# This file is the result of combining several RDB files, specifically # T0289.t04.dssp-ebghstl.rdb (weight 1.53986) # T0289.t04.stride-ebghtl.rdb (weight 1.24869) # T0289.t04.str2.rdb (weight 1.54758) # T0289.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 T0289.t04.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.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 12.0479 # # ============================================ # Comments from T0289.t04.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.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 12.0479 # # ============================================ # Comments from T0289.t04.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.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 12.0479 # # ============================================ # Comments from T0289.t04.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.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 12.0479 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.0618 0.0144 0.9237 2 P 0.0742 0.0740 0.8518 3 C 0.0948 0.1068 0.7984 4 A 0.3881 0.0984 0.5135 5 I 0.6511 0.0326 0.3162 6 D 0.8433 0.0189 0.1378 7 V 0.8733 0.0318 0.0950 8 Y 0.8571 0.0386 0.1043 9 K 0.8438 0.0381 0.1182 10 I 0.7372 0.0629 0.1998 11 M 0.6152 0.0792 0.3055 12 E 0.5127 0.1219 0.3654 13 K 0.5673 0.0748 0.3578 14 V 0.5975 0.0280 0.3745 15 D 0.5213 0.0260 0.4527 16 Y 0.3468 0.0198 0.6334 17 P 0.3306 0.0246 0.6448 18 R 0.3576 0.0468 0.5956 19 N 0.1225 0.0395 0.8380 20 E 0.0484 0.1279 0.8237 21 S 0.0618 0.0264 0.9118 22 G 0.0687 0.0250 0.9063 23 D 0.2674 0.0159 0.7167 24 V 0.7326 0.0133 0.2541 25 A 0.8299 0.0193 0.1508 26 A 0.9001 0.0098 0.0901 27 V 0.9066 0.0091 0.0843 28 I 0.8565 0.0142 0.1293 29 H 0.4349 0.0226 0.5425 30 P 0.0954 0.2654 0.6391 31 N 0.0588 0.2467 0.6945 32 L 0.0889 0.3628 0.5483 33 Q 0.1460 0.2170 0.6370 34 D 0.0863 0.2454 0.6682 35 Q 0.0804 0.2318 0.6878 36 D 0.1313 0.1389 0.7298 37 W 0.1769 0.1650 0.6581 38 K 0.2984 0.0978 0.6038 39 P 0.4427 0.1011 0.4562 40 L 0.3072 0.0672 0.6257 41 H 0.1029 0.0246 0.8725 42 P 0.0316 0.0699 0.8985 43 G 0.0216 0.0400 0.9384 44 D 0.1092 0.0183 0.8724 45 P 0.2435 0.0389 0.7176 46 V 0.5952 0.0655 0.3393 47 F 0.7986 0.0351 0.1664 48 V 0.8329 0.0272 0.1399 49 S 0.7167 0.0221 0.2612 50 L 0.4270 0.0517 0.5213 51 D 0.0926 0.0304 0.8770 52 G 0.0846 0.0337 0.8817 53 K 0.4648 0.0148 0.5204 54 V 0.8476 0.0050 0.1474 55 I 0.8085 0.0073 0.1843 56 P 0.7191 0.0117 0.2692 57 L 0.4266 0.0470 0.5265 58 G 0.1397 0.0547 0.8056 59 G 0.0853 0.0552 0.8595 60 D 0.1165 0.0830 0.8005 61 C 0.2593 0.0645 0.6762 62 T 0.4661 0.0362 0.4976 63 V 0.5558 0.0410 0.4032 64 Y 0.5404 0.0486 0.4109 65 P 0.4615 0.1517 0.3869 66 V 0.5931 0.2132 0.1937 67 F 0.5420 0.3069 0.1510 68 V 0.3239 0.5597 0.1164 69 N 0.1457 0.6411 0.2131 70 E 0.1054 0.6804 0.2142 71 A 0.0297 0.8716 0.0987 72 A 0.0226 0.8864 0.0910 73 Y 0.0180 0.8935 0.0885 74 Y 0.0223 0.8717 0.1059 75 E 0.0206 0.8424 0.1370 76 K 0.0145 0.7381 0.2474 77 K 0.0203 0.6676 0.3120 78 E 0.0399 0.6782 0.2819 79 A 0.0845 0.6869 0.2286 80 F 0.1443 0.6428 0.2129 81 A 0.2521 0.5552 0.1927 82 K 0.2809 0.4989 0.2202 83 T 0.4032 0.3295 0.2673 84 T 0.4679 0.2388 0.2933 85 K 0.5276 0.1921 0.2803 86 L 0.5831 0.1610 0.2559 87 T 0.5928 0.1109 0.2963 88 L 0.5085 0.0731 0.4184 89 N 0.3063 0.0544 0.6393 90 A 0.0844 0.4858 0.4298 91 K 0.0338 0.6946 0.2717 92 S 0.0405 0.6914 0.2681 93 I 0.0515 0.7430 0.2055 94 R 0.0577 0.7283 0.2140 95 S 0.0465 0.7004 0.2530 96 T 0.0434 0.5905 0.3660 97 L 0.0710 0.3888 0.5402 98 H 0.0457 0.1555 0.7988