# This file is the result of combining several RDB files, specifically # T0289.t06.dssp-ebghstl.rdb (weight 1.53986) # T0289.t06.stride-ebghtl.rdb (weight 1.24869) # T0289.t06.str2.rdb (weight 1.54758) # T0289.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 T0289.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0289 # Using neural net t04-2621-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 T0289.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 13.7277 # # ============================================ # Comments from T0289.t06.stride-ebghtl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 13.7277 # # ============================================ # Comments from T0289.t06.str2.rdb # ============================================ # TARGET T0289 # 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 T0289.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 13.7277 # # ============================================ # Comments from T0289.t06.alpha.rdb # ============================================ # TARGET T0289 # 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 T0289.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 13.7277 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0184 0.5564 0.4252 2 L 0.0239 0.7376 0.2385 3 D 0.0258 0.8172 0.1570 4 F 0.0337 0.8615 0.1049 5 I 0.0323 0.8672 0.1004 6 Q 0.0403 0.8663 0.0934 7 R 0.0489 0.8426 0.1085 8 F 0.0381 0.7419 0.2199 9 N 0.0497 0.5619 0.3885 10 E 0.0480 0.2683 0.6837 11 G 0.0304 0.0532 0.9164 12 K 0.0937 0.0409 0.8653 13 E 0.3052 0.0232 0.6716 14 F 0.1603 0.0134 0.8263 15 P 0.0951 0.0147 0.8902 16 P 0.0870 0.2187 0.6943 17 C 0.0966 0.2614 0.6421 18 A 0.3568 0.2007 0.4425 19 I 0.6894 0.0379 0.2727 20 D 0.8443 0.0251 0.1306 21 V 0.8685 0.0390 0.0925 22 Y 0.8601 0.0429 0.0970 23 K 0.8450 0.0425 0.1125 24 I 0.7455 0.0659 0.1886 25 M 0.6174 0.0795 0.3030 26 E 0.5105 0.1180 0.3716 27 K 0.5689 0.0712 0.3599 28 V 0.6037 0.0266 0.3696 29 D 0.5319 0.0241 0.4440 30 Y 0.3566 0.0194 0.6240 31 P 0.3393 0.0243 0.6363 32 R 0.3658 0.0452 0.5890 33 N 0.1204 0.0365 0.8430 34 E 0.0446 0.1270 0.8284 35 S 0.0605 0.0262 0.9133 36 G 0.0677 0.0248 0.9075 37 D 0.2609 0.0159 0.7232 38 V 0.7260 0.0140 0.2600 39 A 0.8268 0.0205 0.1526 40 A 0.8983 0.0107 0.0910 41 V 0.9055 0.0097 0.0848 42 I 0.8542 0.0153 0.1305 43 H 0.4346 0.0236 0.5418 44 P 0.0959 0.2737 0.6304 45 N 0.0590 0.2561 0.6849 46 L 0.0862 0.3771 0.5367 47 Q 0.1445 0.2224 0.6331 48 D 0.0843 0.2469 0.6687 49 Q 0.0819 0.2300 0.6880 50 D 0.1322 0.1384 0.7294 51 W 0.1746 0.1650 0.6604 52 K 0.2942 0.0978 0.6079 53 P 0.4345 0.1020 0.4635 54 L 0.3021 0.0669 0.6310 55 H 0.1015 0.0246 0.8739 56 P 0.0313 0.0705 0.8982 57 G 0.0216 0.0407 0.9377 58 D 0.1099 0.0187 0.8714 59 P 0.2364 0.0429 0.7207 60 V 0.5708 0.0743 0.3549 61 F 0.7831 0.0405 0.1763 62 V 0.8209 0.0307 0.1485 63 S 0.6981 0.0238 0.2782 64 L 0.4037 0.0537 0.5426 65 D 0.0914 0.0307 0.8779 66 G 0.0852 0.0335 0.8812 67 K 0.4545 0.0149 0.5306 68 V 0.8457 0.0053 0.1491 69 I 0.8081 0.0072 0.1846 70 P 0.7198 0.0120 0.2682 71 L 0.4316 0.0461 0.5223 72 G 0.1430 0.0545 0.8026 73 G 0.0871 0.0543 0.8586 74 D 0.1167 0.0819 0.8014 75 C 0.2613 0.0629 0.6758 76 T 0.4677 0.0352 0.4971 77 V 0.5604 0.0393 0.4003 78 Y 0.5480 0.0462 0.4058 79 P 0.4723 0.1442 0.3835 80 V 0.6006 0.2087 0.1907 81 F 0.5445 0.3056 0.1499 82 V 0.3187 0.5668 0.1145 83 N 0.1370 0.6536 0.2094 84 E 0.0992 0.6893 0.2115 85 A 0.0270 0.8797 0.0933 86 A 0.0212 0.8933 0.0855 87 Y 0.0159 0.9019 0.0821 88 Y 0.0191 0.8852 0.0957 89 E 0.0179 0.8598 0.1223 90 K 0.0133 0.7535 0.2332 91 K 0.0179 0.6765 0.3057 92 E 0.0368 0.6882 0.2749 93 A 0.0777 0.6950 0.2273 94 F 0.1354 0.6495 0.2151 95 A 0.2413 0.5615 0.1972 96 K 0.2696 0.5066 0.2238 97 T 0.3982 0.3313 0.2705 98 T 0.4662 0.2396 0.2942 99 K 0.5300 0.1921 0.2779 100 L 0.5856 0.1611 0.2533 101 T 0.5916 0.1112 0.2972 102 L 0.5043 0.0726 0.4231 103 N 0.3025 0.0525 0.6450 104 A 0.0838 0.4821 0.4341 105 K 0.0326 0.6913 0.2761 106 S 0.0397 0.6912 0.2691 107 I 0.0519 0.7454 0.2027 108 R 0.0564 0.7399 0.2038 109 S 0.0477 0.7056 0.2467 110 T 0.0448 0.5899 0.3653 111 L 0.0692 0.3845 0.5464 112 H 0.0432 0.1449 0.8119