# This file is the result of combining several RDB files, specifically # T0289.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0289.t2k.stride-ebghtl.rdb (weight 1.24869) # T0289.t2k.str2.rdb (weight 1.54758) # T0289.t2k.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 T0289.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0289 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0289.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 119 # # ============================================ # Comments from T0289.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0289 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0289.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 119 # # ============================================ # Comments from T0289.t2k.str2.rdb # ============================================ # TARGET T0289 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0289.t2k-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 119 # # ============================================ # Comments from T0289.t2k.alpha.rdb # ============================================ # TARGET T0289 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0289.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 119 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1472 0.0369 0.8159 2 T 0.3447 0.0369 0.6184 3 S 0.4572 0.0319 0.5109 4 C 0.3875 0.0384 0.5741 5 V 0.2285 0.0555 0.7160 6 A 0.1167 0.0793 0.8040 7 E 0.0635 0.0650 0.8714 8 E 0.0713 0.0483 0.8805 9 P 0.1068 0.0566 0.8366 10 I 0.1480 0.0220 0.8300 11 K 0.1573 0.0434 0.7993 12 K 0.7307 0.0073 0.2620 13 I 0.9230 0.0035 0.0735 14 A 0.9302 0.0034 0.0663 15 I 0.9276 0.0035 0.0689 16 F 0.8750 0.0173 0.1077 17 G 0.6814 0.0186 0.3000 18 G 0.4157 0.0314 0.5529 19 T 0.2848 0.0640 0.6512 20 H 0.1718 0.0961 0.7321 21 G 0.0837 0.1486 0.7677 22 N 0.0728 0.1284 0.7988 23 E 0.1211 0.3715 0.5074 24 L 0.1070 0.4747 0.4183 25 T 0.0484 0.5292 0.4224 26 G 0.0166 0.7226 0.2608 27 V 0.0048 0.9543 0.0409 28 F 0.0056 0.9562 0.0381 29 L 0.0047 0.9589 0.0364 30 V 0.0047 0.9594 0.0359 31 T 0.0047 0.9590 0.0363 32 H 0.0048 0.9559 0.0394 33 W 0.0049 0.9472 0.0478 34 L 0.0053 0.9281 0.0665 35 K 0.0107 0.7903 0.1990 36 N 0.0304 0.4909 0.4786 37 G 0.0419 0.3221 0.6360 38 A 0.0285 0.4695 0.5020 39 E 0.0331 0.5042 0.4627 40 V 0.0666 0.4855 0.4479 41 H 0.1332 0.3834 0.4833 42 R 0.1351 0.2802 0.5847 43 A 0.1038 0.2169 0.6793 44 G 0.1176 0.0737 0.8087 45 L 0.3141 0.0262 0.6597 46 E 0.6769 0.0151 0.3080 47 V 0.8556 0.0093 0.1351 48 K 0.8574 0.0119 0.1307 49 P 0.8325 0.0133 0.1541 50 F 0.7464 0.0237 0.2299 51 I 0.5058 0.0501 0.4441 52 T 0.2005 0.0453 0.7542 53 N 0.0929 0.0304 0.8767 54 P 0.0156 0.7764 0.2080 55 R 0.0079 0.9085 0.0837 56 A 0.0074 0.9192 0.0734 57 V 0.0102 0.9164 0.0733 58 E 0.0128 0.9101 0.0771 59 K 0.0266 0.8228 0.1506 60 C 0.0433 0.7350 0.2216 61 T 0.0782 0.6842 0.2376 62 R 0.1176 0.6174 0.2650 63 Y 0.1332 0.5043 0.3625 64 I 0.1589 0.3036 0.5375 65 D 0.1356 0.1702 0.6942 66 C 0.1238 0.2329 0.6433 67 D 0.2011 0.1925 0.6063 68 L 0.0673 0.4808 0.4519 69 N 0.0851 0.4562 0.4587 70 R 0.1506 0.4332 0.4163 71 V 0.2332 0.2456 0.5212 72 F 0.2313 0.1058 0.6629 73 D 0.1319 0.0712 0.7969 74 L 0.0357 0.5959 0.3684 75 E 0.0254 0.6927 0.2819 76 N 0.0300 0.6798 0.2903 77 L 0.0465 0.4812 0.4723 78 S 0.0406 