# This file is the result of combining several RDB files, specifically # T0471.t06.str2.rdb (weight 1.54425) # T0471.t06.str4.rdb (weight 0.924988) # T0471.t06.pb.rdb (weight 0.789901) # T0471.t06.bys.rdb (weight 0.748322) # T0471.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 T0471.t06.str2.rdb # ============================================ # TARGET T0471 # 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 T0471.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 15.2655 # # ============================================ # Comments from T0471.t06.str4.rdb # ============================================ # TARGET T0471 # 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 T0471.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 15.2655 # # ============================================ # Comments from T0471.t06.pb.rdb # ============================================ # TARGET T0471 # 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 T0471.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 15.2655 # # ============================================ # Comments from T0471.t06.bys.rdb # ============================================ # TARGET T0471 # 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 T0471.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 15.2655 # # ============================================ # Comments from T0471.t06.alpha.rdb # ============================================ # TARGET T0471 # 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 T0471.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 15.2655 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1530 0.3956 0.4514 2 W 0.1016 0.5729 0.3255 3 N 0.0587 0.6923 0.2490 4 D 0.0426 0.7399 0.2175 5 L 0.0195 0.8418 0.1387 6 A 0.0134 0.8895 0.0971 7 V 0.0146 0.9079 0.0775 8 Y 0.0209 0.8991 0.0801 9 I 0.0361 0.8716 0.0924 10 I 0.0697 0.7867 0.1435 11 R 0.1210 0.5710 0.3080 12 C 0.1378 0.3353 0.5269 13 S 0.1593 0.1501 0.6906 14 G 0.1656 0.0819 0.7524 15 P 0.1023 0.1746 0.7231 16 G 0.0555 0.1143 0.8302 17 T 0.2492 0.0380 0.7128 18 R 0.5650 0.0202 0.4148 19 V 0.7414 0.0080 0.2506 20 V 0.7807 0.0090 0.2103 21 E 0.7741 0.0072 0.2187 22 V 0.7364 0.0152 0.2484 23 G 0.5424 0.0297 0.4280 24 A 0.3494 0.1145 0.5362 25 G 0.2638 0.1447 0.5915 26 R 0.2044 0.2848 0.5108 27 F 0.1418 0.4581 0.4001 28 L 0.0426 0.7372 0.2202 29 Y 0.0340 0.7950 0.1710 30 V 0.0149 0.8815 0.1036 31 S 0.0096 0.9064 0.0840 32 D 0.0089 0.9097 0.0814 33 Y 0.0092 0.9009 0.0899 34 I 0.0149 0.8696 0.1156 35 R 0.0125 0.7979 0.1897 36 K 0.0217 0.6979 0.2804 37 H 0.0743 0.3672 0.5584 38 S 0.0589 0.2786 0.6625 39 K 0.0637 0.1086 0.8277 40 V 0.3219 0.0173 0.6608 41 D 0.5605 0.0183 0.4212 42 L 0.8081 0.0049 0.1869 43 V 0.7831 0.0084 0.2085 44 L 0.7955 0.0070 0.1975 45 T 0.7644 0.0160 0.2195 46 D 0.6666 0.0201 0.3133 47 I 0.4242 0.0576 0.5181 48 K 0.2826 0.0372 0.6801 49 P 0.2183 0.1538 0.6280 50 S 0.1343 0.1964 0.6692 51 H 0.1353 0.1639 0.7009 52 G 0.1634 0.1184 0.7182 53 G 0.2453 0.0968 0.6579 54 I 0.5123 0.0593 0.4284 55 V 0.6115 0.0626 0.3260 56 R 0.5550 0.0960 0.3490 57 D 0.4116 0.1346 0.4538 58 D 0.2975 0.1871 0.5154 59 I 0.2327 0.2631 0.5042 60 T 0.2154 0.1809 0.6037 61 S 0.2251 0.0859 0.6891 62 P 0.1389 0.2470 0.6141 63 R 0.1537 0.2202 0.6261 64 M 0.3223 0.2043 0.4733 65 E 0.4620 0.1995 0.3385 66 I 0.5202 0.1973 0.2825 67 Y 0.4243 0.2121 0.3636 68 R 0.2456 0.2417 0.5127 69 G 0.1710 0.1525 0.6765 70 A 0.3491 0.0524 0.5985 71 A 0.4815 0.0651 0.4534 72 L 0.7753 0.0269 0.1977 73 I 0.7327 0.0343 0.2331 74 Y 0.7576 0.0401 0.2023 75 S 0.7320 0.0345 0.2335 76 I 0.5805 0.0492 0.3703 77 R 0.3905 0.0230 0.5866 78 P 0.1986 0.0216 0.7798 79 P 0.1115 0.2225 0.6659 80 A 0.0228 0.6149 0.3623 81 E 0.0285 0.6930 0.2785 82 I 0.0418 0.7175 0.2407 83 H 0.0281 0.7949 0.1770 84 S 0.0118 0.8740 0.1142 85 S 0.0097 0.8987 0.0916 86 L 0.0085 0.9178 0.0737 87 M 0.0084 0.9195 0.0721 88 R 0.0086 0.9182 0.0732 89 V 0.0089 0.9080 0.0831 90 A 0.0101 0.8839 0.1059 91 D 0.0110 0.8296 0.1593 92 A 0.0234 0.6990 0.2776 93 V 0.0872 0.2291 0.6837 94 G 0.0864 0.0889 0.8247 95 A 0.3459 0.0258 0.6283 96 R 0.5516 0.0288 0.4196 97 L 0.8003 0.0071 0.1926 98 I 0.7699 0.0088 0.2213 99 I 0.7679 0.0077 0.2244 100 K 0.6689 0.0143 0.3168 101 P 0.3891 0.0293 0.5817 102 L 0.2187 0.1282 0.6532 103 T 0.1396 0.1122 0.7482 104 G 0.0928 0.1012 0.8060 105 E 0.2055 0.1363 0.6582 106 D 0.3167 0.1454 0.5380 107 I 0.3896 0.1609 0.4495 108 V 0.4118 0.1449 0.4433 109 T 0.3593 0.1208 0.5200 110 E 0.2142 0.2269 0.5588 111 R 0.2259 0.1912 0.5828 112 K 0.3112 0.1152 0.5736 113 M 0.4990 0.0392 0.4618 114 K 0.6643 0.0262 0.3095 115 L 0.7001 0.0176 0.2824 116 V 0.6909 0.0304 0.2787 117 N 0.5941 0.0378 0.3681 118 Y 0.3160 0.1043 0.5797 119 G 0.1813 0.0808 0.7379 120 R 0.3615 0.0721 0.5664 121 T 0.6077 0.0434 0.3489 122 Y 0.7181 0.0398 0.2421 123 F 0.7632 0.0298 0.2070 124 Y 0.7715 0.0348 0.1937 125 E 0.7211 0.0647 0.2143 126 Y 0.6594 0.1016 0.2390 127 I 0.5245 0.1987 0.2768 128 A 0.3266 0.3880 0.2855 129 E 0.2552 0.4340 0.3108 130 V 0.2711 0.3599 0.3689 131 R 0.2492 0.2868 0.4640 132 S 0.2072 0.2356 0.5572 133 R 0.1766 0.2057 0.6177