# This file is the result of combining several RDB files, specifically # T0399.t06.str2.rdb (weight 1.54425) # T0399.t06.str4.rdb (weight 0.924988) # T0399.t06.pb.rdb (weight 0.789901) # T0399.t06.bys.rdb (weight 0.748322) # T0399.t06.alpha.rdb (weight 0.678173) # T0399.t04.str2.rdb (weight 1.54425) # T0399.t04.str4.rdb (weight 0.924988) # T0399.t04.pb.rdb (weight 0.789901) # T0399.t04.bys.rdb (weight 0.748322) # T0399.t04.alpha.rdb (weight 0.678173) # T0399.t2k.str2.rdb (weight 1.54425) # T0399.t2k.str4.rdb (weight 0.924988) # T0399.t2k.pb.rdb (weight 0.789901) # T0399.t2k.bys.rdb (weight 0.748322) # T0399.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 T0399.t06.str2.rdb # ============================================ # TARGET T0399 # 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 T0399.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 145 # # ============================================ # Comments from T0399.t06.str4.rdb # ============================================ # TARGET T0399 # 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 T0399.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 145 # # ============================================ # Comments from T0399.t06.pb.rdb # ============================================ # TARGET T0399 # 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 T0399.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 145 # # ============================================ # Comments from T0399.t06.bys.rdb # ============================================ # TARGET T0399 # 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 T0399.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 145 # # ============================================ # Comments from T0399.t06.alpha.rdb # ============================================ # TARGET T0399 # 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 T0399.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 145 # # ============================================ # Comments from T0399.t04.str2.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t04-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 T0399.t04-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 132 # # ============================================ # Comments from T0399.t04.str4.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t04-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 T0399.t04-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 132 # # ============================================ # Comments from T0399.t04.pb.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t04-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 T0399.t04-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 132 # # ============================================ # Comments from T0399.t04.bys.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t04-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 T0399.t04-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 132 # # ============================================ # Comments from T0399.t04.alpha.rdb # ============================================ # TARGET T0399 # Using neural net dunbrack-40pc-3157-t04-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 T0399.t04-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 132 # # ============================================ # Comments from T0399.t2k.str2.rdb # ============================================ # TARGET T0399 # 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 T0399.