# This file is the result of combining several RDB files, specifically # T0321.t06.dssp-ebghstl.rdb (weight 1.53986) # T0321.t06.stride-ebghtl.rdb (weight 1.24869) # T0321.t06.str2.rdb (weight 1.54758) # T0321.t06.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 T0321.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0321.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 49 # # ============================================ # Comments from T0321.t06.stride-ebghtl.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0321.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 49 # # ============================================ # Comments from T0321.t06.str2.rdb # ============================================ # TARGET T0321 # 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 T0321.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 49 # # ============================================ # Comments from T0321.t06.alpha.rdb # ============================================ # TARGET T0321 # Using neural net t04-2621-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 T0321.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 49 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 V 0.0976 0.0617 0.8408 2 E 0.0827 0.1022 0.8150 3 D 0.0607 0.1778 0.7615 4 R 0.0545 0.1479 0.7976 5 M 0.0732 0.0968 0.8299 6 N 0.0562 0.0650 0.8788 7 D 0.0975 0.0359 0.8667 8 P 0.0400 0.5317 0.4283 9 F 0.0609 0.6232 0.3159 10 I 0.1235 0.5927 0.2838 11 M 0.1991 0.5060 0.2949 12 S 0.2773 0.3906 0.3320 13 Q 0.1849 0.4904 0.3247 14 N 0.1980 0.4652 0.3368 15 E 0.1798 0.4442 0.3760 16 V 0.2056 0.2424 0.5520 17 K 0.0596 0.0747 0.8657 18 G 0.0331 0.0356 0.9312 19 K 0.1950 0.0144 0.7906 20 K 0.7493 0.0038 0.2470 21 V 0.9191 0.0039 0.0770 22 G 0.9308 0.0034 0.0658 23 V 0.9295 0.0033 0.0673 24 V 0.8689 0.0222 0.1089 25 G 0.5881 0.0166 0.3953 26 H 0.2481 0.0364 0.7155 27 F 0.1142 0.0910 0.7949 28 P 0.0521 0.2949 0.6530 29 H 0.0563 0.4144 0.5293 30 L 0.0164 0.7889 0.1947 31 E 0.0137 0.8244 0.1619 32 S 0.0125 0.7888 0.1987 33 L 0.0594 0.6230 0.3176 34 L 0.0947 0.4130 0.4923 35 E 0.0933 0.2389 0.6678 36 P 0.0901 0.2511 0.6588 37 I 0.1766 0.1940 0.6293 38 C 0.2349 0.0739 0.6911 39 D 0.4896 0.0298 0.4806 40 L 0.7594 0.0083 0.2323 41 S 0.8551 0.0099 0.1350 42 I 0.8883 0.0136 0.0981 43 L 0.8592 0.0157 0.1250 44 E 0.7846 0.0132 0.2022 45 W 0.4902 0.0204 0.4894 46 S 0.1869 0.0163 0.7968 47 P 0.0587 0.0988 0.8424 48 E 0.0532 0.0724 0.8744 49 E 0.0392 0.1199 0.8409 50 G 0.0393 0.0713 0.8894 51 D 0.1446 0.0564 0.7990 52 Y 0.1675 