# This file is the result of combining several RDB files, specifically # T0382.t04.dssp-ebghstl.rdb (weight 1.53986) # T0382.t04.stride-ebghtl.rdb (weight 1.24869) # T0382.t04.str2.rdb (weight 1.54758) # T0382.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 T0382.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t04.stride-ebghtl.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t04.str2.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ # Comments from T0382.t04.alpha.rdb # ============================================ # TARGET T0382 # 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 T0382.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 8.40194 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0853 0.0426 0.8721 2 S 0.1076 0.0714 0.8210 3 K 0.1117 0.1425 0.7458 4 L 0.1733 0.1210 0.7056 5 D 0.1774 0.0886 0.7340 6 L 0.0792 0.4739 0.4469 7 H 0.0836 0.4489 0.4675 8 Q 0.1842 0.3325 0.4833 9 M 0.2402 0.0776 0.6822 10 T 0.1709 0.0681 0.7610 11 T 0.0100 0.8953 0.0947 12 Q 0.0047 0.9469 0.0483 13 D 0.0047 0.9509 0.0444 14 L 0.0047 0.9566 0.0388 15 V 0.0047 0.9600 0.0353 16 A 0.0046 0.9612 0.0341 17 L 0.0047 0.9599 0.0354 18 F 0.0047 0.9590 0.0364 19 A 0.0047 0.9596 0.0357 20 K 0.0046 0.9587 0.0367 21 V 0.0047 0.9506 0.0447 22 T 0.0048 0.9367 0.0585 23 V 0.0051 0.9129 0.0820 24 E 0.0060 0.8797 0.1143 25 Q 0.0064 0.8828 0.1108 26 D 0.0066 0.8885 0.1049 27 D 0.0071 0.8639 0.1290 28 A 0.0108 0.8644 0.1248 29 L 0.0227 0.7882 0.1891 30 L 0.0263 0.6831 0.2906 31 G 0.0222 0.7059 0.2719 32 N 0.0251 0.6856 0.2893 33 Q 0.0279 0.7325 0.2396 34 I 0.0135 0.8642 0.1223 35 S 0.0087 0.8893 0.1020 36 R 0.0073 0.9196 0.0731 37 F 0.0079 0.9289 0.0632 38 N 0.0082 0.9196 0.0722 39 R 0.0058 0.9311 0.0631 40 L 0.0052 0.9350 0.0598 41 F 0.0053 0.9415 0.0532 42 G 0.0054 0.9411 0.0535 43 V 0.0057 0.9485 0.0459 44 M 0.0047 0.9575 0.0378 45 A 0.0047 0.9585 0.0368 46 E 0.0047 0.9556 0.0397 47 I 0.0049 0.9503 0.0448 48 A 0.0048 0.9520 0.0431 49 D 0.0048 0.9453 0.0499 50 E 0.0050 0.9373 0.0577 51 L 0.0071 0.9089 0.0840 52 K 0.0090 0.8096 0.1814 53 A 0.0146 0.6586 0.3269 54 R 0.0485 0.2761 0.6754 55 D 0.0399 0.1796 0.7805 56 G 0.0260 0.1958 0.7782 57 D 0.0570 0.3366 0.6064 58 Q 0.0279 0.7980 0.1741 59 R 0.0169 0.8995 0.0835 60 T 0.0125 0.9230 0.0644 61 A 0.0134 0.9167 0.0699 62 L 0.0128 0.9073 0.0799 63 L 0.0112 0.9031 0.0857 64 S 0.0120 0.8740 0.1140 65 L 0.0158 0.8198 0.1644 66 F 0.0450 0.6583 0.2967 67 E 0.0638 0.3975 0.5387 68 Y 0.0709 0.0727 0.8564 69 P 0.0140 0.2163 0.7697 70 N 0.0491 0.2321 0.7188 71 M 0.0571 0.7058 0.2371 72 Q 0.0450 0.8557 0.0993 73 V 0.0557 0.8735 0.0708 74 R 0.0251 0.9190 0.0559 75 L 0.0090 0.9497 0.0413 76 Q 0.0084 0.9431 0.0485 77 A 0.0079 0.9432 0.0489 78 A 0.0112 0.9434 0.0454 79 K 0.0095 0.9400 0.0505 80 L 0.0106 0.9203 0.0692 81 T 0.0132 0.8869 0.0999 82 L 0.0308 0.7935 0.1757 83 A 0.0773 0.6840 0.2386 84 V 0.1192 0.5320 0.3488 85 A 0.1019 0.1197 0.7784 86 P 0.0568 0.1721 0.7712 87 V 0.0087 0.8314 0.1599 88 K 0.0118 0.8624 0.1258 89 A 0.0054 0.9313 0.0633 90 R 0.0054 0.9514 0.0432 91 E 0.0050 0.9577 0.0373 92 Q 0.0047 0.9581 0.0372 93 L 0.0047 0.9593 0.0360 94 E 0.0047 0.9594 0.0359 95 A 0.0047 0.9563 0.0390 96 I 0.0049 0.9435 0.0516 97 V 0.0059 0.9067 0.0874 98 S 0.0107 0.7079 0.2814 99 S 0.0446 0.4275 0.5279 100 K 0.0383 0.2206 0.7411 101 W 0.0711 0.1301 0.7987 102 F 0.1020 0.0501 0.8479 103 P 0.0747 0.0815 0.8438 104 Q 0.0638 0.1347 0.8015 105 A 0.0651 0.1830 0.7519 106 G 0.0609 0.1963 0.7427 107 D 0.0660 0.2948 0.6392 108 A 0.0245 0.7992 0.1763 109 G 0.0129 0.8708 0.1163 110 M 0.0230 0.8755 0.1015 111 C 0.0202 0.8992 0.0805 112 L 0.0118 0.9125 0.0757 113 D 0.0122 0.8649 0.1229 114 L 0.0167 0.8292 0.1542 115 L 0.0655 0.6466 0.2879 116 D 0.0567 0.4839 0.4593 117 D 0.0537 0.2473 0.6990 118 G 0.0716 0.0570 0.8714 119 T 0.2382 0.0431 0.7186 120 F 0.4292 0.0221 0.5487 121 K 0.3836 0.0160 0.6004 122 P 0.2059 0.0394 0.7546 123 K 0.0941 0.0605 0.8454