# This file is the result of combining several RDB files, specifically # T0297.t06.dssp-ebghstl.rdb (weight 1.53986) # T0297.t06.stride-ebghtl.rdb (weight 1.24869) # T0297.t06.str2.rdb (weight 1.54758) # T0297.t06.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 T0297.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0297 # 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 T0297.t06-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 1705 # # ============================================ # Comments from T0297.t06.stride-ebghtl.rdb # ============================================ # TARGET T0297 # Using neural net t06-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 T0297.t06-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 1705 # # ============================================ # Comments from T0297.t06.str2.rdb # ============================================ # TARGET T0297 # Using neural net t06-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 T0297.t06-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 1705 # # ============================================ # Comments from T0297.t06.alpha.rdb # ============================================ # TARGET T0297 # Using neural net t06-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 T0297.t06-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 1705 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0876 0.0834 0.8290 2 A 0.1615 0.1335 0.7050 3 V 0.2021 0.2882 0.5097 4 Q 0.2221 0.3841 0.3938 5 L 0.1944 0.5087 0.2968 6 L 0.1667 0.4985 0.3348 7 E 0.1172 0.5842 0.2986 8 N 0.0907 0.6218 0.2875 9 W 0.1279 0.5789 0.2932 10 L 0.2278 0.4720 0.3003 11 L 0.2512 0.3680 0.3809 12 K 0.1747 0.3059 0.5194 13 E 0.1017 0.5222 0.3761 14 Q 0.1386 0.5344 0.3271 15 E 0.2038 0.4876 0.3086 16 K 0.3265 0.4479 0.2256 17 I 0.3859 0.4092 0.2049 18 Q 0.3682 0.4000 0.2317 19 T 0.4282 0.3458 0.2259 20 K 0.4080 0.3491 0.2429 21 Y 0.3313 0.3757 0.2930 22 R 0.2964 0.3619 0.3417 23 H 0.3134 0.3411 0.3455 24 L 0.2663 0.2912 0.4425 25 N 0.2333 0.1980 0.5688 26 H 0.1921 0.1715 0.6364 27 I 0.1604 0.1606 0.6790 28 S 0.1338 0.1293 0.7369 29 V 0.1022 0.1452 0.7526 30 V 0.1049 0.0721 0.8231 31 E 0.0984 0.0247 0.8769 32 P 0.1412 0.0232 0.8356 33 N 0.5645 0.0219 0.4135 34 I 0.9182 0.0035 0.0783 35 L 0.9284 0.0033 0.0683 36 F 0.9212 0.0046 0.0742 37 I 0.7766 0.0315 0.1919 38 G 0.2827 0.0355 0.6817 39 D 0.1244 0.1291 0.7465 40 S 0.1274 0.3245 0.5480 41 I 0.0812 0.6144 0.3044 42 V 0.0842 0.6555 0.2603 43 E 0.0936 0.5373 0.3691 44 Y 0.0824 0.4149 0.5027 45 Y 0.0968 0.1913 0.7119 46 P 0.1020 0.1815 0.7165 47 L 0.0623 0.4774 0.4603 48 Q 0.0567 0.6042 0.3391 49 E 0.0516 0.6526 0.2958 50 L 0.0753 0.5454 0.3793 51 F 0.0984 0.2959 0.6057 52 G 0.0662 0.1393 0.7945 53 T 0.0763 0.0922 0.8315 54 S 0.0974 0.0788 0.8238 55 K 0.2243 0.1042 0.6715 56 T 0.5589 0.0835 0.3575 57 I 0.7914 0.0627 0.1459 58 V 0.7977 0.0583 0.1440 59 N 0.7408 0.0770 0.1822 60 R 0.5665 0.1070 0.3265 61 G 0.4481 0.1006 0.4513 62 I 0.3739 0.1274 0.4987 63 R 0.1939 0.1765 0.6295 64 G 0.0945 0.1920 0.7135 65 Y 0.0971 0.3199 0.5829 66 Q 0.1233 0.3872 0.4895 67 T 0.0615 0.6299 0.3086 68 G 0.0261 0.7420 0.2320 69 L 0.0299 0.7734 0.1967 70 L 0.0201 0.8435 0.1364 71 L 0.0107 0.8960 0.0932 72 E 0.0072 0.9000 0.0928 73 N 0.0070 0.8881 0.1049 74 L 0.0107 0.8812 0.1081 75 D 0.0092 0.8822 0.1086 76 A 0.0097 0.8609 0.1294 77 H 0.0123 0.8275 0.1602 78 L 0.0374 0.6827 0.2799 79 Y 0.0325 0.4490 0.5185 80 G 0.0355 0.1623 0.8022 81 G 0.0494 0.0841 0.8665 82 