# This file is the result of combining several RDB files, specifically # T0443.t06.str2.rdb (weight 1.54425) # T0443.t06.str4.rdb (weight 0.924988) # T0443.t06.pb.rdb (weight 0.789901) # T0443.t06.bys.rdb (weight 0.748322) # T0443.t06.alpha.rdb (weight 0.678173) # T0443.t04.str2.rdb (weight 1.54425) # T0443.t04.str4.rdb (weight 0.924988) # T0443.t04.pb.rdb (weight 0.789901) # T0443.t04.bys.rdb (weight 0.748322) # T0443.t04.alpha.rdb (weight 0.678173) # T0443.t2k.str2.rdb (weight 1.54425) # T0443.t2k.str4.rdb (weight 0.924988) # T0443.t2k.pb.rdb (weight 0.789901) # T0443.t2k.bys.rdb (weight 0.748322) # T0443.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 T0443.t06.str2.rdb # ============================================ # TARGET T0443 # 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 T0443.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 1 # # ============================================ # Comments from T0443.t06.str4.rdb # ============================================ # TARGET T0443 # 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 T0443.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 1 # # ============================================ # Comments from T0443.t06.pb.rdb # ============================================ # TARGET T0443 # 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 T0443.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 1 # # ============================================ # Comments from T0443.t06.bys.rdb # ============================================ # TARGET T0443 # 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 T0443.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 1 # # ============================================ # Comments from T0443.t06.alpha.rdb # ============================================ # TARGET T0443 # 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 T0443.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 1 # # ============================================ # Comments from T0443.t04.str2.rdb # ============================================ # TARGET T0443 # 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 T0443.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 1 # # ============================================ # Comments from T0443.t04.str4.rdb # ============================================ # TARGET T0443 # 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 T0443.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 1 # # ============================================ # Comments from T0443.t04.pb.rdb # ============================================ # TARGET T0443 # 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 T0443.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 1 # # ============================================ # Comments from T0443.t04.bys.rdb # ============================================ # TARGET T0443 # 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 T0443.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 1 # # ============================================ # Comments from T0443.t04.alpha.rdb # ============================================ # TARGET T0443 # 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 T0443.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 1 # # ============================================ # Comments from T0443.t2k.str2.rdb # ============================================ # TARGET T0443 # 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 T0443.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 4 # # ============================================ # Comments from T0443.t2k.str4.rdb # ============================================ # TARGET T0443 # 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 T0443.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 4 # # ============================================ # Comments from T0443.t2k.pb.rdb # ============================================ # TARGET T0443 # 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 T0443.