0524 22 Q 0.0048 0.9443 0.0509 23 R 0.0061 0.9415 0.0524 24 Q 0.0058 0.9372 0.0570 25 V 0.0056 0.9308 0.0635 26 I 0.0071 0.9046 0.0883 27 E 0.0098 0.8396 0.1506 28 A 0.0321 0.6257 0.3422 29 G 0.0340 0.2790 0.6870 30 G 0.0410 0.1814 0.7776 31 G 0.0427 0.2877 0.6697 32 E 0.0243 0.6853 0.2903 33 R 0.0393 0.7490 0.2117 34 R 0.0487 0.7626 0.1887 35 V 0.0525 0.7547 0.1928 36 E 0.0341 0.8033 0.1626 37 K 0.0252 0.7653 0.2095 38 Q 0.0348 0.6119 0.3533 39 H 0.0360 0.4158 0.5482 40 S 0.0492 0.2701 0.6807 41 Q 0.0390 0.1812 0.7798 42 G 0.0405 0.0910 0.8685 43 K 0.1027 0.0406 0.8567 44 Q 0.1350 0.0395 0.8255 45 T 0.1024 0.0288 0.8688 46 A 0.0056 0.9128 0.0816 47 R 0.0045 0.9463 0.0493 48 E 0.0048 0.9514 0.0437 49 R 0.0051 0.9481 0.0467 50 L 0.0064 0.9266 0.0670 51 N 0.0098 0.8951 0.0951 52 N 0.0151 0.8330 0.1519 53 L 0.0260 0.7331 0.2409 54 L 0.1497 0.3852 0.4652 55 D 0.0764 0.0791 0.8445 56 P 0.0271 0.1427 0.8302 57 H 0.0310 0.0833 0.8857 58 S 0.2349 0.0816 0.6835 59 F 0.5172 0.0646 0.4182 60 D 0.6048 0.0796 0.3156 61 E 0.5622 0.1025 0.3353 62 V 0.3123 0.1549 0.5328 63 G 0.1816 0.1762 0.6422 64 A 0.0978 0.2274 0.6748 65 F 0.0912 0.2202 0.6886 66 R 0.0547 0.3562 0.5891 67 K 0.0403 0.3743 0.5854 68 H 0.0592 0.4091 0.5317 69 R 0.0423 0.5404 0.4173 70 T 0.0492 0.6238 0.3270 71 T 0.0427 0.6895 0.2678 72 L 0.0370 0.7163 0.2466 73 F 0.0263 0.7309 0.2428 74 G 0.0257 0.6984 0.2759 75 M 0.0318 0.6278 0.3404 76 D 0.0429 0.5165 0.4406 77 K 0.0469 0.4425 0.5105 78 A 0.0580 0.3063 0.6357 79 V 0.0730 0.1577 0.7693 80 V 0.0830 0.0944 0.8225 81 P 0.0972 0.1073 0.7955 82 A 0.1071 0.0998 0.7930 83 D 0.0967 0.1548 0.7485 84 G 0.3452 0.0883 0.5665 85 V 0.7651 0.0199 0.2150 86 V 0.8644 0.0099 0.1257 87 T 0.8436 0.0225 0.1340 88 G 0.8714 0.0131 0.1154 89 R 0.8527 0.0234 0.1239 90 G 0.8604 0.0128 0.1268 91 T 0.8767 0.0132 0.1101 92 I 0.7946 0.0328 0.1726 93 L 0.0932 0.0344 0.8724 94 G 0.0471 0.0462 0.9067 95 R 0.6038 0.0103 0.3860 96 P 0.8337 0.0040 0.1623 97 V 0.9102 0.0058 0.0840 98 H 0.9314 0.0037 0.0649 99 A 0.9317 0.0035 0.0648 100 A 0.9176 0.0059 0.0765 101 S 0.8635 0.0107 0.1258 102 Q 0.5779 0.0249 0.3972 103 D 0.1829 0.0254 0.7917 104 F 0.1041 0.1174 0.7785 105 T 0.2108 0.1442 0.6450 106 V 0.3635 0.1422 0.4942 107 M 0.3066 0.1260 0.5673 108 G 0.2138 0.1307 0.6554 109 G 0.1602 0.0982 0.7416 110 S 0.1648 0.1068 0.7284 111 A 0.1082 0.1145 0.7772 112 G 0.0557 0.1220 0.8223 113 E 0.0118 