# This file is the result of combining several RDB files, specifically # T0474.t06.str2.rdb (weight 1.54425) # T0474.t06.str4.rdb (weight 0.924988) # T0474.t06.pb.rdb (weight 0.789901) # T0474.t06.bys.rdb (weight 0.748322) # T0474.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 T0474.t06.str2.rdb # ============================================ # TARGET T0474 # 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 T0474.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 19.7804 # # ============================================ # Comments from T0474.t06.str4.rdb # ============================================ # TARGET T0474 # 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 T0474.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 19.7804 # # ============================================ # Comments from T0474.t06.pb.rdb # ============================================ # TARGET T0474 # 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 T0474.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 19.7804 # # ============================================ # Comments from T0474.t06.bys.rdb # ============================================ # TARGET T0474 # 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 T0474.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 19.7804 # # ============================================ # Comments from T0474.t06.alpha.rdb # ============================================ # TARGET T0474 # 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 T0474.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 19.7804 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2527 0.2359 0.5115 2 N 0.2409 0.2650 0.4941 3 S 0.2231 0.4302 0.3467 4 L 0.2151 0.4855 0.2995 5 A 0.2239 0.4721 0.3040 6 G 0.2736 0.4385 0.2878 7 I 0.3061 0.4222 0.2717 8 D 0.3238 0.3407 0.3355 9 M 0.3906 0.2739 0.3355 10 G 0.4692 0.1792 0.3515 11 R 0.6667 0.0880 0.2453 12 I 0.6971 0.0668 0.2361 13 L 0.7145 0.0520 0.2335 14 L 0.6829 0.0353 0.2817 15 D 0.4887 0.0401 0.4711 16 L 0.2402 0.1218 0.6381 17 S 0.1504 0.1444 0.7052 18 N 0.0136 0.7098 0.2766 19 E 0.0101 0.8422 0.1476 20 V 0.0099 0.9087 0.0814 21 I 0.0089 0.9104 0.0807 22 K 0.0086 0.8990 0.0924 23 Q 0.0097 0.8823 0.1080 24 L 0.0120 0.8827 0.1053 25 D 0.0090 0.8988 0.0923 26 D 0.0087 0.9076 0.0837 27 L 0.0090 0.9086 0.0824 28 E 0.0089 0.9051 0.0860 29 V 0.0115 0.8764 0.1121 30 Q 0.0235 0.7405 0.2359 31 R 0.0561 0.3850 0.5588 32 N 0.0372 0.1587 0.8041 33 L 0.1670 0.0380 0.7951 34 P 0.1530 0.0373 0.8096 35 R 0.0144 0.7392 0.2464 36 A 0.0093 0.8700 0.1207 37 D 0.0083 0.9224 0.0693 38 L 0.0083 0.9234 0.0683 39 L 0.0083 0.9211 0.0706 40 R 0.0083 0.9232 0.0685 41 E 0.0083 0.9223 0.0694 42 A 0.0083 0.9224 0.0693 43 V 0.0083 0.9205 0.0711 44 D 0.0084 0.9195 0.0721 45 Q 0.0084 0.9157 0.0759 46 Y 0.0087 0.9081 0.0832 47 L 0.0104 0.8860 0.1037 48 I 0.0142 0.8369 0.1489 49 N 0.0302 0.6507 0.3191 50 Q 0.0841 0.4015 0.5144 51 S 0.0891 0.3162 0.5946 52 Q 0.0936 0.4103 0.4961 53 T 0.1053 0.4736 0.4211 54 A 0.0998 0.5493 0.3509 55 R 0.0979 0.5535 0.3486 56 T 0.1101 0.4517 0.4381 57 S 0.1488 0.3178 0.5334 58 V 0.2386 0.1314 0.6300 59 P 0.1967 0.2103 0.5930 60 G 0.2323 0.1885 0.5791 61 I 0.3260 0.2511 0.4229 62 W 0.3509 0.2411 0.4080 63 Q 0.2531 0.1957 0.5512 64 G 0.1490 0.1170 0.7340 65 C 0.1955 0.1250 0.6795 66 E 0.1917 0.1887 0.6196 67 E 0.1916 0.2597 0.5487 68 D 0.1626 0.2820 0.5555 69 G 0.1581 0.4420 0.4000 70 V 0.1001 0.6754 0.2245 71 E 0.0521 0.7985 0.1493 72 Y 0.0363 0.8401 0.1237 73 Q 0.0168 0.8901 0.0931 74 R 0.0094 0.9090 0.0816 75 K 0.0107 0.9018 0.0875 76 L 0.0166 0.8637 0.1197 77 R 0.0174 0.8629 0.1196 78 E 0.0158 0.8414 0.1428 79 E 0.0281 0.7247 0.2472 80 W 0.0699 0.5008 0.4293