# This file is the result of combining several RDB files, specifically # T0448.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0448.t2k.stride-ebghtl.rdb (weight 1.24869) # T0448.t2k.str.rdb (weight 1.53983) # 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 T0448.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0448 # 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 T0448.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 124 # # ============================================ # Comments from T0448.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0448 # 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 T0448.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 124 # # ============================================ # Comments from T0448.t2k.str.rdb # ============================================ # TARGET T0448 # 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 T0448.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 124 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0254 0.0172 0.9573 2 I 0.2473 0.1200 0.6326 3 A 0.2952 0.2247 0.4801 4 M 0.2906 0.2951 0.4143 5 I 0.3224 0.3516 0.3260 6 V 0.3632 0.3519 0.2849 7 K 0.3490 0.3498 0.3012 8 G 0.3178 0.4027 0.2795 9 G 0.2283 0.4981 0.2736 10 L 0.1430 0.6039 0.2531 11 A 0.1103 0.6553 0.2345 12 M 0.0929 0.6932 0.2139 13 A 0.1225 0.6411 0.2365 14 I 0.1309 0.5848 0.2843 15 S 0.0948 0.5254 0.3798 16 N 0.0706 0.3781 0.5513 17 G 0.0558 0.2600 0.6842 18 H 0.0442 0.2266 0.7291 19 V 0.0392 0.1677 0.7931 20 S 0.0553 0.1031 0.8416 21 F 0.0920 0.0520 0.8559 22 K 0.3085 0.0185 0.6730 23 R 0.8390 0.0067 0.1543 24 P 0.9574 0.0032 0.0394 25 A 0.9718 0.0028 0.0254 26 W 0.9610 0.0028 0.0362 27 L 0.8505 0.0061 0.1434 28 G 0.4614 0.0172 0.5213 29 D 0.1628 0.0422 0.7950 30 S 0.1967 0.0907 0.7126 31 I 0.2424 0.1775 0.5801 32 T 0.2545 0.1963 0.5492 33 A 0.1956 0.1860 0.6184 34 N 0.1121 0.1614 0.7265 35 N 0.1021 0.1177 0.7803 36 G 0.0887 0.0997 0.8116 37 L 0.0832 0.1034 0.8134 38 A 0.0541 0.1215 0.8244 39 T 0.0355 0.1479 0.8166 40 V 0.0312 0.2042 0.7646 41 H 0.0385 0.2969 0.6646 42 Y 0.0764 0.3234 0.6002 43 H 0.0349 0.7431 0.2220 44 D 0.0118 0.9063 0.0818 45 I 0.0075 0.9321 0.0603 46 L 0.0060 0.9425 0.0516 47 A 0.0050 0.9406 0.0544 48 A 0.0056 0.9260 0.0684 49 D 0.0069 0.8517 0.1414 50 W 0.0125 0.7234 0.2642 51 D 0.0316 0.3486 0.6198 52 V 0.0465 0.0671 0.8864 53 E 0.2150 0.0414 0.7435 54 R 0.6703 0.0267 0.3030 55 S 0.8811 0.0196 0.0993 56 D 0.8954 0.0191 0.0855 57 N 0.8108 0.0256 0.1636 58 L 0.5498 0.0429 0.4073 59 G 0.3870 0.0461 0.5669 60 I 0.2792 0.0572 0.6636 61 S 0.1939 0.0765 0.7296 62 G 0.1132 0.2321 0.6547 63 S 0.0974 0.4270 0.4757 64 T 0.1169 0.5423 0.3407 65 I 0.0733 0.6959 0.2308 66 G 0.0733 0.6444 0.2823 67 S 0.0661 0.6348 0.2991 68 R 0.0527 0.6563 0.2910 69 Y 0.0526 0.6723 0.2752 70 D 0.0497 0.6510 0.2993 71 A 0.0354 0.6374 0.3272 72 M 0.0330 0.5880 0.3790 73 A 0.0426 0.5595 0.3979 74 V 0.0417 0.4879 0.4704 75 R 0.0493 0.5589 0.3918 76 Y 0.0365 0.6282 0.3353 77 Q 0.0249 0.6642 0.3109 78 A 0.0278 0.6520 0.3202 79 I 0.0207 0.5987 0.3806 80 P 0.0263 0.4163 0.5574 81 E 0.0396 0.2080 0.7524 82 D 0.0658 0.0413 0.8929 83 A 0.0461 0.0134 0.9405 84 D 0.1520 0.0084 0.8396 85 F 0.9559 0.0025 0.0416 86 I 0.9822 0.0024 0.0155 87 A 0.9824 0.0024 0.0152 88 V 0.9771 0.0024 0.0205 89 F 0.8715 0.0030 0.1255 90 G 0.4841 0.0105 0.5054 91 G 0.3032 0.0271 0.6697 92 V 0.2672 0.0747 0.6581 93 N 0.2456 0.1387 0.6158 94 D 0.1777 0.1900 0.6322 95 Y 0.1242 0.2475 0.6283 96 G 0.0939 0.2440 0.6621 97 R 0.0973 0.1723 0.7304 98 D 0.1167 0.1088 0.7745 99 Q 0.1397 0.0924 0.7679 100 P 