# This file is the result of combining several RDB files, specifically # T0289.t06.dssp-ebghstl.rdb (weight 1.53986) # T0289.t06.stride-ebghtl.rdb (weight 1.24869) # T0289.t06.str2.rdb (weight 1.54758) # T0289.t06.alpha.rdb (weight 0.659012) # T0289.t04.dssp-ebghstl.rdb (weight 1.53986) # T0289.t04.stride-ebghtl.rdb (weight 1.24869) # T0289.t04.str2.rdb (weight 1.54758) # T0289.t04.alpha.rdb (weight 0.659012) # 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.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 991 # # ============================================ # Comments from T0289.t06.stride-ebghtl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 991 # # ============================================ # Comments from T0289.t06.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.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 991 # # ============================================ # Comments from T0289.t06.alpha.rdb # ============================================ # TARGET T0289 # 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 T0289.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 991 # # ============================================ # Comments from T0289.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 959 # # ============================================ # Comments from T0289.t04.stride-ebghtl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 959 # # ============================================ # Comments from T0289.t04.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.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 959 # # ============================================ # Comments from T0289.t04.alpha.rdb # ============================================ # TARGET T0289 # 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 T0289.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 959 # # ============================================ # 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 118 # # ============================================ # 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 118 # # ============================================ # 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 118 # # ============================================ # 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 118 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2541 0.0186 0.7272 2 T 0.4330 0.0206 0.5464 3 S 0.4876 0.0219 0.4905 4 C 0.3828 0.0361 0.5810 5 V 0.2282 0.0590 0.7127 6 A 0.1136 0.0923 0.7941 7 E 0.0601 0.0741 0.8658 8 E 0.0694 0.0522 0.8784 9 P 0.0998 0.0588 0.8415 10 I 0.1432 0.0243 0.8325 11 K 0.1419 0.0494 0.8087 12 K 0.7013 0.0082 0.2905 13 I 0.9213 0.0035 0.0752 14 A 0.9305 0.0034 0.0660 15 I 0.9273 0.0035 0.0692 16 F 0.8767 0.0172 0.1061 17 G 0.6876 0.0183 0.2940 18 G 0.4232 0.0316 0.5452 19 T 0.2898 0.0639 0.6464 20 H 0.1749 0.0963 0.7289 21 G 0.0849 0.1512 0.7639 22 N 0.0718 0.1307 0.7975 23 E 0.1186 0.3736 0.5078 24 L 0.1054 0.4773 0.4173 25 T 0.0481 0.5293 0.4226 26 G 0.0167 0.7207 0.2626 27 V 0.0048 0.9542 0.0410 28 F 0.0056 0.9562 0.0382 29 L 0.0047 0.9588 0.0365 30 V 0.0047 0.9591 0.0362 31 T 0.0047 0.9582 0.0371 32 H 0.0048 0.9547 0.0405 33 W 0.0049 0.9471 0.0480 34 L 0.0056 0.9198 0.0746 35 K 0.0095 0.7804 0.2101 36 N 0.0266 0.5317 0.4417 37 G 0.0300 0.4681 0.5019 38 A 0.0208 0.5844 0.3948 39 E 0.0267 0.6183 0.3550 40 V 0.0491 0.5335 0.4174 41 H 0.0787 0.4372 0.4841 42 R 0.0812 0.2589 0.6598 43 A 0.0590 0.1911 0.7500 44 G 0.0640 0.0719 0.8640 45 L 0.2785 0.0234 0.6981 46 E 0.7167 0.0132 0.2701 47 V 0.8782 0.0072 0.1146 48 K 0.8765 0.0088 0.1147 49 P 0.8531 0.0103 0.1366 50 F 0.7542 0.0209 0.2249 51 I 0.4812 0.0482 0.4706 52 T 0.1827 0.0438 0.7735 53 N 0.0930 0.0288 0.8782 54 P 0.0149 0.7833 0.2017 55 R 0.0076 0.9096 0.0828 56 A 0.0073 0.9203 0.0723 57 V 0.0101 0.9182 0.0718 58 E 0.0130 0.9105 0.0765 59 K 0.0257 0.8234 0.1508 60 C 0.0427 0.7328 0.2246 61 T 0.0763 0.6813 0.2424 62 R 0.1158 0.6174 0.2668 63 Y 0.1326 0.5074 0.3600 64 I 0.1597 0.3163 0.5240 65 D 0.1387 