0.7975 0.1907 114 T 0.0070 0.8998 0.0932 115 Q 0.0065 0.9357 0.0578 116 S 0.0045 0.9530 0.0425 117 T 0.0044 0.9568 0.0388 118 K 0.0044 0.9580 0.0376 119 V 0.0044 0.9595 0.0361 120 V 0.0044 0.9605 0.0351 121 E 0.0044 0.9608 0.0349 122 T 0.0044 0.9604 0.0352 123 M 0.0044 0.9598 0.0358 124 E 0.0044 0.9584 0.0371 125 Q 0.0044 0.9590 0.0366 126 A 0.0046 0.9541 0.0413 127 L 0.0052 0.9402 0.0546 128 L 0.0061 0.8894 0.1045 129 T 0.0454 0.4390 0.5156 130 G 0.0392 0.0266 0.9342 131 T 0.0688 0.0087 0.9224 132 P 0.2770 0.0079 0.7151 133 F 0.8833 0.0036 0.1131 134 L 0.9274 0.0039 0.0687 135 F 0.9314 0.0036 0.0650 136 F 0.9224 0.0043 0.0733 137 Y 0.8520 0.0118 0.1362 138 D 0.4696 0.0277 0.5027 139 S 0.1438 0.0669 0.7893 140 G 0.0700 0.1066 0.8234 141 G 0.0914 0.1305 0.7781 142 A 0.1608 0.1072 0.7320 143 R 0.1788 0.1274 0.6939 144 I 0.0828 0.2656 0.6516 145 Q 0.0435 0.3226 0.6339 146 E 0.0422 0.5267 0.4311 147 G 0.0352 0.5967 0.3682 148 I 0.0199 0.8041 0.1759 149 D 0.0121 0.8494 0.1385 150 S 0.0085 0.8647 0.1268 151 L 0.0071 0.8753 0.1176 152 S 0.0073 0.8574 0.1354 153 G 0.0065 0.8650 0.1285 154 Y 0.0049 0.9278 0.0673 155 G 0.0044 0.9509 0.0447 156 K 0.0044 0.9566 0.0390 157 M 0.0044 0.9591 0.0365 158 F 0.0044 0.9585 0.0371 159 F 0.0044 0.9575 0.0381 160 A 0.0045 0.9554 0.0401 161 N 0.0046 0.9470 0.0484 162 V 0.0051 0.9253 0.0696 163 K 0.0067 0.8686 0.1247 164 L 0.0168 0.6682 0.3150 165 S 0.0319 0.3521 0.6160 166 G 0.0516 0.1546 0.7938 167 V 0.0659 0.0792 0.8548 168 V 0.1554 0.0181 0.8265 169 P 0.3250 0.0085 0.6665 170 Q 0.8745 0.0081 0.1174 171 I 0.9245 0.0036 0.0718 172 A 0.9178 0.0043 0.0779 173 I 0.9070 0.0042 0.0888 174 I 0.7811 0.0110 0.2078 175 A 0.4228 0.0211 0.5561 176 G 0.1649 0.0278 0.8074 177 P 0.0703 0.1045 0.8252 178 C 0.1046 0.0980 0.7973 179 A 0.1263 0.1157 0.7580 180 G 0.1416 0.1042 0.7541 181 G 0.2371 0.1583 0.6046 182 A 0.3750 0.1686 0.4564 183 S 0.5328 0.1721 0.2951 184 Y 0.6187 0.1346 0.2468 185 S 0.5759 0.1272 0.2969 186 P 0.4845 0.1066 0.4089 187 A 0.3053 0.0900 0.6047 188 L 0.2146 0.1349 0.6505 189 T 0.1522 0.1316 0.7162 190 D 0.2775 0.1185 0.6040 191 F 0.7648 0.0281 0.2072 192 I 0.8623 0.0148 0.1228 193 I 0.8780 0.0132 0.1088 194 M 0.8510 0.0116 0.1374 195 T 0.5121 0.0167 0.4712 196 K 0.0678 0.0892 0.8430 197 K 0.0478 0.0480 0.9042 198 A 0.2650 0.0229 0.7122 199 H 0.6139 0.0179 0.3682 200 M 0.8897 0.0080 0.1023 201 F 0.9087 0.0057 0.0856 202 I 