# This file is the result of combining several RDB files, specifically # T0585.t04.dssp-ebghstl.rdb (weight 1.53986) # T0585.t04.stride-ebghtl.rdb (weight 1.24869) # T0585.t04.str2.rdb (weight 1.54758) # T0585.t04.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 T0585.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0585 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0585.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1016.66 # # ============================================ # Comments from T0585.t04.stride-ebghtl.rdb # ============================================ # TARGET T0585 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0585.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1016.66 # # ============================================ # Comments from T0585.t04.str2.rdb # ============================================ # TARGET T0585 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-str2-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0585.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1016.66 # # ============================================ # Comments from T0585.t04.alpha.rdb # ============================================ # TARGET T0585 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-alpha-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0585.t04-thin90.a2m.gz # with weighted counts, using HenikoffWeight(1.3 bits/column, 1) # The weighting was determined by the posterior distribution # after regularizing with /projects/compbio/lib/recode3.20comp. # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1016.66 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0498 0.0584 0.8918 2 N 0.0539 0.0911 0.8550 3 A 0.0637 0.1339 0.8024 4 S 0.1380 0.0445 0.8175 5 F 0.5924 0.0053 0.4023 6 R 0.8960 0.0038 0.1002 7 V 0.9326 0.0031 0.0643 8 V 0.9303 0.0033 0.0663 9 L 0.9083 0.0046 0.0872 10 D 0.5712 0.0068 0.4220 11 P 0.0946 0.0887 0.8167 12 G 0.0591 0.0653 0.8755 13 H 0.1086 0.0554 0.8360 14 G 0.0952 0.0448 0.8599 15 G 0.1113 0.0567 0.8320 16 I 0.1956 0.0651 0.7392 17 D 0.1307 0.0602 0.8091 18 G 0.0583 0.0938 0.8479 19 G 0.0764 0.0976 0.8261 20 A 0.2656 0.1019 0.6325 21 R 0.3815 0.0829 0.5356 22 G 0.2169 0.0596 0.7236 23 V 0.0916 0.1355 0.7729 24 T 0.0612 0.1001 0.8387 25 G 0.1170 0.0854 0.7976 26 I 0.2327 0.1872 0.5801 27 L 0.3812 0.3518 0.2670 28 E 0.1632 0.6733 0.1635 29 K 0.0594 0.8444 0.0962 30 D 0.0364 0.8867 0.0769 31 V 0.0127 0.9328 0.0545 32 T 0.0056 0.9501 0.0443 33 L 0.0047 0.9602 0.0352 34 A 0.0046 0.9616 0.0338 35 F 0.0047 0.9604 0.0349 36 A 0.0047 0.9608 0.0345 37 R 0.0046 0.9613 0.0340 38 A 0.0047 0.9585 0.0368 39 