# This file is the result of combining several RDB files, specifically # T0316.t04.dssp-ebghstl.rdb (weight 1.53986) # T0316.t04.stride-ebghtl.rdb (weight 1.24869) # T0316.t04.str2.rdb (weight 1.54758) # T0316.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 T0316.t04.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.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 1900 # # ============================================ # Comments from T0316.t04.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.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 1900 # # ============================================ # Comments from T0316.t04.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.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 1900 # # ============================================ # Comments from T0316.t04.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.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 1900 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0750 0.1172 0.8078 2 S 0.0977 0.1731 0.7293 3 D 0.0851 0.2215 0.6934 4 N 0.0675 0.1575 0.7750 5 S 0.0450 0.1627 0.7923 6 K 0.0512 0.0995 0.8493 7 T 0.1711 0.0321 0.7967 8 R 0.7209 0.0047 0.2744 9 V 0.9209 0.0034 0.0757 10 V 0.9332 0.0032 0.0635 11 V 0.9314 0.0035 0.0651 12 G 0.9183 0.0054 0.0763 13 M 0.8623 0.0083 0.1294 14 S 0.5177 0.0189 0.4634 15 G 0.1441 0.0354 0.8205 16 G 0.1063 0.0865 0.8072 17 V 0.0583 0.3859 0.5557 18 D 0.0276 0.5788 0.3936 19 S 0.0052 0.9409 0.0539 20 S 0.0047 0.9571 0.0381 21 V 0.0047 0.9601 0.0352 22 T 0.0047 0.9607 0.0347 23 A 0.0046 0.9613 0.0340 24 L 0.0046 0.9616 0.0338 25 L 0.0047 0.9610 0.0344 26 L 0.0047 0.9585 0.0368 27 K 0.0048 0.9522 0.0429 28 E 0.0061 0.9173 0.0766 29 Q 0.0418 0.3855 0.5727 30 G 0.0382 0.0195 0.9423 31 Y 0.0626 0.0132 0.9242 32 D 0.4520 0.0165 0.5315 33 V 0.8579 0.0063 0.1359 34 I 0.8712 0.0123 0.1165 35 G 0.9109 0.0042 0.0849 36 I 0.9134 0.0043 0.0823 37 F 0.8887 0.0079 0.1034 38 M 0.7387 0.0231 0.2382 39 K 0.6603 0.0366 0.3031 40 N 0.5677 0.0460 0.3863 41 W 0.4111 0.0760 0.5129 42 D 0.2982 0.0964 0.6053 43 D 0.2040 0.1707 0.6252 44 T 0.1213 0.1285 0.7502 45 D 0.0694 0.1862 0.7444 46 E 0.0496 0.2120 0.7384 47 N 0.0751 0.1231 0.8018 48 G 0.0605 0.0706 0.8688 49 V 0.1726 0.0642 0.7632 50 C 0.2172 0.0588 0.7241 51 T 0.1148 0.0590 0.8263 52 A 0.0614 0.1373 0.8013 53 T 0.0382 0.5111 0.4507 54 E 0.0381 0.6036 0.3583 55 D 0.0436 0.5952 0.3612 56 Y 0.0075 0.9268 0.0657 57 K 0.0048 0.9559 0.0392 58 D 0.0047 0.9580 0.0373 59 V 0.0047 0.9594 0.0359 60 V 0.0046 0.9611 0.0343 61 A 0.0046 0.9613 0.0341 62 V 0.0046 0.9615 0.0339 63 A 0.0047 0.9605 0.0348 64 D 0.0048 0.9529 0.0423 65 Q 0.0055 0.9293 0.0652 66 I 0.0447 0.6091 0.3462 67 G 0.0453 0.0168 0.9379 68 I 0.0623 0.0079 0.9298 69 P 0.2134 0.0104 0.7762 70 Y 0.7996 0.0075 0.1928 71 Y 0.9068 0.0052 0.0880 72 S 0.9186 0.0037 0.0777 73 V 0.7884 0.0116 0.2000 74 N 0.3759 0.0116 0.6125 75 