# This file is the result of combining several RDB files, specifically # T0387.t06.str2.rdb (weight 1.54425) # T0387.t06.str4.rdb (weight 0.924988) # T0387.t06.pb.rdb (weight 0.789901) # T0387.t06.bys.rdb (weight 0.748322) # T0387.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 T0387.t06.str2.rdb # ============================================ # TARGET T0387 # 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 T0387.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 2612 # # ============================================ # Comments from T0387.t06.str4.rdb # ============================================ # TARGET T0387 # 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 T0387.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 2612 # # ============================================ # Comments from T0387.t06.pb.rdb # ============================================ # TARGET T0387 # 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 T0387.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 2612 # # ============================================ # Comments from T0387.t06.bys.rdb # ============================================ # TARGET T0387 # 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 T0387.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 2612 # # ============================================ # Comments from T0387.t06.alpha.rdb # ============================================ # TARGET T0387 # 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 T0387.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 2612 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.2264 0.0853 0.6883 2 M 0.2434 0.0633 0.6933 3 K 0.3618 0.0234 0.6148 4 P 0.5278 0.0165 0.4558 5 K 0.6847 0.0221 0.2933 6 L 0.7605 0.0062 0.2333 7 C 0.7930 0.0069 0.2001 8 R 0.7997 0.0054 0.1950 9 L 0.7429 0.0081 0.2490 10 A 0.6462 0.0198 0.3340 11 K 0.4364 0.0399 0.5237 12 G 0.2484 0.0547 0.6969 13 E 0.1739 0.1793 0.6467 14 N 0.1404 0.1445 0.7151 15 G 0.1818 0.0873 0.7309 16 Y 0.3547 0.0633 0.5820 17 G 0.5561 0.0286 0.4152 18 F 0.7470 0.0082 0.2448 19 H 0.7798 0.0079 0.2124 20 L 0.7410 0.0118 0.2472 21 N 0.6677 0.0331 0.2992 22 A 0.5119 0.0593 0.4288 23 I 0.3568 0.1141 0.5292 24 R 0.2340 0.1381 0.6279 25 G 0.1310 0.0974 0.7716 26 L 0.2180 0.0431 0.7389 27 P 0.1858 0.1148 0.6994 28 G 0.2918 0.0752 0.6330 29 S 0.6374 0.0185 0.3441 30 F 0.7341 0.0130 0.2529 31 I 0.6895 0.0258 0.2847 32 K 0.6273 0.0603 0.3123 33 E 0.6825 0.0490 0.2685 34 V 0.5463 0.0477 0.4060 35 Q 0.3463 0.0517 0.6021 36 K 0.1261 0.2076 0.6662 37 G 0.0537 0.1418 0.8045 38 G 0.1458 0.1310 0.7232 39 P 0.0938 0.4980 0.4082 40 A 0.0551 0.7183 0.2266 41 D 0.0458 0.7663 0.1878 42 L 0.0528 0.6807 0.2665 43 A 0.0682 0.3145 0.6173 44 G 0.0521 0.1182 0.8297 45 L 0.1811 0.0335 0.7855 46 E 0.1971 0.0250 0.7779 47 D 0.0834 0.2647 0.6519 48 E 0.0639 0.1952 0.7410 49 D 0.2406 0.1171 0.6423 50 V 0.6096 0.0576 0.3328 51 I 0.6807 0.0645 0.2548 52 I 0.7200 0.0417 0.2382 53 E 0.7366 0.0446 0.2188 54 V 0.6163 0.0614 0.3223 55 N 0.3118 0.0714 0.6168 56 G 0.1384 0.0525 0.8091 57 V 0.3650 0.0245 0.6106 58 N 0.4307 0.0296 0.5396 59 V 0.3082 0.1662 0.5256 60 L 0.1871 0.2095 0.6035 61 D 0.1261 0.1075 0.7664 62 E 0.2279 0.0542 0.7179 63 P 0.1726 0.0514 0.7760 64 Y 0.0178 0.7333 0.2489 65 E 0.0093 0.8673 0.1233 66 K 0.0084 0.9216 0.0700 67 V 0.0084 0.9222 0.0694 68 V 0.0083 0.9209 0.0708 69 D 0.0083 0.9223 0.0694 70 R 0.0084 0.9194 0.0721 71 I 0.0106 0.9049 0.0845 72 Q 0.0123 0.8591 0.1286 73 S 0.0245 0.6303 0.3452 74 S 0.0675 0.2136 0.7189 75 G 0.0538 0.0805 0.8657 76 K 0.1902 0.0563 0.7535 77 N 0.4981 0.0236 0.4783 78 V 0.7533 0.0083 0.2384 79 T 0.7968 0.0061 0.1971 80 L 0.8022 0.0052 0.1926 81 L 0.7987 0.0063 0.1950 82 V 0.7503 0.0059 0.2437 83 C 0.6456 0.0196 0.3347 84 G 0.3886 0.0305 0.5810 85 K 0.2561 0.1025 0.6414 86 K 0.2369 0.1319 0.6312 87 A 0.2107 0.1532 0.6361 88 Q 0.1922 0.1727 0.6351 89 D 0.1982 0.1316 0.6702 90 T 0.2170 0.0836 0.6994 91 V 0.1718 0.2116 0.6167