# This file is the result of combining several RDB files, specifically # T0249.t04.dssp-ebghstl.rdb (weight 1.53986) # T0249.t04.stride-ebghtl.rdb (weight 1.24869) # T0249.t04.str2.rdb (weight 1.54758) # T0249.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 T0249.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0249 # 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 T0249.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 56.813 # # ============================================ # Comments from T0249.t04.stride-ebghtl.rdb # ============================================ # TARGET T0249 # 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 T0249.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 56.813 # # ============================================ # Comments from T0249.t04.str2.rdb # ============================================ # TARGET T0249 # 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 T0249.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 56.813 # # ============================================ # Comments from T0249.t04.alpha.rdb # ============================================ # TARGET T0249 # 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 T0249.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 56.813 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0444 0.0988 0.8567 2 Q 0.0437 0.2816 0.6747 3 E 0.0323 0.5010 0.4667 4 Q 0.0252 0.5529 0.4219 5 R 0.0072 0.8763 0.1166 6 Q 0.0059 0.9361 0.0580 7 Q 0.0051 0.9499 0.0449 8 L 0.0050 0.9543 0.0407 9 L 0.0050 0.9540 0.0410 10 R 0.0061 0.9499 0.0439 11 S 0.0093 0.9377 0.0529 12 L 0.0367 0.8795 0.0839 13 E 0.0633 0.8434 0.0934 14 A 0.1558 0.7956 0.0487 15 L 0.1725 0.7798 0.0477 16 I 0.1965 0.7437 0.0599 17 F 0.1652 0.6743 0.1605 18 S 0.1227 0.4395 0.4378 19 S 0.0827 0.1997 0.7175 20 E 0.0428 0.0756 0.8815 21 E 0.0790 0.0227 0.8983 22 P 0.1236 0.0302 0.8462 23 V 0.2346 0.0122 0.7532 24 N 0.1529 0.0112 0.8359 25 L 0.0052 0.9452 0.0496 26 Q 0.0049 0.9570 0.0381 27 T 0.0047 0.9571 0.0382 28 L 0.0050 0.9542 0.0408 29 S 0.0049 0.9436 0.0515 30 Q 0.0058 0.9057 0.0885 31 I 0.0118 0.8473 0.1409 32 T 0.0328 0.5816 0.3856 33 A 0.0191 0.4758 0.5051 34 H 0.0382 0.2344 0.7274 35 K 0.0490 0.1079 0.8431 36 F 0.1170 0.0239 0.8591 37 T 0.0684 0.0113 0.9204 38 P 0.0049 0.9369 0.0582 39 S 0.0047 0.9564 0.0389 40 E 0.0047 0.9589 0.0364 41 L 0.0047 0.9608 0.0345 42 Q 0.0047 0.9608 0.0346 43 E 0.0046 0.9596 0.0357 44 A 0.0047 0.9591 0.0362 45 V 0.0047 0.9603 0.0350 46 D 0.0047 0.9597 0.0357 47 E 0.0048 0.9514 0.0438 48 L 0.0051 0.9292 0.0657 49 N 0.0062 0.9110 0.0828 50 R 0.0072 0.8784 0.1144 51 D 0.0132 0.8370 0.1498 52 Y 0.0297 0.7899 0.1804 53 E 0.0198 0.6526 0.3275 54 A 0.0221 0.5677 0.4102 55 T 0.0451 0.1740 0.7809 56 G 0.0335 0.0314 0.9350 57 R 0.1352 0.0178 0.8470 58 T 0.6922 0.0064 0.3015 59 F 0.8297 0.0040 0.1664 60 R 0.9215 0.0036 0.0749 61 I 0.9268 0.0035 0.0697 62 H 0.9144 0.0059 0.0797 63 A 0.9200 0.0044 0.0755 64 I 0.8539 0.0175 0.1286 65 A 0.5422 0.0324 0.4254 66 G 0.1016 0.0336 0.8647 67 G 0.3480 0.0360 0.6160 68 Y 0.8246 0.0123 0.1631 69 R 0.8816 0.0145 0.1039 70 F 0.8763 0.0128 0.1110 71 L 0.7730 0.0207 0.2063 72 T 0.4404 0.0289 0.5308 73 E 0.0872 0.0925 0.8203 74 P 0.0096 0.8168 0.1736 75 E 0.0144 0.8203 0.1653 76 F 0.0116 0.8716 0.1168 77 A 0.0056 0.9449 0.0495 78 D 0.0047 0.9533 0.0420 79 L 0.0049 0.9560 0.0391 80 V 0.0048 0.9567 0.0385 81 R 0.0048 0.9528 0.0424 82 Q 0.0057 