# 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 144 # # ============================================ # 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 144 # # ============================================ # 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 144 # # ============================================ # 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 144 # # ============================================ # 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 144 # # ============================================ # 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 25 # # ============================================ # 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 25 # # ============================================ # 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 25 # # ============================================ # 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 25 # # ============================================ # 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 25 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2321 0.1245 0.6434 2 S 0.2201 0.0861 0.6938 3 M 0.1345 0.3399 0.5256 4 K 0.1142 0.4255 0.4603 5 K 0.1504 0.3661 0.4835 6 T 0.1885 0.3213 0.4902 7 K 0.1921 0.4540 0.3539 8 N 0.1499 0.6328 0.2173 9 W 0.0990 0.7583 0.1427 10 L 0.0377 0.8671 0.0952 11 L 0.0210 0.9024 0.0766 12 V 0.0131 0.9138 0.0731 13 F 0.0090 0.9217 0.0693 14 L 0.0090 0.9209 0.0701 15 T 0.0085 0.9219 0.0696 16 V 0.0087 0.9214 0.0699 17 T 0.0093 0.9199 0.0708 18 F 0.0107 0.9132 0.0761 19 C 0.0160 0.9015 0.0826 20 F 0.0251 0.8810 0.0939 21 L 0.0442 0.8322 0.1235 22 M 0.0901 0.7164 0.1935 23 L 0.1389 0.5354 0.3257 24 G 0.1587 0.3526 0.4888 25 C 0.1368 0.2288 0.6344 26 Q 0.1387 0.1761 0.6853 27 S 0.1745 0.1751 0.6504 28 K 0.1484 0.3595 0.4921 29 E 0.1856 0.3926 0.4219 30 D 0.2056 0.3435 0.4510 31 K 0.1997 0.3360 0.4643 32 K 0.1782 0.2555 0.5663 33 G 0.1300 0.1487 0.7213 34 G 0.1517 0.1049 0.7434 35 T 0.2241 0.0810 0.6949 36 K 0.2298 0.0435 0.7267 37 P 0.1678 0.1575 0.6746 38 S 0.1143 0.3718 0.5138 39 N 0.1107 0.4206 0.4686 40 E 0.0746 0.6425 0.2830 41 A 0.0499 0.7573 0.1928 42 A 0.0559 0.7545 0.1895 43 L 0.0835 0.6888 0.2277 44 T 0.1076 0.6006 0.2918 45 K 0.0909 0.5656 0.3436 46 T 0.0830 0.4885 0.4285 47 E 0.0866 0.4049 0.5085 48 N 0.1246 0.3197 0.5557 49 L 0.0723 0.5819 0.3458 50 D 0.1269 0.5147 0.3584 51 F 0.2319 0.3978 0.3703 52 R 0.3627 0.2561 0.3812 53 L 0.4507 0.2061 0.3433 54 S 0.3807 0.1698 0.4495 55 F 0.2976 0.2491 0.4533 56 N 0.2111 0.2163 0.5725 57 K 0.3867 0.1287 0.4846 58 I 0.5855 0.0411 0.3734 59 K 0.6248 0.0353 0.3399 60 V 0.6240 0.0569 0.3191 61 T 0.4959 0.0791 0.4250 62 T 0.3992 0.1604 0.4404 63 D 0.3031 0.2169 0.4801 64 Q 0.2592 0.2799 0.4609 65 N 0.2295 0.2374 0.5331 66 H 0.2913 0.1740 0.5347 67 F 0.3553 0.1228 0.5219 68 S 0.2923 0.1301 0.5776 69 G 0.2043 0.1388 0.6569 70 G 0.1544 0.1347 0.7109 71 T 0.1991 0.1495 0.6514 72 S 0.1709 0.1045 0.7246 73 I 0.0119 0.7650 0.2231 74 E 0.0100 0.8683 0.1217 75 Q 0.0098 0.9172 0.0730 76 L 0.0086 0.9182 0.0732 77 K 0.0089 0.9137 0.0774 78 Q 0.0099 0.8954 0.0947 79 W 0.0222 0.7577 0.2201 80 F 0.0582 0.3354 0.6065 81 G 0.0540 0.1037 0.8422 82 D 0.1635 0.0348 0.8017 83 P 0.1413 0.2454 0.6133 84 N 0.1242 0.2180 0.6578 85 K 0.1718 