# This file is the result of combining several RDB files, specifically # T0578.t04.dssp-ebghstl.rdb (weight 1.53986) # T0578.t04.stride-ebghtl.rdb (weight 1.24869) # T0578.t04.str2.rdb (weight 1.54758) # T0578.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 T0578.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0578 # 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 T0578.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 7.82799 # # ============================================ # Comments from T0578.t04.stride-ebghtl.rdb # ============================================ # TARGET T0578 # 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 T0578.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 7.82799 # # ============================================ # Comments from T0578.t04.str2.rdb # ============================================ # TARGET T0578 # 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 T0578.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 7.82799 # # ============================================ # Comments from T0578.t04.alpha.rdb # ============================================ # TARGET T0578 # 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 T0578.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 7.82799 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.0192 0.6007 0.3802 2 N 0.0164 0.7860 0.1975 3 A 0.0123 0.8936 0.0941 4 M 0.0090 0.9193 0.0717 5 K 0.0094 0.9009 0.0896 6 K 0.0073 0.8873 0.1055 7 A 0.0201 0.8072 0.1727 8 T 0.0176 0.6430 0.3394 9 M 0.0067 0.8815 0.1117 10 L 0.0050 0.9413 0.0536 11 T 0.0047 0.9536 0.0417 12 Y 0.0047 0.9572 0.0381 13 L 0.0048 0.9536 0.0416 14 E 0.0047 0.9587 0.0366 15 E 0.0048 0.9570 0.0382 16 Q 0.0050 0.9511 0.0439 17 L 0.0053 0.9400 0.0547 18 E 0.0054 0.9028 0.0918 19 K 0.0071 0.8028 0.1901 20 H 0.0182 0.5868 0.3950 21 L 0.0677 0.2097 0.7227 22 G 0.0493 0.1160 0.8347 23 D 0.0841 0.1178 0.7981 24 Y 0.2203 0.0980 0.6817 25 E 0.4308 0.0632 0.5060 26 V 0.6816 0.0335 0.2850 27 G 0.7582 0.0173 0.2245 28 L 0.6906 0.0207 0.2886 29 D 0.5445 0.0193 0.4361 30 W 0.2569 0.1319 0.6112 31 D 0.2029 0.1233 0.6738 32 R 0.0903 0.2983 0.6113 33 K 0.1235 0.1793 0.6971 34 N 0.1545 0.0840 0.7615 35 H 0.4190 0.0321 0.5489 36 T 0.8274 0.0051 0.1675 37 I 0.9155 0.0036 0.0809 38 E 0.9289 0.0034 0.0677 39 V 0.9298 0.0032 0.0670 40 I 0.9308 0.0032 0.0660 41 V 0.9316 0.0033 0.0651 42 R 0.9296 0.0035 0.0669 43 L 0.9188 0.0042 0.0770 44 Y 0.9100 0.0046 0.0855 45 A 0.8704 0.0091 0.1205 46 E 0.6922 0.0378 0.2700 47 N 0.3380 0.0267 0.6352 48 N 0.1062 0.0860 0.8078 49 E 0.1493 0.1033 0.7475 50 Q 0.4899 0.0600 0.4501 51 V 0.7416 0.0113 0.2471 52 A 0.8550 0.0071 0.1379 53 I 0.8802 0.0082 0.1116 54 D 0.8363 0.0097 0.1540 55 D 0.5278 0.0387 0.4335 56 V 0.1395 0.1320 0.7284 57 D 0.0817 0.0461 0.8722 58 G 0.1130 0.0372 0.8498 