# This file is the result of combining several RDB files, specifically # T0288.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0288.t2k.stride-ebghtl.rdb (weight 1.24869) # T0288.t2k.str2.rdb (weight 1.54758) # T0288.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 T0288.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0288 # 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 T0288.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 1199 # # ============================================ # Comments from T0288.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0288 # 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 T0288.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 1199 # # ============================================ # Comments from T0288.t2k.str2.rdb # ============================================ # TARGET T0288 # 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 T0288.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 195.398 # # ============================================ # Comments from T0288.t2k.alpha.rdb # ============================================ # TARGET T0288 # 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 T0288.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 1199 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1863 0.0533 0.7604 2 M 0.3416 0.0336 0.6248 3 V 0.4113 0.0161 0.5726 4 P 0.4822 0.0202 0.4976 5 G 0.6485 0.0126 0.3389 6 K 0.8840 0.0045 0.1115 7 V 0.9141 0.0034 0.0825 8 T 0.9089 0.0053 0.0858 9 L 0.9079 0.0049 0.0872 10 Q 0.8443 0.0090 0.1467 11 K 0.6889 0.0218 0.2893 12 D 0.3502 0.0327 0.6171 13 A 0.1169 0.0802 0.8030 14 Q 0.0764 0.0930 0.8306 15 N 0.1484 0.0720 0.7796 16 L 0.3897 0.0565 0.5538 17 I 0.6205 0.0209 0.3586 18 G 0.8061 0.0121 0.1819 19 I 0.8895 0.0050 0.1055 20 S 0.8936 0.0047 0.1017 21 I 0.8751 0.0088 0.1161 22 G 0.7207 0.0235 0.2558 23 G 0.3529 0.0336 0.6135 24 G 0.1475 0.0579 0.7946 25 A 0.1326 0.1019 0.7656 26 Q 0.1339 0.1009 0.7652 27 Y 0.1309 0.0854 0.7837 28 C 0.1482 0.0496 0.8022 29 P 0.2114 0.0413 0.7473 30 C 0.5352 0.0180 0.4467 31 L 0.8470 0.0045 0.1485 32 Y 0.8992 0.0042 0.0966 33 I 0.9069 0.0037 0.0894 34 V 0.8296 0.0255 0.1449 35 Q 0.8228 0.0085 0.1687 36 V 0.6813 0.0159 0.3028 37 F 0.2785 0.0203 0.7012 38 D 0.0407 0.0757 0.8836 39 N 0.0282 0.0358 0.9360 40 T 0.0873 0.0374 0.8753 41 P 0.1040 0.3789 0.5171 42 A 0.1181 0.5562 0.3257 43 A 0.1575 0.5761 0.2664 44 L 0.1392 0.5328 0.3280 45 D 0.1148 0.2059 0.6793 46 G 0.0677 0.0808 0.8515 47 T 0.2427 0.0483 0.7090 48 V 0.4690 0.0299 0.5011 49 A 0.2319 0.0280 0.7400 50 A 0.1031 0.1288 0.7682 51 G 0.0723 0.0780 0.8498 52 D 0.3042 0.0923 0.6035 53 E 0.7404 0.0364 0.2232 54 I 0.8572 0.0186 0.1242 55 T 0.8701 0.0195 0.1104 56 G 0.8766 0.0105 0.1129 57 V 0.7440 0.0226 0.2334 58 N 0.2699 0.0322 0.6980 59 G 0.1115 0.0507 0.8378 60 R 0.4752 0.0219 0.5029 61 S 0.5911 0.0262 0.3827 62 I 0.4303 0.0906 0.4791 63 K 0.1647 0.0960 0.7393 64 G 0.0789 0.0624 0.8587 65 K 0.1912 0.0364 0.7723 66 T 0.1577 0.0457 0.7966 67 K 0.0053 0.9282 0.0665 68 V 0.0047 0.9552 0.0401 69 E 0.0047 0.9581 0.0372 70 V 0.0047 0.9594 0.0359 71 A 0.0047 0.9594 0.0359 72 K 0.0047 0.9585 0.0368 73 M 0.0048 0.9550 0.0402 74 I 0.0058 0.9437 0.0505 75 Q 0.0070 0.9146 0.0784 76 E 0.0170 0.7154 0.2676 77 V 0.0572 0.3481 0.5947 78 K 0.0313 0.0937 0.8750 79 G 0.0415 0.0632 0.8953 80 E 0.2924 0.0197 0.6879 81 V 0.7195 0.0048 0.2758 82 T 0.8890 0.0038 0.1072 83 I 0.9138 0.0036 0.0826 84 H 0.9239 0.0033 0.0727 85 Y 0.9131 0.0032 0.0837 86 N 0.8370 0.0053 0.1577 87 K 0.6690 0.0080 0.3229 88 L 0.3595 0.0262 0.6143 89 Q 0.1481 0.0377 0.8143 90 Y 0.0997 0.0493 0.8510 91 Y 0.1344 0.0404 0.8251 92 K 0.2034 0.0461 0.7505 93 V 0.1744 0.0518 0.7738