0.8859 0.0125 0.1016 203 T 0.6787 0.0230 0.2983 204 G 0.1994 0.0309 0.7696 205 P 0.0096 0.7876 0.2028 206 Q 0.0057 0.9003 0.0939 207 V 0.0055 0.9407 0.0538 208 I 0.0076 0.9417 0.0507 209 K 0.0144 0.9202 0.0654 210 S 0.0199 0.8638 0.1163 211 V 0.0265 0.7872 0.1863 212 T 0.0483 0.6055 0.3462 213 G 0.0563 0.3118 0.6319 214 E 0.1000 0.2283 0.6717 215 D 0.1476 0.1726 0.6798 216 V 0.0954 0.1951 0.7095 217 T 0.0828 0.1223 0.7949 218 A 0.0239 0.6176 0.3584 219 D 0.0203 0.6163 0.3633 220 E 0.0226 0.6398 0.3375 221 L 0.0487 0.4640 0.4873 222 G 0.0419 0.2375 0.7206 223 G 0.0617 0.2612 0.6771 224 A 0.0583 0.4288 0.5129 225 E 0.0256 0.8012 0.1732 226 A 0.0254 0.8600 0.1147 227 H 0.0359 0.8500 0.1140 228 M 0.0240 0.8850 0.0910 229 A 0.0274 0.8673 0.1053 230 I 0.0246 0.8043 0.1711 231 S 0.0541 0.4228 0.5231 232 G 0.0632 0.0791 0.8577 233 N 0.2359 0.1013 0.6628 234 I 0.5006 0.1158 0.3836 235 H 0.5009 0.1575 0.3417 236 F 0.5920 0.1309 0.2771 237 V 0.6100 0.0819 0.3082 238 A 0.4330 0.0417 0.5253 239 E 0.1647 0.0389 0.7964 240 D 0.0579 0.0610 0.8811 241 D 0.0216 0.5658 0.4126 242 D 0.0080 0.8547 0.1373 243 A 0.0073 0.8754 0.1173 244 A 0.0056 0.9109 0.0835 245 E 0.0048 0.9419 0.0533 246 L 0.0045 0.9496 0.0460 247 I 0.0044 0.9512 0.0443 248 A 0.0044 0.9561 0.0395 249 K 0.0044 0.9586 0.0370 250 K 0.0044 0.9557 0.0398 251 L 0.0044 0.9537 0.0419 252 L 0.0045 0.9429 0.0526 253 S 0.0047 0.9079 0.0874 254 F 0.0068 0.8346 0.1586 255 L 0.0325 0.6379 0.3297 256 P 0.0190 0.5338 0.4472 257 Q 0.0183 0.4382 0.5435 258 N 0.0362 0.3223 0.6415 259 N 0.0664 0.1875 0.7462 260 T 0.0475 0.1715 0.7810 261 E 0.0591 0.1222 0.8187 262 E 0.0706 0.0769 0.8525 263 A 0.0759 0.0572 0.8669 264 S 0.1045 0.0658 0.8297 265 F 0.1982 0.0970 0.7048 266 V 0.1784 0.0960 0.7255 267 N 0.1024 0.0740 0.8235 268 P 0.0626 0.1017 0.8357 269 N 0.0620 0.0739 0.8640 270 N 0.0638 0.0484 0.8877 271 D 0.0666 0.0781 0.8553 272 V 0.0610 0.1678 0.7713 273 S 0.0639 0.1870 0.7491 274 P 0.0531 0.1794 0.7675 275 N 0.0323 0.5744 0.3933 276 T 0.0293 0.6678 0.3029 277 E 0.0465 0.6469 0.3066 278 L 0.0709 0.6026 0.3264 279 R 0.0591 0.5797 0.3612 280 D 0.0708 0.4516 0.4777 281 I 0.1245 0.3280 0.5475 282 V 0.2079 0.0783 0.7138 283 P 0.1339 0.0602 0.8059 284 I 0.0776 0.0855 0.8369 285 D 0.1003 0.0750 0.8247 286 G 0.0167 0.2174 0.7659 287 K 0.0272 0.1498 0.8229 288 K 0.1040 0.0701 0.8260 289 G 0.0901 0.0724 0.8375 290 Y 0.0454 0.0323 0.9223