# This file is the result of combining several RDB files, specifically # T0347.t04.dssp-ebghstl.rdb (weight 1.53986) # T0347.t04.stride-ebghtl.rdb (weight 1.24869) # T0347.t04.str2.rdb (weight 1.54758) # T0347.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 T0347.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0347 # Using neural net t06-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 T0347.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 13.9885 # # ============================================ # Comments from T0347.t04.stride-ebghtl.rdb # ============================================ # TARGET T0347 # 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 T0347.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 13.9885 # # ============================================ # Comments from T0347.t04.str2.rdb # ============================================ # TARGET T0347 # 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 T0347.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 13.9885 # # ============================================ # Comments from T0347.t04.alpha.rdb # ============================================ # TARGET T0347 # 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 T0347.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 13.9885 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0695 0.0291 0.9013 2 T 0.0871 0.0731 0.8398 3 H 0.0938 0.0949 0.8113 4 I 0.0773 0.1386 0.7842 5 Y 0.0851 0.1063 0.8086 6 E 0.0903 0.0673 0.8424 7 P 0.0794 0.1420 0.7785 8 R 0.1600 0.1554 0.6846 9 L 0.4567 0.1048 0.4385 10 S 0.6596 0.0667 0.2738 11 R 0.8018 0.0320 0.1661 12 I 0.7699 0.0154 0.2147 13 A 0.6180 0.0180 0.3639 14 I 0.0629 0.7009 0.2362 15 D 0.0285 0.7357 0.2358 16 K 0.0186 0.7110 0.2704 17 L 0.1111 0.3363 0.5526 18 R 0.0899 0.1076 0.8025 19 P 0.0651 0.3519 0.5830 20 T 0.1333 0.2879 0.5788 21 Q 0.2547 0.4028 0.3425 22 I 0.3712 0.4281 0.2007 23 A 0.3697 0.4979 0.1323 24 V 0.2860 0.5207 0.1933 25 G 0.1759 0.4461 0.3780 26 F 0.0270 0.8522 0.1208 27 R 0.0200 0.8926 0.0874 28 E 0.0195 0.9129 0.0676 29 V 0.0131 0.9335 0.0533 30 E 0.0090 0.9378 0.0531 31 L 0.0083 0.9253 0.0664 32 K 0.0078 0.8984 0.0939 33 R 0.0086 0.9067 0.0847 34 K 0.0085 0.9092 0.0823 35 E 0.0090 0.9020 0.0890 36 W 0.0091 0.8932 0.0977 37 R 0.0096 0.8493 0.1411 38 E 0.0120 0.7360 0.2520 39 T 0.0316 0.5112 0.4573 40 R 0.0539 0.2849 0.6612 41 K 0.0209 0.5559 0.4231 42 K 0.0239 0.5034 0.4727 43 D 0.0395 0.5098 0.4508 44 G 0.0228 0.6661 0.3111 45 D 0.0156 0.7855 0.1989 46 D 0.0145 0.8112 0.1743 47 F 0.0190 0.8003 0.1807 48 L 0.0395 0.6491 0.3114 49 G 0.0316 0.3271 0.6413 50 N 0.0378 0.1520 0.8102 51 H 0.1139 0.0509 0.8352 52 I 0.2302 0.0136 0.7562 53 V 0.4459 0.0103 0.5438 54 P 0.5903 0.0093 0.4005 55 V 0.8202 0.0118 0.1680 56 V 0.8599 0.0067 0.1334 57 A 0.7889 0.0142 0.1969 58 G 0.3042 0.0130 0.6827 59 P 0.0617 0.0689 0.8694 60 K 0.0402 0.0484 0.9114 61 D 0.0465 0.0417 0.9118 62 R 0.2673 0.0210 0.7117 63 A 0.8241 0.0063 0.1696 64 Y 0.9021 0.0061 0.0919 65 L 0.9105 0.0074 0.0820 66 I 0.8436 0.0210 0.1355 67 D 0.4748 0.0662 0.4590 68 H 0.0796 0.2920 0.6283 69 H 0.0357 0.5280 0.4362 70 H 0.0308 0.7688 0.2004 71 L 0.0182 0.9042 0.0777 72 V 0.0095 0.9390 0.0515 73 L 0.0064 0.9420 0.0516 74 A 0.0059 0.9438 0.0503 75 L 0.0071 0.9290 0.0639 76 S 0.0092 0.9027 0.0881 77 K 0.0111 0.8393 0.1496 78 E 0.0433 0.4400 0.5168 79 G 0.0408 0.0446 0.9146 