# This file is the result of combining several RDB files, specifically # T0388.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0388.t2k.stride-ebghtl.rdb (weight 1.24869) # T0388.t2k.str2.rdb (weight 1.54758) # T0388.t2k.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 T0388.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0388 # 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 T0388.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 960 # # ============================================ # Comments from T0388.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0388 # 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 T0388.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 960 # # ============================================ # Comments from T0388.t2k.str2.rdb # ============================================ # TARGET T0388 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0388.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 960 # # ============================================ # Comments from T0388.t2k.alpha.rdb # ============================================ # TARGET T0388 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0388.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 960 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 E 0.2816 0.1229 0.5954 2 N 0.3561 0.1126 0.5313 3 L 0.4240 0.1676 0.4084 4 Y 0.6040 0.1398 0.2561 5 F 0.6831 0.1231 0.1938 6 Q 0.5937 0.1064 0.2999 7 S 0.4205 0.1019 0.4776 8 M 0.2452 0.1348 0.6199 9 I 0.1656 0.1264 0.7080 10 N 0.1894 0.0972 0.7134 11 S 0.2369 0.0735 0.6897 12 F 0.2069 0.1193 0.6738 13 Y 0.2113 0.1112 0.6775 14 A 0.3373 0.0923 0.5704 15 F 0.5639 0.0192 0.4169 16 E 0.7534 0.0072 0.2393 17 V 0.7958 0.0076 0.1966 18 K 0.8169 0.0106 0.1726 19 D 0.3908 0.0146 0.5946 20 A 0.0532 0.1196 0.8272 21 K 0.0517 0.0213 0.9270 22 G 0.0379 0.0323 0.9298 23 R 0.2694 0.0098 0.7209 24 T 0.8231 0.0041 0.1728 25 V 0.7741 0.0059 0.2199 26 S 0.5782 0.0122 0.4096 27 L 0.0333 0.6967 0.2700 28 E 0.0118 0.7266 0.2616 29 K 0.0229 0.7131 0.2641 30 Y 0.0917 0.3628 0.5454 31 K 0.0718 0.1055 0.8227 32 G 0.1034 0.0353 0.8612 33 K 0.3388 0.0116 0.6496 34 V 0.6257 0.0044 0.3699 35 S 0.8787 0.0078 0.1135 36 L 0.9305 0.0034 0.0661 37 V 0.9234 0.0042 0.0725 38 V 0.8610 0.0174 0.1215 39 N 0.6337 0.0207 0.3456 40 V 0.3259 0.0700 0.6041 41 A 0.2594 0.1558 0.5848 42 S 0.1239 0.2790 0.5970 43 D 0.0779 0.2219 0.7002 44 C 0.0758 0.1191 0.8050 45 Q 0.0501 0.1052 0.8447 46 L 0.0748 0.1050 0.8202 47 T 0.0712 0.0962 0.8326 48 D 0.0139 0.7070 0.2791 49 R 0.0110 0.6926 0.2964 50 N 0.0129 0.7325 0.2545 51 Y 0.0138 0.7478 0.2383 52 L 0.0057 0.8879 0.1064 53 G 0.0060 0.9072 0.0868 54 L 0.0048 0.9504 0.0448 55 K 0.0048 0.9549 0.0403 56 E 0.0047 0.9556 0.0397 57 L 0.0048 0.9516 0.0435 58 H 0.0053 0.9436 0.0510 59 K 0.0056 0.9318 0.0626 60 E 0.0097 0.8907 0.0996 61 F 0.0418 0.7613 0.1969 62 G 0.0276 0.5245 0.4479 63 P 0.0201 0.3900 0.5898 64 S 0.0519 0.1373 