# This file is the result of combining several RDB files, specifically # T0582.t06.str2.rdb (weight 1.54425) # T0582.t06.str4.rdb (weight 0.924988) # T0582.t06.pb.rdb (weight 0.789901) # T0582.t06.bys.rdb (weight 0.748322) # T0582.t06.alpha.rdb (weight 0.678173) # T0582.t04.str2.rdb (weight 1.54425) # T0582.t04.str4.rdb (weight 0.924988) # T0582.t04.pb.rdb (weight 0.789901) # T0582.t04.bys.rdb (weight 0.748322) # T0582.t04.alpha.rdb (weight 0.678173) # T0582.t2k.str2.rdb (weight 1.54425) # T0582.t2k.str4.rdb (weight 0.924988) # T0582.t2k.pb.rdb (weight 0.789901) # T0582.t2k.bys.rdb (weight 0.748322) # T0582.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 T0582.t06.str2.rdb # ============================================ # TARGET T0582 # 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 T0582.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 2410 # # ============================================ # Comments from T0582.t06.str4.rdb # ============================================ # TARGET T0582 # 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 T0582.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 2410 # # ============================================ # Comments from T0582.t06.pb.rdb # ============================================ # TARGET T0582 # 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 T0582.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 2410 # # ============================================ # Comments from T0582.t06.bys.rdb # ============================================ # TARGET T0582 # 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 T0582.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 2410 # # ============================================ # Comments from T0582.t06.alpha.rdb # ============================================ # TARGET T0582 # 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 T0582.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 2410 # # ============================================ # Comments from T0582.t04.str2.rdb # ============================================ # TARGET T0582 # 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 T0582.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 1685 # # ============================================ # Comments from T0582.t04.str4.rdb # ============================================ # TARGET T0582 # 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 T0582.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 1685 # # ============================================ # Comments from T0582.t04.pb.rdb # ============================================ # TARGET T0582 # 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 T0582.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 1685 # # ============================================ # Comments from T0582.t04.bys.rdb # ============================================ # TARGET T0582 # 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 T0582.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 1685 # # ============================================ # Comments from T0582.t04.alpha.rdb # ============================================ # TARGET T0582 # 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 T0582.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 1685 # # ============================================ # Comments from T0582.t2k.str2.rdb # ============================================ # TARGET T0582 # 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 T0582.