0.0197 0.8128 53 P 0.1142 0.0338 0.8520 54 L 0.0475 0.4213 0.5312 55 P 0.0187 0.6366 0.3447 56 A 0.0150 0.7692 0.2158 57 S 0.0312 0.7384 0.2304 58 E 0.0181 0.6160 0.3658 59 F 0.0314 0.4441 0.5244 60 I 0.0735 0.4340 0.4925 61 L 0.0704 0.1487 0.7809 62 P 0.0170 0.3226 0.6604 63 E 0.0336 0.2284 0.7380 64 C 0.1755 0.0832 0.7414 65 D 0.1636 0.0678 0.7686 66 Y 0.8311 0.0331 0.1359 67 V 0.9100 0.0154 0.0746 68 Y 0.9056 0.0268 0.0676 69 I 0.8027 0.0729 0.1245 70 T 0.4916 0.1248 0.3836 71 C 0.1990 0.4690 0.3320 72 A 0.0827 0.6279 0.2894 73 S 0.0708 0.7758 0.1534 74 V 0.0754 0.8111 0.1135 75 V 0.0698 0.7442 0.1859 76 D 0.0606 0.5754 0.3640 77 K 0.0170 0.5511 0.4319 78 T 0.0250 0.6458 0.3292 79 L 0.0049 0.9445 0.0506 80 P 0.0048 0.9530 0.0423 81 R 0.0047 0.9539 0.0413 82 L 0.0048 0.9536 0.0416 83 L 0.0048 0.9364 0.0587 84 E 0.0053 0.8689 0.1258 85 L 0.0085 0.7793 0.2122 86 S 0.0270 0.5465 0.4265 87 R 0.0173 0.4604 0.5224 88 N 0.0313 0.2739 0.6948 89 A 0.1016 0.1301 0.7683 90 R 0.3464 0.0399 0.6137 91 R 0.8213 0.0090 0.1697 92 I 0.9217 0.0035 0.0748 93 T 0.9297 0.0034 0.0669 94 L 0.9229 0.0037 0.0734 95 V 0.8117 0.0140 0.1743 96 G 0.2965 0.0166 0.6869 97 P 0.1172 0.0575 0.8254 98 G 0.0959 0.0985 0.8056 99 T 0.0735 0.1827 0.7438 100 P 0.0477 0.3928 0.5595 101 L 0.0651 0.4530 0.4820 102 A 0.0500 0.4221 0.5280 103 P 0.0146 0.8345 0.1509 104 V 0.0131 0.8572 0.1297 105 L 0.0100 0.8844 0.1056 106 F 0.0123 0.8364 0.1514 107 E 0.0124 0.7167 0.2709 108 H 0.0412 0.4702 0.4886 109 G 0.0616 0.0871 0.8513 110 L 0.1976 0.1145 0.6879 111 Q 0.3413 0.1339 0.5248 112 E 0.6929 0.1214 0.1857 113 L 0.7991 0.0630 0.1379 114 S 0.7281 0.0666 0.2053 115 G 0.6111 0.0455 0.3434 116 F 0.6293 0.0212 0.3495 117 M 0.7105 0.0184 0.2711 118 V 0.6250 0.0175 0.3575 119 K 0.3093 0.0414 0.6493 120 D 0.1184 0.0428 0.8388 121 N 0.0059 0.8959 0.0982 122 A 0.0072 0.9383 0.0544 123 R 0.0067 0.9415 0.0519 124 A 0.0057 0.9550 0.0393 125 F 0.0070 0.9545 0.0385 126 R 0.0088 0.9531 0.0381 127 I 0.0101 0.9481 0.0418 128 V 0.0118 0.9269 0.0613 129 A 0.0225 0.8133 0.1642 130 G 0.0333 0.4939 0.4727 131 A 0.0634 0.2759 0.6607 132 E 0.0708 0.2192 0.7100 133 K 0.1691 0.2027 0.6282 134 V 0.3002 0.1486 0.5512 135 K 0.4636 0.1144 0.4221 136 I 0.5098 0.1375 0.3527 137 Y 0.4097 0.1223 0.4680 138 S 0.3079 0.1146 0.5774 139 A 0.1793 0.1226 0.6981 140 G 0.3674 0.0555 0.5771 141 Q 0.6894 0.0204 0.2902 142 K 0.8798 0.0087 0.1115 143 V 0.8901 0.0081 0.1018 144 T 0.9051 0.0077 0.0872 145 I 0.8535 0.0114 0.1351 146 K 0.5654 0.0259 0.4087 147 K 0.1696 0.0257 0.8047