# This file is the result of combining several RDB files, specifically # T0293.t04.dssp-ebghstl.rdb (weight 1.53986) # T0293.t04.stride-ebghtl.rdb (weight 1.24869) # T0293.t04.str2.rdb (weight 1.54758) # T0293.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 T0293.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 2191 # # ============================================ # Comments from T0293.t04.stride-ebghtl.rdb # ============================================ # TARGET T0293 # 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 T0293.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 2191 # # ============================================ # Comments from T0293.t04.str2.rdb # ============================================ # TARGET T0293 # 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 T0293.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 2191 # # ============================================ # Comments from T0293.t04.alpha.rdb # ============================================ # TARGET T0293 # 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 T0293.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 2191 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.1175 0.0419 0.8406 2 I 0.1745 0.0137 0.8118 3 P 0.0998 0.0165 0.8837 4 L 0.0146 0.4923 0.4931 5 E 0.0244 0.4430 0.5326 6 R 0.1585 0.4293 0.4121 7 L 0.4079 0.1054 0.4867 8 I 0.2475 0.0658 0.6867 9 P 0.1492 0.0854 0.7654 10 T 0.1531 0.0878 0.7591 11 V 0.1365 0.0662 0.7973 12 P 0.1013 0.1109 0.7878 13 L 0.0996 0.1563 0.7441 14 R 0.0842 0.1741 0.7417 15 L 0.0412 0.4217 0.5371 16 N 0.0506 0.4799 0.4695 17 Y 0.0640 0.6380 0.2979 18 I 0.0596 0.7614 0.1789 19 H 0.0559 0.7843 0.1598 20 W 0.0327 0.8420 0.1253 21 V 0.0096 0.9357 0.0547 22 E 0.0071 0.9411 0.0518 23 D 0.0076 0.9299 0.0626 24 L 0.0094 0.9062 0.0844 25 I 0.0200 0.8159 0.1641 26 G 0.0211 0.6526 0.3263 27 H 0.0214 0.5668 0.4118 28 Q 0.0262 0.5392 0.4347 29 D 0.0432 0.3768 0.5800 30 S 0.0511 0.2648 0.6841 31 D 0.0563 0.1976 0.7462 32 K 0.0468 0.2845 0.6687 33 S 0.0523 0.2373 0.7105 34 T 0.0569 0.2402 0.7028 35 L 0.1113 0.0932 0.7955 36 R 0.2043 0.0535 0.7422 37 R 0.6846 0.0197 0.2957 38 G 0.8957 0.0063 0.0980 39 I 0.9084 0.0065 0.0850 40 D 0.8658 0.0112 0.1230 41 I 0.5882 0.0688 0.3430 42 G 0.2147 0.0663 0.7190 43 T 0.1183 0.0935 0.7882 44 G 0.0699 0.1597 0.7703 45 A 0.0353 0.5000 0.4647 46 S 0.0149 0.7808 0.2043 47 C 0.0107 0.9021 0.0871 48 I 0.0057 0.9399 0.0544 49 Y 0.0051 0.9549 0.0400 50 P 0.0050 0.9576 0.0374 51 L 0.0052 0.9547 0.0402 52 L 0.0050 0.9438 0.0513 53 G 0.0051 0.9122 0.0827 54 A 0.0060 0.8365 0.1575 55 T 0.0140 0.7425 0.2435 56 L 0.0660 0.1257 0.8083 57 N 0.0293 0.0951 0.8756 58 G 0.0384 0.0448 0.9167 59 W 0.3395 0.0152 0.6453 60 Y 0.8656 0.0058 0.1286 61 F 0.9224 0.0033 0.0743 62 L 0.9154 0.0064 0.0781 63 A 0.9045 0.0055 0.0900 64 T 0.8309 0.0096 0.1595 65 E 0.6273 0.0104 0.3623 66 V 0.1666 0.0315 0.8019 67 D 0.0768 0.0146 0.9086 68 D 0.0053 0.9062 0.0885 69 M 0.0050 0.9440 0.0510 70 C 0.0049 0.9522 0.0429 71 F 0.0047 0.9578 0.0375 72 N 0.0047 0.9589 0.0364 73 Y 0.0047 0.9596 0.0356 74 A 0.0047 0.9592 0.0361 75 K 0.0047 0.9574 0.0379 76 K 0.0050 0.9536 0.0414 77 N 0.0049 0.9537 0.0414 78 V 0.0049 0.9540 0.0411 79 E 0.0050 0.9422 0.0528 80 Q 0.0068 0.8721 0.1210 81 N 0.0475 0.3710 0.5815 82 N 0.0456 0.0384 0.9160 83 L 0.0594 0.1353 0.8053 84 S 0.0458 0.3866 0.5676 85 D 0.0819 0.3668 0.5513 86 L 0.4377 0.1204 0.4419 87 I 0.7727 0.0120 0.2153 88 K 0.8950 0.0066 0.0984 89 V 0.9140 0.0045 0.0815 90 V 0.8730 0.0089 0.1181 91 K 0.8071 0.0085 0.1844 92 V 