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 133.033 # # ============================================ # Comments from T0582.t2k.str4.rdb # ============================================ # TARGET T0582 # 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 T0582.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 133.033 # # ============================================ # Comments from T0582.t2k.pb.rdb # ============================================ # TARGET T0582 # 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 T0582.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 133.033 # # ============================================ # Comments from T0582.t2k.bys.rdb # ============================================ # TARGET T0582 # 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 T0582.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 133.033 # # ============================================ # Comments from T0582.t2k.alpha.rdb # ============================================ # TARGET T0582 # 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 T0582.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 133.033 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.4559 0.0821 0.4620 2 E 0.4947 0.0639 0.4414 3 I 0.4991 0.0627 0.4383 4 N 0.3199 0.0452 0.6349 5 A 0.1839 0.2619 0.5542 6 D 0.1686 0.1724 0.6589 7 F 0.1696 0.2211 0.6093 8 T 0.2008 0.1415 0.6576 9 K 0.3200 0.0653 0.6147 10 P 0.4442 0.0570 0.4988 11 V 0.6796 0.0256 0.2948 12 V 0.7202 0.0153 0.2646 13 I 0.6849 0.0201 0.2950 14 D 0.3489 0.0170 0.6341 15 T 0.1617 0.3425 0.4959 16 D 0.1072 0.3358 0.5571 17 Q 0.1646 0.2662 0.5692 18 L 0.2736 0.1428 0.5835 19 E 0.2765 0.1203 0.6032 20 W 0.3527 0.1088 0.5385 21 R 0.3635 0.0420 0.5945 22 P 0.3214 0.0808 0.5977 23 S 0.2561 0.0541 0.6898 24 P 0.1554 0.2036 0.6409 25 M 0.1764 0.1676 0.6561 26 K 0.1385 0.1816 0.6800 27 G 0.1297 0.1464 0.7239 28 V 0.3086 0.1995 0.4920 29 E 0.4392 0.2246 0.3362 30 R 0.5360 0.1964 0.2676 31 R 0.5109 0.2068 0.2823 32 M 0.4266 0.2772 0.2962 33 L 0.2947 0.4154 0.2899 34 D 0.1985 0.4495 0.3520 35 R 0.1971 0.3315 0.4714 36 I 0.1520 0.1968 0.6512 37 G 0.0897 0.1244 0.7859 38 G 0.1276 0.1593 0.7131 39 E 0.2302 0.1952 0.5746 40 V 0.3614 0.2107 0.4279 41 A 0.3786 0.2118 0.4096 42 R 0.5105 0.1874 0.3022 43 A 0.6255 0.1256 0.2489 44 T 0.6982 0.0774 0.2244 45 S 0.7436 0.0514 0.2050 46 I 0.7623 0.0312 0.2065 47 V 0.7538 0.0340 0.2122 48 R 0.7200 0.0318 0.2482 49 Y 0.5585 0.0521 0.3895 50 A 0.3226 0.0397 0.6377 51 P 0.1324 0.1495 0.7181 52 G 0.0718 0.1021 0.8260 53 S 0.2010 0.0996 0.6994 54 R 0.3409 0.0886 0.5704 55 F 0.3831 0.0507 0.5661 56 S 0.2754 0.0885 0.6361 57 A 0.2372 0.2436 0.5193 58 H 0.3099 0.1498 0.5403 59 T 0.3058 0.1189 0.5753 60 H 0.2533 0.0710 0.6757 61 D 0.1470 0.1561 0.6968 62 G 0.0889 0.1252 0.7859 63 G 0.1953 0.0976 0.7071 64 E 0.4829 0.0506 0.4666 65 E 0.6895 0.0289 0.2817 66 F 0.8017 0.0080 0.1904 67 I 0.8101 0.0058 0.1841 68 V 0.8045 0.0075 0.1880 69 L 0.7621 0.0137 0.2242 70 D 0.6624 0.0345 0.3030 71 G 0.5370 0.0426 0.4204 72 V 0.6242 0.0511 0.3247 73 F 0.6408 0.0464 0.3128 74 Q 0.5665 0.0664 0.3671 75 D 0.3899 0.0904 0.5196 76 E 0.1622 0.3382 0.4995 77 H 0.1080 0.1881 0.7039 78 G 0.1118 0.0987 0.7895 79 D 0.2750 0.0724 0.6525 80 Y 0.2943 0.0348 0.6708 81 P 0.2630 0.0700 0.6669 82 A 0.1992 0.1797 0.6211 83 G 0.1940 0.1175 0.6885 84 T 0.4176 0.0599 0.5225 85 Y 0.6520 0.0458 0.3022 86 V 0.7032 0.0384 0.2584 87 R 0.6679 0.0378 0.2943 88 N 0.4441 0.0237 0.5322 89 P 0.2307 0.0535 0.7157 90 P 0.1241 0.2328 0.6431 91 T 0.1390 0.1641 0.6970 92 T 0.2121 