# This file is the result of combining several RDB files, specifically # T0555.t06.str2.rdb (weight 1.54425) # T0555.t06.str4.rdb (weight 0.924988) # T0555.t06.pb.rdb (weight 0.789901) # T0555.t06.bys.rdb (weight 0.748322) # T0555.t06.alpha.rdb (weight 0.678173) # 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 T0555.t06.str2.rdb # ============================================ # TARGET T0555 # Using neural net dunbrack-40pc-3157-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 T0555.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 27.539 # # ============================================ # Comments from T0555.t06.str4.rdb # ============================================ # TARGET T0555 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0555.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 27.539 # # ============================================ # Comments from T0555.t06.pb.rdb # ============================================ # TARGET T0555 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0555.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 27.539 # # ============================================ # Comments from T0555.t06.bys.rdb # ============================================ # TARGET T0555 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0555.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 27.539 # # ============================================ # Comments from T0555.t06.alpha.rdb # ============================================ # TARGET T0555 # Using neural net dunbrack-40pc-3157-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 T0555.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 27.539 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2579 0.0491 0.6930 2 P 0.1857 0.0826 0.7316 3 Q 0.1610 0.2559 0.5830 4 S 0.1996 0.3235 0.4770 5 Y 0.2856 0.2463 0.4681 6 F 0.3048 0.2209 0.4743 7 N 0.2183 0.2437 0.5380 8 A 0.1328 0.4268 0.4404 9 A 0.1341 0.4021 0.4638 10 A 0.1444 0.3693 0.4863 11 K 0.1985 0.2663 0.5352 12 R 0.2554 0.1835 0.5612 13 Q 0.3701 0.1420 0.4879 14 K 0.4604 0.1283 0.4112 15 Y 0.5154 0.1018 0.3828 16 A 0.5225 0.0885 0.3890 17 M 0.4521 0.0635 0.4845 18 K 0.3139 0.0340 0.6520 19 P 0.1825 0.1248 0.6927 20 G 0.1142 0.1238 0.7620 21 L 0.1713 0.1168 0.7119 22 S 0.1733 0.0841 0.7427 23 A 0.0252 0.6594 0.3153 24 L 0.0169 0.7852 0.1979 25 E 0.0155 0.8708 0.1136 26 K 0.0097 0.9079 0.0824 27 N 0.0084 0.9187 0.0728 28 A 0.0083 0.9234 0.0683 29 V 0.0083 0.9243 0.0675 30 I 0.0083 0.9238 0.0679 31 K 0.0083 0.9240 0.0677 32 A 0.0083 0.9228 0.0689 33 A 0.0083 0.9234 0.0684 34 Y 0.0084 0.9191 0.0725 35 R 0.0084 0.9161 0.0755 36 Q 0.0089 0.9089 0.0822 37 I 0.0146 0.8358 0.1495 38 F 0.0262 0.7089 0.2649 39 E 0.0302 0.5500 0.4198 40 R 0.0556 0.4817 0.4627 41 D 0.1015 0.4148 0.4836 42 I 0.1460 0.4213 0.4327 43 T 