# This file is the result of combining several RDB files, specifically # T0460.t06.str2.rdb (weight 1.54425) # T0460.t06.str4.rdb (weight 0.924988) # T0460.t06.pb.rdb (weight 0.789901) # T0460.t06.bys.rdb (weight 0.748322) # T0460.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 T0460.t06.str2.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.18387 # # ============================================ # Comments from T0460.t06.str4.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.18387 # # ============================================ # Comments from T0460.t06.pb.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.18387 # # ============================================ # Comments from T0460.t06.bys.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.18387 # # ============================================ # Comments from T0460.t06.alpha.rdb # ============================================ # TARGET T0460 # 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 T0460.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 2.18387 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1687 0.2257 0.6055 2 N 0.1182 0.3318 0.5500 3 S 0.0316 0.7256 0.2428 4 E 0.0187 0.8557 0.1256 5 V 0.0167 0.8973 0.0859 6 I 0.0117 0.9099 0.0784 7 K 0.0089 0.9164 0.0746 8 E 0.0098 0.9090 0.0812 9 F 0.0141 0.8880 0.0979 10 L 0.0131 0.8765 0.1104 11 E 0.0131 0.8593 0.1277 12 D 0.0259 0.7263 0.2478 13 I 0.0659 0.4675 0.4666 14 G 0.0655 0.2924 0.6422 15 E 0.0948 0.3635 0.5417 16 D 0.1303 0.3205 0.5491 17 Y 0.3309 0.2573 0.4119 18 I 0.5469 0.1322 0.3209 19 E 0.6078 0.1159 0.2763 20 L 0.5253 0.1393 0.3353 21 E 0.3564 0.1601 0.4835 22 N 0.2596 0.1096 0.6308 23 E 0.4909 0.0639 0.4452 24 I 0.6180 0.0444 0.3376 25 H 0.5645 0.0466 0.3888 26 L 0.4725 0.0582 0.4694 27 K 0.2959 0.0361 0.6680 28 P 0.2077 0.2589 0.5334 29 E 0.2783 0.3026 0.4190 30 V 0.4729 0.2792 0.2479 31 F 0.4186 0.3898 0.1916 32 Y 0.4815 0.3537 0.1648 33 E 0.4297 0.4093 0.1610 34 V 0.4293 0.4227 0.1480 35 W 0.3853 0.4478 0.1669 36 K 0.2984 0.5046 0.1971 37 Y 0.2789 0.3845 0.3366 38 V 0.2493 0.2016 0.5491 39 G 0.1462 0.1186 0.7352 40 E 0.2279 0.0684 0.7037 41 P 0.2203 0.2335 0.5462 42 E 0.2723 0.1959 0.5318 43 L 0.4783 0.0924 0.4292 44 K 0.5591 0.0751 0.3657 45 T 0.7177 0.0268 0.2555 46 Y 0.7407 0.0205 0.2388 47 V 0.7568 0.0152 0.2280 48 I 0.6942 0.0266 0.2792 49 E 0.5111 0.0794 0.4095 50 D 0.3511 0.1129 0.5360 51 E 0.4808 0.0966 0.4226 52 I 0.5729 0.0600 0.3672 53 V 0.5543 0.0506 0.3951 54 E 0.3975 0.0334 0.5691 55 P 0.2743 0.1300 0.5957 56 G 0.1824 0.1221 0.6956 57 E 0.2447 0.1275 0.6278 58 Y 0.3069 0.0871 0.6060 59 D 0.2353 0.0362 0.7285 60 P 0.1365 0.2607 0.6028 61 P 0.0798 0.4869 0.4332 62 E 0.1490 0.3929 0.4581 63 M 0.3399 0.1620 0.4981 64 K 0.4276 0.1308 0.4416 65 Y 0.5120 0.1062 0.3818 66 T 0.4273 0.1205 0.4522 67 N 0.4319 0.0933 0.4748 68 V 0.5069 0.0842 0.4088 69 K 0.5199 0.0890 0.3911 70 K 0.6704 0.0322 0.2974 71 V 0.6497 0.0191 0.3312 72 K 0.6848 0.0165 0.2987 73 I 0.6575 0.0183 0.3243 74 K 0.5762 0.0519 0.3719 75 K 0.7363 0.0182 0.2455 76 V 0.7447 0.0132 0.2422 77 Y 0.7637 0.0139 0.2224 78 F 0.7118 0.0276 0.2606 79 E 0.6572 0.0587 0.2841 80 T 0.5936 0.0721 0.3343 81 L 0.3873 0.1393 0.4734 82 D 0.2068 0.1386 0.6545 83 N 0.1390 0.1118 0.7493 84 V 0.3509 0.0375 0.6116 85 R 0.5832 0.0295 0.3874 86 V 0.7018 0.0196 0.2786 87 V 0.6707 0.0329 0.2965 88 T 0.5269 0.0532 0.4199 89 D 0.2801 0.0884 0.6315 90 Y 0.0657 0.5226 0.4117 91 S 0.0252 0.7580 0.2168 92 E 0.0142 0.8544 0.1314 93 F 0.0108 0.8966 0.0925 94 Q 0.0091 0.9146 0.0763 95 K 0.0086 0.9217 0.0697 96 I 0.0098 0.9151 0.0751 97 L 0.0167 0.8864 0.0969 98 K 0.0205 0.8603 0.1192 99 K 0.0357 0.7285 0.2358 100 R 0.0709 0.4112 0.5179 101 G 0.0661 0.1677 0.7662 102 T 0.1933 0.1499 0.6568 103 K 0.2699 0.2008 0.5294 104 L 0.2917 0.2511 0.4572 105 E 0.2579 0.3023 0.4398 106 H 0.2629 0.2788 0.4583 107 H 0.2252 0.2603 0.5145 108 H 0.2144 0.2365 0.5491 109 H 0.2086 0.2070 0.5844 110 H 0.1989 0.1752 0.6260 111 H 0.1991 0.1445 0.6564