L 0.0048 0.9533 0.0419 40 R 0.0047 0.9566 0.0387 41 D 0.0048 0.9537 0.0415 42 E 0.0053 0.9401 0.0546 43 L 0.0069 0.8921 0.1011 44 Q 0.0093 0.7216 0.2691 45 K 0.0401 0.3471 0.6127 46 G 0.0291 0.0589 0.9119 47 S 0.0694 0.0266 0.9040 48 H 0.2480 0.0103 0.7417 49 T 0.7078 0.0071 0.2851 50 I 0.8985 0.0040 0.0976 51 V 0.8843 0.0070 0.1088 52 A 0.8265 0.0065 0.1670 53 L 0.5296 0.0150 0.4554 54 T 0.3970 0.0183 0.5847 55 R 0.2171 0.0684 0.7144 56 D 0.1040 0.1087 0.7873 57 S 0.0681 0.1113 0.8206 58 D 0.1167 0.0765 0.8068 59 I 0.2451 0.0964 0.6585 60 F 0.3795 0.0547 0.5658 61 L 0.3589 0.0264 0.6146 62 R 0.1842 0.0198 0.7960 63 L 0.0072 0.9195 0.0733 64 S 0.0051 0.9515 0.0434 65 E 0.0055 0.9515 0.0430 66 R 0.0064 0.9514 0.0422 67 V 0.0052 0.9572 0.0376 68 K 0.0047 0.9574 0.0380 69 K 0.0047 0.9534 0.0419 70 A 0.0047 0.9443 0.0510 71 Q 0.0051 0.9047 0.0902 72 E 0.0068 0.7562 0.2369 73 F 0.0482 0.3063 0.6454 74 D 0.0699 0.0182 0.9119 75 A 0.0931 0.0152 0.8917 76 D 0.2064 0.0612 0.7324 77 L 0.9093 0.0055 0.0851 78 F 0.9316 0.0034 0.0651 79 I 0.9310 0.0040 0.0650 80 S 0.9154 0.0040 0.0806 81 I 0.7971 0.0182 0.1847 82 H 0.6465 0.0174 0.3361 83 A 0.3962 0.0706 0.5332 84 D 0.2657 0.0732 0.6611 85 T 0.1516 0.1302 0.7181 86 I 0.1318 0.0786 0.7896 87 D 0.1058 0.0923 0.8019 88 V 0.0863 0.1442 0.7695 89 H 0.0760 0.2134 0.7107 90 S 0.1192 0.2176 0.6632 91 L 0.2844 0.1163 0.5994 92 R 0.2577 0.0668 0.6755 93 G 0.4778 0.0267 0.4955 94 A 0.6995 0.0058 0.2947 95 T 0.8936 0.0042 0.1022 96 V 0.9246 0.0033 0.0722 97 Y 0.9188 0.0039 0.0773 98 T 0.8822 0.0040 0.1139 99 I 0.5916 0.0109 0.3975 100 S 0.1761 0.0198 0.8041 101 D 0.0386 0.1210 0.8404 102 E 0.0421 0.1593 0.7986 103 A 0.0580 0.2188 0.7232 104 S 0.0442 0.2426 0.7131 105 D 0.0225 0.7501 0.2274 106 A 0.0056 0.9332 0.0612 107 I 0.0052 0.9385 0.0563 108 A 0.0047 0.9455 0.0498 109 K 0.0047 0.9541 0.0412 110 S 0.0047 0.9493 0.0460 111 L 0.0048 0.9411 0.0541 112 A 0.0051 0.9237 0.0712 113 E 0.0057 0.8953 0.0990 114 S 0.0078 0.8443 0.1479 115 E 0.0145 0.7169 0.2686 116 N 0.0376 0.4606 0.5018 117 K 0.0404 0.5311 0.4285 118 V 0.0598 0.5659 0.3744 119 D 0.0680 0.6345 0.2975 120 L 0.0874 0.6852 0.2274 121 L 0.0892 0.5700 0.3408 122 D 0.0533 0.3093 0.6374 123 G 0.0414 0.1110 0.8477 124 L 0.0880 0.0326 0.8795 125 P 0.0917 0.0393 0.8690 126 K 0.0427 0.2413 0.7160 127 E 0.0444 0.3179 0.6377 128 E 0.0338 0.3922 0.5740 129 S 0.0546 0.3190 0.6265 130 L 0.0301 0.6473 0.3226 131 E 0.0240 0.7987 0.1773 132 L 0.0145 0.8881 0.0974 133 T 0.0185 0.8825 0.0990 134 D 0.0203 0.8800 0.0997 135 I 0.0287 0.8787 0.0926 136 L 0.0242 0.8762 0.0996 137 L 0.0379 0.8307 0.1314 138 