# This file is the result of combining several RDB files, specifically # T0389.t06.str2.rdb (weight 1.54425) # T0389.t06.str4.rdb (weight 0.924988) # T0389.t06.pb.rdb (weight 0.789901) # T0389.t06.bys.rdb (weight 0.748322) # T0389.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 T0389.t06.str2.rdb # ============================================ # TARGET T0389 # 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 T0389.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 3182 # # ============================================ # Comments from T0389.t06.str4.rdb # ============================================ # TARGET T0389 # 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 T0389.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 3182 # # ============================================ # Comments from T0389.t06.pb.rdb # ============================================ # TARGET T0389 # 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 T0389.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 3182 # # ============================================ # Comments from T0389.t06.bys.rdb # ============================================ # TARGET T0389 # 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 T0389.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 3182 # # ============================================ # Comments from T0389.t06.alpha.rdb # ============================================ # TARGET T0389 # 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 T0389.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 3182 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2827 0.0637 0.6535 2 I 0.2277 0.0687 0.7036 3 G 0.2409 0.0885 0.6705 4 T 0.3094 0.1245 0.5661 5 Q 0.4437 0.0820 0.4743 6 I 0.4453 0.0479 0.5068 7 V 0.2135 0.0261 0.7604 8 T 0.0171 0.7371 0.2458 9 E 0.0094 0.8672 0.1235 10 R 0.0087 0.9184 0.0729 11 L 0.0084 0.9224 0.0692 12 V 0.0084 0.9189 0.0728 13 A 0.0083 0.9184 0.0732 14 L 0.0090 0.9054 0.0856 15 L 0.0120 0.8714 0.1166 16 E 0.0171 0.6617 0.3212 17 S 0.0552 0.2624 0.6824 18 G 0.0440 0.1087 0.8472 19 T 0.1682 0.0737 0.7581 20 E 0.1741 0.1508 0.6751 21 K 0.3713 0.0581 0.5705 22 V 0.7275 0.0081 0.2643 23 L 0.7655 0.0094 0.2251 24 L 0.7678 0.0064 0.2258 25 I 0.7693 0.0128 0.2179 26 D 0.6818 0.0167 0.3015 27 S 0.4881 0.0641 0.4477 28 R 0.3401 0.0329 0.6270 29 P 0.2093 0.0710 0.7197 30 F 0.0834 0.4717 0.4449 31 V 0.0649 0.6259 0.3092 32 E 0.1094 0.5992 0.2914 33 Y 0.1485 0.5446 0.3069 34 N 0.1339 0.4699 0.3962 35 T 0.1406 0.4315 0.4279 36 S 0.1650 0.3036 0.5314 37 H 0.2383 0.2163 0.5454 38 I 0.2619 0.1419 0.5963 39 L 0.1338 0.3307 0.5356 40 E 0.1126 0.2529 0.6345 41 A 0.3068 0.1952 0.4979 42 I 0.4710 0.1188 0.4102 43 N 0.4611 0.0807 0.4582 44 I 0.3893 0.0607 0.5500 45 N 0.2053 0.0499 0.7448 46 C 0.0460 0.6545 0.2995 47 S 0.0196 0.7968 0.1836 