# This file is the result of combining several RDB files, specifically # T0385.t06.dssp-ebghstl.rdb (weight 1.53986) # T0385.t06.stride-ebghtl.rdb (weight 1.24869) # T0385.t06.str2.rdb (weight 1.54758) # T0385.t06.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 T0385.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0385 # Using neural net t06-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 T0385.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 36.4986 # # ============================================ # Comments from T0385.t06.stride-ebghtl.rdb # ============================================ # TARGET T0385 # Using neural net t06-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 T0385.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 36.4986 # # ============================================ # Comments from T0385.t06.str2.rdb # ============================================ # TARGET T0385 # Using neural net t06-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 T0385.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 36.4986 # # ============================================ # Comments from T0385.t06.alpha.rdb # ============================================ # TARGET T0385 # Using neural net t06-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 T0385.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 36.4986 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0857 0.0460 0.8684 2 T 0.1568 0.0757 0.7676 3 S 0.1567 0.0859 0.7574 4 S 0.1337 0.0990 0.7673 5 E 0.1010 0.0765 0.8225 6 P 0.0856 0.1390 0.7754 7 A 0.0941 0.1625 0.7433 8 H 0.0927 0.1813 0.7260 9 G 0.0890 0.1351 0.7759 10 A 0.1306 0.0885 0.7809 11 T 0.1172 0.0486 0.8342 12 P 0.0886 0.1333 0.7781 13 K 0.0711 0.1751 0.7538 14 R 0.1023 0.1161 0.7816 15 S 0.0980 0.0311 0.8709 16 P 0.0698 0.0726 0.8576 17 S 0.0811 0.0658 0.8531 18 E 0.0554 0.1213 0.8233 19 G 0.0441 0.1064 0.8495 20 S 0.0543 0.3440 0.6017 21 A 0.0376 0.6240 0.3384 22 D 0.0187 0.8369 0.1445 23 N 0.0055 0.9320 0.0625 24 A 0.0048 0.9470 0.0482 25 A 0.0047 0.9529 0.0424 26 L 0.0047 0.9581 0.0373 27 C 0.0047 0.9602 0.0352 28 D 0.0047 0.9593 0.0361 29 A 0.0047 0.9601 0.0352 30 L 0.0047 0.9587 0.0366 31 A 0.0047 0.9589 0.0364 32 V 0.0047 0.9585 0.0368 33 E 0.0047 0.9567 0.0386 34 H 0.0047 0.9546 0.0407 35 A 0.0048 0.9485 0.0467 36 T 0.0048 0.9470 0.0481 37 I 0.0057 0.9388 0.0556 38 Y 0.0090 0.9141 0.0768 39 G 0.0162 0.8687 0.1151 40 Y 0.0283 0.8030 0.1687 41 G 0.0636 0.6319 0.3046 42 I 0.0842 0.6670 0.2488 43 V 0.1146 0.6145 0.2709 44 S 0.0871 0.4946 0.4183 45 A 0.0667 0.3485 0.5848 46 L 0.0948 0.1919 0.7133 47 S 0.0805 0.0792 0.8403 48 P 0.0512 0.0798 0.8690 49 P 0.0265 0.2316 0.7419 50 G 0.0381 0.2959 0.6660 51 V 0.0287 0.7291 0.2422 52 N 0.0079 0.8946 0.0975 53 F 0.0050 0.9447 0.0503 54 L 0.0055 0.9497 0.0448 55 V 0.0047 0.9557 0.0396 56 A 