# This file is the result of combining several RDB files, specifically # T0332.t04.dssp-ebghstl.rdb (weight 1.53986) # T0332.t04.stride-ebghtl.rdb (weight 1.24869) # T0332.t04.str2.rdb (weight 1.54758) # T0332.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 T0332.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0332 # 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 T0332.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 1414 # # ============================================ # Comments from T0332.t04.stride-ebghtl.rdb # ============================================ # TARGET T0332 # 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 T0332.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 1414 # # ============================================ # Comments from T0332.t04.str2.rdb # ============================================ # TARGET T0332 # 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 T0332.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 1414 # # ============================================ # Comments from T0332.t04.alpha.rdb # ============================================ # TARGET T0332 # 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 T0332.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 1414 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 L 0.0692 0.0685 0.8623 2 G 0.0593 0.0749 0.8658 3 K 0.0611 0.1473 0.7916 4 S 0.0679 0.1733 0.7588 5 I 0.1142 0.1590 0.7268 6 S 0.1377 0.0641 0.7982 7 R 0.2969 0.0316 0.6714 8 L 0.8142 0.0045 0.1814 9 I 0.9269 0.0034 0.0697 10 V 0.9327 0.0032 0.0641 11 V 0.9274 0.0038 0.0689 12 A 0.8966 0.0056 0.0978 13 S 0.6719 0.0352 0.2929 14 L 0.3427 0.0271 0.6302 15 I 0.1858 0.0595 0.7547 16 D 0.1116 0.0797 0.8088 17 K 0.0820 0.0484 0.8696 18 P 0.0415 0.2487 0.7098 19 T 0.0506 0.3732 0.5762 20 N 0.0330 0.7091 0.2580 21 L 0.0065 0.9210 0.0725 22 G 0.0050 0.9515 0.0435 23 G 0.0047 0.9579 0.0373 24 L 0.0047 0.9590 0.0363 25 C 0.0047 0.9603 0.0350 26 R 0.0047 0.9591 0.0362 27 T 0.0047 0.9592 0.0362 28 C 0.0047 0.9576 0.0377 29 E 0.0048 0.9459 0.0492 30 V 0.0053 0.9150 0.0797 31 F 0.0422 0.4162 0.5415 32 G 0.0601 0.0150 0.9250 33 A 0.0968 0.0143 0.8889 34 S 0.1732 0.0550 0.7718 35 V 0.8476 0.0116 0.1408 36 L 0.9242 0.0045 0.0714 37 V 0.9284 0.0040 0.0676 38 V 0.8802 0.0056 0.1142 39 G 0.4724 0.0151 0.5125 40 S 0.2129 0.0331 0.7540 41 L 0.0841 0.1451 0.7708 42 Q 0.0844 0.1314 0.7842 43 C 0.0963 0.0862 0.8175 44 I 0.0740 0.0822 0.8438 45 S 0.0749 0.0843 0.8408 46 D 0.0760 0.1391 0.7849 47 K 0.0076 0.8282 0.1641 48 Q 0.0127 0.8605 0.1268 49 F 0.0221 0.8940 0.0840 50 Q 0.0346 0.8879 0.0775 51 H 0.0478 0.8691 0.0830 52 L 0.0432 0.8186 0.1382 53 S 0.0675 0.6975 0.2351 54 V 0.0681 0.5665 0.3654 55 S 0.0914 0.3650 0.5436 56 A 0.0476 