# This file is the result of combining several RDB files, specifically # T0316.t06.dssp-ebghstl.rdb (weight 1.53986) # T0316.t06.stride-ebghtl.rdb (weight 1.24869) # T0316.t06.str2.rdb (weight 1.54758) # T0316.t06.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 T0316.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0316 # 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 T0316.t06-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 2231 # # ============================================ # Comments from T0316.t06.stride-ebghtl.rdb # ============================================ # TARGET T0316 # 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 T0316.t06-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 2231 # # ============================================ # Comments from T0316.t06.str2.rdb # ============================================ # TARGET T0316 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0316.t06-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 2231 # # ============================================ # Comments from T0316.t06.alpha.rdb # ============================================ # TARGET T0316 # 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 T0316.t06-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 2231 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0766 0.0234 0.9001 2 S 0.0927 0.0425 0.8649 3 D 0.0593 0.1682 0.7725 4 N 0.0448 0.2296 0.7256 5 S 0.0481 0.2165 0.7354 6 K 0.0702 0.0904 0.8395 7 T 0.1990 0.0255 0.7755 8 R 0.7195 0.0050 0.2755 9 V 0.9186 0.0035 0.0779 10 V 0.9327 0.0032 0.0640 11 V 0.9310 0.0036 0.0655 12 G 0.9172 0.0054 0.0774 13 M 0.8545 0.0090 0.1364 14 S 0.5108 0.0198 0.4694 15 G 0.1438 0.0355 0.8206 16 G 0.1006 0.0888 0.8105 17 V 0.0543 0.3980 0.5477 18 D 0.0281 0.5816 0.3903 19 S 0.0053 0.9414 0.0533 20 S 0.0048 0.9565 0.0387 21 V 0.0047 0.9603 0.0350 22 T 0.0047 0.9605 0.0348 23 A 0.0046 0.9614 0.0340 24 L 0.0046 0.9616 0.0338 25 L 0.0047 0.9613 0.0341 26 L 0.0047 0.9595 0.0358 27 K 0.0049 0.9541 0.0410 28 E 0.0057 0.9194 0.0749 29 Q 0.0412 0.3469 0.6119 30 G 0.0370 0.0159 0.9471 31 Y 0.0621 0.0087 0.9292 32 D 0.5511 0.0118 0.4372 33 V 0.8992 0.0034 0.0974 34 I 0.9113 0.0068 0.0819 35 G 0.9280 0.0035 0.0685 36 I 0.9257 0.0034 0.0709 37 F 0.9049 0.0037 0.0914 38 M 0.7092 0.0090 0.2818 39 K 0.4025 0.0272 0.5703 40 N 0.1796 0.0318 0.7887 41 W 0.1353 0.2361 0.6286 42 D 0.1307 0.3060 0.5633 43 D 0.1313 0.3313 0.5374 44 T 0.1185 0.1830 0.6985 45 D 0.0572 0.2713 0.6715 46 E 0.0415 0.2894 0.6692 47 N 0.0751 0.1556 0.7693 48 G 0.0664 0.0483 0.8853 49 V 0.2103 0.0456 0.7440 50 C 0.2352 0.0463 0.7184 51 T 0.1041 0.0596 0.8363 52 A 0.0636 0.1652 0.7712 53 T 0.0331 0.5681 0.3988 54 E 0.0311 0.6441 0.3248 55 D 0.0374 0.6374 0.3251 56 Y 0.0082 0.9084 0.0834 57 K 0.0049 0.9521 0.0429 58 D 0.0048 0.9552 0.0400 59 V 0.0047 0.9589 0.0364 60 V 0.0046 0.9609 0.0344 61 A 0.0046 0.9615 0.0339 62 V 0.0046 0.9616 0.0337 63 A 0.0047 0.9604 0.0350 64 D 0.0048 0.9522 0.0430 65 Q 0.0057 0.9253 0.0690 66 I 0.0451 0.5997 0.3552 67 G 0.0453 0.0166 0.9381 68 I 0.0604 0.0079 