0.9253 0.0690 83 L 0.0080 0.8638 0.1282 84 L 0.0168 0.6914 0.2918 85 A 0.0257 0.3485 0.6258 86 P 0.0212 0.4076 0.5712 87 V 0.0281 0.4287 0.5432 88 I 0.0521 0.4020 0.5459 89 Q 0.0493 0.3689 0.5818 90 R 0.0479 0.4550 0.4971 91 R 0.0842 0.4139 0.5019 92 L 0.0796 0.4118 0.5085 93 S 0.0524 0.4441 0.5035 94 R 0.0049 0.9468 0.0483 95 S 0.0048 0.9575 0.0377 96 M 0.0048 0.9574 0.0379 97 L 0.0047 0.9595 0.0358 98 E 0.0047 0.9604 0.0350 99 V 0.0046 0.9613 0.0341 100 L 0.0047 0.9604 0.0349 101 A 0.0046 0.9604 0.0349 102 V 0.0047 0.9571 0.0382 103 V 0.0049 0.9503 0.0449 104 A 0.0063 0.9092 0.0845 105 W 0.0124 0.7871 0.2005 106 H 0.0259 0.4305 0.5437 107 Q 0.0518 0.0416 0.9066 108 P 0.0655 0.0750 0.8595 109 V 0.1132 0.0864 0.8004 110 T 0.1296 0.1013 0.7691 111 K 0.0361 0.8086 0.1553 112 G 0.0356 0.8475 0.1170 113 E 0.0545 0.8388 0.1067 114 I 0.0363 0.8925 0.0712 115 Q 0.0631 0.8595 0.0773 116 Q 0.0461 0.8531 0.1007 117 I 0.1242 0.6861 0.1897 118 R 0.1603 0.3931 0.4466 119 G 0.0924 0.0756 0.8321 120 A 0.1098 0.0372 0.8530 121 S 0.1083 0.0293 0.8624 122 P 0.0286 0.4755 0.4959 123 D 0.0136 0.7734 0.2131 124 Y 0.0083 0.8908 0.1009 125 S 0.0069 0.9349 0.0582 126 I 0.0049 0.9575 0.0375 127 D 0.0049 0.9597 0.0354 128 R 0.0047 0.9602 0.0351 129 L 0.0047 0.9586 0.0367 130 L 0.0048 0.9522 0.0429 131 A 0.0059 0.9012 0.0929 132 R 0.0438 0.3789 0.5773 133 G 0.0357 0.0565 0.9078 134 L 0.1758 0.0720 0.7522 135 I 0.6648 0.0393 0.2959 136 E 0.8092 0.0256 0.1652 137 V 0.7969 0.0242 0.1789 138 R 0.5425 0.0467 0.4108 139 G 0.2476 0.0371 0.7153 140 R 0.3430 0.0475 0.6095 141 A 0.3795 0.0445 0.5760 142 D 0.1909 0.0507 0.7584 143 S 0.1122 0.0348 0.8530 144 P 0.0702 0.0556 0.8743 145 G 0.0681 0.0397 0.8922 146 R 0.1788 0.0408 0.7803 147 P 0.3052 0.1119 0.5829 148 L 0.4443 0.2080 0.3477 149 Q 0.5576 0.2205 0.2219 150 Y 0.4892 0.2448 0.2660 151 G 0.4345 0.1690 0.3965 152 T 0.2864 0.2015 0.5122 153 T 0.0644 0.4770 0.4586 154 E 0.0048 0.9480 0.0472 155 V 0.0048 0.9535 0.0418 156 F 0.0048 0.9551 0.0401 157 L 0.0048 0.9492 0.0460 158 D 0.0054 0.9147 0.0799 159 L 0.0103 0.7985 0.1912 160 F 0.0587 0.2879 0.6534 161 H 0.0541 0.0604 0.8855 162 L 0.0633 0.0513 0.8854 163 P 0.0317 0.3136 0.6547 164 S 0.0525 0.4880 0.4595 165 L 0.0081 0.8739 0.1180 166 K 0.0068 0.8235 0.1697 167 D 0.0117 0.6901 0.2982 168 L 0.0498 0.2747 0.6755 169 P 0.0267 0.3450 0.6283 170 K 0.0353 0.2987 0.6660 171 L 0.0136 0.7333 0.2531 172 R 0.0078 0.8611 0.1310 173 E 0.0105 0.8582 0.1313 174 I 0.0071 0.8904 0.1025 175 K 0.0053 0.9365 0.0582 176 E 0.0053 0.9303 0.0645 177 I 0.0053 0.9216 0.0730 178 L 0.0066 0.9041 0.0893 179 Q 0.0062 0.8501 0.1437 180 E 0.0078 0.8180 0.1742 181 H 0.0139 0.7459 0.2403 182 E 0.0149 0.7191 0.2661 183 E 0.0103 0.8324 0.1573 184 Q 0.0184 0.8236 0.1579 185 Q 0.0290 0.7983 0.1727 186 Y 0.0434 0.7745 0.1821 187 L 0.0615 0.6978 0.2407 188 A 0.0694 0.5779 0.3527 189 A 0.0556 0.3828 0.5616 190 D 0.0717 0.1448 0.7835 191 G 0.0689 0.0986 0.8325 192 D 0.1073 0.0823 0.8104 193 L 0.1145 0.0785 0.8070 194 P 0.0997 0.1609 0.7393 195 V 0.1022 0.2975 0.6003 196 A 0.1109 0.2574 0.6317 197 A 0.0936 0.2494 0.6570 198 D 0.0770 0.2245 0.6985 199 E 0.0288 0.4969 0.4743 200 D 0.0330 0.4190 0.5480 201 E 0.0381 0.3294 0.6325 202 K 0.0643 0.1801 0.7556 203 P 0.0569 0.2725 0.6706 204 R 0.0649 0.3504 0.5847 205 M 0.0512 0.5867 0.3621 206 E 0.0596 0.5572 0.3831 207 R 0.0758 0.4279 0.4963 208 I 0.0891 0.2049 0.7060 209 E 0.0554 0.1182 0.8265