# This file is the result of combining several RDB files, specifically # T0286.t06.dssp-ebghstl.rdb (weight 1.53986) # T0286.t06.stride-ebghtl.rdb (weight 1.24869) # T0286.t06.str2.rdb (weight 1.54758) # T0286.t06.alpha.rdb (weight 0.659012) # T0286.t04.dssp-ebghstl.rdb (weight 1.53986) # T0286.t04.stride-ebghtl.rdb (weight 1.24869) # T0286.t04.str2.rdb (weight 1.54758) # T0286.t04.alpha.rdb (weight 0.659012) # T0286.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0286.t2k.stride-ebghtl.rdb (weight 1.24869) # T0286.t2k.str2.rdb (weight 1.54758) # T0286.t2k.alpha.rdb (weight 0.659012) # 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 T0286.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0286 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0286.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 1642 # # ============================================ # Comments from T0286.t06.stride-ebghtl.rdb # ============================================ # TARGET T0286 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0286.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 1642 # # ============================================ # Comments from T0286.t06.str2.rdb # ============================================ # TARGET T0286 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0286.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 1642 # # ============================================ # Comments from T0286.t06.alpha.rdb # ============================================ # TARGET T0286 # Using neural net t04-2621-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 T0286.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 1642 # # ============================================ # Comments from T0286.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0286 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0286.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 1461 # # ============================================ # Comments from T0286.t04.stride-ebghtl.rdb # ============================================ # TARGET T0286 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0286.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 1461 # # ============================================ # Comments from T0286.t04.str2.rdb # ============================================ # TARGET T0286 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0286.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 1461 # # ============================================ # Comments from T0286.t04.alpha.rdb # ============================================ # TARGET T0286 # Using neural net t04-2621-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 T0286.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 1461 # # ============================================ # Comments from T0286.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0286 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0286.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 83 # # ============================================ # Comments from T0286.