# This file is the result of combining several RDB files, specifically # T0177.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0177.t2k.stride-ebghtl.rdb (weight 1.24869) # T0177.t2k.str.rdb (weight 1.53983) # T0177.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 T0177.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0177 # 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 T0177.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 63 # # ============================================ # Comments from T0177.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0177 # 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 T0177.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 63 # # ============================================ # Comments from T0177.t2k.str.rdb # ============================================ # TARGET T0177 # 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 T0177.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 63 # # ============================================ # Comments from T0177.t2k.alpha.rdb # ============================================ # TARGET T0177 # 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 T0177.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 63 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0452 0.0460 0.9088 2 G 0.0627 0.1472 0.7901 3 R 0.0764 0.2436 0.6799 4 A 0.0312 0.5356 0.4331 5 F 0.0173 0.7271 0.2556 6 E 0.0187 0.7690 0.2122 7 Y 0.0135 0.7847 0.2018 8 R 0.0089 0.8652 0.1259 9 R 0.0070 0.8791 0.1139 10 A 0.0073 0.8622 0.1304 11 A 0.0084 0.8586 0.1330 12 K 0.0102 0.8108 0.1790 13 E 0.0104 0.8298 0.1598 14 K 0.0097 0.8771 0.1131 15 R 0.0075 0.8745 0.1179 16 W 0.0077 0.8749 0.1175 17 D 0.0052 0.8948 0.1000 18 K 0.0050 0.8685 0.1265 19 M 0.0053 0.8335 0.1612 20 S 0.0060 0.8208 0.1732 21 K 0.0055 0.8860 0.1084 22 V 0.0049 0.9183 0.0769 23 F 0.0045 0.9438 0.0517 24 P 0.0044 0.9540 0.0416 25 K 0.0045 0.9537 0.0418 26 L 0.0044 0.9568 0.0387 27 A 0.0044 0.9578 0.0378 28 K 0.0044 0.9603 0.0353 29 A 0.0043 0.9610 0.0347 30 I 0.0043 0.9612 0.0345 31 T 0.0043 0.9612 0.0344 32 L 0.0043 0.9615 0.0341 33 A 0.0044 0.9603 0.0353 34 A 0.0045 0.9547 0.0407 35 K 0.0053 0.9351 0.0596 36 D 0.0344 0.6263 0.3393 37 G 0.0450 0.0871 0.8679 38 G 0.0599 0.0324 0.9078 39 S 0.1023 0.0611 0.8366 40 E 0.0853 0.0831 0.8317 41 P 0.0135 0.3735 0.6129 42 D 0.0141 0.3409 0.6451 43 T 0.0256 0.2937 0.6807 44 N 0.0608 0.2020 0.7372 45 A 0.0068 0.8361 0.1571 46 K 0.0081 0.8878 0.1041 47 L 0.0045 0.9470 0.0484 48 R 0.0044 0.9554 0.0402 49 T 0.0044 0.9566 0.0390 50 