# This file is the result of combining several RDB files, specifically # T0296.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0296.t2k.stride-ebghtl.rdb (weight 1.24869) # T0296.t2k.str2.rdb (weight 1.54758) # T0296.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 T0296.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0296 # 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 T0296.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 49 # # ============================================ # Comments from T0296.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0296 # 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 T0296.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 49 # # ============================================ # Comments from T0296.t2k.str2.rdb # ============================================ # TARGET T0296 # 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 T0296.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 7.47333 # # ============================================ # Comments from T0296.t2k.alpha.rdb # ============================================ # TARGET T0296 # 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 T0296.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 49 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.0733 0.0591 0.8676 2 L 0.2775 0.0299 0.6926 3 S 0.3875 0.0340 0.5785 4 L 0.3813 0.0554 0.5633 5 A 0.3135 0.0472 0.6394 6 P 0.2263 0.0382 0.7355 7 T 0.1113 0.0353 0.8534 8 P 0.0526 0.2113 0.7360 9 A 0.0459 0.1948 0.7593 10 V 0.0559 0.2735 0.6706 11 G 0.0468 0.2129 0.7402 12 D 0.0773 0.2876 0.6351 13 S 0.1692 0.4475 0.3834 14 V 0.0112 0.9246 0.0642 15 A 0.0050 0.9528 0.0422 16 R 0.0047 0.9599 0.0354 17 V 0.0047 0.9602 0.0351 18 L 0.0047 0.9573 0.0379 19 E 0.0052 0.9459 0.0489 20 E 0.0071 0.8884 0.1045 21 M 0.0341 0.5796 0.3863 22 G 0.0607 0.1963 0.7430 23 L 0.0659 0.2219 0.7122 24 E 0.0819 0.3784 0.5397 25 T 0.1666 0.3518 0.4816 26 V 0.1549 0.2310 0.6141 27 G 0.0732 0.0883 0.8385 28 T 0.0660 0.1656 0.7685 29 H 0.0485 0.3536 0.5979 30 G 0.0294 0.5799 0.3907 31 T 0.0086 0.8902 0.1012 32 T 0.0047 0.9581 0.0372 33 A 0.0047 0.9604 0.0349 34 A 0.0047 0.9603 0.0350 35 L 0.0047 0.9597 0.0356 36 A 0.0047 0.9593 0.0360 37 L 0.0048 0.9565 0.0387 38 L 0.0052 0.9528 0.0420 39 N 0.0088 0.9451 0.0461 40 D 0.0053 0.9510 0.0437 41 Q 0.0052 0.9480 0.0468 42 V 0.0058 0.9354 0.0588 43 K 0.0095 0.9091 0.0814 44 K 0.0142 0.8320 0.1538 45 G 0.0350 0.7313 0.2337 46 G 0.0341 0.7036 0.2623 47 V 0.0535 0.7330 0.2135 48 M 0.0634 0.7525 0.1841 49 A 0.1262 0.6316 0.2422 50 C 0.1546 0.4229 0.4226 51 N 0.1243 0.2538 0.6219 52 Q 0.1680 0.1436 0.6884 53 V 0.3067 0.1103 0.5830 54 G 0.2543 0.0957 0.6500 55 G 0.2566 0.0782 0.6653 56 L 0.3013 0.1201 0.5787 57 S 0.2493 0.1279 0.6228 58 G 0.2561 0.1554 0.5885 59 A 0.4249 0.1082 0.4669 60 F 0.5156 0.0574 0.4270 61 I 0.4758 0.0341 0.4901 62 P 0.3206 0.0706 0.6088 63 V 0.1202 0.5212 0.3586 64 S 0.0671 0.5362 0.3968 65 E 0.0292 0.5833 0.3875 66 D 0.0186 0.6023 