F 0.0564 0.4697 0.4739 76 E 0.0305 0.6986 0.2709 77 K 0.0130 0.8449 0.1421 78 E 0.0192 0.8204 0.1604 79 Y 0.0130 0.8173 0.1698 80 W 0.0078 0.9158 0.0765 81 D 0.0071 0.9253 0.0676 82 R 0.0079 0.9223 0.0699 83 V 0.0134 0.9047 0.0819 84 F 0.0152 0.8850 0.0997 85 E 0.0176 0.8660 0.1164 86 Y 0.0243 0.8393 0.1364 87 F 0.0339 0.6958 0.2703 88 L 0.0170 0.8442 0.1388 89 A 0.0071 0.9233 0.0696 90 E 0.0086 0.9267 0.0647 91 Y 0.0237 0.8894 0.0869 92 R 0.0261 0.8224 0.1515 93 A 0.0356 0.4267 0.5378 94 G 0.0271 0.0933 0.8796 95 R 0.0867 0.0319 0.8814 96 T 0.1129 0.0154 0.8717 97 P 0.0832 0.0305 0.8863 98 N 0.0953 0.0325 0.8722 99 P 0.0575 0.1672 0.7753 100 D 0.0951 0.2279 0.6771 101 V 0.1537 0.2933 0.5531 102 M 0.1308 0.2975 0.5717 103 C 0.0786 0.3792 0.5422 104 N 0.0332 0.5016 0.4652 105 K 0.0120 0.7988 0.1892 106 E 0.0154 0.8633 0.1213 107 I 0.0338 0.8601 0.1061 108 K 0.0249 0.8642 0.1109 109 F 0.0086 0.9341 0.0573 110 K 0.0068 0.9439 0.0492 111 A 0.0051 0.9544 0.0405 112 F 0.0048 0.9566 0.0386 113 L 0.0047 0.9604 0.0349 114 D 0.0047 0.9611 0.0342 115 Y 0.0047 0.9612 0.0341 116 A 0.0047 0.9599 0.0354 117 I 0.0048 0.9533 0.0419 118 T 0.0052 0.9428 0.0521 119 L 0.0405 0.5737 0.3858 120 G 0.0613 0.0199 0.9188 121 A 0.0910 0.0192 0.8897 122 D 0.1133 0.0589 0.8278 123 Y 0.8641 0.0168 0.1191 124 V 0.9191 0.0079 0.0730 125 A 0.9100 0.0103 0.0798 126 T 0.7911 0.0321 0.1768 127 G 0.4908 0.0346 0.4746 128 H 0.3358 0.0675 0.5967 129 Y 0.2188 0.1414 0.6398 130 A 0.1345 0.3016 0.5640 131 R 0.1017 0.3458 0.5526 132 V 0.1484 0.3596 0.4920 133 A 0.2766 0.2992 0.4242 134 R 0.3599 0.2303 0.4098 135 D 0.2471 0.1695 0.5834 136 E 0.1549 0.1871 0.6580 137 D 0.0977 0.1130 0.7893 138 G 0.0918 0.1001 0.8082 139 T 0.2734 0.1732 0.5534 140 V 0.4252 0.2460 0.3288 141 H 0.3317 0.3253 0.3430 142 M 0.2867 0.3769 0.3364 143 L 0.2434 0.3214 0.4352 144 R 0.1647 0.2866 0.5488 145 G 0.1179 0.2233 0.6588 146 V 0.1200 0.2452 0.6348 147 D 0.0865 0.2452 0.6683 148 N 0.0458 0.2676 0.6866 149 G 0.0656 0.2923 0.6422 150 K 0.1127 0.4268 0.4605 151 D 0.1258 0.4360 0.4382 152 Q 0.1127 0.5114 0.3758 153 T 0.1397 0.5220 0.3384 154 Y 0.1353 0.5090 0.3557 155 F 0.1310 0.4502 0.4188 156 L 0.1138 0.4709 0.4153 157 S 0.1084 0.3767 0.5150 158 Q 0.1082 0.2920 0.5999 159 L 0.1286 0.1298 0.7416 160 S 0.0832 0.1039 0.8129 161 Q 0.0071 0.7838 0.2091 162 E 0.0074 0.8099 0.1827 163 Q 0.0162 0.7756 0.2083 164 L 0.0529 0.6858 0.2613 165 Q 0.1323 0.5574 0.3103 166 K 0.2829 0.4719 0.2453 167 T 0.3812 0.3797 0.2391 168 M 0.3978 0.3021 0.3001 169 F 0.3488 0.1526 0.4986 170 P 0.1821 0.1781 0.6398 171 L 0.0685 0.3977 0.5338 172 G 0.0507 0.3665 0.5829 173 H 0.0567 0.2633 0.6800 174 L 0.1149 0.0614 0.8237 175 E 0.0657 0.0431 0.8912 176 K 0.0111 0.8783 0.1106 177 P 0.0047 0.9515 0.0437 178 E 0.0048 0.9544 0.0407 179 V 0.0056 0.9536 0.0408 180 R 0.0067 0.9424 0.0510 181 R 0.0087 0.8963 0.0950 182 L 0.0135 0.7939 0.1926 183 A 0.0292 0.4067 0.5641