# This file is the result of combining several RDB files, specifically # T0507.t04.dssp-ebghstl.rdb (weight 1.53986) # T0507.t04.stride-ebghtl.rdb (weight 1.24869) # T0507.t04.str2.rdb (weight 1.54758) # T0507.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 T0507.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0507 # 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 T0507.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 2067 # # ============================================ # Comments from T0507.t04.stride-ebghtl.rdb # ============================================ # TARGET T0507 # 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 T0507.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 2067 # # ============================================ # Comments from T0507.t04.str2.rdb # ============================================ # TARGET T0507 # 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 T0507.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 2067 # # ============================================ # Comments from T0507.t04.alpha.rdb # ============================================ # TARGET T0507 # 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 T0507.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 2067 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1491 0.0075 0.8434 2 K 0.7648 0.0067 0.2284 3 V 0.8916 0.0040 0.1043 4 A 0.9111 0.0042 0.0847 5 L 0.8338 0.0178 0.1485 6 G 0.5236 0.0285 0.4479 7 G 0.2601 0.0294 0.7105 8 T 0.2299 0.0434 0.7267 9 F 0.1871 0.0666 0.7464 10 E 0.0908 0.0931 0.8160 11 P 0.0405 0.3639 0.5956 12 L 0.0454 0.3563 0.5983 13 H 0.0422 0.5545 0.4033 14 E 0.0083 0.8435 0.1483 15 G 0.0065 0.8908 0.1027 16 H 0.0055 0.9395 0.0550 17 K 0.0047 0.9572 0.0381 18 K 0.0047 0.9600 0.0353 19 L 0.0047 0.9603 0.0350 20 I 0.0047 0.9609 0.0345 21 D 0.0046 0.9616 0.0337 22 V 0.0047 0.9608 0.0346 23 A 0.0047 0.9587 0.0366 24 I 0.0050 0.9531 0.0419 25 K 0.0062 0.9136 0.0801 26 L 0.0220 0.6986 0.2794 27 G 0.0522 0.2327 0.7151 28 G 0.0461 0.0982 0.8557 29 R 0.0698 0.0602 0.8700 30 D 0.0932 0.0685 0.8384 31 I 0.7168 0.0089 0.2742 32 T 0.9114 0.0032 0.0854 33 I 0.9230 0.0050 0.0720 34 G 0.9060 0.0050 0.0890 35 V 0.8321 0.0073 0.1606 36 T 0.5369 0.0145 0.4487 37 S 0.1558 0.0295 0.8147 38 D 0.0815 0.0927 0.8258 39 R 0.0280 0.5289 0.4432 40 M 0.0263 0.6571 0.3166 41 A 0.0279 0.7615 0.2106 42 R 0.0406 0.7290 0.2304 43 A 0.0500 0.6712 0.2788 44 R 0.0678 0.5534 0.3788 45 I 0.0860 0.3017 0.6124 46 R 0.0933 0.1084 0.7983 47 S 0.0909 0.0984 0.8107 48 V 0.1281 0.0562 0.8158 49 L 0.1146 0.0168 0.8685 50 P 0.0705 0.0224 0.9071 