# This file is the result of combining several RDB files, specifically # T0273.t04.dssp-ebghstl.rdb (weight 1.53986) # T0273.t04.stride-ebghtl.rdb (weight 1.24869) # T0273.t04.str2.rdb (weight 1.54758) # T0273.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 T0273.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0273 # 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 T0273.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 402 # # ============================================ # Comments from T0273.t04.stride-ebghtl.rdb # ============================================ # TARGET T0273 # 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 T0273.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 402 # # ============================================ # Comments from T0273.t04.str2.rdb # ============================================ # TARGET T0273 # 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 T0273.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 402 # # ============================================ # Comments from T0273.t04.alpha.rdb # ============================================ # TARGET T0273 # 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 T0273.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 402 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0882 0.0182 0.8936 2 P 0.2031 0.0352 0.7617 3 L 0.3171 0.0726 0.6103 4 V 0.3929 0.0995 0.5076 5 L 0.2897 0.0894 0.6209 6 D 0.1589 0.0920 0.7492 7 L 0.0747 0.1075 0.8179 8 A 0.0942 0.0655 0.8403 9 R 0.0914 0.0306 0.8780 10 P 0.1513 0.0226 0.8261 11 V 0.2117 0.0109 0.7774 12 S 0.1020 0.0107 0.8873 13 E 0.0048 0.9513 0.0439 14 E 0.0047 0.9603 0.0350 15 E 0.0047 0.9607 0.0347 16 L 0.0047 0.9573 0.0380 17 R 0.0051 0.9190 0.0759 18 R 0.0054 0.7763 0.2184 19 L 0.0100 0.6757 0.3143 20 S 0.0258 0.5816 0.3926 21 E 0.0241 0.4956 0.4803 22 L 0.0550 0.3228 0.6222 23 N 0.0727 0.0340 0.8933 24 P 0.0271 0.1197 0.8532 25 G 0.0366 0.0879 0.8756 26 Y 0.2299 0.0699 0.7001 27 Q 0.5402 0.0505 0.4093 28 W 0.7516 0.0336 0.2147 29 E 0.8161 0.0174 0.1665 30 R 0.7621 0.0133 0.2247 31 S 0.1804 0.0149 0.8047 32 P 0.0498 0.1045 0.8457 33 E 0.0501 0.0252 0.9247 34 G 0.1572 0.0314 0.8114 35 R 0.6152 0.0081 0.3767 36 L 0.9082 0.0034 0.0884 37 W 0.8133 0.0104 0.1764 38 V 0.5749 0.0082 0.4169 39 S 0.2652 0.0104 0.7245 40 P 0.1224 0.0380 0.8396 41 T 0.1108 0.0443 0.8450 42 G 0.0901 0.0561 0.8539 43 G 0.0493 0.1951 0.7555 44 E 0.0575 0.3263 0.6161 45 S 0.0589 0.4209 0.5202 46 G 0.0328 0.6024 0.3648 47 R 0.0257 0.8523 0.1220 48 R 0.0265 0.9051 0.0684 49 S 0.0127 0.9373 0.0499 50 L 0.0103 0.9467 0.0430 51 Q 0.0089 0.9514 0.0397 52 L 0.0047 0.9587 0.0366 53 A 0.0047 0.9609 0.0344 54 Y 0.0046 0.9615 0.0338 55 Q 0.0047 0.9608 0.0346 56 L 0.0047 0.9584 0.0369 57 A 0.0047 0.9570 0.0382 58 R 0.0049 0.9529 0.0422 59 W 0.0050 0.9504 0.0446 60 N 0.0057 0.9343 0.0599 61 E 0.0060 0.8950 0.0990 62 E 0.0097 0.8112 0.1791 63 R 0.0466 0.4216 0.5318 64 G 0.0471 0.0528 0.9001 65 L 0.1019 0.0333 0.8648 66 G 0.2776 0.0510 0.6713 67 V 0.6640 0.0253 0.3106 68 V 0.7910 0.0139 0.1951 69 F 0.7193 0.0144 0.2663 70 D 0.4761 0.0275 0.4964 71 S 