# This file is the result of combining several RDB files, specifically # T0380.t06.dssp-ebghstl.rdb (weight 1.53986) # T0380.t06.stride-ebghtl.rdb (weight 1.24869) # T0380.t06.str2.rdb (weight 1.54758) # T0380.t06.alpha.rdb (weight 0.659012) # T0380.t04.dssp-ebghstl.rdb (weight 1.53986) # T0380.t04.stride-ebghtl.rdb (weight 1.24869) # T0380.t04.str2.rdb (weight 1.54758) # T0380.t04.alpha.rdb (weight 0.659012) # T0380.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0380.t2k.stride-ebghtl.rdb (weight 1.24869) # T0380.t2k.str2.rdb (weight 1.54758) # T0380.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 T0380.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0380 # 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 T0380.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 1013 # # ============================================ # Comments from T0380.t06.stride-ebghtl.rdb # ============================================ # TARGET T0380 # 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 T0380.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 1013 # # ============================================ # Comments from T0380.t06.str2.rdb # ============================================ # TARGET T0380 # 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 T0380.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 1013 # # ============================================ # Comments from T0380.t06.alpha.rdb # ============================================ # TARGET T0380 # 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 T0380.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 1013 # # ============================================ # Comments from T0380.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0380 # 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 T0380.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 1009 # # ============================================ # Comments from T0380.t04.stride-ebghtl.rdb # ============================================ # TARGET T0380 # 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 T0380.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 1009 # # ============================================ # Comments from T0380.t04.str2.rdb # ============================================ # TARGET T0380 # 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 T0380.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 1009 # # ============================================ # Comments from T0380.t04.alpha.rdb # ============================================ # TARGET T0380 # 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 T0380.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 1009 # # ============================================ # Comments from T0380.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0380 # 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 T0380.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 104 # # ============================================ # Comments from T0380.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0380 # 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 T0380.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 104 # # ============================================ # Comments from T0380.t2k.str2.rdb # ============================================ # TARGET T0380 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0380.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 104 # # ============================================ # Comments from T0380.t2k.alpha.rdb # ============================================ # TARGET T0380 # 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 T0380.