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0286 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0286.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 83 # # ============================================ # Comments from T0286.t2k.str2.rdb # ============================================ # TARGET T0286 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0286.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 83 # # ============================================ # Comments from T0286.t2k.alpha.rdb # ============================================ # TARGET T0286 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0286.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 83 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0657 0.0737 0.8606 2 A 0.0764 0.1034 0.8203 3 S 0.0813 0.0519 0.8668 4 K 0.1900 0.0172 0.7927 5 T 0.5387 0.0086 0.4527 6 I 0.8143 0.0053 0.1804 7 K 0.8949 0.0038 0.1013 8 I 0.9160 0.0034 0.0807 9 M 0.8644 0.0049 0.1307 10 P 0.6847 0.0068 0.3085 11 V 0.3312 0.0582 0.6106 12 G 0.1716 0.0826 0.7458 13 D 0.1291 0.1858 0.6851 14 S 0.2073 0.2006 0.5921 15 C 0.2538 0.2481 0.4982 16 T 0.3359 0.1992 0.4649 17 E 0.2719 0.1699 0.5582 18 G 0.1646 0.1239 0.7115 19 M 0.1612 0.1105 0.7283 20 G 0.1392 0.0776 0.7832 21 G 0.1102 0.0859 0.8039 22 G 0.0480 0.1886 0.7634 23 E 0.0404 0.1913 0.7683 24 M 0.0401 0.1970 0.7628 25 G 0.0473 0.1894 0.7633 26 S 0.0832 0.2415 0.6754 27 Y 0.1277 0.3577 0.5146 28 R 0.0807 0.5578 0.3614 29 T 0.0259 0.7990 0.1751 30 E 0.0155 0.8347 0.1498 31 L 0.0088 0.8920 0.0992 32 Y 0.0075 0.9073 0.0852 33 R 0.0074 0.9260 0.0667 34 L 0.0061 0.9310 0.0629 35 L 0.0088 0.9159 0.0754 36 T 0.0086 0.8976 0.0938 37 Q 0.0125 0.8168 0.1707 38 A 0.0403 0.3551 0.6045 39 G 0.0339 0.0388 0.9273 40 L 0.0960 0.0257 0.8783 41 S 0.3269 0.0253 0.6478 42 I 0.6357 0.0350 0.3293 43 D 0.7279 0.0384 0.2338 44 F 0.7628 0.0336 0.2037 45 V 0.6250 0.0506 0.3244 46 G 0.4187 0.0405 0.5408 47 S 0.2535 0.0874 0.6591 48 Q 0.2091 0.0785 0.7124 49 R 0.2148 0.0737 0.7115 50 S 0.1673 0.0609 0.7717 51 G 0.1126 0.0650 0.8224 52 P 0.1201 0.0885 0.7914 53 S 0.1295 0.1515 0.7191 54 S 0.1028 0.1717 0.7255 55 L 0.0758 0.2381 0.6861 56 P 0.0645 0.2697 0.6657 57 D 0.0765 0.3488 0.5747 58 K 0.0834 0.4303 0.4862 59 D 0.0746 0.3971 0.5283 60 H 0.0688 0.3613 0.5699 61 E 0.0651 0.2948 0.6401 62 G 0.0604 0.2157 0.7239 63 H 0.0696 0.1925 0.7379 64 S 0.0653 0.2809 0.6538 65 G 0.0654 0.3126 0.6220 66 W 0.1041 0.3908 0.5052 67 T 0.1539 0.4420 0.4041 68 I 0.0497 0.7509 0.1994 69 P 0.0320 0.8350 0.1331 70 Q 0.0281 0.8477 0.1242 71 I 0.0263 0.8465 0.1273 72 A 0.0191 0.8259 0.1550 73 S 0.0230 0.7415 0.2354 74 N 0.0273 0.6445 0.3282 75 I 0.0485 0.5835 0.3680 76 N 0.0473 0.5160 0.4368 77 N 0.0449 0.4306 0.5245 78 W 0.0704 0.4365 0.4931 79 L 0.0902 0.3974 0.5125 80 N 0.0903 0.3634 0.5463 81 T 0.1032 0.2841 0.6127 82 H 0.1224 0.1473 0.7303 83 N 0.1159 0.0364 0.8477 84 P 0.1139 0.0473 0.8388 85 D 0.1587 0.0621 0.7792 86 V 0.9048 0.0049 0.0903 87 V 0.9333 0.0032 0.0635 88 F 0.9323 0.0032 0.0644 89 L 0.9170 0.0049 0.0781 90 W 0.8234 0.0116 0.1650 91 I 0.3621 0.0433 