# This file is the result of combining several RDB files, specifically # T0393.t2k.str2.rdb (weight 1.54425) # T0393.t2k.str4.rdb (weight 0.924988) # T0393.t2k.pb.rdb (weight 0.789901) # T0393.t2k.bys.rdb (weight 0.748322) # T0393.t2k.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 T0393.t2k.str2.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t2k-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 T0393.t2k-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 715 # # ============================================ # Comments from T0393.t2k.str4.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t2k-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 T0393.t2k-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 715 # # ============================================ # Comments from T0393.t2k.pb.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t2k-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 T0393.t2k-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 715 # # ============================================ # Comments from T0393.t2k.bys.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t2k-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 T0393.t2k-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 715 # # ============================================ # Comments from T0393.t2k.alpha.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t2k-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 T0393.t2k-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 715 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3814 0.1470 0.4716 2 K 0.2884 0.1499 0.5617 3 R 0.2441 0.2033 0.5526 4 S 0.2094 0.1483 0.6424 5 I 0.0863 0.4163 0.4974 6 E 0.0748 0.3230 0.6022 7 D 0.0676 0.1579 0.7745 8 T 0.2940 0.0186 0.6874 9 P 0.4951 0.0166 0.4883 10 I 0.7961 0.0064 0.1975 11 V 0.8193 0.0047 0.1760 12 L 0.7760 0.0051 0.2189 13 I 0.7442 0.0178 0.2381 14 G 0.5828 0.0257 0.3916 15 A 0.1988 0.2204 0.5809 16 G 0.0694 0.4126 0.5180 17 N 0.0215 0.7789 0.1996 18 L 0.0121 0.8842 0.1038 19 A 0.0083 0.9202 0.0715 20 T 0.0083 0.9215 0.0701 21 N 0.0083 0.9251 0.0667 22 L 0.0083 0.9231 0.0686 23 A 0.0083 0.9224 0.0693 24 K 0.0083 0.9237 0.0680 25 A 0.0083 0.9245 0.0672 26 L 0.0083 0.9203 0.0713 27 Y 0.0087 0.8894 0.1019 28 R 0.0115 0.8208 0.1677 29 K 0.0538 0.2144 0.7318 30 G 0.0492 0.0630 0.8879 31 F 0.2230 0.0231 0.7539 32 R 0.4669 0.0312 0.5018 33 I 0.7643 0.0112 0.2246 34 V 0.8007 0.0072 0.1921 35 Q 0.8034 0.0056 0.1911 36 V 0.7874 0.0092 0.2034 37 Y 0.6979 0.0331 0.2690 38 S 0.4410 0.0480 0.5109 39 R 0.2156 0.1258 0.6586 40 T 0.1638 0.0454 0.7909 41 E 0.0120 0.7364 0.2517 42 E 0.0093 0.8664 0.1242 43 S 0.0090 0.9106 0.0804 44 A 0.0085 0.9155 0.0759 45 R 0.0083 0.9239 0.0679 46 E 0.0083 0.9240 0.0678 47 L 0.0084 0.9185 0.0731 48 A 0.0086 0.9056 0.0858 49 Q 0.0090 0.8910 0.0999 50 K 0.0188 0.7422 0.2390 51 V 0.0678 0.4273 0.5049 52 E 0.0679 0.1310 0.8011 53 A 0.1898 0.1134 0.6969 54 E 