0.8108 65 H 0.0738 0.0387 0.8875 66 F 0.4606 0.0061 0.5333 67 S 0.8874 0.0036 0.1090 68 V 0.9240 0.0032 0.0729 69 L 0.9085 0.0062 0.0853 70 A 0.8996 0.0052 0.0952 71 F 0.8209 0.0093 0.1698 72 P 0.6372 0.0107 0.3521 73 C 0.2863 0.0598 0.6539 74 N 0.1498 0.0721 0.7780 75 Q 0.0596 0.1587 0.7817 76 F 0.0526 0.1396 0.8078 77 G 0.0562 0.1211 0.8227 78 E 0.0768 0.0978 0.8254 79 S 0.1702 0.0858 0.7440 80 E 0.1159 0.0596 0.8245 81 P 0.0787 0.0993 0.8221 82 R 0.0661 0.1032 0.8307 83 P 0.0567 0.1182 0.8251 84 S 0.0205 0.7470 0.2325 85 K 0.0068 0.9216 0.0717 86 E 0.0064 0.9369 0.0567 87 V 0.0058 0.9440 0.0502 88 E 0.0050 0.9513 0.0437 89 S 0.0053 0.9489 0.0458 90 F 0.0052 0.9453 0.0495 91 A 0.0056 0.9408 0.0536 92 R 0.0060 0.9325 0.0614 93 K 0.0082 0.8844 0.1074 94 N 0.0150 0.7390 0.2460 95 Y 0.0589 0.2674 0.6738 96 G 0.0574 0.0455 0.8971 97 V 0.1129 0.0241 0.8630 98 T 0.1674 0.0275 0.8050 99 F 0.3452 0.0389 0.6159 100 P 0.4559 0.0688 0.4753 101 I 0.4775 0.1195 0.4030 102 F 0.5253 0.1163 0.3584 103 H 0.4302 0.1227 0.4470 104 K 0.3157 0.1495 0.5348 105 I 0.3146 0.1764 0.5091 106 K 0.2795 0.1615 0.5590 107 I 0.2311 0.1361 0.6328 108 L 0.1524 0.1132 0.7343 109 G 0.0745 0.2135 0.7120 110 S 0.0332 0.3321 0.6346 111 E 0.0428 0.3327 0.6245 112 G 0.0420 0.3483 0.6097 113 E 0.0464 0.4225 0.5310 114 P 0.0148 0.8915 0.0937 115 A 0.0068 0.9342 0.0590 116 F 0.0059 0.9485 0.0456 117 R 0.0053 0.9504 0.0443 118 F 0.0052 0.9481 0.0467 119 L 0.0059 0.9361 0.0580 120 V 0.0072 0.9022 0.0906 121 D 0.0119 0.7921 0.1960 122 S 0.0326 0.5478 0.4196 123 S 0.0541 0.1899 0.7560 124 K 0.0382 0.1680 0.7938 125 K 0.0553 0.1774 0.7673 126 E 0.1113 0.1127 0.7760 127 P 0.2621 0.0556 0.6823 128 R 0.4160 0.0419 0.5420 129 W 0.4878 0.0307 0.4816 130 N 0.3642 0.0168 0.6190 131 F 0.3674 0.0489 0.5838 132 W 0.5701 0.0434 0.3865 133 K 0.8093 0.0157 0.1750 134 Y 0.8685 0.0064 0.1252 135 L 0.8824 0.0058 0.1118 136 V 0.8602 0.0055 0.1343 137 N 0.2245 0.0128 0.7626 138 P 0.0196 0.1108 0.8696 139 E 0.0517 0.0173 0.9310 140 G 0.0905 0.0204 0.8891 141 Q 0.2961 0.0086 0.6952 142 V 0.8815 0.0030 0.1156 143 V 0.8501 0.0157 0.1342 144 K 0.8545 0.0078 0.1377 145 F 0.7757 0.0200 0.2043 146 W 0.6300 0.0220 0.3480 147 R 0.3288 0.0297 0.6415 148 P 0.0834 0.0739 0.8427 149 E 0.0995 0.0649 0.8356 150 E 0.1356 0.0293 0.8350 151 P 0.0834 0.0246 0.8921 152 I 0.0158 0.7749 0.2093 153 E 0.0070 0.8037 0.1894 154 V 0.0118 0.8245 0.1637 155 I 0.0094 0.8459 0.1447 156 R 0.0060 0.9204 0.0736 157 P 0.0052 0.9339 0.0609 158 D 0.0059 0.9449 0.0492 159 I 0.0051 0.9511 0.0439 160 A 0.0049 0.9549 0.0402 161 A 0.0052 0.9487 0.0461 162 L 0.0062 0.9336 0.0603 163 V 0.0115 0.9153 0.0732 164 R 0.0065 0.8952 0.0983 165 Q 0.0075 0.8383 0.1542 166 V 0.0151 0.7983 0.1866 167 I 0.0274 0.7609 0.2117 168 I 0.0365 0.7225 0.2411 169 K 0.0600 0.5415 0.3985 170 K 0.0743 0.4822 0.4435 171 K 0.0713 0.5171 0.4116 172 E 0.0599 0.4120 0.5281 173 D 0.0588 0.3087 0.6325 174 L 0.0322 0.1193 0.8485