0.1963 0.0837 0.7200 72 S 0.2117 0.0804 0.7078 73 T 0.3587 0.0535 0.5879 74 G 0.6211 0.0281 0.3507 75 F 0.8302 0.0087 0.1611 76 K 0.8105 0.0081 0.1814 77 F 0.4299 0.0092 0.5608 78 P 0.1244 0.0376 0.8380 79 D 0.0466 0.0548 0.8986 80 G 0.0527 0.0570 0.8904 81 S 0.1263 0.0477 0.8260 82 I 0.3187 0.0340 0.6473 83 L 0.4040 0.0223 0.5737 84 S 0.4446 0.0280 0.5274 85 P 0.4199 0.0161 0.5640 86 D 0.4734 0.0325 0.4941 87 A 0.8752 0.0088 0.1160 88 A 0.9208 0.0041 0.0751 89 F 0.9256 0.0050 0.0694 90 V 0.8931 0.0097 0.0972 91 E 0.7546 0.0221 0.2233 92 R 0.2361 0.0528 0.7111 93 G 0.1199 0.0833 0.7967 94 A 0.1132 0.1721 0.7147 95 W 0.0627 0.5386 0.3988 96 E 0.0504 0.6288 0.3207 97 A 0.0425 0.6313 0.3262 98 L 0.0763 0.4738 0.4499 99 S 0.0578 0.4250 0.5173 100 E 0.0362 0.5592 0.4046 101 A 0.0613 0.5407 0.3979 102 E 0.0996 0.5019 0.3985 103 R 0.1455 0.3757 0.4788 104 E 0.0854 0.2792 0.6354 105 G 0.0651 0.1280 0.8070 106 F 0.0941 0.0622 0.8437 107 P 0.0804 0.0708 0.8489 108 P 0.0767 0.1065 0.8168 109 L 0.1124 0.0828 0.8048 110 A 0.1200 0.0326 0.8475 111 P 0.1760 0.0282 0.7959 112 K 0.4866 0.0422 0.4711 113 A 0.8882 0.0043 0.1075 114 V 0.9297 0.0032 0.0671 115 F 0.9296 0.0034 0.0670 116 E 0.9214 0.0036 0.0750 117 V 0.8642 0.0047 0.1312 118 R 0.5789 0.0105 0.4106 119 S 0.1668 0.0195 0.8136 120 A 0.0170 0.1315 0.8515 121 S 0.0509 0.0405 0.9086 122 Q 0.0530 0.0314 0.9155 123 D 0.0709 0.0164 0.9128 124 P 0.0103 0.8895 0.1003 125 E 0.0050 0.9431 0.0519 126 E 0.0050 0.9505 0.0445 127 L 0.0047 0.9549 0.0403 128 R 0.0047 0.9539 0.0413 129 A 0.0049 0.9476 0.0475 130 K 0.0049 0.9433 0.0518 131 M 0.0071 0.9450 0.0478 132 G 0.0053 0.9547 0.0399 133 I 0.0057 0.9572 0.0371 134 Y 0.0057 0.9558 0.0386 135 L 0.0059 0.9488 0.0453 136 R 0.0066 0.9091 0.0843 137 N 0.0426 0.3272 0.6303 138 G 0.0379 0.0173 0.9448 139 V 0.0978 0.0078 0.8944 140 L 0.4203 0.0113 0.5684 141 L 0.8541 0.0049 0.1410 142 G 0.9130 0.0037 0.0834 143 V 0.9301 0.0033 0.0666 144 L 0.9285 0.0033 0.0682 145 V 0.8890 0.0080 0.1030 146 D 0.5618 0.0050 0.4332 147 P 0.0282 0.1262 0.8456 148 Y 0.0244 0.0997 0.8759 149 A 0.0960 0.0751 0.8289 150 R 0.3087 0.0258 0.6655 151 A 0.8303 0.0074 0.1623 152 V 0.9138 0.0036 0.0826 153 E 0.9207 0.0045 0.0748 154 V 0.9183 0.0043 0.0773 155 F 0.8727 0.0078 0.1194 156 R 0.6586 0.0086 0.3328 157 P 0.1327 0.0579 0.8094 158 G 0.0490 0.0403 0.9107 159 K 0.0915 0.0221 0.8864 160 P 0.1254 0.0220 0.8525 161 P 0.3044 0.0405 0.6551 162 L 0.7175 0.0153 0.2672 163 R 0.8303 0.0089 0.1608 164 L 0.8503 0.0090 0.1407 165 E 0.6781 0.0283 0.2936 166 G 0.4114 0.0299 0.5587 167 V 0.2334 0.0642 0.7023 168 E 0.3062 0.0844 0.6094 169 R 0.5304 0.0671 0.4025 170 V 0.5914 0.0314 0.3772 171 S 0.5843 0.0315 0.3842 172 L 0.3880 0.0358 0.5762 173 D 0.1493 0.0266 0.8242 174 P 0.0214 0.2283 0.7503 175 E 0.0321 0.1747 0.7931 176 L 0.0845 0.0938 0.8217 177 P 0.0352 0.0979 0.8669 178 G 0.0629 0.0777 0.8594 179 F 0.3355 0.0327 0.6317 180 A 0.6902 0.0158 0.2940 181 L 0.7012 0.0145 0.2843 182 S 0.5066 0.0201 0.4733 183 L 0.1871 0.1205 0.6924 184 P 0.1055 0.3350 0.5595 185 P 0.0794 0.4814 0.4392 186 L 0.1038 0.3227 0.5736 187 W 0.1021 0.1299 0.7680