0.1824 0.6789 66 C 0.1271 0.2444 0.6285 67 D 0.2005 0.2022 0.5973 68 L 0.0639 0.4972 0.4388 69 N 0.0792 0.4732 0.4476 70 R 0.1389 0.4538 0.4073 71 V 0.2211 0.2627 0.5162 72 F 0.2190 0.1137 0.6673 73 D 0.1262 0.0735 0.8003 74 L 0.0348 0.6034 0.3617 75 E 0.0245 0.7016 0.2739 76 N 0.0297 0.6890 0.2813 77 L 0.0461 0.4901 0.4639 78 S 0.0413 0.3147 0.6440 79 K 0.0568 0.2521 0.6911 80 E 0.0477 0.3136 0.6387 81 M 0.0570 0.2970 0.6459 82 S 0.0468 0.3393 0.6139 83 E 0.0374 0.3141 0.6485 84 D 0.0448 0.3595 0.5957 85 L 0.0157 0.6107 0.3736 86 P 0.0077 0.8661 0.1262 87 Y 0.0058 0.9312 0.0630 88 E 0.0058 0.9388 0.0554 89 V 0.0061 0.9406 0.0533 90 R 0.0061 0.9449 0.0490 91 R 0.0069 0.9420 0.0511 92 A 0.0052 0.9438 0.0510 93 Q 0.0055 0.9452 0.0493 94 E 0.0049 0.9471 0.0480 95 I 0.0049 0.9477 0.0474 96 N 0.0053 0.9405 0.0542 97 H 0.0056 0.9192 0.0752 98 L 0.0069 0.8699 0.1232 99 F 0.0191 0.6902 0.2906 100 G 0.0525 0.3113 0.6362 101 P 0.0528 0.1850 0.7622 102 K 0.0449 0.2674 0.6878 103 N 0.0347 0.2455 0.7197 104 S 0.0519 0.1860 0.7621 105 D 0.0644 0.1248 0.8108 106 D 0.0777 0.1421 0.7802 107 A 0.1883 0.1379 0.6738 108 Y 0.4026 0.0576 0.5398 109 D 0.6046 0.0475 0.3479 110 V 0.8904 0.0151 0.0945 111 V 0.9106 0.0114 0.0780 112 F 0.9002 0.0123 0.0875 113 D 0.8107 0.0152 0.1740 114 L 0.3387 0.1158 0.5455 115 H 0.1667 0.1460 0.6873 116 N 0.1412 0.1976 0.6612 117 T 0.1584 0.2108 0.6308 118 T 0.1231 0.1922 0.6847 119 S 0.0459 0.2675 0.6866 120 N 0.0433 0.1920 0.7648 121 M 0.1026 0.1573 0.7402 122 G 0.1582 0.0760 0.7658 123 C 0.3776 0.0647 0.5576 124 T 0.6456 0.0545 0.2999 125 L 0.7850 0.0387 0.1763 126 I 0.8199 0.0338 0.1463 127 L 0.7657 0.0336 0.2006 128 E 0.5866 0.0316 0.3818 129 D 0.2177 0.0330 0.7493 130 S 0.0611 0.0887 0.8502 131 R 0.0478 0.1165 0.8357 132 N 0.0410 0.2469 0.7121 133 D 0.0404 0.3165 0.6431 134 F 0.0361 0.5352 0.4287 135 L 0.0240 0.7355 0.2404 136 I 0.0182 0.8249 0.1569 137 Q 0.0135 0.8690 0.1175 138 M 0.0123 0.8856 0.1021 139 F 0.0113 0.8797 0.1090 140 H 0.0146 0.8580 0.1275 141 Y 0.0164 0.8370 0.1466 142 I 0.0219 0.8224 0.1557 143 K 0.0191 0.8183 0.1627 144 T 0.0217 0.7703 0.2081 145 C 0.0442 0.6461 0.3097 146 M 0.0781 0.4265 0.4954 147 A 0.0750 0.2527 0.6723 148 P 0.0983 0.2530 0.6486 149 L 0.1279 0.2509 0.6212 150 P 0.2102 0.2316 0.5582 151 C 0.3511 0.1831 0.4659 152 S 0.4985 0.1772 0.3244 153 V 0.4715 0.2210 0.3075 154 Y 0.4394 0.2011 0.3595 155 L 0.3940 0.1257 0.4803 156 I 0.2512 0.0842 0.6646 157 E 0.1628 0.0984 0.7388 158 H 0.1211 0.1045 0.7744 159 P 0.0918 0.1685 0.7398 160 S 0.0962 0.2791 0.6247 161 L 0.1059 0.3752 0.5189 162 K 0.1061 0.3461 0.5477 163 Y 0.1543 0.3253 0.5204 164 A 0.2182 0.2675 0.5143 165 T 0.2298 0.2485 0.5216 166 T 0.0875 0.6882 0.2242 167 R 0.0555 0.7635 0.1811 168 S 0.0697 0.6959 0.2344 169 I 0.1110 0.5566 0.3324 170 A 0.1136 0.3971 0.4893 171 K 0.0843 0.3259 0.5898 172 Y 0.1343 0.1449 0.7208 173 P 0.3240 0.0598 0.6163 174 V 0.7247 0.0213 0.2540 175 G 0.8924 0.0109 0.0967 176 I 0.8977 0.0077 0.0946 177 E 0.8766 0.0084 0.1150 178 V 0.6892 0.0230 0.2878 179 G 0.4189 0.0159 0.5652 180 P 0.2943 0.0346 0.6711 181 Q 0.2458 0.0255 0.7287 182 P 0.1240 0.0711 0.8049 183 H 0.0663 0.1063 0.8273 184 G 0.0748 0.1146 0.8107 185 V 0.1476 0.1750 0.6773 186 L 0.1607 0.1914 0.6480 187 R 0.0784 0.2492 0.6724 188 A 0.0069 0.8876 0.1055 189 D 0.0066 0.9020 0.0913 190 I 0.0055 0.9323 0.0622 191 L 0.0048 0.9511 0.0441 192 D 0.0048 0.9534 0.0418 193 Q 0.0048 0.9548 0.0405 194 M 0.0047 0.9584 0.0369 195 R 0.0047 0.9599 0.0354 196 R 0.0047 0.9595 0.0357 197 M 0.0047 0.9594 0.0359 198 L 0.0047 0.9594 0.0359 199 K 0.0047 0.9597 0.0356 200 H 0.0047 0.9558 0.0394 201 A 0.0047 0.9538 0.0414 202 L 0.0048 0.9496 0.0456 203 D 0.0050 0.9302 0.0649 204 F 0.0051 0.9191 0.0759 205 I 0.0100 0.9000 0.0900 206 Q 0.0152 0.8510 0.1337 207 R 0.0224 0.7658 0.2117 208 F 0.0376 0.6291 0.3333 209 N 0.0496 0.3839 0.5665 210 E 0.0559 0.2037 0.7404 211 G 0.0470 0.0960 0.8570 212 K 0.1532 0.0834 0.7633 213 E 0.3362 0.0664 0.5975 214 F 0.1499 0.0335 0.8166