0.3791 67 E 0.0081 0.9234 0.0686 68 G 0.0064 0.9416 0.0520 69 M 0.0048 0.9538 0.0414 70 I 0.0049 0.9582 0.0369 71 A 0.0049 0.9594 0.0357 72 A 0.0048 0.9591 0.0361 73 V 0.0052 0.9513 0.0435 74 Q 0.0054 0.9334 0.0612 75 N 0.0424 0.5597 0.3979 76 G 0.0250 0.1593 0.8157 77 S 0.0742 0.0711 0.8547 78 L 0.2887 0.0384 0.6729 79 N 0.2216 0.0366 0.7418 80 L 0.0095 0.8712 0.1194 81 E 0.0062 0.9064 0.0875 82 K 0.0081 0.8961 0.0958 83 L 0.0162 0.8899 0.0939 84 E 0.0263 0.8390 0.1347 85 A 0.0363 0.8026 0.1611 86 M 0.0534 0.7253 0.2213 87 T 0.1065 0.6173 0.2762 88 A 0.1949 0.4968 0.3083 89 I 0.3182 0.4119 0.2699 90 C 0.3660 0.3226 0.3115 91 S 0.3403 0.2239 0.4358 92 V 0.2392 0.2106 0.5501 93 G 0.2465 0.1231 0.6304 94 L 0.3059 0.1343 0.5598 95 D 0.3597 0.1433 0.4970 96 M 0.5743 0.0739 0.3518 97 I 0.6344 0.0321 0.3336 98 A 0.6576 0.0184 0.3239 99 I 0.4461 0.0193 0.5346 100 P 0.1601 0.1217 0.7182 101 E 0.0484 0.1304 0.8212 102 D 0.0519 0.1777 0.7704 103 T 0.0834 0.0495 0.8671 104 P 0.0597 0.1044 0.8358 105 A 0.0050 0.9374 0.0576 106 E 0.0048 0.9524 0.0429 107 T 0.0048 0.9565 0.0388 108 I 0.0047 0.9584 0.0369 109 A 0.0047 0.9577 0.0376 110 A 0.0047 0.9527 0.0425 111 M 0.0047 0.9516 0.0436 112 I 0.0054 0.9444 0.0502 113 A 0.0048 0.9327 0.0625 114 D 0.0055 0.9033 0.0913 115 E 0.0053 0.9330 0.0617 116 A 0.0063 0.9347 0.0591 117 A 0.0092 0.9311 0.0596 118 I 0.0130 0.9296 0.0574 119 G 0.0367 0.8925 0.0708 120 V 0.0395 0.8627 0.0978 121 I 0.0447 0.7388 0.2165 122 N 0.0339 0.3283 0.6379 123 M 0.0303 0.0768 0.8928 124 K 0.1658 0.0197 0.8145 125 T 0.3294 0.0094 0.6611 126 T 0.6347 0.0273 0.3380 127 A 0.8804 0.0067 0.1129 128 V 0.9188 0.0037 0.0775 129 R 0.9222 0.0037 0.0742 130 I 0.8883 0.0054 0.1063 131 I 0.8059 0.0054 0.1887 132 P 0.6081 0.0094 0.3825 133 K 0.2756 0.0318 0.6925 134 G 0.0816 0.0599 0.8585 135 K 0.0467 0.0633 0.8900 136 E 0.0638 0.0558 0.8804 137 G 0.1048 0.0634 0.8318 138 D 0.2877 0.0866 0.6256 139 M 0.6891 0.0648 0.2460 140 I 0.7951 0.0468 0.1581 141 E 0.7693 0.0601 0.1706 142 F 0.5848 0.0907 0.3245 143 G 0.3241 0.1218 0.5541 144 G 0.2440 0.1629 0.5932 145 L 0.2978 0.2019 0.5004 146 L 0.2839 0.1739 0.5422 147 G 0.1851 0.0925 0.7225 148 T 0.2443 0.0488 0.7069 149 A 0.3226 0.0134 0.6640 150 P 0.4033 0.0129 0.5837 151 V 0.7721 0.0150 0.2129 152 M 0.8170 0.0121 0.1710 153 K 0.7900 0.0111 0.1989 154 V 0.5407 0.0331 0.4262 155 N 0.2334 0.0556 0.7109 156 G 0.0883 0.0980 0.8137 157 A 0.1099 0.0732 0.8169 158 S 0.1342 0.0508 0.8149 159 S 0.0557 0.5330 0.4113 160 V 0.0551 0.7509 0.1940 161 D 0.0902 0.7814 0.1284 162 F 0.1392 0.7334 0.1274 163 I 0.1432 0.6804 0.1764 164 S 0.1172 0.6099 0.2729 165 R 0.0615 0.4472 0.4914 166 G 0.0565 0.1376 0.8059 167 G 0.1086 0.0578 0.8336 168 Q 0.2694 0.0362 0.6945 169 I 0.2720 0.0376 0.6904 170 P 0.2566 0.0420 0.7014 171 A 0.2205 0.1307 0.6488 172 P 0.2047 0.1983 0.5970 173 I 0.1857 0.3804 0.4339 174 H 0.1765 0.4123 0.4111 175 S 0.1698 0.3556 0.4746 176 F 0.2085 0.2075 0.5840 177 K 0.1463 0.1178 0.7359 178 N 0.0747 0.0310 0.8943