51 F 0.0050 0.9478 0.0472 52 A 0.0047 0.9611 0.0342 53 I 0.0047 0.9600 0.0353 54 R 0.0047 0.9603 0.0350 55 A 0.0047 0.9605 0.0348 56 E 0.0047 0.9607 0.0346 57 N 0.0047 0.9605 0.0349 58 V 0.0047 0.9595 0.0358 59 K 0.0047 0.9596 0.0357 60 R 0.0049 0.9551 0.0400 61 Y 0.0052 0.9406 0.0542 62 V 0.0075 0.8885 0.1040 63 M 0.0131 0.7250 0.2620 64 R 0.0280 0.4008 0.5712 65 K 0.0694 0.1581 0.7724 66 Y 0.0554 0.1205 0.8241 67 G 0.1683 0.0584 0.7732 68 F 0.5532 0.0119 0.4349 69 E 0.7592 0.0069 0.2340 70 P 0.7605 0.0061 0.2334 71 E 0.6996 0.0172 0.2832 72 I 0.6720 0.0271 0.3009 73 V 0.5483 0.0371 0.4146 74 K 0.4436 0.0419 0.5145 75 I 0.2688 0.0666 0.6647 76 T 0.1901 0.0649 0.7450 77 N 0.1240 0.0286 0.8474 78 P 0.0884 0.1555 0.7562 79 Y 0.0974 0.3596 0.5431 80 G 0.0976 0.3954 0.5070 81 K 0.1243 0.4819 0.3939 82 T 0.1843 0.4790 0.3366 83 L 0.1661 0.4648 0.3690 84 D 0.2029 0.3024 0.4948 85 V 0.1932 0.1222 0.6847 86 D 0.1729 0.0196 0.8075 87 F 0.1889 0.0320 0.7790 88 E 0.3252 0.0596 0.6153 89 Y 0.9020 0.0087 0.0892 90 L 0.9301 0.0033 0.0666 91 V 0.9256 0.0034 0.0710 92 V 0.8242 0.0118 0.1640 93 S 0.2128 0.0119 0.7753 94 P 0.0256 0.2508 0.7235 95 E 0.0280 0.3391 0.6329 96 T 0.0414 0.5255 0.4331 97 Y 0.0397 0.6423 0.3180 98 E 0.0327 0.7251 0.2421 99 M 0.0331 0.7858 0.1811 100 A 0.0185 0.8741 0.1073 101 L 0.0180 0.8802 0.1018 102 K 0.0169 0.8913 0.0918 103 I 0.0141 0.8833 0.1026 104 N 0.0215 0.7633 0.2152 105 Q 0.0288 0.8020 0.1692 106 K 0.0120 0.8954 0.0926 107 R 0.0100 0.9231 0.0668 108 E 0.0092 0.9214 0.0694 109 E 0.0101 0.8946 0.0953 110 L 0.0305 0.7140 0.2555 111 G 0.0213 0.4383 0.5404 112 K 0.0386 0.2912 0.6702 113 R 0.1028 0.1147 0.7825 114 K 0.1349 0.0488 0.8163 115 I 0.4415 0.0183 0.5402 116 T 0.7779 0.0104 0.2117 117 I 0.9005 0.0055 0.0940 118 V 0.9069 0.0047 0.0884 119 K 0.8927 0.0044 0.1029 120 V 0.7766 0.0108 0.2126 121 D 0.5428 0.0247 0.4325 122 W 0.3702 0.0767 0.5531 123 M 0.3778 0.0742 0.5479 124 M 0.3373 0.0986 0.5641 125 A 0.1508 0.1121 0.7371 126 E 0.0767 0.1551 0.7682 127 D 0.0691 0.0791 0.8518 128 G 0.0639 0.0454 0.8907 129 K 0.1182 0.0241 0.8577 130 P 0.3830 0.0324 0.5846 131 I 0.4929 0.0496 0.4574 132 S 0.5035 0.0603 0.4361 133 S 0.2657 0.4119 0.3224 134 T 0.1030 0.6927 0.2043 135 R 0.0717 0.8008 0.1275 136 I 0.0661 0.8442 0.0897 137 K 0.0607 0.8496 0.0897 138 R 0.0463 0.8700 0.0837 139 G 0.0369 0.8523 0.1108 140 E 0.0288 0.8461 0.1251 141 I 0.0274 0.8270 0.1456 142 D 0.0399 0.6288 0.3313 143 R 0.0310 0.2537 0.7154 144 Y 0.0557 0.0805 0.8638 145 G 0.0459 0.0743 0.8798 146 G 0.0633 0.0585 0.8782 147 I 0.1243 0.0304 0.8454 148 I 0.0945 0.0231 0.8824