# This file is the result of combining several RDB files, specifically # T0472.t06.str2.rdb (weight 1.54425) # T0472.t06.str4.rdb (weight 0.924988) # T0472.t06.pb.rdb (weight 0.789901) # T0472.t06.bys.rdb (weight 0.748322) # T0472.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 T0472.t06.str2.rdb # ============================================ # TARGET T0472 # 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 T0472.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 26.5762 # # ============================================ # Comments from T0472.t06.str4.rdb # ============================================ # TARGET T0472 # 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 T0472.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 26.5762 # # ============================================ # Comments from T0472.t06.pb.rdb # ============================================ # TARGET T0472 # 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 T0472.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 26.5762 # # ============================================ # Comments from T0472.t06.bys.rdb # ============================================ # TARGET T0472 # 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 T0472.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 26.5762 # # ============================================ # Comments from T0472.t06.alpha.rdb # ============================================ # TARGET T0472 # 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 T0472.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 26.5762 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2445 0.1274 0.6281 2 S 0.2635 0.1069 0.6296 3 G 0.3424 0.1005 0.5571 4 W 0.5784 0.0544 0.3672 5 Y 0.7429 0.0171 0.2400 6 E 0.7760 0.0128 0.2113 7 L 0.7653 0.0128 0.2218 8 S 0.7258 0.0217 0.2525 9 K 0.6200 0.0528 0.3272 10 S 0.3994 0.0711 0.5295 11 S 0.1729 0.2345 0.5926 12 N 0.1328 0.1319 0.7352 13 D 0.1532 0.0839 0.7629 14 Q 0.5183 0.0303 0.4514 15 F 0.7354 0.0097 0.2549 16 K 0.8061 0.0062 0.1877 17 F 0.8286 0.0042 0.1672 18 V 0.8165 0.0048 0.1787 19 L 0.7923 0.0068 0.2009 20 K 0.7732 0.0126 0.2142 21 A 0.6367 0.0291 0.3342 22 G 0.2574 0.1334 0.6092 23 N 0.1291 0.1210 0.7498 24 G 0.1689 0.0674 0.7637 25 E 0.5518 0.0251 0.4231 26 V 0.7383 0.0133 0.2484 27 I 0.7575 0.0193 0.2232 28 L 0.7544 0.0248 0.2208 29 T 0.6822 0.0455 0.2723 30 S 0.5095 0.0619 0.4285 31 E 0.2486 0.2606 0.4909 32 L 0.2095 0.3037 0.4868 33 Y 0.2417 0.2338 0.5244 34 T 0.2105 0.2177 0.5719 35 G 0.1451 0.2072 0.6477 36 K 0.0547 0.6072 0.3382 37 S 0.0436 0.7133 0.2430 38 G 0.0382 0.7392 0.2227 39 A 0.0255 0.8379 0.1366 40 M 0.0175 0.8423 0.1403 41 N 0.0208 0.7936 0.1856 42 G 0.0277 0.7976 0.1747 43 I 0.0228 0.8421 0.1351 44 E 0.0181 0.8584 0.1235 45 S 0.0233 0.8405 0.1363 46 V 0.0527 0.7676 0.1797 47 Q 0.0656 0.6917 0.2427 48 T 0.0841 0.5153 0.4006 49 N 0.0895 0.2568 0.6538 50 S 0.1732 0.1135 0.7133 51 P 0.1096 0.2397 0.6507 52 I 0.0934 0.4147 0.4919 53 E 0.0866 0.5598 0.3537 54 A 0.1201 0.5775 0.3024 55 R 0.2128 0.5113 0.2759 56 Y 0.2838 0.4597 0.2565 57 A 0.3360 0.4025 0.2615 58 K 0.3960 0.3498 0.2542 59 E 0.4395 0.2803 0.2802 60 V 0.4343 0.2428 0.3229 61 A 0.2794 0.2653 0.4553 62 K 0.1239 0.2919 0.5843 63 N 0.1074 0.1422 0.7504 64 D 0.0923 0.0912 0.8166 65 K 0.3676 0.0217 0.6107 66 P 0.5596 0.0262 0.4142 67 Y 0.7269 0.0176 0.2555 68 F 0.8019 0.0078 0.1903 69 N 0.7740 0.0082 0.2178 70 L 0.7719 0.0130 0.2151 71 K 0.7232 0.0264 0.2504 72 A 0.5650 0.0717 0.3633 73 A 0.2243 0.1952 0.5805 74 N 0.0981 0.1252 0.7767 75 H 0.1721 0.0771 0.7509 76 Q 0.5033 0.0283 0.4685 77 I 0.6717 0.0193 0.3090 78 I 0.6715 0.0295 0.2989 79 G 0.6203 0.0456 0.3341 80 T 0.4962 0.1217 0.3821 81 S 0.3526 0.1742 0.4732 82 Q 0.1908 0.3801 0.4291 83 M 0.1768 0.4558 0.3673 84 Y 0.1874 0.4431 0.3695 85 S 0.1723 0.4459 0.3818 86 S 0.1019 0.5806 0.3176 87 T 0.0227 0.7868 0.1904 88 A 0.0190 0.8451 0.1359 89 A 0.0218 0.8539 0.1243 90 R 0.0202 0.8541 0.1257 91 D 0.0251 0.7406 0.2343 92 N 0.0398 0.5168 0.4434 93 G 0.0421 0.5235 0.4344 94 I 0.0488 0.7290 0.2221 95 K 0.0262 0.8279 0.1459 96 S 0.0352 0.8485 0.1163 97 V 0.0493 0.8255 0.1252 98 M 0.0521 0.7989 0.1489 99 E 0.0497 0.6476 0.3027 100 N 0.0590 0.3478 0.5932 101 G 0.1195 0.1424 0.7380 102 K 0.1092 0.2091 0.6817 103 T 0.1465 0.1670 0.6865 104 T 0.2740 0.1299 0.5961 105 T 0.4067 0.1290 0.4644 106 I 0.4611 0.1682 0.3707 107 K 0.3725 0.2160 0.4115 108 D 0.3126 0.2008 0.4866 109 L 0.2216 0.2219 0.5565 110 T 0.2059 0.1555 0.6386