0.1526 0.1107 0.7367 101 L 0.0902 0.2101 0.6997 102 G 0.0607 0.2011 0.7382 103 Q 0.0724 0.1736 0.7540 104 Y 0.0886 0.1448 0.7666 105 G 0.0745 0.0892 0.8363 106 D 0.0822 0.0736 0.8442 107 C 0.1486 0.0390 0.8124 108 D 0.0767 0.0442 0.8791 109 M 0.0043 0.9074 0.0883 110 T 0.0045 0.9262 0.0693 111 T 0.0038 0.9354 0.0607 112 F 0.0041 0.9449 0.0510 113 Y 0.0037 0.9617 0.0345 114 G 0.0038 0.9649 0.0314 115 A 0.0037 0.9688 0.0275 116 L 0.0037 0.9755 0.0208 117 M 0.0037 0.9755 0.0207 118 M 0.0037 0.9748 0.0215 119 L 0.0037 0.9759 0.0204 120 L 0.0037 0.9755 0.0208 121 T 0.0037 0.9729 0.0234 122 G 0.0037 0.9630 0.0333 123 L 0.0038 0.9517 0.0445 124 Q 0.0043 0.9111 0.0845 125 T 0.0051 0.7297 0.2651 126 N 0.0100 0.4441 0.5459 127 W 0.0228 0.0613 0.9158 128 P 0.0400 0.0435 0.9164 129 T 0.1554 0.0430 0.8015 130 V 0.5864 0.0160 0.3977 131 P 0.8998 0.0055 0.0947 132 K 0.9657 0.0030 0.0313 133 L 0.9655 0.0028 0.0318 134 F 0.9507 0.0031 0.0462 135 I 0.8176 0.0053 0.1771 136 S 0.4694 0.0167 0.5140 137 A 0.2465 0.0587 0.6948 138 I 0.1659 0.0958 0.7383 139 H 0.1310 0.1077 0.7613 140 I 0.0916 0.1135 0.7949 141 G 0.0811 0.1499 0.7691 142 S 0.0635 0.3212 0.6153 143 D 0.0685 0.3586 0.5729 144 F 0.0822 0.3236 0.5942 145 G 0.0794 0.2181 0.7025 146 G 0.0849 0.1622 0.7529 147 S 0.0746 0.2163 0.7091 148 F 0.0560 0.2661 0.6779 149 S 0.0419 0.3324 0.6257 150 A 0.0419 0.4011 0.5570 151 V 0.0476 0.5215 0.4309 152 T 0.0428 0.5657 0.3915 153 N 0.0346 0.5674 0.3980 154 G 0.0238 0.6044 0.3718 155 L 0.0164 0.6558 0.3278 156 G 0.0130 0.7095 0.2775 157 Y 0.0114 0.7899 0.1987 158 R 0.0106 0.8155 0.1740 159 Q 0.0054 0.9001 0.0945 160 S 0.0051 0.9128 0.0821 161 D 0.0045 0.9182 0.0774 162 Y 0.0041 0.9493 0.0466 163 E 0.0038 0.9662 0.0300 164 A 0.0038 0.9700 0.0262 165 A 0.0037 0.9715 0.0248 166 I 0.0037 0.9733 0.0229 167 A 0.0038 0.9712 0.0250 168 Q 0.0038 0.9712 0.0250 169 M 0.0037 0.9721 0.0242 170 T 0.0038 0.9641 0.0321 171 A 0.0039 0.9395 0.0566 172 D 0.0042 0.8647 0.1311 173 Y 0.0065 0.4194 0.5741 174 G 0.0102 0.0189 0.9709 175 V 0.0468 0.0100 0.9432 176 P 0.2730 0.0168 0.7102 177 H 0.7326 0.0315 0.2359 178 L 0.8188 0.0275 0.1537 179 S 0.6705 0.0384 0.2912 180 L 0.2247 0.3160 0.4593 181 Y 0.0880 0.3866 0.5254 182 R 0.0513 0.5234 0.4253 183 D 0.0503 0.5554 0.3943 184 A 0.0496 0.5101 0.4402 185 G 0.0671 0.4442 0.4887 186 M 0.0615 0.4261 0.5124 187 T 0.0548 0.3526 0.5927 188 F 0.0394 0.3800 0.5806 189 A 0.0346 0.3495 0.6159 190 I 0.0269 0.3598 0.6133 191 P 0.0169 0.5112 0.4718 192 A 0.0186 0.5152 0.4662 193 Q 0.0263 0.5749 0.3988 194 A 0.0254 0.6467 0.3279 195 A 0.0324 0.6023 0.3653 196 I 0.0584 0.5131 0.4285 197 Y 0.1122 0.3066 0.5812 198 S 0.0972 0.1626 0.7402 199 V 0.0659 0.1448 0.7894 200 D 0.0624 0.0958 0.8417 201 T 0.0692 0.0735 0.8573 202 L 0.1416 0.0718 0.7867 203 H 0.1413 0.0440 0.8147 204 P 0.1051 0.0516 0.8432 205 N 0.0261 0.0769 0.8971 206 N 0.0039 0.9250 0.0711 207 A 0.0037 0.9622 0.0341 208 G 0.0037 0.9646 0.0317 209 H 0.0037 0.9746 0.0217 210 R 0.0037 0.9755 0.0208 211 V 0.0037 0.9748 0.0215 212 I 0.0037 0.9741 0.0222 213 A 0.0037 0.9752 0.0211 214 R 0.0037 0.9734 0.0229 215 K 0.0037 0.9683 0.0280 216 L 0.0037 0.9712 0.0251 217 Q 0.0037 0.9723 0.0239 218 S 0.0038 0.9654 0.0308 219 F 0.0037 0.9591 0.0372 220 L 0.0041 0.9493 0.0466 221 D 0.0038 0.9046 0.0916 222 S 0.0046 0.8042 0.1912 223 H 0.0095 0.6798 0.3107 224 F 0.0270 0.5012 0.4718 225 L 0.0276 0.4117 0.5608 226 E 0.0256 0.3645 0.6099 227 H 0.0284 0.2795 0.6921 228 H 0.0310 0.2583 0.7107 229 H 0.0371 0.2150 0.7478 230 H 0.0472 0.1864 0.7664 231 H 0.0445 0.0952 0.8603 232 H 0.0109 0.0128 0.9763