A 0.0044 0.9580 0.0376 51 I 0.0045 0.9582 0.0373 52 L 0.0045 0.9557 0.0399 53 N 0.0045 0.9509 0.0446 54 A 0.0048 0.9376 0.0576 55 K 0.0053 0.8920 0.1026 56 A 0.0068 0.8252 0.1680 57 Q 0.0367 0.4016 0.5617 58 N 0.0369 0.0876 0.8756 59 M 0.0554 0.0279 0.9167 60 P 0.0580 0.0562 0.8858 61 K 0.0133 0.6633 0.3234 62 D 0.0095 0.7825 0.2080 63 N 0.0109 0.8470 0.1421 64 I 0.0066 0.9429 0.0506 65 D 0.0050 0.9541 0.0409 66 A 0.0044 0.9544 0.0412 67 A 0.0044 0.9515 0.0441 68 I 0.0046 0.9460 0.0494 69 K 0.0056 0.9130 0.0813 70 R 0.0161 0.7765 0.2073 71 A 0.0484 0.5203 0.4313 72 S 0.0586 0.2775 0.6640 73 S 0.0477 0.1128 0.8395 74 K 0.0542 0.0754 0.8704 75 E 0.0623 0.0833 0.8544 76 G 0.2013 0.0696 0.7291 77 N 0.3933 0.0416 0.5651 78 L 0.6776 0.0230 0.2995 79 S 0.7807 0.0214 0.1979 80 E 0.8904 0.0060 0.1036 81 I 0.8908 0.0080 0.1012 82 T 0.9136 0.0038 0.0825 83 Y 0.9065 0.0057 0.0878 84 E 0.8908 0.0100 0.0992 85 G 0.8633 0.0080 0.1287 86 K 0.7976 0.0164 0.1860 87 A 0.4833 0.0174 0.4993 88 N 0.0614 0.0957 0.8429 89 F 0.0402 0.0636 0.8961 90 G 0.1522 0.0657 0.7821 91 V 0.5105 0.0645 0.4251 92 L 0.8210 0.0361 0.1429 93 I 0.8850 0.0319 0.0831 94 I 0.9066 0.0228 0.0706 95 M 0.8716 0.0415 0.0869 96 E 0.7903 0.0725 0.1373 97 C 0.7006 0.1020 0.1974 98 M 0.4955 0.1234 0.3811 99 T 0.2499 0.1229 0.6272 100 D 0.0892 0.0806 0.8302 101 N 0.0979 0.1203 0.7817 102 P 0.0304 0.4306 0.5391 103 T 0.0302 0.6770 0.2929 104 R 0.0314 0.7752 0.1934 105 T 0.0337 0.8294 0.1369 106 I 0.0069 0.9401 0.0530 107 A 0.0063 0.9463 0.0474 108 N 0.0056 0.9379 0.0565 109 L 0.0059 0.9450 0.0491 110 K 0.0053 0.9521 0.0426 111 S 0.0050 0.9451 0.0499 112 Y 0.0054 0.9400 0.0546 113 F 0.0119 0.9172 0.0709 114 N 0.0149 0.8295 0.1556 115 K 0.0184 0.7017 0.2799 116 T 0.0595 0.3615 0.5790 117 Q 0.0578 0.1037 0.8386 118 G 0.0903 0.1291 0.7806 119 A 0.2371 0.1648 0.5981 120 S 0.2753 0.1610 0.5637 121 I 0.2637 0.1451 0.5912 122 V 0.1940 0.0820 0.7240 123 P 0.1233 0.0884 0.7882 124 N 0.0622 0.0955 0.8423 125 G 0.0858 0.0776 0.8366 126 S 0.3391 0.0710 0.5899 127 L 0.5787 0.1122 0.3091 128 E 0.5728 0.1611 0.2661 129 F 0.6024 0.1714 0.2262 130 M 0.6073 0.1332 0.2596 131 F 0.5877 0.1105 0.3019 132 N 0.4506 0.1018 0.4477 133 R 0.4791 0.0677 0.4533 134 K 0.4813 0.0403 0.4784 135 S 0.5269 0.0194 0.4537 136 V 0.8321 0.0070 0.1609 137 F 0.8964 0.0048 0.0988 138 E 0.8895 0.0045 0.1060 139 C 0.8037 0.0062 0.1901 140 L 0.5873 0.0100 0.4027 141 K 0.2093 0.0350 0.7557 142 N 0.0519 0.0484 0.8996 143 E 0.0315 0.3451 0.6233 144 V 0.0236 0.3831 0.5933 145 E 0.0286 0.4474 0.5239 146 N 0.0399 