80 V 0.0927 0.0517 0.8556 81 E 0.2713 0.1035 0.6252 82 H 0.6157 0.0664 0.3179 83 V 0.6986 0.0456 0.2558 84 L 0.7653 0.0407 0.1940 85 T 0.7281 0.0993 0.1725 86 S 0.7443 0.0803 0.1754 87 E 0.7875 0.0764 0.1361 88 V 0.7272 0.1129 0.1600 89 A 0.5722 0.1406 0.2872 90 K 0.4227 0.1470 0.4303 91 F 0.1622 0.3333 0.5045 92 S 0.0710 0.3805 0.5485 93 H 0.0496 0.2995 0.6509 94 L 0.0833 0.1335 0.7832 95 G 0.0558 0.0717 0.8725 96 K 0.0288 0.5762 0.3949 97 D 0.0128 0.8062 0.1809 98 E 0.0117 0.8639 0.1243 99 F 0.0105 0.9150 0.0745 100 W 0.0079 0.9323 0.0598 101 S 0.0087 0.9295 0.0618 102 V 0.0121 0.9188 0.0691 103 M 0.0240 0.8640 0.1120 104 D 0.0190 0.7316 0.2494 105 H 0.0197 0.4611 0.5192 106 R 0.0530 0.1258 0.8212 107 N 0.0520 0.0513 0.8967 108 L 0.3124 0.0217 0.6659 109 I 0.5731 0.0149 0.4120 110 Y 0.5808 0.0156 0.4036 111 P 0.4678 0.0825 0.4497 112 F 0.3560 0.0965 0.5475 113 D 0.1563 0.0709 0.7728 114 A 0.0267 0.2241 0.7491 115 Q 0.0538 0.0968 0.8494 116 G 0.0699 0.0927 0.8374 117 L 0.1672 0.0359 0.7969 118 R 0.3172 0.0307 0.6522 119 R 0.1890 0.0395 0.7714 120 Q 0.1181 0.0532 0.8287 121 S 0.0235 0.6158 0.3607 122 G 0.0189 0.5163 0.4648 123 D 0.0306 0.5128 0.4565 124 I 0.0842 0.1207 0.7950 125 P 0.0821 0.1357 0.7821 126 K 0.0631 0.4080 0.5290 127 N 0.0828 0.3925 0.5247 128 I 0.0868 0.5573 0.3559 129 H 0.0844 0.4459 0.4696 130 D 0.0871 0.3945 0.5184 131 L 0.0702 0.3712 0.5586 132 E 0.0514 0.2829 0.6657 133 D 0.0603 0.1502 0.7895 134 D 0.0916 0.0532 0.8552 135 P 0.0110 0.6143 0.3747 136 F 0.0167 0.7304 0.2529 137 R 0.0137 0.8328 0.1535 138 S 0.0140 0.9044 0.0817 139 L 0.0093 0.9344 0.0563 140 A 0.0068 0.9522 0.0409 141 G 0.0050 0.9592 0.0359 142 A 0.0050 0.9594 0.0356 143 L 0.0059 0.9558 0.0382 144 R 0.0066 0.9437 0.0497 145 M 0.0081 0.9102 0.0817 146 A 0.0405 0.5261 0.4334 147 G 0.0322 0.0730 0.8948 148 G 0.0631 0.0733 0.8637 149 Y 0.1590 0.0936 0.7474 150 A 0.1549 0.1219 0.7232 151 K 0.1535 0.0871 0.7593 152 V 0.1591 0.0688 0.7721 153 I 0.2125 0.0498 0.7377 154 I 0.1829 0.0260 0.7911 155 P 0.1522 0.0743 0.7735 156 F 0.1026 0.4068 0.4906 157 S 0.0585 0.5784 0.3632 158 E 0.0636 0.6615 0.2749 159 F 0.0849 0.6545 0.2605 160 G 0.0748 0.6986 0.2266 161 W 0.0175 0.8803 0.1022 162 A 0.0076 0.9353 0.0571 163 D 0.0053 0.9525 0.0423 164 F 0.0054 0.9520 0.0426 165 L 0.0055 0.9409 0.0536 166 R 0.0070 0.8967 0.0963 167 R 0.0095 0.8253 0.1652 168 R 0.0200 0.6459 0.3341 169 I 0.0598 0.3546 0.5856 170 D 0.0607 0.1683 0.7710 171 R 0.0214 0.6160 0.3625 172 D 0.0162 0.6523 0.3315 173 L 0.0176 0.7009 0.2815 174 L 0.0384 0.4705 0.4912 175 S 0.0297 0.4091 0.5611 176 D 0.0126 0.4298 0.5576 177 S 0.0267 0.3938 0.5795 178 F 0.0189 0.6329 0.3482 179 D 0.0064 0.8961 0.0975 180 D 0.0048 0.9213 0.0739 181 A 0.0048 0.9356 0.0595 182 L 0.0047 0.9505 0.0448 183 A 0.0047 0.9530 0.0423 184 E 0.0048 0.9459 0.0494 185 A 0.0048 0.9444 0.0508 186 M 0.0048 0.9430 0.0522 187 K 0.0048 0.9230 0.0722 188 L 0.0051 0.8645 0.1304 189 A 0.0074 0.7698 0.2228 190 K 0.0149 0.6050 0.3802 191 S 0.0528 0.3909 0.5563 192 R 0.0066 0.6550 0.3384 193 E 0.0101 0.6027 0.3872 194 A 0.0196 0.7115 0.2689 195 R 0.0241 0.5718 0.4041 196 H 0.0351 0.3560 0.6089 197 L 0.1019 0.0590 0.8390 198 P 0.0584 0.1260 0.8156 199 G 0.1000 0.1010 0.7990 200 W 0.1815 0.1200 0.6985 201 C 0.1723 0.1101 0.7176 202 G 0.1003 0.0751 0.8246 203 V 0.0874 0.0626 0.8500 204 E 0.0769 0.0528 0.8703 205 E 0.0510 0.0409 0.9081