59 T 0.3329 0.0225 0.6446 60 L 0.5433 0.0143 0.4424 61 S 0.2342 0.0225 0.7434 62 E 0.0866 0.4078 0.5055 63 E 0.0684 0.5222 0.4094 64 E 0.0900 0.4765 0.4335 65 F 0.4073 0.2432 0.3495 66 I 0.6931 0.0804 0.2265 67 E 0.7462 0.0662 0.1876 68 F 0.5940 0.1444 0.2616 69 E 0.4938 0.1220 0.3842 70 D 0.4464 0.1044 0.4492 71 G 0.6823 0.0418 0.2758 72 L 0.8628 0.0207 0.1165 73 L 0.9078 0.0114 0.0808 74 F 0.9000 0.0069 0.0932 75 Y 0.8068 0.0137 0.1795 76 N 0.2769 0.0115 0.7115 77 P 0.0165 0.1420 0.8415 78 Q 0.0250 0.1368 0.8382 79 K 0.0953 0.1835 0.7212 80 S 0.1756 0.0863 0.7381 81 V 0.3347 0.0744 0.5909 82 V 0.2567 0.0504 0.6929 83 D 0.1500 0.0429 0.8071 84 D 0.0378 0.5595 0.4027 85 E 0.0287 0.5908 0.3806 86 E 0.0727 0.4805 0.4468 87 Y 0.4000 0.2329 0.3670 88 L 0.6564 0.1216 0.2220 89 V 0.7761 0.0785 0.1454 90 T 0.8036 0.0481 0.1483 91 I 0.6536 0.0324 0.3140 92 P 0.3895 0.0390 0.5714 93 Y 0.1957 0.0813 0.7230 94 E 0.0948 0.1272 0.7780 95 G 0.0421 0.1726 0.7853 96 K 0.0537 0.3142 0.6321 97 K 0.0513 0.4011 0.5475 98 G 0.0471 0.4897 0.4633 99 L 0.0752 0.5819 0.3428 100 R 0.0466 0.7811 0.1723 101 K 0.0057 0.9441 0.0503 102 A 0.0051 0.9512 0.0436 103 V 0.0047 0.9561 0.0392 104 L 0.0047 0.9591 0.0362 105 D 0.0047 0.9608 0.0345 106 G 0.0047 0.9603 0.0350 107 F 0.0047 0.9599 0.0354 108 I 0.0047 0.9609 0.0345 109 H 0.0047 0.9611 0.0342 110 Y 0.0047 0.9582 0.0372 111 L 0.0047 0.9571 0.0382 112 K 0.0047 0.9602 0.0351 113 V 0.0047 0.9600 0.0353 114 V 0.0047 0.9564 0.0389 115 L 0.0052 0.9464 0.0484 116 D 0.0078 0.8932 0.0990 117 E 0.0380 0.5789 0.3831 118 G 0.0330 0.2104 0.7566 119 Q 0.0359 0.4143 0.5498 120 S 0.0337 0.6319 0.3344 121 D 0.0245 0.7380 0.2375 122 L 0.0105 0.8870 0.1024 123 L 0.0067 0.9101 0.0832 124 D 0.0059 0.9004 0.0936 125 F 0.0093 0.8486 0.1421 126 L 0.0357 0.6109 0.3533 127 S 0.0582 0.3079 0.6339 128 D 0.0456 0.1115 0.8429 129 E 0.0208 0.2275 0.7517 130 T 0.0488 0.1779 0.7733 131 A 0.1310 0.1505 0.7185 132 E 0.3143 0.0748 0.6108 133 V 0.7816 0.0265 0.1919 134 F 0.8539 0.0078 0.1383 135 E 0.8858 0.0081 0.1061 136 L 0.8573 0.0085 0.1342 137 H 0.6629 0.0098 0.3272 138 W 0.3772 0.0111 0.6117 139 E 0.1036 0.0080 0.8883 140 P 0.0065 0.8830 0.1105 141 A 0.0048 0.9330 0.0622 142 D 0.0053 0.9405 0.0541 143 F 0.0056 0.9508 0.0436 144 E 0.0052 0.9587 0.0361 145 A 0.0049 0.9588 0.0363 146 M 0.0052 0.9546 0.0401 147 I 0.0052 0.9514 0.0434 148 K 0.0058 0.9381 0.0562 149 K 0.0075 0.8973 0.0952 150 V 0.0168 0.8180 0.1651 151 A 0.0271 0.7317 0.2412 152 E 0.0280 0.7140 0.2581 153 T 0.0337 0.5246 0.4417 154 E 0.0376 0.4044 0.5580 155 K 0.0266 0.4356 0.5378 156 E 0.0497 0.4122 0.5381 157 Q 0.1395 0.3292 0.5313 158 W 0.2905 0.1974 0.5121 159 I 0.3315 0.0848 0.5837 160 A 0.2773 0.0682 0.6545 161 Y 0.1459 0.0339 0.8202 162 P 0.1033 0.0643 0.8323 163 S 0.1009 0.0937 0.8054 164 Y 0.0988 0.0723 0.8290