0.2998 0.6603 147 L 0.0610 0.3067 0.6323 148 K 0.1233 0.1988 0.6779 149 L 0.1238 0.0989 0.7773 150 S 0.0891 0.0758 0.8351 151 L 0.0050 0.9226 0.0725 152 E 0.0047 0.9403 0.0550 153 D 0.0046 0.9527 0.0427 154 L 0.0044 0.9544 0.0411 155 E 0.0047 0.9534 0.0419 156 F 0.0048 0.9512 0.0440 157 A 0.0045 0.9487 0.0468 158 L 0.0050 0.9465 0.0486 159 I 0.0053 0.9334 0.0613 160 D 0.0089 0.8604 0.1307 161 Y 0.0433 0.4537 0.5029 162 G 0.0579 0.0380 0.9041 163 L 0.0998 0.1068 0.7934 164 E 0.1956 0.3328 0.4716 165 E 0.3491 0.3308 0.3201 166 L 0.5134 0.1817 0.3049 167 E 0.5913 0.1247 0.2840 168 E 0.4879 0.1291 0.3830 169 V 0.3068 0.1232 0.5700 170 E 0.1050 0.0954 0.7996 171 D 0.1249 0.0738 0.8012 172 K 0.5689 0.0166 0.4145 173 I 0.8483 0.0047 0.1469 174 I 0.9070 0.0038 0.0893 175 I 0.9109 0.0037 0.0854 176 R 0.8754 0.0056 0.1190 177 G 0.6192 0.0079 0.3728 178 D 0.2137 0.0110 0.7753 179 Y 0.0227 0.4193 0.5580 180 N 0.0115 0.5736 0.4149 181 S 0.0256 0.6466 0.3278 182 F 0.0060 0.8830 0.1109 183 K 0.0051 0.9324 0.0625 184 L 0.0048 0.9425 0.0526 185 L 0.0047 0.9514 0.0439 186 N 0.0045 0.9567 0.0388 187 E 0.0045 0.9570 0.0385 188 G 0.0045 0.9572 0.0384 189 F 0.0044 0.9545 0.0411 190 E 0.0046 0.9454 0.0500 191 S 0.0049 0.8956 0.0995 192 L 0.0419 0.3472 0.6109 193 K 0.0367 0.0180 0.9453 194 L 0.0986 0.0109 0.8905 195 P 0.4835 0.0128 0.5037 196 I 0.6712 0.0165 0.3124 197 L 0.7375 0.0326 0.2299 198 K 0.7644 0.0171 0.2185 199 A 0.7694 0.0192 0.2114 200 S 0.8492 0.0089 0.1418 201 L 0.8714 0.0071 0.1215 202 Q 0.8312 0.0111 0.1578 203 R 0.8174 0.0092 0.1734 204 I 0.5783 0.0133 0.4084 205 A 0.3217 0.0291 0.6492 206 T 0.1399 0.0650 0.7951 207 T 0.2610 0.0259 0.7131 208 P 0.3850 0.0272 0.5877 209 I 0.5843 0.0116 0.4041 210 E 0.6160 0.0099 0.3741 211 L 0.2968 0.0132 0.6900 212 N 0.1050 0.0171 0.8779 213 D 0.0056 0.8313 0.1631 214 E 0.0051 0.8806 0.1143 215 Q 0.0057 0.9077 0.0866 216 M 0.0045 0.9471 0.0483 217 E 0.0051 0.9470 0.0479 218 L 0.0050 0.9429 0.0521 219 T 0.0045 0.9516 0.0439 220 E 0.0044 0.9578 0.0378 221 K 0.0044 0.9542 0.0414 222 L 0.0044 0.9526 0.0430 223 L 0.0045 0.9510 0.0445 224 D 0.0046 0.9308 0.0647 225 R 0.0050 0.8690 0.1260 226 I 0.0098 0.7909 0.1992 227 E 0.0091 0.5705 0.4204 228 D 0.0207 0.4009 0.5784 229 D 0.0584 0.2951 0.6465 230 D 0.0175 0.4374 0.5451 231 D 0.0628 0.4172 0.5200 232 V 0.1743 0.4499 0.3758 233 V 0.2570 0.4325 0.3105 234 A 0.4108 0.3822 0.2070 235 L 0.4091 0.3603 0.2306 236 Y 0.3805 0.3292 0.2903 237 T 0.3053 0.1810 0.5137 238 N 0.1890 0.1140 0.6970 239 I 0.1235 0.1022 0.7743 240 E 0.0406 0.0448 0.9146