# This file is the result of combining several RDB files, specifically # T0507.t06.str2.rdb (weight 1.54425) # T0507.t06.str4.rdb (weight 0.924988) # T0507.t06.pb.rdb (weight 0.789901) # T0507.t06.bys.rdb (weight 0.748322) # T0507.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 T0507.t06.str2.rdb # ============================================ # TARGET T0507 # 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 T0507.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 2928 # # ============================================ # Comments from T0507.t06.str4.rdb # ============================================ # TARGET T0507 # 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 T0507.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 2928 # # ============================================ # Comments from T0507.t06.pb.rdb # ============================================ # TARGET T0507 # 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 T0507.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 2928 # # ============================================ # Comments from T0507.t06.bys.rdb # ============================================ # TARGET T0507 # 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 T0507.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 2928 # # ============================================ # Comments from T0507.t06.alpha.rdb # ============================================ # TARGET T0507 # 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 T0507.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 2928 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4011 0.0334 0.5655 2 K 0.5299 0.0228 0.4474 3 V 0.7785 0.0105 0.2110 4 A 0.7547 0.0127 0.2325 5 L 0.7156 0.0246 0.2598 6 G 0.5906 0.0389 0.3705 7 G 0.4723 0.0572 0.4705 8 T 0.4186 0.0709 0.5106 9 F 0.3249 0.0778 0.5973 10 E 0.2301 0.0521 0.7177 11 P 0.1167 0.3214 0.5620 12 L 0.0886 0.4180 0.4934 13 H 0.1060 0.4911 0.4029 14 E 0.0288 0.7178 0.2534 15 G 0.0244 0.8085 0.1670 16 H 0.0119 0.8979 0.0902 17 K 0.0084 0.9178 0.0738 18 K 0.0083 0.9238 0.0679 19 L 0.0083 0.9244 0.0673 20 I 0.0083 0.9229 0.0688 21 D 0.0083 0.9241 0.0676 22 V 0.0083 0.9242 0.0675 23 A 0.0083 0.9231 0.0686 24 I 0.0086 0.9111 0.0803 25 K 0.0111 0.8414 0.1475 26 L 0.0365 0.5644 0.3991 27 G 0.0572 0.2252 0.7176 28 G 0.0774 0.1848 0.7379 29 R 0.1248 0.1536 0.7216 30 D 0.3651 0.0588 0.5761 31 I 0.7304 0.0104 0.2592 32 T 0.7776 0.0084 0.2140 33 I 0.7966 0.0063 0.1971 34 G 0.7562 0.0123 0.2315 35 V 0.6857 0.0170 0.2972 36 T 0.4987 0.0346 0.4667 37 S 0.2573 0.0919 0.6508 38 D 0.1486 0.2187 0.6328 39 R 0.1171 0.3985 0.4844 40 M 0.1060 0.4445 0.4495 41 A 0.1275 0.4415 0.4310 42 R 0.1245 0.3781 0.4974 43 A 0.1211 0.3365 0.5423 44 R 0.1650 0.2428 0.5922 45 I 