0.3164 0.6429 79 K 0.0544 0.2600 0.6856 80 E 0.0454 0.3347 0.6199 81 M 0.0534 0.3264 0.6202 82 S 0.0447 0.3648 0.5905 83 E 0.0368 0.3358 0.6275 84 D 0.0422 0.3862 0.5716 85 L 0.0165 0.6010 0.3825 86 P 0.0076 0.8734 0.1190 87 Y 0.0060 0.9301 0.0639 88 E 0.0060 0.9371 0.0570 89 V 0.0063 0.9385 0.0553 90 R 0.0063 0.9430 0.0506 91 R 0.0073 0.9404 0.0523 92 A 0.0054 0.9405 0.0541 93 Q 0.0056 0.9423 0.0521 94 E 0.0051 0.9433 0.0516 95 I 0.0053 0.9417 0.0530 96 N 0.0054 0.9317 0.0629 97 H 0.0061 0.9054 0.0885 98 L 0.0078 0.8539 0.1383 99 F 0.0225 0.6814 0.2961 100 G 0.0553 0.3070 0.6377 101 P 0.0544 0.1874 0.7583 102 K 0.0462 0.2657 0.6880 103 N 0.0369 0.2442 0.7189 104 S 0.0542 0.1867 0.7591 105 D 0.0653 0.1245 0.8101 106 D 0.0753 0.1487 0.7760 107 A 0.1791 0.1463 0.6747 108 Y 0.3844 0.0645 0.5511 109 D 0.5849 0.0512 0.3639 110 V 0.8849 0.0172 0.0979 111 V 0.9084 0.0127 0.0788 112 F 0.8969 0.0141 0.0890 113 D 0.8030 0.0179 0.1790 114 L 0.3255 0.1209 0.5536 115 H 0.1590 0.1523 0.6887 116 N 0.1341 0.2034 0.6625 117 T 0.1520 0.2194 0.6286 118 T 0.1186 0.2026 0.6787 119 S 0.0440 0.2768 0.6792 120 N 0.0426 0.1987 0.7586 121 M 0.1029 0.1629 0.7342 122 G 0.1551 0.0785 0.7664 123 C 0.3678 0.0690 0.5632 124 T 0.6318 0.0580 0.3102 125 L 0.7756 0.0414 0.1829 126 I 0.8125 0.0361 0.1514 127 L 0.7579 0.0360 0.2061 128 E 0.5807 0.0337 0.3857 129 D 0.2174 0.0353 0.7473 130 S 0.0636 0.0884 0.8480 131 R 0.0469 0.1308 0.8223 132 N 0.0405 0.2669 0.6926 133 D 0.0410 0.3302 0.6289 134 F 0.0372 0.5314 0.4314 135 L 0.0263 0.7099 0.2638 136 I 0.0196 0.8048 0.1756 137 Q 0.0132 0.8585 0.1283 138 M 0.0134 0.8730 0.1136 139 F 0.0124 0.8670 0.1206 140 H 0.0173 0.8421 0.1406 141 Y 0.0189 0.8223 0.1588 142 I 0.0266 0.8073 0.1661 143 K 0.0236 0.8120 0.1644 144 T 0.0249 0.7739 0.2012 145 C 0.0495 0.6574 0.2931 146 M 0.0831 0.4476 0.4693 147 A 0.0783 0.2800 0.6416 148 P 0.1020 0.2752 0.6228 149 L 0.1299 0.2795 0.5905 150 P 0.1842 0.2605 0.5554 151 C 0.3029 0.2143 0.4828 152 S 0.4526 0.2054 0.3420 153 V 0.4354 0.2420 0.3226 154 Y 0.4111 0.2245 0.3644 155 L 0.3826 0.1354 0.4820 156 I 0.2560 0.0908 0.6532 157 E 0.1640 0.1023 0.7338 158 H 0.1172 0.1114 0.7713 159 P 0.0897 0.1830 0.7273 160 S 0.0941 0.2987 0.6071 161 L 0.1053 0.3824 0.5123 162 K 0.1026 0.3562 0.5412 163 Y 0.1420 0.3377 0.5204 164 A 0.2012 0.2848 0.5140 165 T 0.2194 0.2685 0.5120 166 T 0.0974 0.6637 0.2389 167 R 0.0676 0.7371 0.1952 168 S 0.0847 0.6720 0.2433 169 I 0.1198 0.5431 0.3371 170 A 0.1207 0.3954 0.4838 171 K 0.0859 0.3267 0.5874 172 Y 0.1381 0.1441 0.7178 173 P 0.3289 0.0617 0.6095 174 V 0.7331 0.0235 0.2434 175 G 0.8927 0.0117 0.0957 176 I 0.8959 0.0090 0.0951 177 E 0.8636 0.0112 0.1253 178 V 0.6306 0.0282 0.3412 179 G 0.2916 0.0238 0.6846 180 P 0.2054 0.0605 0.7340 181 Q 0.2224 0.0628 0.7148 182 P 0.1138 0.1190 0.7673 183 H 0.0592 0.2510 0.6898 184 G 0.0542 0.3383 0.6075 185 V 0.1066 0.4046 0.4888 186 L 0.1451 0.3847 0.4702 187 R 0.0802 0.5082 0.4116 188 A 0.0076 0.9049 0.0875 189 D 0.0064 0.9308 0.0628 190 I 0.0049 0.9489 0.0462 191 L 0.0047 0.9587 0.0366 192 D 0.0048 0.9583 0.0369 193 Q 0.0048 0.9574 0.0378 194 M 0.0047 0.9577 0.0375 195 R 0.0048 0.9543 0.0409 196 R 0.0057 0.9444 0.0499 197 M 0.0058 0.9184 0.0758 198 L 0.0164 0.8338 0.1498 199 K 0.0192 0.6122 0.3686 200 H 0.0315 0.1219 0.8467