# This file is the result of combining several RDB files, specifically # TR389.t06.str2.rdb (weight 1.54425) # TR389.t06.str4.rdb (weight 0.924988) # TR389.t06.pb.rdb (weight 0.789901) # TR389.t06.bys.rdb (weight 0.748322) # TR389.t06.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 TR389.t06.str2.rdb # ============================================ # TARGET TR389 # 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 TR389.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 2430 # # ============================================ # Comments from TR389.t06.str4.rdb # ============================================ # TARGET TR389 # 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 TR389.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 2430 # # ============================================ # Comments from TR389.t06.pb.rdb # ============================================ # TARGET TR389 # 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 TR389.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 2430 # # ============================================ # Comments from TR389.t06.bys.rdb # ============================================ # TARGET TR389 # 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 TR389.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 2430 # # ============================================ # Comments from TR389.t06.alpha.rdb # ============================================ # TARGET TR389 # 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 TR389.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 2430 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2437 0.1183 0.6380 2 I 0.1792 0.1594 0.6614 3 G 0.1471 0.1196 0.7333 4 T 0.2329 0.1024 0.6647 5 Q 0.2963 0.1296 0.5741 6 I 0.3541 0.1335 0.5125 7 V 0.2854 0.1666 0.5480 8 T 0.1502 0.2735 0.5763 9 E 0.0120 0.7585 0.2295 10 R 0.0102 0.8729 0.1169 11 L 0.0089 0.9191 0.0720 12 V 0.0084 0.9193 0.0723 13 A 0.0084 0.9169 0.0748 14 L 0.0094 0.9028 0.0878 15 L 0.0140 0.8710 0.1150 16 E 0.0195 0.6736 0.3069 17 S 0.0564 0.2574 0.6862 18 G 0.0478 0.1122 0.8401 19 T 0.1730 0.0660 0.7611 20 E 0.1771 0.1489 0.6740 21 K 0.3988 0.0584 0.5428 22 V 0.7421 0.0077 0.2502 23 L 0.7603 0.0097 0.2300 24 L 0.7690 0.0064 0.2246 25 I 0.7678 0.0131 0.2190 26 D 0.6795 0.0167 0.3038 27 S 0.4869 0.0661 0.4471 28 R 0.3374 0.0323 0.6303 29 P 0.2053 0.0659 0.7288 30 F 0.0775 0.4897 0.4328 31 V 0.0576 0.6486 0.2938 32 E 0.0974 0.6268 0.2758 33 Y 0.1328 0.5768 0.2904 34 N 0.1212 0.5034 0.3754 35 T 0.1297 0.4580 0.4123 36 S 0.1545 0.3199 0.5256 37 H 0.2284 0.2272 0.5444 38 I 0.2595 0.1485 0.5921 39 L 0.1365 0.3268 0.5367 40 E 0.1173 0.2505 0.6322 41 A 0.3157 0.1924 0.4918 42 I 0.4857 0.1151 0.3991 43 N 0.4762 0.0770 0.4467 44 I 0.4075 0.0539 0.5386 45 N 0.2132 0.0428 0.7440 46 C 0.0560 0.6291 0.3149 47 S 0.0215 0.7758 0.2026 48 K 0.0247 0.8294 0.1459 49 L 0.0271 0.8328 0.1401 50 M 0.0300 0.8226 0.1474 51 K 0.0397 0.7620 0.1983 52 R 0.0584 0.6748 0.2669 53 R 0.0702 0.5797 0.3501 54 L 0.0811 0.4798 0.4391 55 Q 0.0811 0.4193 0.4996 56 Q 0.0969 0.3601 0.5430 57 D 0.0974 0.3853 0.5174 58 K 0.1213 0.4430 0.4357 59 V 0.1906 0.3772 0.4322 60 L 0.1827 0.3542 0.4631 61 I 0.1023 0.5710 0.3268 62 T 0.0556 0.6993 0.2451 63 E 0.0325 0.7756 0.1918 64 L 0.0402 0.7748 0.1850 65 I 0.0420 0.7844 0.1736 66 Q 0.0233 0.8386 0.1381 67 H 0.0190 0.8529 0.1281 68 S 0.0196 0.8550 0.1254 69 A 0.0197 0.8547 0.1255 70 K 0.0289 0.8091 0.1620 71 H 0.0481 0.7068 0.2452 72 K 0.0906 0.5388 0.3706 73 V 0.1632 0.2877 0.5491 74 D 0.1641 0.1741 0.6618 75 I 0.2369 0.1153 0.6478 76 D 0.1650 0.0870 0.7479 77 C 0.0843 0.3109 0.6048 78 S 0.1195 0.1807 0.6998 79 Q 0.3191 0.0435 0.6374 80 K 0.5949 0.0169 0.3881 81 V 0.7844 0.0064 0.2092 82 V 0.8038 0.0054 0.1908 83 V 0.7965 0.0054 0.1982 84 Y 0.7619 0.0101 0.2280 85 D 0.4814 0.0183 0.5002 86 Q 0.1978 0.1833 0.6189 87 S 0.1406 0.1973 0.6622 88 S 0.1395 0.1635 0.6971 89 Q 0.0868 0.3083 0.6049 90 D 0.1158 0.3398 0.5443 91 V 0.0847 0.5453 0.3700 92 A 0.0580 0.6118 0.3302 93 S 0.0618 0.6028 0.3354 94 L 0.0789 0.5760 0.3450 95 S 0.0729 0.5772 0.3498 96 S 0.0433 0.6939 0.2628 97 D 0.0232 0.8051 0.1717 98 C 0.0125 0.8853 0.1022 99 F 0.0093 0.9086 0.0821 100 L 0.0084 0.9212 0.0704 101 T 0.0083 0.9233 0.0684 102 V 0.0083 0.9240 0.0678 103 L 0.0084 0.9203 0.0713 104 L 0.0085 0.9141 0.0774 105 G 0.0086 0.8692 0.1222 106 K 0.0099 0.8547 0.1353 107 L 0.0200 0.7823 0.1976 108 E 0.0254 0.6725 0.3021 109 K 0.0404 0.4398 0.5198 110 S 0.0601 0.2303 0.7096 111 F 0.1595 0.1585 0.6820 112 N 0.1657 0.1703 0.6640 113 S 0.3596 0.0951 0.5452 114 V 0.6604 0.0249 0.3147 115 H 0.7539 0.0250 0.2211 116 L 0.7365 0.0214 0.2420 117 L 0.6577 0.0603 0.2820 118 A 0.3786 0.1131 0.5083 119 G 0.1692 0.1383 0.6925 120 G 0.1323 0.2688 0.5989 121 F 0.0628 0.6842 0.2529 122 A 0.0187 0.8322 0.1491 123 E 0.0171 0.8650 0.1179 124 F 0.0219 0.8486 0.1295 125 S 0.0186 0.8281 0.1533 126 R 0.0247 0.6622 0.3131 127 C 0.0528 0.4890 0.4583 128 F 0.1430 0.1488 0.7081 129 P 0.0991 0.2777 0.6232 130 G 0.1011 0.3000 0.5990 131 L 0.1946 0.2757 0.5297 132 C 0.2637 0.1795 0.5568 133 E 0.2399 0.1138 0.6464 134 G 0.1620 0.0783 0.7597 135 K 0.1946 0.1171 0.6883