48 K 0.0221 0.8467 0.1312 49 L 0.0270 0.8306 0.1424 50 M 0.0364 0.7903 0.1733 51 K 0.0473 0.7163 0.2364 52 R 0.0731 0.6013 0.3256 53 R 0.0969 0.4997 0.4034 54 L 0.0834 0.4573 0.4593 55 Q 0.0958 0.4113 0.4929 56 Q 0.0764 0.3830 0.5406 57 D 0.0957 0.3092 0.5951 58 K 0.1213 0.3613 0.5174 59 V 0.2026 0.2968 0.5006 60 L 0.1909 0.2716 0.5376 61 I 0.1303 0.4423 0.4273 62 T 0.0204 0.7983 0.1813 63 E 0.0111 0.8698 0.1191 64 L 0.0125 0.8875 0.1000 65 I 0.0131 0.8938 0.0930 66 Q 0.0089 0.9098 0.0813 67 H 0.0089 0.9107 0.0804 68 S 0.0102 0.8975 0.0923 69 A 0.0121 0.8775 0.1104 70 K 0.0141 0.8336 0.1523 71 H 0.0264 0.7396 0.2340 72 K 0.0633 0.5389 0.3977 73 V 0.1304 0.2864 0.5832 74 D 0.1332 0.1661 0.7007 75 I 0.2142 0.1139 0.6719 76 D 0.1636 0.0883 0.7481 77 C 0.0854 0.3110 0.6036 78 S 0.1240 0.1803 0.6958 79 Q 0.3339 0.0418 0.6243 80 K 0.5973 0.0165 0.3862 81 V 0.7860 0.0064 0.2077 82 V 0.8051 0.0055 0.1894 83 V 0.7934 0.0057 0.2009 84 Y 0.7505 0.0111 0.2384 85 D 0.4656 0.0183 0.5161 86 Q 0.2025 0.1412 0.6563 87 S 0.1650 0.1587 0.6763 88 S 0.1305 0.2319 0.6376 89 Q 0.0692 0.4038 0.5270 90 D 0.0943 0.4230 0.4827 91 V 0.1388 0.3838 0.4773 92 A 0.1132 0.3597 0.5271 93 S 0.1064 0.3547 0.5389 94 L 0.0901 0.4740 0.4359 95 S 0.0739 0.5704 0.3557 96 S 0.0244 0.7816 0.1940 97 D 0.0101 0.8774 0.1125 98 C 0.0085 0.9171 0.0744 99 F 0.0083 0.9220 0.0696 100 L 0.0083 0.9223 0.0694 101 T 0.0083 0.9233 0.0684 102 V 0.0084 0.9201 0.0715 103 L 0.0091 0.9047 0.0862 104 L 0.0108 0.8452 0.1440 105 G 0.0163 0.6379 0.3458 106 K 0.0358 0.6608 0.3034 107 L 0.0324 0.6901 0.2776 108 E 0.0322 0.6260 0.3419 109 K 0.0638 0.4318 0.5044 110 S 0.1024 0.2111 0.6865 111 F 0.1820 0.1769 0.6411 112 N 0.1830 0.1749 0.6421 113 S 0.3521 0.1147 0.5332 114 V 0.6628 0.0310 0.3062 115 H 0.7385 0.0331 0.2284 116 L 0.7284 0.0288 0.2428 117 L 0.6503 0.0667 0.2830 118 A 0.3646 0.1216 0.5138 119 G 0.1663 0.1456 0.6881 120 G 0.1314 0.2830 0.5856 121 F 0.0592 0.6992 0.2416 122 A 0.0186 0.8372 0.1442 123 E 0.0172 0.8657 0.1171 124 F 0.0221 0.8486 0.1293 125 S 0.0186 0.8266 0.1547 126 R 0.0251 0.6628 0.3121 127 C 0.0540 0.4844 0.4616 128 F 0.1412 0.1528 0.7059 129 P 0.0972 0.2803 0.6225 130 G 0.0968 0.3135 0.5897 131 L 0.1792 0.3124 0.5085 132 C 0.2414 0.2215 0.5372 133 E 0.1967 0.1478 0.6555 134 G 0.1343 0.0937 0.7720 135 K 0.2322 0.0806 0.6872 136 S 0.3030 0.0865 0.6105 137 T 0.3969 0.0626 0.5405 138 L 0.3952 0.0545 0.5503 139 V 0.3501 0.0299 0.6199 140 P 0.2709 0.1066 0.6225 141 T 0.2487 0.1570 0.5943 142 C 0.2749 0.1483 0.5768 143 I 0.2881 0.1191 0.5927 144 S 0.2834 0.0818 0.6348 145 Q 0.2876 0.0494 0.6630 146 P 0.2423 0.0881 0.6696 147 A 0.2639 0.1443 0.5917 148 H 0.2809 0.1287 0.5904 149 H 0.2786 0.1587 0.5626 150 H 0.2384 0.1673 0.5943 151 H 0.2219 0.1743 0.6038 152 H 0.2276 0.1486 0.6239 153 H 0.2180 0.1370 0.6450