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 27 # # ============================================ # Comments from T0399.t2k.str4.rdb # ============================================ # TARGET T0399 # 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 T0399.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 27 # # ============================================ # Comments from T0399.t2k.pb.rdb # ============================================ # TARGET T0399 # 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 T0399.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 27 # # ============================================ # Comments from T0399.t2k.bys.rdb # ============================================ # TARGET T0399 # 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 T0399.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 27 # # ============================================ # Comments from T0399.t2k.alpha.rdb # ============================================ # TARGET T0399 # 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 T0399.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 27 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2278 0.1302 0.6420 2 S 0.2131 0.0938 0.6931 3 M 0.1250 0.3564 0.5186 4 K 0.0972 0.4599 0.4428 5 K 0.1265 0.4220 0.4515 6 T 0.1578 0.3818 0.4604 7 K 0.1524 0.5192 0.3284 8 N 0.1012 0.7134 0.1854 9 W 0.0552 0.8282 0.1166 10 L 0.0210 0.8963 0.0827 11 L 0.0117 0.9161 0.0721 12 V 0.0094 0.9197 0.0709 13 F 0.0088 0.9215 0.0696 14 L 0.0086 0.9218 0.0696 15 T 0.0085 0.9223 0.0691 16 V 0.0091 0.9206 0.0703 17 T 0.0115 0.9156 0.0729 18 F 0.0180 0.8988 0.0833 19 C 0.0261 0.8740 0.0999 20 F 0.0520 0.8211 0.1269 21 L 0.0992 0.7204 0.1804 22 M 0.1839 0.5257 0.2904 23 L 0.2338 0.3119 0.4543 24 G 0.2050 0.1864 0.6086 25 C 0.1616 0.1844 0.6539 26 Q 0.1491 0.1732 0.6777 27 S 0.1786 0.1676 0.6538 28 K 0.1317 0.4022 0.4661 29 E 0.1578 0.4078 0.4344 30 D 0.1875 0.3114 0.5011 31 K 0.1633 0.2936 0.5431 32 K 0.1494 0.2139 0.6367 33 G 0.1161 0.1518 0.7321 34 G 0.1445 0.1181 0.7374 35 T 0.1896 0.1038 0.7066 36 K 0.2235 0.0633 0.7132 37 P 0.1660 0.1962 0.6379 38 S 0.1347 0.3951 0.4702 39 N 0.1088 0.5289 0.3622 40 E 0.0914 0.6435 0.2651 41 A 0.0658 0.7350 0.1991 42 A 0.0661 0.7304 0.2035 43 L 0.0977 0.6414 0.2609 44 T 0.1188 0.5646 0.3166 45 K 0.0966 0.5494 0.3540 46 T 0.0885 0.5032 0.4083 47 E 0.0881 0.4613 0.4505 48 N 0.1147 0.4118 0.4734 49 L 0.0913 0.6051 0.3036 50 D 0.1423 0.5513 0.3063 51 F 0.2073 0.4717 0.3210 52 R 0.2893 0.3431 0.3676 53 L 0.3303 0.2941 0.3756 54 S 0.2798 0.2064 0.5138 55 F 0.2273 0.2691 0.5036 56 N 0.1760 0.2228 0.6011 57 K 0.3432 0.1337 0.5231 58 I 0.5607 0.0442 0.3951 59 K 0.6456 0.0326 0.3218 60 V 0.6523 0.0423 0.3054 61 T 0.5091 0.0613 0.4296 62 T 0.3938 0.1485 0.4576 63 D 0.2904 0.2344 0.4752 64 Q 0.2584 0.2866 0.4550 65 N 0.2470 0.2376 0.5154 66 H 0.3278 0.1624 0.5099 67 F 0.3910 0.1149 0.4941 68 S 0.3154 0.1255 0.5591 69 G 0.2169 0.1342 0.6489 70 G 0.1588 0.1293 0.7119 71 T 0.1990 0.1440 0.6570 72 S 0.1701 0.0917 0.7382 73 I 0.0122 0.7629 0.2250 74 E 0.0102 0.8641 0.1257 75 Q 0.0102 0.9150 0.0748 76 L 0.0088 0.9171 0.0741 77 K 0.0093 0.9141 0.0766 78 Q 0.0099 0.8977 0.0924 79 W 0.0229 0.7594 0.2177 80 F 0.0573 0.3357 0.6070 81 G 0.0531 0.0974 