0.9317 69 P 0.2007 0.0116 0.7878 70 Y 0.7766 0.0085 0.2149 71 Y 0.9053 0.0056 0.0891 72 S 0.9198 0.0039 0.0763 73 V 0.8240 0.0096 0.1664 74 N 0.4668 0.0084 0.5249 75 F 0.0900 0.3202 0.5898 76 E 0.0480 0.5348 0.4172 77 K 0.0124 0.8376 0.1500 78 E 0.0171 0.8399 0.1430 79 Y 0.0128 0.8578 0.1294 80 W 0.0083 0.9177 0.0740 81 D 0.0074 0.9250 0.0676 82 R 0.0076 0.9223 0.0701 83 V 0.0097 0.9149 0.0754 84 F 0.0107 0.9084 0.0810 85 E 0.0101 0.9138 0.0761 86 Y 0.0150 0.8907 0.0943 87 F 0.0190 0.8223 0.1587 88 L 0.0124 0.9075 0.0800 89 A 0.0071 0.9408 0.0522 90 E 0.0080 0.9383 0.0537 91 Y 0.0192 0.8994 0.0813 92 R 0.0205 0.8344 0.1451 93 A 0.0367 0.4599 0.5034 94 G 0.0276 0.1008 0.8716 95 R 0.0803 0.0380 0.8817 96 T 0.1094 0.0181 0.8725 97 P 0.0869 0.0381 0.8750 98 N 0.0983 0.0387 0.8631 99 P 0.0639 0.1691 0.7670 100 D 0.0942 0.2267 0.6790 101 V 0.1949 0.2964 0.5087 102 M 0.1611 0.3042 0.5347 103 C 0.0867 0.3950 0.5183 104 N 0.0340 0.5096 0.4564 105 K 0.0124 0.7605 0.2270 106 E 0.0117 0.8599 0.1284 107 I 0.0291 0.8539 0.1171 108 K 0.0186 0.8767 0.1046 109 F 0.0065 0.9448 0.0487 110 K 0.0056 0.9530 0.0415 111 A 0.0047 0.9568 0.0385 112 F 0.0048 0.9580 0.0372 113 L 0.0047 0.9609 0.0345 114 D 0.0047 0.9615 0.0338 115 Y 0.0047 0.9615 0.0339 116 A 0.0047 0.9604 0.0349 117 I 0.0048 0.9537 0.0415 118 T 0.0052 0.9415 0.0533 119 L 0.0407 0.5513 0.4080 120 G 0.0592 0.0183 0.9225 121 A 0.0896 0.0126 0.8978 122 D 0.1363 0.0543 0.8094 123 Y 0.8703 0.0119 0.1177 124 V 0.9201 0.0057 0.0743 125 A 0.9089 0.0080 0.0830 126 T 0.7574 0.0268 0.2158 127 G 0.3927 0.0340 0.5733 128 H 0.2164 0.0762 0.7074 129 Y 0.1539 0.1942 0.6519 130 A 0.0801 0.4860 0.4340 131 R 0.0538 0.5753 0.3709 132 V 0.0658 0.6211 0.3131 133 A 0.0967 0.5975 0.3059 134 R 0.1082 0.5015 0.3903 135 D 0.1002 0.3750 0.5248 136 E 0.1038 0.3510 0.5452 137 D 0.1073 0.2793 0.6134 138 G 0.0789 0.3219 0.5992 139 T 0.1027 0.5146 0.3827 140 V 0.1208 0.6210 0.2582 141 H 0.0935 0.6564 0.2501 142 M 0.1055 0.6353 0.2592 143 L 0.1071 0.5169 0.3760 144 R 0.0654 0.2898 0.6448 145 G 0.0700 0.2066 0.7235 146 V 0.0982 0.2197 0.6822 147 D 0.0855 0.3113 0.6032 148 N 0.0493 0.3506 0.6001 149 G 0.0489 0.3882 0.5629 150 K 0.0682 0.5163 0.4156 151 D 0.0816 0.4926 0.4259 152 Q 0.0925 0.4805 0.4271 153 T 0.1273 0.4332 0.4395 154 Y 0.1109 0.4796 0.4095 155 F 0.1118 0.4537 0.4344 156 L 0.1016 0.4782 0.4201 157 S 0.0795 0.4132 0.5073 158 Q 0.0767 0.3439 0.5794 159 L 0.0948 0.1871 0.7180 160 S 0.0685 0.1494 0.7822 161 Q 0.0084 0.7839 0.2077 162 E 0.0089 0.8145 0.1766 163 Q 0.0184 0.7936 0.1880 164 L 0.0401 0.7615 0.1983 165 Q 0.0915 0.6496 0.2590 166 K 0.2083 0.5579 0.2338 167 T 0.3119 0.4387 0.2494 168 M 0.3541 0.3330 0.3128 169 F 0.3386 0.1579 0.5034 170 P 0.1899 0.1797 0.6304 171 L 0.0626 0.4153 0.5221 172 G 0.0395 0.3857 0.5748 173 H 0.0469 0.2694 0.6837 174 L 0.1110 0.0558 0.8331 175 E 0.0642 0.0391 0.8967 176 K 0.0102 0.8877 0.1022 177 P 0.0047 0.9521 0.0432 178 E 0.0048 0.9544 0.0407 179 V 0.0056 0.9537 0.0407 180 R 0.0063 0.9424 0.0513 181 R 0.0084 0.8929 0.0987 182 L 0.0136 0.7938 0.1926 183 A 0.0290 0.4018 0.5691