D 0.0356 0.8290 0.1354 139 L 0.0169 0.8566 0.1265 140 T 0.0261 0.7976 0.1763 141 R 0.0392 0.7301 0.2307 142 R 0.0406 0.6715 0.2879 143 E 0.0314 0.6095 0.3592 144 T 0.0346 0.5692 0.3963 145 H 0.0372 0.6087 0.3541 146 A 0.0234 0.7494 0.2273 147 F 0.0285 0.7311 0.2404 148 S 0.0132 0.8185 0.1683 149 I 0.0057 0.9486 0.0457 150 N 0.0050 0.9538 0.0412 151 F 0.0048 0.9555 0.0397 152 A 0.0047 0.9597 0.0356 153 N 0.0047 0.9607 0.0347 154 N 0.0047 0.9588 0.0365 155 V 0.0047 0.9565 0.0388 156 V 0.0047 0.9568 0.0385 157 S 0.0047 0.9526 0.0426 158 N 0.0049 0.9361 0.0590 159 L 0.0054 0.9114 0.0832 160 S 0.0079 0.8403 0.1518 161 K 0.0128 0.7510 0.2361 162 S 0.0300 0.6142 0.3558 163 H 0.0593 0.3339 0.6068 164 I 0.0716 0.2947 0.6337 165 N 0.0937 0.2285 0.6778 166 L 0.1365 0.2092 0.6543 167 I 0.1433 0.1726 0.6840 168 N 0.1071 0.1258 0.7671 169 N 0.1013 0.0731 0.8256 170 P 0.1035 0.1257 0.7709 171 H 0.2421 0.1481 0.6097 172 R 0.3550 0.1175 0.5275 173 Y 0.3370 0.1047 0.5583 174 A 0.2697 0.1036 0.6267 175 D 0.3081 0.0620 0.6299 176 F 0.6305 0.0392 0.3303 177 Q 0.8125 0.0313 0.1562 178 V 0.8596 0.0330 0.1074 179 L 0.7911 0.0326 0.1763 180 K 0.4928 0.0478 0.4594 181 A 0.1226 0.0306 0.8468 182 P 0.0580 0.0837 0.8583 183 D 0.0639 0.0755 0.8607 184 V 0.1033 0.0363 0.8604 185 P 0.1486 0.0500 0.8014 186 S 0.6741 0.0694 0.2565 187 V 0.8874 0.0271 0.0855 188 L 0.9179 0.0141 0.0680 189 I 0.9049 0.0163 0.0787 190 E 0.8413 0.0299 0.1288 191 I 0.6499 0.0541 0.2960 192 G 0.4414 0.0781 0.4804 193 Y 0.4105 0.1040 0.4855 194 L 0.2824 0.0779 0.6397 195 S 0.1259 0.0306 0.8436 196 N 0.0684 0.0369 0.8947 197 K 0.0051 0.9143 0.0807 198 E 0.0050 0.9411 0.0539 199 D 0.0055 0.9413 0.0532 200 E 0.0049 0.9500 0.0451 201 K 0.0051 0.9330 0.0619 202 L 0.0062 0.8235 0.1702 203 L 0.0187 0.6738 0.3075 204 N 0.0343 0.2965 0.6693 205 N 0.0763 0.0148 0.9089 206 P 0.0050 0.8675 0.1275 207 Q 0.0051 0.9322 0.0628 208 W 0.0047 0.9561 0.0392 209 R 0.0047 0.9602 0.0352 210 K 0.0046 0.9611 0.0343 211 Q 0.0047 0.9613 0.0340 212 M 0.0047 0.9609 0.0344 213 A 0.0047 0.9609 0.0345 214 A 0.0046 0.9616 0.0338 215 S 0.0046 0.9616 0.0338 216 I 0.0047 0.9608 0.0346 217 A 0.0047 0.9610 0.0343 218 Y 0.0046 0.9604 0.0350 219 S 0.0046 0.9584 0.0370 220 I 0.0047 0.9593 0.0361 221 R 0.0047 0.9581 0.0372 222 Q 0.0048 0.9509 0.0443 223 F 0.0052 0.9298 0.0650 224 A 0.0053 0.9360 0.0587 225 E 0.0058 0.9226 0.0717 226 Y 0.0103 0.8866 0.1031 227 R 0.0179 0.8473 0.1348 228 Q 0.0247 0.7830 0.1923 229 K 0.0421 0.7022 0.2556 230 I 0.0651 0.5438 0.3912 231 M 0.0852 0.2481 0.6667 232 Q 0.0807 0.1067 0.8125 233 P 0.0587 0.0335 0.9078 234 L 0.0498 0.0293 0.9209