0.8494 82 D 0.1623 0.0295 0.8082 83 P 0.1242 0.2806 0.5952 84 N 0.1111 0.2721 0.6167 85 K 0.1619 0.2478 0.5903 86 S 0.1913 0.1824 0.6263 87 E 0.2481 0.2141 0.5378 88 Q 0.3222 0.1918 0.4860 89 R 0.3611 0.1596 0.4793 90 N 0.3140 0.1731 0.5129 91 A 0.2179 0.1677 0.6144 92 G 0.1300 0.1290 0.7410 93 N 0.2549 0.0748 0.6703 94 I 0.5393 0.0222 0.4384 95 T 0.6738 0.0190 0.3071 96 L 0.7132 0.0265 0.2603 97 D 0.6700 0.0459 0.2841 98 S 0.7052 0.0470 0.2477 99 Y 0.6944 0.0460 0.2596 100 T 0.6812 0.0459 0.2729 101 W 0.5960 0.0650 0.3390 102 V 0.4441 0.0780 0.4779 103 K 0.2900 0.1293 0.5807 104 D 0.1573 0.1044 0.7384 105 G 0.2072 0.0763 0.7166 106 A 0.5391 0.0177 0.4432 107 V 0.7319 0.0083 0.2598 108 I 0.8043 0.0063 0.1894 109 N 0.8131 0.0045 0.1824 110 A 0.8177 0.0050 0.1773 111 Q 0.8057 0.0052 0.1891 112 L 0.7238 0.0103 0.2659 113 Y 0.5059 0.0442 0.4499 114 K 0.2103 0.0744 0.7152 115 N 0.1182 0.0987 0.7831 116 S 0.3029 0.1139 0.5833 117 T 0.5503 0.1081 0.3416 118 V 0.6177 0.1401 0.2422 119 A 0.5744 0.2135 0.2121 120 R 0.4339 0.3646 0.2016 121 S 0.2683 0.4923 0.2393 122 I 0.2519 0.4488 0.2994 123 S 0.1409 0.2994 0.5597 124 N 0.1110 0.1596 0.7294 125 F 0.2726 0.1127 0.6148 126 S 0.3469 0.1200 0.5331 127 F 0.3564 0.1671 0.4765 128 S 0.2458 0.2284 0.5258 129 R 0.1315 0.4607 0.4078 130 E 0.1080 0.4817 0.4103 131 A 0.1122 0.4373 0.4505 132 K 0.1551 0.2624 0.5825 133 I 0.2440 0.1418 0.6142 134 G 0.1738 0.0620 0.7642 135 K 0.0421 0.6124 0.3455 136 E 0.0258 0.7454 0.2288 137 D 0.0549 0.6877 0.2574 138 Y 0.0457 0.7523 0.2020 139 D 0.0284 0.7902 0.1814 140 E 0.0492 0.6955 0.2553 141 L 0.0950 0.6499 0.2551 142 K 0.1238 0.4938 0.3824 143 I 0.1106 0.2566 0.6328 144 G 0.0642 0.1440 0.7918 145 E 0.1144 0.2479 0.6377 146 S 0.1320 0.2518 0.6162 147 Y 0.0256 0.7399 0.2345 148 K 0.0113 0.8648 0.1239 149 K 0.0120 0.9068 0.0812 150 V 0.0119 0.9105 0.0775 151 V 0.0104 0.9095 0.0801 152 E 0.0099 0.9019 0.0883 153 K 0.0236 0.7628 0.2137 154 L 0.0600 0.3701 0.5699 155 G 0.0551 0.0948 0.8501 156 E 0.1690 0.0415 0.7895 157 P 0.1630 0.1920 0.6449 158 D 0.1357 0.2563 0.6080 159 V 0.2190 0.2731 0.5079 160 L 0.2961 0.2479 0.4560 161 S 0.3242 0.2359 0.4399 162 Q 0.2874 0.3320 0.3806 163 S 0.2552 0.3090 0.4358 164 M 0.2450 0.2592 0.4958 165 S 0.2407 0.1919 0.5673 166 S 0.1688 0.1680 0.6631 167 D 0.1529 0.1437 0.7035 168 K 0.1134 0.3263 0.5603 169 E 0.1568 0.3540 0.4893 170 E 0.3498 0.2500 0.4002 171 M 0.5105 0.1866 0.3029 172 Q 0.6480 0.1390 0.2130 173 T 0.7252 0.0852 0.1896 174 V 0.7065 0.1028 0.1908 175 W 0.6335 0.1409 0.2256 176 S 0.5148 0.1864 0.2988 177 S 0.2876 0.1643 0.5481 178 G 0.1827 0.0859 0.7314 179 I 0.3476 0.0954 0.5570 180 K 0.3726 0.1127 0.5147 181 T 0.2839 0.1305 0.5856 182 K 0.1689 0.1114 0.7198 183 S 0.1975 0.1061 0.6964 184 S 0.1584 0.1777 0.6639 185 S 0.2496 0.1111 0.6393 186 A 0.3773 0.0650 0.5577 187 T 0.6117 0.0264 0.3619 188 I 0.7511 0.0083 0.2406 189 E 0.8016 0.0052 0.1932 190 L 0.8143 0.0049 0.1809 191 Y 0.8013 0.0052 0.1935 192 F 0.6804 0.0097 0.3099 193 E 0.4783 0.0667 0.4550 194 N 0.2201 0.0671 0.7128 195 G 0.1441 0.0847 0.7712 196 L 0.4590 0.0513 0.4897 197 L 0.6170 0.0453 0.3377 198 K 0.5890 0.0835 0.3275 199 N 0.5096 0.1442 0.3463 200 K 0.2528 0.3684 0.3788 201 T 0.2155 0.3738 0.4107 202 Q 0.1898 0.3753 0.4349 203 K 0.1592 0.2927 0.5481 204 D 0.1529 0.1797 0.6674 205 L 0.1952 0.2488 0.5559 206 E 0.2374 0.2292 0.5334