# This file is the result of combining several RDB files, specifically # T0178.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0178.t2k.stride-ebghtl.rdb (weight 1.24869) # T0178.t2k.str.rdb (weight 1.53983) # T0178.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 T0178.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0178 # 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 T0178.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 52 # # ============================================ # Comments from T0178.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0178 # 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 T0178.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 52 # # ============================================ # Comments from T0178.t2k.str.rdb # ============================================ # TARGET T0178 # 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 T0178.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 52 # # ============================================ # Comments from T0178.t2k.alpha.rdb # ============================================ # TARGET T0178 # 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 T0178.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 52 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0131 0.2461 0.7409 2 I 0.0339 0.6458 0.3203 3 D 0.0261 0.7035 0.2704 4 V 0.0131 0.8429 0.1440 5 R 0.0127 0.8671 0.1203 6 K 0.0114 0.8726 0.1160 7 Y 0.0218 0.8508 0.1275 8 I 0.0459 0.7892 0.1648 9 D 0.0468 0.7270 0.2263 10 N 0.0311 0.6861 0.2828 11 A 0.0384 0.5102 0.4513 12 A 0.0563 0.2700 0.6737 13 L 0.1009 0.1039 0.7952 14 K 0.0650 0.0577 0.8772 15 P 0.0159 0.2139 0.7702 16 H 0.0182 0.1318 0.8500 17 L 0.0733 0.0529 0.8738 18 S 0.0626 0.0273 0.9101 19 E 0.0046 0.9247 0.0706 20 K 0.0044 0.9491 0.0465 21 E 0.0045 0.9539 0.0417 22 I 0.0044 0.9600 0.0357 23 E 0.0044 0.9596 0.0360 24 E 0.0044 0.9582 0.0374 25 F 0.0044 0.9555 0.0401 26 V 0.0045 0.9554 0.0401 27 L 0.0045 0.9537 0.0419 28 K 0.0046 0.9431 0.0523 29 S 0.0056 0.9314 0.0630 30 E 0.0068 0.8831 0.1101 31 E 0.0124 0.7310 0.2566 32 L 0.0471 0.3071 0.6458 33 G 0.0484 0.0363 0.9153 34 I 0.1691 0.0156 0.8153 35 Y 0.5980 0.0165 0.3855 36 A 0.8787 0.0069 0.1144 37 V 0.9147 0.0042 0.0810 38 C 0.8901 0.0056 0.1042 39 V 0.6810 0.0121 0.3069 40 N 0.2092 0.0156 0.7753 41 P 0.0235 0.4204 0.5561 42 Y 0.0233 0.5886 0.3880 43 H 0.0208 0.7043 0.2750 44 V 0.0107 0.8494 0.1399 45 K 0.0049 0.9388 0.0562 46 L 0.0046 0.9434 0.0520 47 A 0.0046 0.9474 0.0480 48 S 0.0047 0.9399 0.0554 49 S 0.0058 0.9147 0.0795 50 I 0.0100 0.8034 0.1867 51 A 0.0614 0.5586 0.3800 52 K 0.0287 0.3484 0.6229 53 K 0.0463 0.1000 0.8537 54 V 0.2260 0.0229 0.7511 55 K 0.5566 0.0153 0.4281 56 V 0.8866 0.0062 0.1072 57 C 0.8739 0.0100 0.1161 58 C 0.8313 0.0134 0.1553 59 V 0.7692 0.0247 0.2061 60 I 0.4622 0.0470 0.4909 61 G 0.2331 0.0312 0.7357 62 F 0.1705 0.0271 0.8025 63 P 0.1418 0.0585 0.7996 64 L 0.0733 0.0954 0.8313 65 G 0.0508 0.0830 0.8661 66 L 0.0632 0.1197 0.8171 67 N 0.0943 0.1426 0.7631 68 K 0.0729 0.4629 0.4642 69 T 0.0401 0.7765 0.1834 70 S 0.0291 0.8921 0.0788 71 V 0.0251 0.9124 0.0625 72 K 0.0149 0.9370 0.0481 73 V 0.0097 0.9521 0.0382 74 K 0.0077 0.9563 0.0360 75 E 0.0063 0.9564 0.0374 76 A 0.0068 0.9535 0.0397 77 V 0.0059 0.9553 0.0388 78 E 0.0052 0.9534 0.0415 79 A 0.0048 0.9441 0.0511 80 V 0.0049 0.9159 0.0792 81 R 0.0059 0.8271 0.1670 82 D 0.0371 0.3368 0.6261 83 G 0.0481 0.0991 0.8528 84 A 0.0943 0.0638 0.8419 85 Q 0.1858 0.1244 0.6899 86 E 0.5486 0.0764 0.3750 87 L 0.6808 0.0281 0.2911 88 D 