0.2808 0.1198 0.5994 55 Y 0.3401 0.1581 0.5018 56 T 0.2425 0.2590 0.4985 57 T 0.1743 0.3507 0.4750 58 D 0.1486 0.2693 0.5821 59 L 0.0278 0.6974 0.2749 60 A 0.0130 0.8051 0.1818 61 E 0.0167 0.7531 0.2302 62 V 0.0508 0.6302 0.3190 63 N 0.1131 0.4063 0.4806 64 P 0.0377 0.5108 0.4515 65 Y 0.0740 0.2776 0.6484 66 A 0.2037 0.1832 0.6132 67 K 0.3758 0.0837 0.5404 68 L 0.7468 0.0138 0.2393 69 Y 0.7691 0.0083 0.2226 70 I 0.8042 0.0066 0.1893 71 V 0.7973 0.0118 0.1909 72 S 0.7507 0.0138 0.2355 73 L 0.4469 0.0293 0.5238 74 K 0.2424 0.0572 0.7004 75 D 0.1196 0.2504 0.6300 76 S 0.0509 0.4521 0.4970 77 A 0.0626 0.5370 0.4005 78 F 0.0476 0.7085 0.2439 79 A 0.0301 0.8194 0.1505 80 E 0.0282 0.8511 0.1206 81 L 0.0259 0.8622 0.1120 82 L 0.0180 0.8702 0.1118 83 Q 0.0143 0.8609 0.1247 84 G 0.0225 0.8010 0.1765 85 I 0.0400 0.7468 0.2132 86 V 0.0696 0.6171 0.3134 87 E 0.0648 0.4820 0.4532 88 G 0.0621 0.2817 0.6562 89 K 0.1429 0.2034 0.6538 90 R 0.1825 0.1167 0.7008 91 E 0.1795 0.1759 0.6446 92 E 0.2230 0.1224 0.6546 93 A 0.5769 0.0229 0.4002 94 L 0.7595 0.0076 0.2329 95 M 0.8027 0.0055 0.1918 96 V 0.8031 0.0074 0.1896 97 H 0.7014 0.0144 0.2842 98 T 0.5257 0.0724 0.4019 99 A 0.3212 0.0921 0.5867 100 G 0.2311 0.0815 0.6874 101 S 0.2361 0.1004 0.6635 102 I 0.2591 0.0560 0.6848 103 P 0.1935 0.1176 0.6889 104 M 0.1418 0.4318 0.4264 105 N 0.1181 0.5180 0.3639 106 V 0.0622 0.7053 0.2326 107 W 0.0573 0.7207 0.2220 108 E 0.0534 0.6848 0.2618 109 G 0.0423 0.5745 0.3832 110 H 0.0786 0.4338 0.4876 111 V 0.1466 0.2567 0.5967 112 P 0.0683 0.4521 0.4796 113 H 0.0793 0.3980 0.5227 114 Y 0.1448 0.2466 0.6086 115 G 0.2088 0.1407 0.6505 116 V 0.4449 0.0928 0.4623 117 F 0.5006 0.0688 0.4306 118 Y 0.3996 0.0550 0.5454 119 P 0.2610 0.2376 0.5014 120 M 0.2146 0.2608 0.5246 121 Q 0.2648 0.1706 0.5646 122 T 0.2174 0.2202 0.5624 123 F 0.2092 0.2086 0.5821 124 S 0.1594 0.2305 0.6101 125 K 0.0922 0.3972 0.5106 126 Q 0.1014 0.4376 0.4610 127 R 0.1083 0.4849 0.4069 128 E 0.0852 0.6129 0.3019 129 V 0.0779 0.6711 0.2510 130 D 0.0782 0.6252 0.2966 131 F 0.0875 0.5771 0.3354 132 K 0.0822 0.5424 0.3754 133 E 0.1194 0.4100 0.4706 134 I 0.2195 0.3106 0.4699 135 P 0.2176 0.4659 0.3165 136 F 0.2664 0.4933 0.2403 137 F 0.2811 0.4957 0.2232 138 I 0.2414 0.4882 0.2704 139 E 0.2020 0.4335 0.3646 140 A 0.1691 0.2844 0.5465 141 S 0.1687 0.1680 0.6633 142 S 0.1591 0.1442 0.6967 143 T 0.0155 0.7265 0.2580 144 E 0.0104 0.8565 0.1332 145 D 0.0111 0.9019 0.0870 146 A 0.0086 0.9136 0.0778 147 A 0.0084 0.9189 0.0728 148 F 0.0083 0.9227 0.0690 149 L 0.0083 0.9209 0.0708 150 K 0.0083 0.9227 0.0690 151 A 0.0083 0.9239 0.0678 152 I 0.0084 0.9183 0.0733 153 A 0.0085 0.9096 0.0819 154 S 0.0090 0.8859 0.1051 155 T 0.0182 0.7585 0.2232 156 L 0.0587 0.4695 0.4717 157 S 0.0873 0.2473 0.6654 158 N 0.1917 0.1510 0.6573 159 R 0.4068 0.0588 0.5344 160 V 0.5714 0.0363 0.3923 161 Y 0.6227 0.0307 0.3466 162 D 0.5025 0.0357 0.4618 163 A 0.2994 0.1289 0.5717 164 D 0.1761 0.0925 0.7314