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 4 # # ============================================ # Comments from T0443.t2k.bys.rdb # ============================================ # TARGET T0443 # 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 T0443.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 4 # # ============================================ # Comments from T0443.t2k.alpha.rdb # ============================================ # TARGET T0443 # 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 T0443.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 4 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.1958 0.0685 0.7357 2 I 0.2090 0.0974 0.6936 3 P 0.1717 0.1667 0.6616 4 D 0.2829 0.1358 0.5813 5 I 0.4346 0.0709 0.4945 6 H 0.5083 0.0589 0.4328 7 Y 0.4352 0.0722 0.4926 8 S 0.2646 0.0881 0.6473 9 N 0.1372 0.2599 0.6030 10 D 0.1354 0.2071 0.6575 11 S 0.2040 0.1432 0.6528 12 K 0.1870 0.1897 0.6233 13 Y 0.2380 0.1239 0.6381 14 T 0.2487 0.0490 0.7023 15 P 0.2535 0.0928 0.6537 16 S 0.2050 0.0526 0.7423 17 P 0.0846 0.5379 0.3775 18 A 0.1183 0.6173 0.2643 19 A 0.2636 0.5352 0.2012 20 F 0.3652 0.4321 0.2026 21 I 0.3806 0.3966 0.2227 22 R 0.3464 0.3634 0.2902 23 Q 0.3542 0.2435 0.4023 24 Y 0.3918 0.1284 0.4798 25 R 0.3882 0.1068 0.5050 26 Y 0.4070 0.1370 0.4560 27 D 0.3526 0.1519 0.4955 28 V 0.3042 0.2871 0.4086 29 T 0.2209 0.2875 0.4916 30 H 0.1697 0.3622 0.4681 31 D 0.1449 0.3424 0.5127 32 L 0.1087 0.4530 0.4383 33 Q 0.1297 0.3962 0.4742 34 E 0.1656 0.2601 0.5743 35 A 0.2206 0.1315 0.6479 36 E 0.2201 0.1617 0.6181 37 T 0.3327 0.0939 0.5734 38 A 0.5614 0.0401 0.3985 39 L 0.7622 0.0108 0.2269 40 L 0.7999 0.0063 0.1937 41 I 0.8061 0.0077 0.1862 42 W 0.7380 0.0142 0.2478 43 R 0.5948 0.0442 0.3610 44 N 0.3403 0.0406 0.6191 45 A 0.1386 0.3427 0.5187 46 E 0.0902 0.4324 0.4774 47 D 0.1122 0.4121 0.4757 48 D 0.2090 0.3316 0.4594 49 V 0.3381 0.3402 0.3217 50 M 0.3335 0.3582 0.3082 51 Y 0.4205 0.3153 0.2642 52 Q 0.4420 0.2527 0.3052 53 T 0.3323 0.2530 0.4147 54 L 0.1876 0.2937 0.5187 55 D 0.0918 0.3487 0.5594 56 G 0.0516 0.4255 0.5229 57 F 0.0843 0.6713 0.2444 58 D 0.0351 0.8294 0.1355 59 M 0.0204 0.8782 0.1014 60 M 0.0149 0.9031 0.0820 61 L 0.0129 0.9142 0.0729 62 L 0.0103 0.9138 0.0759 63 E 0.0103 0.9076 0.0821 64 I 0.0164 0.8401 0.1435 65 M 0.0364 0.6651 0.2984 66 G 0.0433 0.4889 0.4678 67 S 0.0659 0.4383 0.4958 68 S 0.1169 0.2484 0.6347 69 A 0.0744 0.4723 0.4533 70 L 0.1031 0.3882 0.5087 71 S 0.1222 0.3375 0.5403 72 F 0.0209 0.7693 0.2098 73 D 0.0110 0.8634 0.1256 74 T 0.0089 0.9068 0.0843 75 L 0.0085 0.9157 0.0759 76 A 0.0083 0.9205 0.0712 77 Q 0.0083 0.9215 0.0702 78 T 0.0084 0.9205 0.0711 79 L 0.0087 0.9066 0.0848 80 V 0.0087 0.8938 0.0975 81 E 0.0100 0.7949 0.1952 82 F 0.0237 0.6342 0.3422 83 M 0.1276 0.2859 0.5864 84 P 0.0833 0.4298 0.4869 85 K 0.0391 0.5416 0.4193 86 A 0.0319 0.6572 0.3109 87 D 0.0305 0.6806 0.2889 88 N 0.0349 0.6705 0.2946 89 W 0.0385 0.7620 0.1995 90 K 0.0312 0.8460 0.1228 91 N 0.0208 0.8765 0.1027 92 I 0.0226 0.8784 0.0990 93 L 0.0307 0.8274 0.1419 94 L 0.0486 0.7189 0.2325 95 G 0.0446 0.5961 0.3594 96 K 0.0676 0.5990 0.3334 97 W 0.0866 0.5566 0.3568 98 S 0.0728 0.5466 0.3806 99 G 0.0777 0.4824 0.4399 100 W 0.1589 0.5120 0.3291 101 I 0.2597 0.4199 0.3204 102 E 0.2694 0.3509 0.3797 103 Q 0.3006 0.2596 0.4397 104 R 0.4483 0.1331 0.4186 105 I 0.6090 0.0614 0.3296 106 I 0.6350 0.0426 0.3225 107 I 0.4529 0.0309 0.5162 108 P 0.2715 0.1141 0.6144 109 S 0.2047 0.1797 0.6156 110 L 0.1640 0.3495 0.4866 111 S 0.1731 0.4075 0.4194 112 A 0.1857 0.4588 0.3555 113 I 0.2254 0.3773 0.3972 114 S 0.2022 0.3508 0.4470 115 E 0.1210 0.4171 0.4619 116 N 0.1224 0.2684 0.6091 117 M 0.1464 0.2689 0.5847 118 E 0.1531 0.2027 0.6442 119 G 0.1286 0.1488 0.7226 120 N 0.1752 0.1201 0.7047 121 S 0.2017 0.0625 0.7358 122 P 0.1233 0.2607 0.6160 123 S 0.1281 0.2666 0.6052 124 Q 0.1197 0.3904 0.4899 125 N 0.1375 0.3051 0.5574 126 H 0.2119 0.2337 0.5544 127 L 0.2786 0.1694 0.5521 128 S 0.2611 0.1430 0.5959 129 A 0.1981 0.2449 0.5570