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 104 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0406 0.1194 0.8400 2 I 0.0485 0.2247 0.7269 3 D 0.0252 0.4960 0.4788 4 E 0.0102 0.8042 0.1856 5 K 0.0099 0.8402 0.1499 6 F 0.0074 0.8850 0.1076 7 L 0.0059 0.9345 0.0596 8 I 0.0057 0.9451 0.0493 9 E 0.0049 0.9514 0.0437 10 S 0.0051 0.9498 0.0451 11 N 0.0048 0.9504 0.0448 12 E 0.0049 0.9393 0.0558 13 L 0.0061 0.9042 0.0896 14 V 0.0168 0.8169 0.1663 15 E 0.0104 0.5802 0.4095 16 S 0.0277 0.1927 0.7796 17 S 0.0886 0.0261 0.8852 18 K 0.0743 0.0583 0.8674 19 I 0.8324 0.0103 0.1573 20 V 0.9014 0.0044 0.0942 21 M 0.9209 0.0035 0.0756 22 V 0.9021 0.0045 0.0934 23 G 0.8168 0.0072 0.1759 24 T 0.7315 0.0065 0.2620 25 N 0.7413 0.0140 0.2447 26 G 0.2264 0.0187 0.7549 27 E 0.0348 0.1045 0.8607 28 N 0.0480 0.0209 0.9311 29 G 0.0561 0.0296 0.9143 30 Y 0.1971 0.0133 0.7896 31 P 0.5691 0.0201 0.4108 32 N 0.4820 0.0437 0.4742 33 I 0.5902 0.0284 0.3814 34 K 0.5617 0.0305 0.4078 35 A 0.6046 0.0407 0.3547 36 M 0.6413 0.0530 0.3057 37 M 0.6672 0.0490 0.2838 38 R 0.6390 0.0732 0.2878 39 L 0.6152 0.0654 0.3195 40 K 0.6036 0.0619 0.3345 41 H 0.4907 0.0864 0.4229 42 D 0.2976 0.1302 0.5722 43 G 0.1679 0.1005 0.7316 44 L 0.0882 0.0685 0.8433 45 K 0.0980 0.0452 0.8569 46 K 0.6622 0.0083 0.3295 47 F 0.8963 0.0035 0.1003 48 W 0.9170 0.0039 0.0791 49 L 0.9110 0.0045 0.0845 50 S 0.8511 0.0081 0.1408 51 T 0.5476 0.0193 0.4331 52 N 0.1276 0.0446 0.8278 53 T 0.0225 0.1184 0.8591 54 S 0.0303 0.1071 0.8626 55 T 0.0567 0.2586 0.6847 56 R 0.0594 0.5745 0.3660 57 M 0.0773 0.7163 0.2064 58 V 0.0513 0.8413 0.1075 59 E 0.0474 0.8680 0.0847 60 R 0.0335 0.8671 0.0994 61 L 0.0351 0.8540 0.1110 62 K 0.0356 0.7578 0.2066 63 K 0.0359 0.5163 0.4479 64 N 0.0789 0.0712 0.8499 65 N 0.0443 0.0823 0.8734 66 K 0.2057 0.0578 0.7364 67 I 0.7110 0.0088 0.2802 68 C 0.8603 0.0074 0.1323 69 L 0.9217 0.0034 0.0748 70 Y 0.9129 0.0039 0.0832 71 F 0.8870 0.0047 0.1083 72 V 0.7616 0.0155 0.2230 73 D 0.3528 0.0188 0.6283 74 D 0.0492 0.1651 0.7858 75 N 0.0367 0.2125 0.7508 76 K 0.1065 0.2053 0.6882 77 F 0.3363 0.0574 0.6063 78 A 0.7095 0.0275 0.2630 79 G 0.8998 0.0048 0.0955 80 L 0.9214 0.0034 0.0753 81 M 0.9255 0.0036 0.0709 82 L 0.9215 0.0036 0.0748 83 V 0.8663 0.0182 0.1155 84 G 0.8457 0.0075 0.1468 85 T 0.8776 0.0079 0.1145 86 I 0.8824 0.0070 0.1106 87 E 0.8865 0.0053 0.1082 88 I 0.8785 0.0052 0.1163 89 L 0.6664 0.0208 0.3128 90 H 0.3502 0.0221 0.6277 91 D 0.1143 0.0734 0.8124 92 R 0.0069 0.8631 0.1300 93 A 0.0070 0.9040 0.0890 94 S 0.0068 0.9172 0.0760 95 K 0.0083 0.9142 0.0774 96 E 0.0108 0.8956 0.0937 97 M 0.0105 0.8504 0.1391 98 L 0.0178 0.7575 0.2247 99 W 0.0273 0.6183 0.3543 100 T 0.0440 0.4862 0.4697 101 D 0.0241 0.7098 0.2662 102 G 0.0243 0.7609 0.2148 103 C 0.0216 0.8054 0.1730 104 E 0.0283 0.8041 0.1676 105 I 0.0391 0.7091 0.2519 106 Y 0.0664 0.5568 0.3768 107 Y 0.1017 0.2532 0.6451 108 P 0.0444 0.2567 0.6989 109 L 0.0452 0.1473 0.8075 110 G 0.0511 0.0907 0.8581 111 I 0.0545 0.1395 0.8060 112 D 0.0595 0.1130 0.8275 113 D 0.0982 0.0552 0.8466 114 P 0.0490 0.1322 0.8188 115 D 0.0951 0.0906 0.8143 116 Y 0.6100 0.0232 0.3668 117 T 0.8528 0.0057 0.1414 118 A 0.9126 0.0032 0.0842 119 L 0.9103 0.0042 0.0855 120 C 0.9046 0.0039 0.0914 121 F 0.8363 0.0072 0.1565 122 T 0.5592 0.0101 0.4308 123 A 0.1743 0.2175 0.6083 124 E 0.0940 0.2418 0.6641 125 W 0.2762 0.2187 0.5051 126 G 0.5735 0.0421 0.3845 127 N 0.8218 0.0239 0.1544 128 Y 0.8689 0.0207 0.1105 129 Y 0.7843 0.0448 0.1709 130 R 0.6161 0.0470 0.3368 131 H 0.2091 0.0608 0.7301 132 L 0.0564 0.1362 0.8074 133 K 0.0530 0.2654 0.6816 134 N 0.1109 0.3925 0.4966 135 I 0.2188 0.5584 0.2227 136 T 0.2527 0.6403 0.1071 137 F 0.2459 0.6753 0.0787 138 K 0.2161 0.7117 0.0722 139 I 0.1443 0.7903 0.0655 140 D 0.1412 0.7841 0.0747 141 E 0.1354 0.7636 0.1009 142 I 0.1231 0.7079 0.1690 143 Y 0.1368 0.4936 0.3696 144 N 0.0756 0.2868 0.6376 145 Y 0.0375 0.0617 0.9008