A 0.0899 0.0474 0.8627 83 V 0.1356 0.0343 0.8301 84 D 0.1783 0.0574 0.7643 85 K 0.8966 0.0044 0.0990 86 I 0.9309 0.0032 0.0659 87 F 0.9337 0.0031 0.0632 88 L 0.9264 0.0040 0.0696 89 L 0.8912 0.0048 0.1040 90 I 0.6423 0.0298 0.3278 91 G 0.3188 0.0318 0.6494 92 T 0.2084 0.1548 0.6368 93 N 0.1283 0.2834 0.5883 94 D 0.0984 0.3590 0.5425 95 I 0.0654 0.2979 0.6366 96 G 0.0520 0.1808 0.7672 97 K 0.0479 0.1137 0.8384 98 D 0.0627 0.0686 0.8687 99 V 0.0994 0.0197 0.8809 100 P 0.0973 0.0199 0.8828 101 V 0.0055 0.9311 0.0633 102 N 0.0047 0.9563 0.0389 103 E 0.0048 0.9546 0.0406 104 A 0.0047 0.9561 0.0392 105 L 0.0047 0.9542 0.0411 106 N 0.0048 0.9408 0.0544 107 N 0.0048 0.9355 0.0597 108 L 0.0047 0.9572 0.0381 109 E 0.0046 0.9611 0.0343 110 A 0.0046 0.9609 0.0345 111 I 0.0046 0.9612 0.0341 112 I 0.0047 0.9609 0.0344 113 Q 0.0047 0.9603 0.0351 114 S 0.0047 0.9580 0.0373 115 V 0.0050 0.9484 0.0467 116 A 0.0057 0.9290 0.0654 117 R 0.0081 0.8125 0.1794 118 D 0.0183 0.5553 0.4264 119 Y 0.0776 0.0554 0.8670 120 P 0.0192 0.1257 0.8551 121 L 0.0350 0.0789 0.8861 122 T 0.2521 0.0177 0.7302 123 E 0.6000 0.0055 0.3945 124 I 0.9175 0.0033 0.0793 125 K 0.9251 0.0036 0.0713 126 L 0.9267 0.0032 0.0701 127 L 0.8628 0.0153 0.1219 128 S 0.7223 0.0084 0.2694 129 I 0.4052 0.0230 0.5718 130 L 0.2247 0.0296 0.7457 131 P 0.1524 0.0482 0.7994 132 V 0.0535 0.3554 0.5911 133 N 0.0549 0.3254 0.6197 134 E 0.0601 0.3697 0.5702 135 R 0.0712 0.3719 0.5570 136 E 0.0303 0.7020 0.2677 137 E 0.0332 0.7392 0.2276 138 Y 0.0432 0.7300 0.2268 139 Q 0.0475 0.6887 0.2638 140 Q 0.0370 0.7542 0.2088 141 A 0.0407 0.7513 0.2080 142 V 0.0566 0.7397 0.2037 143 Y 0.0853 0.6949 0.2197 144 I 0.0690 0.6747 0.2563 145 R 0.0523 0.6238 0.3240 146 S 0.0316 0.6500 0.3184 147 N 0.0168 0.7734 0.2098 148 E 0.0060 0.9042 0.0899 149 K 0.0057 0.9223 0.0719 150 I 0.0049 0.9392 0.0559 151 Q 0.0047 0.9536 0.0416 152 N 0.0047 0.9521 0.0431 153 W 0.0048 0.9523 0.0429 154 N 0.0047 0.9568 0.0385 155 Q 0.0047 0.9579 0.0374 156 A 0.0047 0.9575 0.0378 157 Y 0.0047 0.9583 0.0370 158 Q 0.0047 0.9605 0.0349 159 E 0.0047 0.9600 0.0353 160 L 0.0048 0.9542 0.0410 161 A 0.0049 0.9464 0.0487 162 S 0.0054 0.8813 0.1133 163 A 0.0093 0.7179 0.2728 164 Y 0.0490 0.3963 0.5548 165 M 0.0297 0.1299 0.8405 166 Q 0.0745 0.0498 0.8757 167 V 0.4899 0.0108 0.4993 168 E 0.7904 0.0255 0.1841 169 F 0.9115 0.0042 0.0844 170 V 0.8445 0.0057 0.1497 171 P 0.7192 0.0077 0.2731 172 V 0.2863 0.1285 0.5852 173 F 0.0907 0.3460 0.5633 174 D 0.0432 0.5706 0.3862 175 C 0.0410 0.6716 0.2873 176 L 0.0539 0.6866 0.2595 177 T 0.0528 0.6428 0.3044 178 D 0.0386 0.6011 0.3603 179 Q 0.0248 0.6599 0.3153 180 A 0.0373 0.6346 0.3281 181 G 0.0420 0.5180 0.4400 182 Q 0.0530 0.4769 0.4701 183 L 0.0681 0.5119 0.4200 184 K 0.0529 0.5132 0.4339 185 K 0.0526 0.5180 0.4294 186 E 0.0778 0.4361 0.4861 187 Y 0.1536 0.2625 0.5839 188 T 0.1486 0.1509 0.7006 189 T 0.1039 0.1657 0.7304 190 D 0.0963 0.1084 0.7953 191 G 0.1066 0.0894 0.8040 192 L 0.2050 0.0633 0.7317 193 H 0.2555 0.0437 0.7008 194 L 0.1138 0.0616 0.8246 195 S 0.0561 0.0561 0.8878 196 I 0.0050 0.9441 0.0509 197 A 0.0047 0.9509 0.0444 198 G 0.0047 0.9568 0.0385 199 Y 0.0047 0.9604 0.0350 200 Q 0.0047 0.9606 0.0347 201 A 0.0047 0.9583 0.0370 202 L 0.0049 0.9519 0.0432 203 S 0.0047 0.9552 0.0401 204 K 0.0050 0.9496 0.0454 205 S 0.0051 0.9307 0.0642 206 L 0.0053 0.9196 0.0751 207 K 0.0052 0.9247 0.0700 208 D 0.0058 0.8988 0.0954 209 Y 0.0080 0.7811 0.2109 210 L 0.0355 0.5433 0.4212 211 Y 0.0233 0.0907 0.8861