# This file is the result of combining several RDB files, specifically # T0557.t06.str2.rdb (weight 1.54425) # T0557.t06.str4.rdb (weight 0.924988) # T0557.t06.pb.rdb (weight 0.789901) # T0557.t06.bys.rdb (weight 0.748322) # T0557.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 T0557.t06.str2.rdb # ============================================ # TARGET T0557 # 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 T0557.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 904 # # ============================================ # Comments from T0557.t06.str4.rdb # ============================================ # TARGET T0557 # 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 T0557.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 904 # # ============================================ # Comments from T0557.t06.pb.rdb # ============================================ # TARGET T0557 # 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 T0557.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 904 # # ============================================ # Comments from T0557.t06.bys.rdb # ============================================ # TARGET T0557 # 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 T0557.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 904 # # ============================================ # Comments from T0557.t06.alpha.rdb # ============================================ # TARGET T0557 # 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 T0557.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 904 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1950 0.1879 0.6171 2 R 0.2079 0.1555 0.6366 3 S 0.1799 0.0968 0.7232 4 A 0.0205 0.6976 0.2818 5 T 0.0107 0.8479 0.1414 6 D 0.0102 0.9035 0.0863 7 L 0.0113 0.8992 0.0896 8 L 0.0092 0.9067 0.0842 9 D 0.0086 0.9078 0.0835 10 E 0.0089 0.9022 0.0889 11 L 0.0163 0.8513 0.1324 12 N 0.0217 0.7497 0.2286 13 A 0.0414 0.4966 0.4620 14 V 0.1106 0.2348 0.6547 15 D 0.1049 0.1632 0.7318 16 E 0.0969 0.3143 0.5887 17 S 0.1704 0.2055 0.6241 18 A 0.2905 0.2145 0.4950 19 R 0.5491 0.0996 0.3513 20 I 0.6775 0.0663 0.2562 21 E 0.6934 0.0634 0.2433 22 A 0.6826 0.0807 0.2367 23 K 0.5947 0.1476 0.2577 24 R 0.5574 0.1407 0.3019 25 A 0.3035 0.2680 0.4285 26 S 0.1470 0.3667 0.4863 27 D 0.1051 0.3565 0.5384 28 M 0.0952 0.3967 0.5080 29 G 0.0545 0.5636 0.3820 30 K 0.0392 0.7185 0.2423 31 S 0.0344 0.7826 0.1830 32 V 0.0241 0.8377 0.1382 33 M 0.0139 0.8925 0.0937 34 E 0.0142 0.8952 0.0906 35 T 0.0207 0.8934 0.0859 36 V 0.0420 0.8628 0.0952 37 I 0.0895 0.7975 0.1130 38 A 0.1303 0.7122 0.1575 39 F 0.1540 0.5856 0.2604 40 A 0.2536 0.3094 0.4370 41 N 0.1962 0.1705 0.6333 42 E 0.1998 0.0815 0.7187 43 P 0.1243 0.1761 