0.0047 0.9587 0.0367 57 D 0.0047 0.9552 0.0401 58 A 0.0048 0.9453 0.0499 59 L 0.0048 0.9443 0.0509 60 K 0.0048 0.9351 0.0601 61 Q 0.0052 0.9038 0.0909 62 H 0.0058 0.8990 0.0952 63 R 0.0064 0.9126 0.0810 64 H 0.0064 0.8783 0.1153 65 R 0.0076 0.8979 0.0945 66 R 0.0049 0.9452 0.0499 67 D 0.0047 0.9574 0.0379 68 D 0.0047 0.9584 0.0369 69 V 0.0047 0.9603 0.0351 70 I 0.0046 0.9615 0.0339 71 V 0.0046 0.9612 0.0341 72 M 0.0047 0.9603 0.0350 73 L 0.0047 0.9579 0.0374 74 S 0.0050 0.9396 0.0554 75 A 0.0056 0.8746 0.1198 76 R 0.0430 0.3913 0.5657 77 G 0.0370 0.0245 0.9385 78 V 0.0828 0.0165 0.9007 79 T 0.2087 0.0334 0.7579 80 A 0.2136 0.0485 0.7379 81 P 0.1876 0.0797 0.7327 82 I 0.2034 0.1740 0.6226 83 A 0.1601 0.2576 0.5823 84 A 0.1240 0.3739 0.5021 85 A 0.1285 0.2474 0.6242 86 G 0.1968 0.0839 0.7193 87 Y 0.4978 0.0183 0.4839 88 Q 0.5332 0.0150 0.4517 89 L 0.4281 0.0152 0.5568 90 P 0.2806 0.0213 0.6980 91 M 0.2305 0.0388 0.7307 92 Q 0.2084 0.0325 0.7591 93 V 0.1387 0.0602 0.8012 94 S 0.0879 0.0554 0.8568 95 S 0.0692 0.0305 0.9003 96 A 0.0048 0.9490 0.0462 97 A 0.0047 0.9571 0.0382 98 D 0.0047 0.9582 0.0370 99 A 0.0047 0.9602 0.0351 100 A 0.0047 0.9606 0.0347 101 R 0.0046 0.9608 0.0346 102 L 0.0047 0.9600 0.0353 103 A 0.0047 0.9586 0.0367 104 V 0.0047 0.9527 0.0426 105 R 0.0050 0.9241 0.0709 106 M 0.0058 0.8822 0.1120 107 E 0.0095 0.8456 0.1449 108 N 0.0085 0.8507 0.1408 109 D 0.0143 0.8501 0.1355 110 G 0.0104 0.9140 0.0755 111 A 0.0091 0.9402 0.0506 112 T 0.0110 0.9441 0.0449 113 A 0.0093 0.9428 0.0479 114 W 0.0089 0.9357 0.0554 115 R 0.0088 0.9203 0.0709 116 A 0.0102 0.8745 0.1153 117 V 0.0125 0.8506 0.1369 118 V 0.0157 0.8639 0.1205 119 E 0.0113 0.8327 0.1560 120 H 0.0157 0.7338 0.2506 121 A 0.0592 0.4467 0.4941 122 E 0.0450 0.2884 0.6666 123 T 0.0591 0.0944 0.8464 124 A 0.0067 0.7080 0.2853 125 D 0.0117 0.8143 0.1741 126 D 0.0070 0.9285 0.0646 127 R 0.0051 0.9513 0.0436 128 V 0.0079 0.9497 0.0423 129 F 0.0081 0.9471 0.0447 130 A 0.0056 0.9503 0.0441 131 S 0.0055 0.9479 0.0465 132 T 0.0062 0.9371 0.0568 133 A 0.0062 0.9231 0.0707 134 L 0.0068 0.8977 0.0955 135 T 0.0060 0.9074 0.0866 136 E 0.0048 0.9474 0.0478 137 S 0.0047 0.9562 0.0390 138 A 0.0047 0.9596 0.0357 139 V 0.0047 0.9608 0.0346 140 M 0.0047 0.9605 0.0348 141 A 0.0047 0.9603 0.0350 142 T 0.0047 0.9600 0.0353 143 R 0.0047 0.9574 0.0380 144 W 0.0047 0.9562 0.0391 145 N 0.0049 0.9515 0.0437 146 R 0.0052 0.9374 0.0574 147 V 0.0065 0.8984 0.0951 148 L 0.0430 0.6355 0.3216 149 G 0.0272 0.2237 0.7491 150 A 0.0580 0.1527 0.7894 151 W 0.0953 0.0520 0.8527 152 P 0.1273 0.0473 0.8253 153 I 0.2383 0.0586 0.7031 154 T 0.2486 0.0709 0.6804 155 A 0.2524 0.1048 0.6428 156 A 0.2685 0.0886 0.6429 157 F 0.2224 0.0490 0.7286 158 P 0.1401 0.0658 0.7942 159 G 0.0914 0.0501 0.8585 160 G 0.0622 0.0653 0.8724 161 D 0.0619 0.0636 0.8745 162 E 0.0446 0.1004 0.8550