0.1351 0.6528 93 S 0.2609 0.1469 0.5922 94 H 0.3402 0.1013 0.5585 95 V 0.3412 0.0486 0.6103 96 P 0.2855 0.0894 0.6251 97 G 0.3365 0.0954 0.5681 98 S 0.2568 0.0826 0.6607 99 A 0.1553 0.2967 0.5480 100 E 0.1057 0.1833 0.7110 101 G 0.1166 0.1087 0.7747 102 C 0.4235 0.0500 0.5265 103 T 0.6669 0.0358 0.2973 104 I 0.7855 0.0206 0.1939 105 F 0.7971 0.0189 0.1839 106 V 0.7958 0.0221 0.1822 107 K 0.7550 0.0438 0.2012 108 L 0.6850 0.0781 0.2369 109 W 0.5139 0.1295 0.3566 110 Q 0.3514 0.1557 0.4930 111 F 0.2684 0.1081 0.6235 112 D 0.1965 0.0417 0.7617 113 P 0.0508 0.4386 0.5106 114 A 0.0472 0.4647 0.4882 115 D 0.0878 0.3910 0.5211 116 R 0.1310 0.3624 0.5067 117 T 0.2037 0.2923 0.5040 118 Q 0.2684 0.2593 0.4723 119 F 0.3747 0.2104 0.4149 120 S 0.3866 0.2027 0.4107 121 K 0.3310 0.2615 0.4076 122 N 0.2658 0.1948 0.5394 123 M 0.1348 0.4183 0.4468 124 E 0.1247 0.3939 0.4815 125 A 0.1533 0.3109 0.5359 126 E 0.1166 0.4243 0.4591 127 L 0.1365 0.2455 0.6180 128 G 0.1344 0.1436 0.7220 129 A 0.2690 0.0400 0.6910 130 P 0.3095 0.0680 0.6225 131 V 0.2835 0.0909 0.6256 132 E 0.1925 0.1401 0.6674 133 G 0.1632 0.1067 0.7301 134 I 0.4149 0.0547 0.5304 135 S 0.6053 0.0402 0.3545 136 T 0.6953 0.0280 0.2768 137 S 0.6456 0.0247 0.3296 138 L 0.5390 0.0565 0.4045 139 L 0.4145 0.0961 0.4894 140 H 0.3060 0.0881 0.6059 141 E 0.1730 0.2137 0.6133 142 D 0.1632 0.1653 0.6715 143 E 0.1398 0.2556 0.6047 144 R 0.2404 0.1999 0.5597 145 E 0.4635 0.1077 0.4288 146 T 0.6339 0.0437 0.3224 147 V 0.7281 0.0268 0.2451 148 T 0.7446 0.0278 0.2276 149 H 0.7447 0.0298 0.2255 150 R 0.7221 0.0304 0.2475 151 K 0.6819 0.0265 0.2916 152 L 0.4823 0.0419 0.4759 153 E 0.2687 0.0396 0.6916 154 P 0.1230 0.1576 0.7193 155 G 0.0598 0.1114 0.8287 156 A 0.2308 0.0940 0.6752 157 N 0.4348 0.0709 0.4944 158 L 0.5182 0.0635 0.4182 159 T 0.4446 0.0936 0.4618 160 S 0.3656 0.1741 0.4603 161 E 0.2731 0.2422 0.4846 162 A 0.2366 0.2112 0.5522 163 A 0.1665 0.1724 0.6611 164 G 0.1145 0.1224 0.7630 165 G 0.2391 0.1032 0.6577 166 I 0.5778 0.0431 0.3791 167 E 0.7218 0.0232 0.2550 168 V 0.8050 0.0064 0.1886 169 L 0.8069 0.0056 0.1875 170 V 0.8020 0.0061 0.1919 171 L 0.7559 0.0116 0.2325 172 D 0.6676 0.0256 0.3068 173 G 0.5701 0.0360 0.3939 174 D 0.6699 0.0250 0.3052 175 V 0.7117 0.0209 0.2674 176 T 0.6174 0.0313 0.3513 177 V 0.4381 0.0965 0.4654 178 N 0.2135 0.1288 0.6577 179 D 0.1547 0.1556 0.6896 180 E 0.2826 0.1767 0.5407 181 V 0.4568 0.1393 0.4039 182 L 0.4195 0.0905 0.4900 183 G 0.3488 0.0993 0.5519 184 R 0.2083 0.1838 0.6079 185 N 0.2158 0.1241 0.6600 186 A 0.4138 0.0740 0.5122 187 W 0.6056 0.0631 0.3313 188 L 0.6868 0.0414 0.2718 189 R 0.6508 0.0325 0.3167 190 L 0.3735 0.0258 0.6007 191 P 0.2147 0.0865 0.6989 192 E 0.1157 0.1867 0.6975 193 G 0.0813 0.1348 0.7839 194 E 0.1844 0.1612 0.6544 195 A 0.2561 0.2203 0.5236 196 L 0.3361 0.1841 0.4798 197 S 0.4522 0.1274 0.4204 198 A 0.4649 0.1606 0.3746 199 T 0.5283 0.1059 0.3658 200 A 0.4609 0.1163 0.4228 201 G 0.2855 0.1058 0.6087 202 A 0.2049 0.2617 0.5334 203 R 0.1391 0.1420 0.7189 204 G 0.1655 0.0795 0.7550 205 A 0.4522 0.0131 0.5347 206 K 0.7258 0.0102 0.2640 207 I 0.8090 0.0062 0.1848 208 W 0.8068 0.0061 0.1871 209 M 0.7655 0.0118 0.2227 210 K 0.5783 0.0463 0.3755 211 T 0.3323 0.0889 0.5788 212 G 0.1942 0.1053 0.7006 213 H 0.2492 0.1153 0.6355 214 L 0.2625 0.1727 0.5649 215 R 0.1989 0.3053 0.4958 216 F 0.2566 0.2403 0.5031 217 V 0.3188 0.1476 0.5335 218 R 0.2925 0.0651 0.6423 219 T 0.2094 0.0498 0.7407 220 P 0.0914 0.3069 0.6018 221 E 0.1615 0.2243 0.6142 222 V 0.2390 0.1443 0.6167