0.3424 0.0203 0.6374 93 P 0.0914 0.0529 0.8557 94 Q 0.0354 0.3413 0.6233 95 A 0.0171 0.6901 0.2928 96 T 0.0180 0.7894 0.1926 97 L 0.0289 0.8343 0.1368 98 L 0.0293 0.8590 0.1118 99 M 0.0183 0.8886 0.0930 100 D 0.0142 0.8640 0.1218 101 A 0.0110 0.8620 0.1270 102 L 0.0249 0.7866 0.1886 103 K 0.0400 0.6799 0.2800 104 E 0.0335 0.5998 0.3667 105 E 0.0460 0.4416 0.5124 106 S 0.0509 0.4054 0.5437 107 E 0.0443 0.2246 0.7310 108 I 0.1283 0.1166 0.7551 109 I 0.3984 0.0278 0.5738 110 Y 0.6264 0.0065 0.3671 111 D 0.6599 0.0159 0.3242 112 F 0.9176 0.0041 0.0783 113 C 0.9296 0.0034 0.0670 114 M 0.9192 0.0053 0.0755 115 C 0.7775 0.0139 0.2086 116 N 0.2162 0.0200 0.7637 117 P 0.0832 0.0695 0.8473 118 P 0.0455 0.2221 0.7324 119 F 0.0820 0.2958 0.6222 120 F 0.0774 0.2221 0.7005 121 A 0.0673 0.2868 0.6459 122 N 0.0645 0.3895 0.5460 123 Q 0.0387 0.6190 0.3423 124 L 0.0289 0.7256 0.2454 125 E 0.0348 0.7378 0.2274 126 A 0.0441 0.6690 0.2869 127 K 0.0558 0.4735 0.4707 128 G 0.0462 0.2404 0.7133 129 V 0.0778 0.2441 0.6781 130 N 0.1077 0.1915 0.7008 131 S 0.0836 0.1887 0.7277 132 R 0.0925 0.1535 0.7539 133 N 0.1081 0.0702 0.8218 134 P 0.1016 0.1099 0.7885 135 R 0.1392 0.0953 0.7655 136 R 0.0982 0.0390 0.8628 137 P 0.0645 0.0239 0.9116 138 P 0.0611 0.0278 0.9111 139 P 0.0602 0.1746 0.7653 140 S 0.0260 0.5384 0.4356 141 S 0.0248 0.6532 0.3220 142 V 0.0378 0.6540 0.3082 143 N 0.0514 0.5855 0.3631 144 T 0.0456 0.6636 0.2908 145 G 0.0185 0.7618 0.2197 146 G 0.0231 0.7977 0.1792 147 I 0.0197 0.8701 0.1102 148 T 0.0159 0.8946 0.0895 149 E 0.0208 0.8882 0.0911 150 I 0.0308 0.8557 0.1135 151 M 0.0957 0.6532 0.2511 152 A 0.0720 0.4162 0.5119 153 E 0.0226 0.1917 0.7856 154 G 0.0271 0.0788 0.8941 155 G 0.1700 0.0498 0.7802 156 E 0.5753 0.0978 0.3269 157 L 0.7775 0.1072 0.1153 158 E 0.6914 0.2021 0.1065 159 F 0.6203 0.2759 0.1039 160 V 0.4167 0.4440 0.1393 161 K 0.1879 0.6756 0.1365 162 R 0.0716 0.8029 0.1255 163 I 0.0468 0.8054 0.1479 164 I 0.0260 0.8371 0.1369 165 H 0.0149 0.8577 0.1274 166 D 0.0140 0.8132 0.1728 167 S 0.0163 0.8232 0.1605 168 L 0.0103 0.8513 0.1385 169 Q 0.0104 0.8202 0.1694 170 L 0.0171 0.7102 0.2727 171 G 0.0324 0.4914 0.4762 172 K 0.0467 0.3961 0.5572 173 R 0.0859 0.3725 0.5416 174 L 0.1626 0.1995 0.6379 175 R 0.3543 0.1023 0.5434 176 W 0.7195 0.0523 0.2281 177 Y 0.8487 0.0323 0.1190 178 S 0.8729 0.0255 0.1016 179 C 0.8557 0.0308 0.1135 180 M 0.8150 0.0325 0.1525 181 L 0.6025 0.0618 0.3356 182 G 0.2296 0.0640 0.7064 183 K 0.1373 0.1327 0.7300 184 A 0.1066 0.2503 0.6431 185 C 0.0625 0.2430 0.6945 186 S 0.0596 0.2143 0.7262 187 L 0.0422 0.4655 0.4923 188 A 0.0134 0.8842 0.1025 189 P 0.0080 0.9381 0.0539 190 L 0.0057 0.9494 0.0449 191 K 0.0047 0.9590 0.0364 192 E 0.0047 0.9600 0.0353 193 E 0.0047 0.9609 0.0344 194 L 0.0048 0.9580 0.0372 195 R 0.0050 0.9470 0.0480 196 I 0.0071 0.8912 0.1017 197 Q 0.0426 0.3904 0.5670 198 G 0.0377 0.0247 0.9376 199 V 0.0674 0.0115 0.9211 200 P 0.0954 0.0650 0.8397 201 K 0.4065 0.0745 0.5190 202 V 0.7049 0.0233 0.2718 203 T 0.8465 0.0112 0.1423 204 Y 0.8567 0.0140 0.1293 205 T 0.7584 0.0281 0.2135 206 E 0.6797 0.0502 0.2701 207 F 0.3998 0.1384 0.4618 208 C 0.2732 0.1797 0.5471 209 Q 0.0932 0.1111 0.7957 210 G 0.0572 0.0678 0.8749 211 R 0.2358 0.0589 0.7053 212 T 0.5133 0.0524 0.4343 213 M 0.7407 0.0495 0.2098 214 R 0.8453 0.0420 0.1127 215 W 0.8734 0.0430 0.0836 216 A 0.8532 0.0554 0.0914 217 L 0.8123 0.0578 0.1298 218 A 0.7246 0.0841 0.1914 219 W 0.5601 0.1403 0.2996 220 S 0.3736 0.1955 0.4309 221 F 0.2177 0.2064 0.5759 222 Y 0.1357 0.0857 0.7786 223 D 0.0710 0.0345 0.8945