0.1838 0.1641 0.6521 46 R 0.1998 0.1388 0.6614 47 S 0.2089 0.1669 0.6242 48 V 0.2392 0.1346 0.6261 49 L 0.2583 0.0537 0.6879 50 P 0.1635 0.0784 0.7582 51 F 0.0129 0.7512 0.2359 52 A 0.0094 0.8710 0.1196 53 I 0.0084 0.9224 0.0692 54 R 0.0084 0.9221 0.0695 55 A 0.0084 0.9214 0.0702 56 E 0.0083 0.9218 0.0699 57 N 0.0083 0.9209 0.0707 58 V 0.0083 0.9213 0.0704 59 K 0.0084 0.9186 0.0731 60 R 0.0086 0.9077 0.0837 61 Y 0.0102 0.8770 0.1128 62 V 0.0180 0.8144 0.1675 63 M 0.0430 0.7336 0.2234 64 R 0.0669 0.5433 0.3899 65 K 0.1129 0.3145 0.5726 66 Y 0.1200 0.1837 0.6963 67 G 0.1333 0.0840 0.7827 68 F 0.3385 0.0378 0.6237 69 E 0.4720 0.0230 0.5050 70 P 0.5524 0.0344 0.4132 71 E 0.6074 0.0508 0.3418 72 I 0.6566 0.0342 0.3091 73 V 0.5842 0.0350 0.3808 74 K 0.5042 0.0431 0.4527 75 I 0.3548 0.1255 0.5196 76 T 0.2865 0.1435 0.5700 77 N 0.2775 0.0707 0.6518 78 P 0.2048 0.2026 0.5926 79 Y 0.1825 0.2035 0.6140 80 G 0.1823 0.1442 0.6735 81 K 0.2550 0.1206 0.6244 82 T 0.3271 0.0909 0.5821 83 L 0.3434 0.0779 0.5787 84 D 0.3123 0.0428 0.6449 85 V 0.2750 0.1518 0.5732 86 D 0.2408 0.0909 0.6684 87 F 0.3302 0.1622 0.5076 88 E 0.4052 0.1056 0.4892 89 Y 0.7170 0.0231 0.2599 90 L 0.7216 0.0155 0.2629 91 V 0.7489 0.0121 0.2390 92 V 0.6863 0.0212 0.2925 93 S 0.3444 0.0174 0.6383 94 P 0.0720 0.3706 0.5574 95 E 0.0543 0.4257 0.5200 96 T 0.0792 0.4944 0.4264 97 Y 0.0650 0.6198 0.3152 98 E 0.0497 0.6672 0.2831 99 M 0.0482 0.6765 0.2752 100 A 0.0526 0.7404 0.2070 101 L 0.0515 0.7429 0.2055 102 K 0.0650 0.6776 0.2574 103 I 0.0627 0.6363 0.3010 104 N 0.0479 0.6276 0.3245 105 Q 0.0480 0.6976 0.2543 106 K 0.0233 0.8351 0.1416 107 R 0.0143 0.8821 0.1035 108 E 0.0129 0.8913 0.0959 109 E 0.0199 0.8376 0.1425 110 L 0.0367 0.6705 0.2928 111 G 0.0432 0.4495 0.5073 112 K 0.1250 0.2733 0.6017 113 R 0.1876 0.1210 0.6914 114 K 0.2800 0.0637 0.6563 115 I 0.5290 0.0161 0.4549 116 T 0.6792 0.0173 0.3035 117 I 0.7472 0.0089 0.2439 118 V 0.7369 0.0156 0.2475 119 K 0.6880 0.0145 0.2975 120 V 0.5690 0.0269 0.4041 121 D 0.3999 0.0580 0.5421 122 W 0.3314 0.2162 0.4524 123 M 0.4234 0.1817 0.3949 124 M 0.4182 0.1552 0.4266 125 A 0.2476 0.2114 0.5411 126 E 0.1091 0.3352 0.5557 127 D 0.0812 0.1861 0.7326 128 G 0.0787 0.0787 0.8425 129 K 0.2630 0.0269 0.7101 130 P 0.3859 0.0253 0.5888 131 I 0.4832 0.0358 0.4810 132 S 0.4954 0.0472 0.4574 133 S 0.4424 0.1616 0.3960 134 T 0.4112 0.2295 0.3593 135 R 0.4081 0.2611 0.3308 136 I 0.3705 0.2448 0.3847 137 K 0.2728 0.2268 0.5004 138 R 0.1666 0.2030 0.6304 139 G 0.1056 0.1752 0.7192 140 E 0.1812 0.2728 0.5460 141 I 0.1866 0.4704 0.3431 142 D 0.1132 0.5815 0.3053 143 R 0.1094 0.5429 0.3476 144 Y 0.1083 0.4268 0.4648 145 G 0.0827 0.3614 0.5559 146 G 0.1103 0.2689 0.6208 147 I 0.2333 0.1687 0.5980 148 I 0.2436 0.1604 0.5960