# This file is the result of combining several RDB files, specifically # T0632.t04.dssp-ebghstl.rdb (weight 1.53986) # T0632.t04.stride-ebghtl.rdb (weight 1.24869) # T0632.t04.str2.rdb (weight 1.54758) # T0632.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 T0632.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0632 # 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 T0632.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 T0632.t04.stride-ebghtl.rdb # ============================================ # TARGET T0632 # 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 T0632.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 T0632.t04.str2.rdb # ============================================ # TARGET T0632 # 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 T0632.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 T0632.t04.alpha.rdb # ============================================ # TARGET T0632 # 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 T0632.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 0.0529 0.2877 0.6594 2 D 0.0642 0.4515 0.4843 3 K 0.0593 0.6661 0.2746 4 R 0.0694 0.6886 0.2420 5 L 0.0772 0.6250 0.2978 6 Q 0.0630 0.5109 0.4261 7 Q 0.0419 0.5469 0.4112 8 D 0.0233 0.7302 0.2465 9 R 0.0335 0.7283 0.2382 10 I 0.0427 0.7431 0.2143 11 V 0.0515 0.7448 0.2037 12 D 0.0328 0.7814 0.1858 13 K 0.0172 0.8748 0.1080 14 M 0.0220 0.8771 0.1009 15 E 0.0194 0.8389 0.1416 16 R 0.0342 0.7947 0.1711 17 F 0.0447 0.7258 0.2295 18 L 0.0391 0.6184 0.3425 19 S 0.0480 0.5179 0.4341 20 T 0.0613 0.2423 0.6963 21 A 0.0380 0.3200 0.6420 22 N 0.0430 0.2899 0.6671 23 E 0.0205 0.6921 0.2873 24 E 0.0236 0.7341 0.2423 25 E 0.0260 0.7603 0.2137 26 K 0.0251 0.7929 0.1821 27 D 0.0280 0.7451 0.2269 28 V 0.0241 0.7718 0.2042 29 L 0.0301 0.7199 0.2501 30 S 0.0162 0.7810 0.2028 31 S 0.0162 0.7700 0.2137 32 I 0.0171 0.7959 0.1870 33 V 0.0185 0.7925 0.1890 34 D 0.0147 0.8069 0.1783 35 G 0.0089 0.8860 0.1051 36 L 0.0090 0.9146 0.0764 37 L 0.0094 0.9112 0.0794 38 A 0.0095 0.9061 0.0845 39 K 0.0101 0.9016 0.0884 40 Q 0.0090 0.8819 0.1091 41 E 0.0102 0.8552 0.1346 42 R 0.0150 0.8247 0.1603 43 R 0.0220 0.7467 0.2314 44 Y 0.0287 0.6852 0.2860 45 A 0.0307 0.6812 0.2881 46 T 0.0384 0.6630 0.2985 47 Y 0.0217 0.7709 0.2075 48 L 0.0212 0.8268 0.1521 49 A 0.0334 0.7659 0.2007 50 S 0.0380 0.6951 0.2668 51 L 0.0659 0.5873 0.3468 52 T 0.1265 0.2350 0.6385 53 Q 0.2282 0.0476 0.7242 54 I 0.5407 0.0124 0.4470 55 E 0.8138 0.0079 0.1783 56 S 0.8781 0.0052 0.1167 57 Q 0.8494 0.0110 0.1395 58 E 0.8732 0.0053 0.1215 59 R 0.7342 0.0180 0.2478 60 E 0.4724 0.0260 0.5016 61 D 0.0776 0.0470 0.8754 62 G 0.0767 0.0337 0.8897 63 R 0.7847 0.0084 0.2070 64 F 0.9168 0.0035 0.0798 65 E 0.9282 0.0038 0.0679 66 V 0.9259 