0.2396 0.5885 86 S 0.1925 0.1792 0.6284 87 E 0.2462 0.2065 0.5473 88 Q 0.3215 0.1647 0.5138 89 R 0.3698 0.1287 0.5016 90 N 0.3171 0.1343 0.5486 91 A 0.2228 0.1478 0.6294 92 G 0.1507 0.1152 0.7340 93 N 0.3211 0.0645 0.6144 94 I 0.6042 0.0148 0.3810 95 T 0.7183 0.0107 0.2710 96 L 0.7704 0.0116 0.2180 97 D 0.7190 0.0229 0.2581 98 S 0.7405 0.0288 0.2307 99 Y 0.7183 0.0309 0.2508 100 T 0.6946 0.0313 0.2741 101 W 0.6000 0.0562 0.3439 102 V 0.4410 0.0713 0.4877 103 K 0.3029 0.1147 0.5824 104 D 0.1812 0.1025 0.7164 105 G 0.2683 0.0659 0.6658 106 A 0.5858 0.0146 0.3996 107 V 0.7437 0.0072 0.2491 108 I 0.8076 0.0061 0.1863 109 N 0.8124 0.0044 0.1832 110 A 0.8160 0.0050 0.1790 111 Q 0.8083 0.0053 0.1864 112 L 0.7425 0.0094 0.2482 113 Y 0.5432 0.0396 0.4172 114 K 0.2609 0.0806 0.6585 115 N 0.1530 0.1105 0.7365 116 S 0.2350 0.2026 0.5624 117 T 0.4939 0.1743 0.3317 118 V 0.5717 0.1888 0.2396 119 A 0.5612 0.2311 0.2077 120 R 0.4648 0.3333 0.2019 121 S 0.3076 0.4415 0.2509 122 I 0.2989 0.3927 0.3085 123 S 0.1558 0.2742 0.5701 124 N 0.1125 0.1567 0.7308 125 F 0.2714 0.1252 0.6034 126 S 0.3561 0.1428 0.5011 127 F 0.3678 0.1829 0.4493 128 S 0.2593 0.2451 0.4956 129 R 0.1382 0.4548 0.4070 130 E 0.1102 0.5035 0.3863 131 A 0.0987 0.4431 0.4582 132 K 0.1361 0.2582 0.6057 133 I 0.2252 0.1443 0.6305 134 G 0.1713 0.0692 0.7595 135 K 0.0442 0.6115 0.3442 136 E 0.0262 0.7486 0.2252 137 D 0.0537 0.6988 0.2475 138 Y 0.0440 0.7635 0.1925 139 D 0.0271 0.8064 0.1665 140 E 0.0457 0.7185 0.2358 141 L 0.0857 0.6776 0.2367 142 K 0.1124 0.5235 0.3641 143 I 0.1045 0.2607 0.6348 144 G 0.0614 0.1452 0.7933 145 E 0.1117 0.2607 0.6276 146 S 0.1286 0.2748 0.5967 147 Y 0.0284 0.7404 0.2312 148 K 0.0118 0.8640 0.1242 149 K 0.0126 0.9046 0.0828 150 V 0.0126 0.9084 0.0790 151 V 0.0108 0.9080 0.0812 152 E 0.0103 0.9003 0.0894 153 K 0.0250 0.7590 0.2160 154 L 0.0619 0.3661 0.5719 155 G 0.0561 0.0948 0.8491 156 E 0.1698 0.0399 0.7903 157 P 0.1624 0.1907 0.6469 158 D 0.1326 0.2555 0.6119 159 V 0.2189 0.2695 0.5116 160 L 0.2946 0.2432 0.4622 161 S 0.3240 0.2335 0.4425 162 Q 0.2915 0.3222 0.3863 163 S 0.2543 0.3078 0.4379 164 M 0.2402 0.2686 0.4912 165 S 0.2408 0.1973 0.5620 166 S 0.1687 0.1639 0.6675 167 D 0.1581 0.1326 0.7093 168 K 0.0942 0.3702 0.5356 169 E 0.1277 0.4129 0.4593 170 E 0.2974 0.3066 0.3959 171 M 0.4475 0.2420 0.3105 172 Q 0.5978 0.1781 0.2241 173 T 0.6954 0.1111 0.1935 174 V 0.6887 0.1192 0.1921 175 W 0.6213 0.1547 0.2241 176 S 0.5021 0.1986 0.2993 177 S 0.2759 0.1653 0.5588 178 G 0.1689 0.0833 0.7478 179 I 0.3387 0.0860 0.5753 180 K 0.3776 0.1007 0.5218 181 T 0.3034 0.1207 0.5758 182 K 0.1819 0.1168 0.7014 183 S 0.1910 0.1303 0.6788 184 S 0.1617 0.1651 0.6732 185 S 0.2551 0.1019 0.6429 186 A 0.3970 0.0574 0.5456 187 T 0.6305 0.0228 0.3467 188 I 0.7593 0.0074 0.2333 189 E 0.8051 0.0050 0.1899 190 L 0.8158 0.0048 0.1794 191 Y 0.8052 0.0050 0.1898 192 F 0.6852 0.0091 0.3057 193 E 0.4751 0.0654 0.4595 194 N 0.2181 0.0661 0.7158 195 G 0.1471 0.0831 0.7698 196 L 0.4487 0.0543 0.4971 197 L 0.6011 0.0551 0.3438 198 K 0.5567 0.0973 0.3460 199 N 0.4772 0.1626 0.3602 200 K 0.2412 0.3791 0.3797 201 T 0.2104 0.3906 0.3990 202 Q 0.1839 0.3923 0.4238 203 K 0.1576 0.3054 0.5370 204 D 0.1492 0.1821 0.6687 205 L 0.1846 0.2570 0.5584 206 E 0.2184 0.2387 0.5428