# This file is the result of combining several RDB files, specifically # T0283.t06.dssp-ebghstl.rdb (weight 1.53986) # T0283.t06.stride-ebghtl.rdb (weight 1.24869) # T0283.t06.str2.rdb (weight 1.54758) # T0283.t06.alpha.rdb (weight 0.659012) # T0283.t04.dssp-ebghstl.rdb (weight 1.53986) # T0283.t04.stride-ebghtl.rdb (weight 1.24869) # T0283.t04.str2.rdb (weight 1.54758) # T0283.t04.alpha.rdb (weight 0.659012) # T0283.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0283.t2k.stride-ebghtl.rdb (weight 1.24869) # T0283.t2k.str2.rdb (weight 1.54758) # T0283.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 T0283.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0283 # 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 T0283.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 7.00874 # # ============================================ # Comments from T0283.t06.stride-ebghtl.rdb # ============================================ # TARGET T0283 # 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 T0283.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 7.00874 # # ============================================ # Comments from T0283.t06.str2.rdb # ============================================ # TARGET T0283 # 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 T0283.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 7.00874 # # ============================================ # Comments from T0283.t06.alpha.rdb # ============================================ # TARGET T0283 # 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 T0283.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 7.00874 # # ============================================ # Comments from T0283.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0283 # 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 T0283.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 7.04591 # # ============================================ # Comments from T0283.t04.stride-ebghtl.rdb # ============================================ # TARGET T0283 # 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 T0283.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 7.04591 # # ============================================ # Comments from T0283.t04.str2.rdb # ============================================ # TARGET T0283 # 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 T0283.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 7.04591 # # ============================================ # Comments from T0283.t04.alpha.rdb # ============================================ # TARGET T0283 # 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 T0283.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 7.04591 # # ============================================ # Comments from T0283.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0283 # 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 T0283.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 17 # # ============================================ # Comments from T0283.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0283 # 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 T0283.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 17 # # ============================================ # Comments from T0283.t2k.str2.rdb # ============================================ # TARGET T0283 # 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 T0283.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 12.5344 # # ============================================ # Comments from T0283.t2k.alpha.rdb # ============================================ # TARGET T0283 # 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 T0283.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 17 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0419 0.2301 0.7280 2 S 0.0442 0.4585 0.4973 3 F 0.0215 0.7406 0.2379 4 I 0.0144 0.8478 0.1378 5 E 0.0104 0.8968 0.0929 6 K 0.0116 0.8934 0.0950 7 M 0.0171 0.8801 0.1028 8 I 0.0152 0.8577 0.1272 9 G 0.0193 0.7565 0.2243 10 S 0.0235 0.7000 0.2765 11 L 0.0200 0.7068 0.2731 12 N 0.0125 0.6820 0.3054 13 D 0.0123 0.7324 0.2553 14 K 0.0068 0.8951 0.0980 15 R 0.0062 0.9311 0.0627 16 E 0.0049 0.9416 0.0535 17 W 0.0049 0.9498 0.0453 18 K 0.0047 0.9578 0.0375 19 A 0.0048 0.9557 0.0396 20 M 0.0048 0.9552 0.0401 21 E 0.0049 0.9569 0.0382 22 A 0.0051 0.9494 0.0455 23 R 0.0049 0.9410 0.0540 24 A 0.0054 0.9198 0.0748 25 K 0.0090 0.8170 0.1741 26 A 0.0112 0.5835 0.4053 27 L 0.0308 0.3752 0.5940 28 P 0.0174 0.5152 0.4673 29 K 0.0065 0.8606 0.1329 30 E 0.0066 0.8574 0.1360 31 Y 0.0057 0.9284 0.0659 32 H 0.0049 0.9451 0.0500 33 H 0.0048 0.9483 0.0468 34 A 0.0049 0.9504 0.0447 35 Y 0.0048 0.9537 0.0415 36 K 0.0048 0.9534 0.0418 37 A 0.0048 0.9539 0.0413 38 I 0.0048 0.9547 0.0405 39 Q 0.0048 0.9547 0.0405 40 K 0.0055 0.9495 0.0450 41 Y 0.0064 0.9414 0.0521 42 M 0.0080 0.9286 0.0633 43 W 0.0131 0.8911 0.0958 44 T 0.0208 0.7839 0.1953 45 S 0.0361 0.4923 0.4716 46 G 0.0509 0.1235 0.8256 47 G 0.0413 0.1142 0.8445 48 P 0.0426 0.2117 0.7457 49 T 0.0336 0.2891 0.6772 50 D 0.0357 0.3087 0.6555 51 W 0.0402 0.7261 0.2338 52 Q 0.0133 0.8081 0.1785 53 D 0.0149 0.7898 0.1953 54 T 0.0079 0.8959 0.0962 55 K 0.0071 0.9285 0.0643 56 R 0.0055 0.9255 0.0690 57 I 0.0060 0.9322 0.0618 58 F 0.0057 0.9442 0.0501 59 G 0.0051 0.9470 0.0479 60 G 0.0051 0.9436 0.0513 61 I 0.0048 0.9532 0.0420 62 L 0.0047 0.9526 0.0427 63 D 0.0047 0.9527 0.0426 64 L 0.0048 0.9508 0.0444 65 F 0.0048 0.9506 0.0446 66 E 0.0051 0.9416 0.0533 67 E 0.0060 0.9283 0.0657 68 G 0.0077 0.8988 0.0935 69 A 0.0101 0.8487 0.1412 70 A 0.0139 0.7193 0.2668 71 E 0.0355 0.3517 0.6128 72 G 0.0305 0.0562 0.9133 73 K 0.1111 0.0353 0.8535 74 K 0.2995 0.0498 0.6506 75 V 0.2075 0.5269 0.2655 76 T 0.1574 0.6308 0.2118 77 D 0.1700 0.6175 0.2126 78 L 0.1642 0.4976 0.3382 79 T 0.1445 0.3099 0.5455 80 G 0.0768 0.3603 0.5629 81 E 0.0408 0.5019 0.4573 82 D 0.0746 0.5708 0.3546 83 V 0.0065 0.9247 0.0688 84 A 0.0049 0.9354 0.0597 85 A 0.0050 0.9093 0.0858 86 F 0.0098 0.9160 0.0743 87 C 0.0048 0.9463 0.0489 88 D 0.0047 0.9490 0.0463 89 E 0.0048 0.9467 0.0485 90 L 0.0055 0.9391 0.0553 91 M 0.0066 0.8970 0.0964 92 K 0.0070 0.8259 0.1671 93 D 0.0143 0.7024 0.2833 94 T 0.0563 0.4954 0.4483 95 K 0.0229 0.4103 0.5668 96 T 0.0311 0.5126 0.4563 97 W 0.0482 0.5388 0.4130 98 M 0.0598 0.6139 0.3263 99 D 0.0536 0.6798 0.2666 100 K 0.0286 0.8360 0.1353 101 Y 0.0286 0.8469 0.1244 102 R 0.0296 0.8475 0.1229 103 T 0.0317 0.8469 0.1215 104 K 0.0429 0.7849 0.1722 105 L 0.0345 0.7202 0.2453 106 N 0.0394 0.5905 0.3701 107 D 0.0441 0.5711 0.3848 108 S 0.0594 0.5528 0.3879 109 I 0.0871 0.4598 0.4531 110 G 0.1161 0.2697 0.6142 111 R 0.0982 0.1982 0.7035 112 D 0.0510 0.0387 0.9103