0.0035 0.0706 67 R 0.9124 0.0035 0.0842 68 L 0.8108 0.0053 0.1839 69 P 0.6035 0.0057 0.3908 70 I 0.2521 0.0493 0.6986 71 G 0.0969 0.0961 0.8070 72 P 0.0365 0.4683 0.4952 73 L 0.0634 0.4673 0.4693 74 V 0.1701 0.3654 0.4645 75 N 0.1653 0.2096 0.6251 76 N 0.0961 0.0580 0.8459 77 P 0.0537 0.1635 0.7828 78 L 0.0596 0.1641 0.7762 79 N 0.1050 0.1428 0.7522 80 M 0.2896 0.1811 0.5293 81 V 0.3921 0.1728 0.4351 82 H 0.1940 0.3772 0.4289 83 G 0.0457 0.7221 0.2322 84 G 0.0104 0.9168 0.0728 85 I 0.0066 0.9477 0.0457 86 T 0.0051 0.9559 0.0390 87 A 0.0047 0.9590 0.0363 88 T 0.0047 0.9592 0.0361 89 L 0.0047 0.9574 0.0379 90 L 0.0047 0.9570 0.0383 91 D 0.0047 0.9582 0.0371 92 T 0.0047 0.9585 0.0368 93 A 0.0047 0.9561 0.0392 94 M 0.0047 0.9578 0.0375 95 G 0.0047 0.9598 0.0356 96 Q 0.0047 0.9585 0.0368 97 M 0.0048 0.9549 0.0403 98 V 0.0054 0.9379 0.0567 99 N 0.0082 0.8913 0.1006 100 R 0.0207 0.7545 0.2249 101 Q 0.0528 0.4113 0.5359 102 L 0.0749 0.0273 0.8978 103 P 0.0510 0.0309 0.9180 104 D 0.0229 0.0739 0.9032 105 G 0.0273 0.0506 0.9221 106 Q 0.2124 0.0286 0.7590 107 S 0.5789 0.0136 0.4076 108 A 0.7633 0.0139 0.2229 109 V 0.8246 0.0115 0.1638 110 T 0.8270 0.0135 0.1595 111 S 0.7941 0.0249 0.1809 112 E 0.8502 0.0159 0.1339 113 L 0.8510 0.0110 0.1380 114 N 0.8259 0.0070 0.1671 115 I 0.7548 0.0146 0.2307 116 H 0.7235 0.0475 0.2289 117 Y 0.7788 0.0214 0.1999 118 V 0.6838 0.0219 0.2943 119 K 0.5251 0.0211 0.4538 120 P 0.2831 0.0493 0.6676 121 G 0.1581 0.0413 0.8007 122 M 0.1024 0.0616 0.8360 123 G 0.0710 0.0524 0.8765 124 T 0.2313 0.0291 0.7396 125 Y 0.7814 0.0061 0.2126 126 L 0.9020 0.0036 0.0944 127 R 0.9293 0.0032 0.0675 128 A 0.9175 0.0039 0.0786 129 V 0.9143 0.0038 0.0819 130 A 0.9109 0.0044 0.0847 131 S 0.9159 0.0044 0.0797 132 I 0.9272 0.0031 0.0697 133 V 0.8471 0.0166 0.1363 134 H 0.7784 0.0119 0.2097 135 Q 0.3090 0.0375 0.6535 136 G 0.1451 0.0291 0.8258 137 K 0.5158 0.0188 0.4655 138 Q 0.8240 0.0064 0.1696 139 R 0.8918 0.0053 0.1029 140 I 0.9221 0.0035 0.0743 141 V 0.9311 0.0030 0.0658 142 V 0.9223 0.0040 0.0736 143 E 0.9217 0.0033 0.0750 144 G 0.9177 0.0035 0.0787 145 K 0.9267 0.0035 0.0698 146 V 0.9281 0.0035 0.0685 147 Y 0.9025 0.0076 0.0899 148 T 0.5229 0.0146 0.4625 149 D 0.0293 0.1102 0.8605 150 Q 0.0460 0.0252 0.9288 151 G 0.0589 0.0273 0.9137 152 E 0.2525 0.0084 0.7391 153 T 0.8866 0.0032 0.1102 154 V 0.9088 0.0071 0.0842 155 A 0.9218 0.0041 0.0742 156 M 0.9184 0.0053 0.0763 157 G 0.9035 0.0060 0.0905 158 T 0.8805 0.0168 0.1027 159 G 0.8741 0.0080 0.1179 160 S 0.8611 0.0160 0.1229 161 F 0.8902 0.0104 0.0994 162 F 0.8799 0.0114 0.1088 163 V 0.8637 0.0135 0.1228 164 L 0.6525 0.0290 0.3185 165 R 0.3061 0.0459 0.6480 166 S 0.1176 0.0889 0.7935 167 R 0.0743 0.0590 0.8666 168 G 0.0454 0.0308 0.9238