0.5946 92 G 0.1746 0.0508 0.7747 93 G 0.1359 0.2260 0.6380 94 N 0.1328 0.3128 0.5545 95 D 0.1026 0.4650 0.4323 96 L 0.0431 0.5933 0.3637 97 L 0.0505 0.5139 0.4357 98 L 0.0548 0.3688 0.5764 99 N 0.0583 0.1549 0.7868 100 G 0.0542 0.1814 0.7644 101 N 0.0530 0.2829 0.6641 102 L 0.0326 0.5125 0.4550 103 N 0.0207 0.6903 0.2890 104 A 0.0087 0.8585 0.1328 105 T 0.0065 0.8789 0.1146 106 G 0.0060 0.8974 0.0967 107 L 0.0049 0.9434 0.0517 108 S 0.0049 0.9490 0.0462 109 N 0.0048 0.9482 0.0471 110 L 0.0047 0.9548 0.0405 111 I 0.0050 0.9576 0.0374 112 D 0.0048 0.9571 0.0381 113 Q 0.0048 0.9568 0.0384 114 I 0.0051 0.9509 0.0441 115 F 0.0060 0.9280 0.0661 116 T 0.0073 0.8431 0.1496 117 V 0.0187 0.6749 0.3064 118 K 0.0752 0.0680 0.8568 119 P 0.0180 0.1180 0.8640 120 N 0.0268 0.0585 0.9146 121 V 0.3069 0.0161 0.6771 122 T 0.7633 0.0049 0.2318 123 L 0.9286 0.0034 0.0680 124 F 0.9310 0.0033 0.0658 125 V 0.9223 0.0037 0.0741 126 A 0.8499 0.0137 0.1365 127 D 0.5692 0.0147 0.4160 128 Y 0.3320 0.0218 0.6462 129 Y 0.2216 0.0284 0.7501 130 P 0.1004 0.0466 0.8531 131 W 0.0583 0.0738 0.8679 132 P 0.0317 0.3297 0.6386 133 E 0.0284 0.4154 0.5562 134 A 0.0361 0.5204 0.4435 135 I 0.0265 0.7050 0.2685 136 K 0.0111 0.8589 0.1299 137 Q 0.0090 0.9043 0.0868 138 Y 0.0061 0.9292 0.0648 139 N 0.0057 0.9365 0.0578 140 A 0.0054 0.9216 0.0730 141 V 0.0055 0.9265 0.0680 142 I 0.0061 0.9216 0.0724 143 P 0.0058 0.9283 0.0659 144 G 0.0064 0.9295 0.0640 145 I 0.0064 0.9334 0.0602 146 V 0.0063 0.9392 0.0545 147 Q 0.0049 0.9465 0.0486 148 Q 0.0050 0.9476 0.0474 149 K 0.0051 0.9420 0.0529 150 A 0.0062 0.9191 0.0747 151 N 0.0073 0.8133 0.1794 152 A 0.0221 0.4692 0.5087 153 G 0.0459 0.1809 0.7732 154 K 0.0647 0.0845 0.8508 155 K 0.2014 0.0682 0.7305 156 V 0.3379 0.0819 0.5802 157 Y 0.5136 0.0759 0.4105 158 F 0.6009 0.0735 0.3256 159 V 0.6385 0.0906 0.2709 160 K 0.6245 0.1146 0.2610 161 L 0.5263 0.1680 0.3057 162 S 0.4267 0.2060 0.3673 163 E 0.3407 0.2267 0.4325 164 I 0.2396 0.2187 0.5417 165 Q 0.1834 0.1941 0.6224 166 F 0.1537 0.1516 0.6947 167 D 0.1198 0.1062 0.7740 168 R 0.0945 0.1545 0.7509 169 N 0.0987 0.1952 0.7060 170 T 0.0828 0.3710 0.5462 171 D 0.1018 0.3931 0.5052 172 I 0.1442 0.3191 0.5367 173 S 0.1459 0.2463 0.6078 174 W 0.1134 0.2025 0.6841 175 D 0.0866 0.1298 0.7836 176 G 0.1163 0.0876 0.7961 177 L 0.2657 0.0591 0.6752 178 H 0.3028 0.0495 0.6477 179 L 0.1410 0.1609 0.6982 180 S 0.0560 0.2139 0.7301 181 E 0.0155 0.8088 0.1757 182 I 0.0192 0.8487 0.1321 183 G 0.0098 0.8910 0.0992 184 Y 0.0050 0.9560 0.0390 185 K 0.0047 0.9583 0.0370 186 K 0.0048 0.9557 0.0395 187 I 0.0048 0.9532 0.0420 188 A 0.0048 0.9523 0.0429 189 N 0.0054 0.9417 0.0529 190 I 0.0053 0.9312 0.0635 191 W 0.0061 0.9258 0.0681 192 Y 0.0053 0.9425 0.0522 193 K 0.0048 0.9505 0.0447 194 Y 0.0048 0.9548 0.0404 195 T 0.0048 0.9546 0.0407 196 I 0.0048 0.9523 0.0429 197 D 0.0050 0.9418 0.0532 198 I 0.0051 0.9403 0.0547 199 L 0.0060 0.9218 0.0723 200 R 0.0065 0.8831 0.1104 201 A 0.0107 0.8302 0.1590 202 L 0.0209 0.7193 0.2598 203 A 0.0292 0.4700 0.5008 204 G 0.0277 0.2300 0.7424 205 E 0.0317 0.0870 0.8813