0.6597 0.2927 57 E 0.0387 0.7128 0.2485 58 Q 0.0734 0.6308 0.2959 59 W 0.1791 0.4240 0.3969 60 L 0.3413 0.0701 0.5886 61 P 0.4020 0.0593 0.5386 62 L 0.6483 0.1114 0.2402 63 V 0.7316 0.0744 0.1940 64 E 0.7726 0.0356 0.1918 65 V 0.5820 0.0165 0.4015 66 K 0.1994 0.0190 0.7816 67 P 0.0558 0.3816 0.5626 68 P 0.0165 0.5046 0.4789 69 Q 0.0331 0.4909 0.4760 70 L 0.0050 0.9442 0.0508 71 I 0.0048 0.9548 0.0404 72 D 0.0047 0.9567 0.0386 73 Y 0.0050 0.9557 0.0393 74 L 0.0048 0.9537 0.0415 75 Q 0.0051 0.9319 0.0631 76 Q 0.0063 0.8851 0.1086 77 K 0.0131 0.8361 0.1508 78 K 0.0135 0.7489 0.2376 79 T 0.0148 0.6418 0.3434 80 E 0.0387 0.2576 0.7037 81 G 0.0392 0.0224 0.9384 82 Y 0.2434 0.0071 0.7495 83 T 0.8182 0.0047 0.1772 84 I 0.9165 0.0032 0.0803 85 I 0.8947 0.0071 0.0982 86 G 0.8620 0.0052 0.1328 87 V 0.6812 0.0156 0.3032 88 E 0.4018 0.0195 0.5786 89 Q 0.1521 0.1114 0.7365 90 T 0.0961 0.1719 0.7320 91 A 0.0529 0.3812 0.5659 92 K 0.0566 0.2641 0.6793 93 S 0.1200 0.1681 0.7119 94 L 0.2137 0.0478 0.7385 95 D 0.2141 0.0341 0.7518 96 L 0.0631 0.5878 0.3490 97 T 0.0531 0.6199 0.3270 98 Q 0.0759 0.6479 0.2762 99 Y 0.1912 0.2758 0.5330 100 C 0.1906 0.1117 0.6977 101 F 0.1144 0.0389 0.8467 102 P 0.0806 0.0514 0.8681 103 E 0.0675 0.0757 0.8567 104 K 0.1229 0.0455 0.8316 105 S 0.6336 0.0119 0.3545 106 L 0.9247 0.0035 0.0718 107 L 0.9325 0.0032 0.0643 108 L 0.9287 0.0033 0.0680 109 L 0.8408 0.0154 0.1438 110 G 0.3914 0.0157 0.5929 111 N 0.1730 0.0395 0.7875 112 E 0.0869 0.1778 0.7353 113 R 0.0626 0.2525 0.6849 114 E 0.0440 0.2181 0.7380 115 G 0.0409 0.1143 0.8448 116 I 0.0851 0.0161 0.8988 117 P 0.0682 0.0444 0.8874 118 A 0.0051 0.9331 0.0618 119 N 0.0048 0.9505 0.0447 120 L 0.0055 0.9426 0.0519 121 I 0.0074 0.9344 0.0582 122 Q 0.0106 0.8689 0.1205 123 Q 0.0220 0.5012 0.4769 124 L 0.0766 0.1737 0.7497 125 D 0.0798 0.1141 0.8061 126 V 0.6363 0.0484 0.3153 127 C 0.8937 0.0121 0.0942 128 V 0.9136 0.0078 0.0787 129 E 0.8815 0.0071 0.1115 130 I 0.6657 0.0120 0.3223 131 P 0.3503 0.0258 0.6239 132 Q 0.1601 0.0509 0.7890 133 Q 0.0839 0.1349 0.7812 134 G 0.0599 0.1170 0.8231 135 I 0.1458 0.1609 0.6932 136 I 0.2588 0.1907 0.5504 137 R 0.2197 0.2588 0.5215 138 S 0.2700 0.3420 0.3880 139 L 0.1259 0.6520 0.2221 140 N 0.0342 0.8343 0.1315 141 V 0.0055 0.9530 0.0415 142 H 0.0047 0.9596 0.0357 143 V 0.0047 0.9600 0.0353 144 S 0.0047 0.9608 0.0345 145 G 0.0046 0.9612 0.0342 146 A 0.0046 0.9614 0.0339 147 L 0.0046 0.9616 0.0338 148 L 0.0046 0.9616 0.0338 149 I 0.0046 0.9616 0.0338 150 W 0.0046 0.9615 0.0338 151 E 0.0046 0.9612 0.0341 152 Y 0.0047 0.9590 0.0364 153 T 0.0048 0.9540 0.0412 154 R 0.0050 0.9415 0.0534 155 Q 0.0076 0.9050 0.0874 156 Q 0.0136 0.8061 0.1804 157 L 0.0267 0.4906 0.4826 158 L 0.0448 0.1254 0.8298 159 S 0.0397 0.0426 0.9176