0.7204 0.0423 0.2373 89 I 0.8263 0.0261 0.1476 90 V 0.7396 0.0381 0.2223 91 W 0.5977 0.0634 0.3389 92 N 0.3098 0.0776 0.6126 93 L 0.0381 0.6844 0.2775 94 S 0.0205 0.7787 0.2008 95 A 0.0235 0.8293 0.1472 96 F 0.0411 0.8067 0.1522 97 K 0.0424 0.6651 0.2925 98 S 0.0411 0.3795 0.5793 99 E 0.0378 0.1166 0.8456 100 K 0.0678 0.2218 0.7104 101 Y 0.0135 0.8756 0.1108 102 D 0.0053 0.9290 0.0657 103 F 0.0058 0.9362 0.0580 104 V 0.0049 0.9484 0.0468 105 V 0.0044 0.9580 0.0376 106 E 0.0044 0.9583 0.0373 107 E 0.0044 0.9582 0.0374 108 L 0.0044 0.9601 0.0356 109 K 0.0044 0.9601 0.0355 110 E 0.0044 0.9589 0.0367 111 I 0.0045 0.9554 0.0402 112 F 0.0046 0.9471 0.0483 113 R 0.0051 0.9302 0.0647 114 E 0.0100 0.8504 0.1396 115 T 0.0550 0.4919 0.4531 116 P 0.0289 0.1748 0.7964 117 S 0.0233 0.0852 0.8915 118 A 0.2197 0.0378 0.7425 119 V 0.6238 0.0121 0.3641 120 H 0.8640 0.0109 0.1251 121 K 0.8946 0.0130 0.0924 122 V 0.9048 0.0095 0.0857 123 I 0.8732 0.0177 0.1091 124 V 0.7793 0.0411 0.1797 125 E 0.5993 0.0737 0.3271 126 T 0.3404 0.1562 0.5034 127 P 0.2314 0.1913 0.5772 128 Y 0.2611 0.1278 0.6111 129 L 0.1379 0.0661 0.7960 130 N 0.0674 0.0300 0.9026 131 E 0.0051 0.9248 0.0701 132 E 0.0045 0.9487 0.0468 133 E 0.0045 0.9543 0.0411 134 I 0.0044 0.9592 0.0364 135 K 0.0044 0.9591 0.0365 136 K 0.0044 0.9588 0.0369 137 A 0.0044 0.9588 0.0369 138 V 0.0044 0.9595 0.0361 139 E 0.0044 0.9601 0.0355 140 I 0.0044 0.9606 0.0351 141 C 0.0044 0.9592 0.0364 142 I 0.0047 0.9514 0.0438 143 E 0.0059 0.9162 0.0779 144 A 0.0411 0.5126 0.4463 145 G 0.0501 0.0478 0.9021 146 A 0.0856 0.0249 0.8896 147 D 0.1427 0.0871 0.7701 148 F 0.6310 0.1331 0.2359 149 I 0.6974 0.1162 0.1864 150 K 0.6683 0.0838 0.2479 151 T 0.3165 0.1294 0.5540 152 S 0.1236 0.1300 0.7464 153 T 0.0911 0.1035 0.8054 154 G 0.0854 0.0618 0.8528 155 F 0.1335 0.0672 0.7993 156 A 0.1364 0.0700 0.7937 157 P 0.0923 0.0901 0.8176 158 R 0.0544 0.0898 0.8557 159 G 0.0485 0.0555 0.8960 160 T 0.0951 0.0264 0.8785 161 T 0.0943 0.0660 0.8397 162 L 0.0057 0.9356 0.0587 163 E 0.0044 0.9549 0.0407 164 E 0.0044 0.9584 0.0372 165 V 0.0044 0.9604 0.0352 166 R 0.0044 0.9607 0.0349 167 L 0.0044 0.9604 0.0352 168 I 0.0044 0.9599 0.0358 169 K 0.0045 0.9558 0.0397 170 S 0.0050 0.9452 0.0498 171 S 0.0073 0.8965 0.0962 172 A 0.0290 0.7129 0.2582 173 K 0.0292 0.4925 0.4783 174 G 0.0245 0.3783 0.5971 175 R 0.0408 0.2576 0.7016 176 I 0.1584 0.1059 0.7357 177 K 0.2483 0.0307 0.7210 178 V 0.5498 0.0212 0.4290 179 K 0.6113 0.0241 0.3645 180 A 0.4727 0.0526 0.4747 181 S 0.2155 0.0958 0.6886 182 G 0.1126 0.0777 0.8098 183 G 0.1104 0.1137 0.7759 184 I 0.2154 0.0998 0.6849 185 R 0.1582 0.0997 0.7421 186 D 0.0965 0.0463 0.8572 187 L 0.0048 0.9251 0.0701 188 E 0.0045 0.9509 0.0446 189 T 0.0045 0.9543 0.0411 190 A 0.0044 0.9581 0.0375 191 I 0.0044 0.9589 0.0367 192 S 0.0044 0.9589 0.0367 193 M 0.0045 0.9561 0.0394 194 I 0.0048 0.9540 0.0413 195 E 0.0048 0.9375 0.0577 196 A 0.0065 0.8796 0.1139 197 G 0.0088 0.8249 0.1664 198 A 0.0115 0.8055 0.1830 199 D 0.0186 0.8163 0.1651 200 R 0.0429 0.7670 0.1901 201 I 0.0697 0.6067 0.3237 202 G 0.0810 0.3930 0.5260 203 T 0.0592 0.4722 0.4686 204 S 0.0310 0.5876 0.3814 205 S 0.0165 0.7436 0.2399 206 G 0.0153 0.8627 0.1220 207 I 0.0104 0.9328 0.0568 208 S 0.0120 0.9402 0.0478 209 I 0.0100 0.9385 0.0514 210 A 0.0128 0.9096 0.0777 211 E 0.0136 0.8143 0.1720 212 E 0.0182 0.6035 0.3783 213 F 0.0354 0.4332 0.5314 214 L 0.0601 0.2983 0.6415 215 K 0.0636 0.1934 0.7430 216 R 0.0522 0.2000 0.7478 217 H 0.1089 0.1630 0.7281 218 L 0.1206 0.0842 0.7952 219 I 0.0548 0.0290 0.9162