0.2135 0.3776 0.4089 44 K 0.2080 0.4658 0.3261 45 A 0.1715 0.4893 0.3392 46 Y 0.1691 0.4703 0.3606 47 S 0.1571 0.4157 0.4271 48 Q 0.1502 0.4137 0.4362 49 S 0.1930 0.3836 0.4234 50 I 0.1782 0.4657 0.3560 51 S 0.1478 0.5387 0.3135 52 Y 0.1433 0.6024 0.2543 53 L 0.0535 0.8083 0.1383 54 E 0.0447 0.8382 0.1171 55 S 0.0510 0.8273 0.1217 56 Q 0.0563 0.7798 0.1639 57 V 0.1163 0.6250 0.2587 58 R 0.0913 0.5220 0.3866 59 N 0.0880 0.1489 0.7631 60 G 0.0562 0.0855 0.8582 61 D 0.2282 0.0735 0.6982 62 I 0.3946 0.0544 0.5510 63 S 0.3235 0.1207 0.5558 64 M 0.0872 0.6723 0.2405 65 K 0.0126 0.8665 0.1209 66 E 0.0091 0.9185 0.0724 67 F 0.0083 0.9237 0.0680 68 V 0.0083 0.9220 0.0696 69 R 0.0083 0.9206 0.0711 70 R 0.0085 0.9141 0.0774 71 L 0.0102 0.8807 0.1090 72 A 0.0147 0.8078 0.1774 73 K 0.0299 0.6255 0.3445 74 S 0.1060 0.4510 0.4429 75 P 0.0117 0.7508 0.2376 76 L 0.0107 0.8251 0.1642 77 Y 0.0177 0.8691 0.1133 78 R 0.0154 0.8804 0.1042 79 K 0.0262 0.8371 0.1367 80 Q 0.0417 0.7139 0.2445 81 F 0.0885 0.5375 0.3741 82 F 0.1497 0.3996 0.4507 83 E 0.2108 0.2845 0.5047 84 P 0.1331 0.3900 0.4768 85 F 0.1382 0.3429 0.5190 86 I 0.1267 0.3770 0.4963 87 N 0.0865 0.4995 0.4140 88 S 0.0795 0.6749 0.2456 89 R 0.0450 0.8169 0.1381 90 A 0.0377 0.8656 0.0968 91 L 0.0221 0.8997 0.0783 92 E 0.0126 0.9145 0.0729 93 L 0.0100 0.9171 0.0729 94 A 0.0098 0.9149 0.0753 95 F 0.0103 0.9063 0.0835 96 R 0.0106 0.9024 0.0870 97 H 0.0147 0.8778 0.1075 98 I 0.0311 0.7472 0.2218 99 L 0.0555 0.3857 0.5588 100 G 0.0635 0.1343 0.8023 101 R 0.1591 0.0849 0.7560 102 G 0.1748 0.0542 0.7710 103 P 0.1218 0.1679 0.7103 104 S 0.1170 0.1767 0.7062 105 S 0.1589 0.0780 0.7631 106 R 0.0149 0.7267 0.2584 107 E 0.0099 0.8607 0.1295 108 E 0.0097 0.9132 0.0771 109 V 0.0092 0.9132 0.0776 110 Q 0.0084 0.9152 0.0764 111 K 0.0087 0.9106 0.0808 112 Y 0.0102 0.9069 0.0829 113 F 0.0113 0.9039 0.0848 114 S 0.0129 0.9035 0.0836 115 I 0.0214 0.8810 0.0977 116 V 0.0371 0.8311 0.1318 117 S 0.0439 0.7335 0.2226 118 S 0.0404 0.5261 0.4335 119 G 0.0494 0.2221 0.7285 120 G 0.0829 0.1289 0.7882 121 L 0.1446 0.1837 0.6718 122 P 0.0584 0.6324 0.3092 123 A 0.0468 0.8046 0.1486 124 L 0.0564 0.8353 0.1083 125 V 0.0715 0.8313 0.0972 126 D 0.0490 0.8323 0.1187 127 A 0.0424 0.7468 0.2108 128 L 0.0606 0.6572 0.2822 129 V 0.1218 0.4610 0.4172 130 D 0.1170 0.2577 0.6252 131 S 0.1086 0.3830 0.5083 132 Q 0.0126 0.7521 0.2353 133 E 0.0113 0.8465 0.1422 134 Y 0.0168 0.8737 0.1095 135 A 0.0134 0.8699 0.1167 136 D 0.0184 0.8228 0.1588 137 Y 0.0328 0.6607 0.3065 138 F 0.0841 0.2678 0.6482 139 G 0.0770 0.1516 0.7714 140 E 0.1338 0.2447 0.6215 141 E 0.1837 0.2384 0.5779 142 T 0.3164 0.1603 0.5232 143 V 0.4652 0.0543 0.4804 144 P 0.4514 0.0897 0.4589 145 Y 0.4425 0.1264 0.4310 146 L 0.4175 0.1348 0.4476 147 R 0.3008 0.1323 0.5669 148 G 0.2206 0.0947 0.6848