0.6996 44 G 0.0977 0.1644 0.7379 45 L 0.1248 0.1855 0.6897 46 D 0.1380 0.1328 0.7293 47 G 0.2212 0.0696 0.7092 48 G 0.5223 0.0305 0.4472 49 Y 0.7756 0.0075 0.2169 50 L 0.7983 0.0065 0.1952 51 L 0.7862 0.0081 0.2057 52 L 0.7467 0.0155 0.2378 53 G 0.6595 0.0213 0.3192 54 V 0.5230 0.0711 0.4059 55 D 0.3984 0.1131 0.4885 56 W 0.2517 0.2761 0.4723 57 A 0.1743 0.3596 0.4661 58 I 0.1569 0.3532 0.4899 59 N 0.1493 0.2965 0.5543 60 D 0.1481 0.2500 0.6019 61 K 0.1174 0.1978 0.6848 62 G 0.0956 0.1297 0.7747 63 D 0.1680 0.0995 0.7325 64 T 0.2573 0.0971 0.6456 65 V 0.3915 0.0947 0.5138 66 Y 0.4828 0.0469 0.4703 67 R 0.5964 0.0183 0.3853 68 P 0.5437 0.0270 0.4293 69 V 0.4604 0.0499 0.4898 70 G 0.3122 0.0413 0.6465 71 L 0.2869 0.0506 0.6625 72 P 0.2181 0.0697 0.7122 73 D 0.1905 0.0357 0.7738 74 P 0.0168 0.6911 0.2921 75 D 0.0121 0.8283 0.1596 76 K 0.0115 0.8956 0.0929 77 V 0.0116 0.9031 0.0853 78 Q 0.0088 0.9134 0.0778 79 R 0.0085 0.9171 0.0744 80 D 0.0086 0.9170 0.0744 81 L 0.0087 0.9162 0.0751 82 A 0.0084 0.9153 0.0762 83 S 0.0084 0.9177 0.0739 84 Q 0.0087 0.9118 0.0795 85 C 0.0108 0.8960 0.0932 86 A 0.0129 0.8391 0.1480 87 S 0.0201 0.6778 0.3021 88 M 0.0538 0.4409 0.5054 89 L 0.1451 0.2335 0.6214 90 N 0.1940 0.1067 0.6993 91 V 0.2855 0.1179 0.5966 92 A 0.3412 0.0840 0.5747 93 L 0.4567 0.0656 0.4776 94 R 0.4840 0.0212 0.4948 95 P 0.5780 0.0338 0.3883 96 E 0.6663 0.0232 0.3106 97 M 0.7444 0.0092 0.2464 98 Q 0.7502 0.0117 0.2381 99 L 0.7552 0.0073 0.2374 100 E 0.7555 0.0132 0.2313 101 Q 0.6913 0.0136 0.2951 102 V 0.5543 0.0402 0.4055 103 G 0.1689 0.0790 0.7521 104 G 0.0818 0.0989 0.8193 105 K 0.4114 0.0206 0.5680 106 T 0.7025 0.0121 0.2854 107 L 0.7871 0.0058 0.2071 108 L 0.8012 0.0061 0.1927 109 V 0.8030 0.0050 0.1919 110 V 0.7795 0.0092 0.2113 111 Y 0.7496 0.0075 0.2429 112 V 0.5660 0.0120 0.4219 113 P 0.2664 0.0194 0.7142 114 E 0.1276 0.2451 0.6273 115 A 0.1300 0.2325 0.6375 116 D 0.1599 0.2174 0.6227 117 V 0.1241 0.3257 0.5502 118 T 0.1861 0.2214 0.5925 119 H 0.2504 0.1059 0.6438 120 K 0.3610 0.0300 0.6090 121 P 0.4341 0.0431 0.5227 122 I 0.6063 0.0637 0.3301 123 Y 0.6799 0.0511 0.2690 124 K 0.6359 0.0739 0.2902 125 K 0.4945 0.1119 0.3936 126 A 0.3108 0.1937 0.4955 127 T 0.1663 0.1567 0.6770 128 G 0.1193 0.0809 0.7998 129 L 0.2492 0.0330 0.7178 130 P 0.1781 0.1032 0.7187 131 G 0.1603 0.0807 0.7589 132 G 0.4693 0.0349 0.4959 133 A 0.7254 0.0128 0.2618 134 Y 0.7839 0.0091 0.2070 135 R 0.7899 0.0103 0.1997 136 R 0.7231 0.0162 0.2608 137 I 0.5838 0.0442 0.3720 138 G 0.3323 0.0431 0.6246 139 S 0.2787 0.1110 0.6103 140 S 0.2026 0.2061 0.5912 141 D 0.2246 0.1561 0.6193 142 Q 0.3017 0.1585 0.5398 143 R 0.3321 0.1541 0.5138 144 C 0.3721 0.1068 0.5211 145 V 0.3408 0.0846 0.5746