# This file is the result of combining several RDB files, specifically # T0496.t06.str2.rdb (weight 1.54425) # T0496.t06.str4.rdb (weight 0.924988) # T0496.t06.pb.rdb (weight 0.789901) # T0496.t06.bys.rdb (weight 0.748322) # T0496.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 T0496.t06.str2.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.5976 # # ============================================ # Comments from T0496.t06.str4.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.5976 # # ============================================ # Comments from T0496.t06.pb.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.5976 # # ============================================ # Comments from T0496.t06.bys.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.5976 # # ============================================ # Comments from T0496.t06.alpha.rdb # ============================================ # TARGET T0496 # 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 T0496.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 20.5976 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2503 0.1165 0.6332 2 N 0.2284 0.0865 0.6852 3 T 0.3218 0.0387 0.6395 4 P 0.3217 0.0534 0.6249 5 V 0.4024 0.0445 0.5531 6 S 0.2994 0.0491 0.6515 7 V 0.0802 0.5989 0.3210 8 N 0.0376 0.7725 0.1899 9 E 0.0388 0.8242 0.1370 10 K 0.0218 0.8705 0.1077 11 K 0.0116 0.8951 0.0933 12 D 0.0089 0.9068 0.0843 13 F 0.0088 0.9191 0.0721 14 V 0.0085 0.9211 0.0704 15 K 0.0084 0.9221 0.0695 16 W 0.0086 0.9167 0.0747 17 F 0.0096 0.9097 0.0807 18 L 0.0144 0.8697 0.1159 19 N 0.0273 0.7069 0.2658 20 N 0.0392 0.4451 0.5157 21 Y 0.1083 0.3799 0.5118 22 Q 0.1471 0.3840 0.4689 23 L 0.1665 0.3588 0.4747 24 K 0.1526 0.3796 0.4678 25 Q 0.1118 0.5557 0.3325 26 R 0.0452 0.7307 0.2241 27 E 0.0322 0.8193 0.1485 28 C 0.0193 0.8935 0.0872 29 V 0.0120 0.9150 0.0730 30 W 0.0102 0.9195 0.0703 31 I 0.0090 0.9208 0.0702 32 L 0.0085 0.9193 0.0722 33 N 0.0087 0.9127 0.0785 34 Y 0.0104 0.8875 0.1021 35 L 0.0175 0.8377 0.1448 36 M 0.0295 0.7035 0.2669 37 S 0.0506 0.4479 0.5015 38 H 0.0693 0.5497 0.3810 39 D 0.0169 0.7838 0.1993 40 Q 0.0147 0.8465 0.1388 41 L 0.0233 0.8051 0.1715 42 M 0.0393 0.7533 0.2075 43 H 0.0505 0.6382 0.3114 44 K 0.1165 0.4448 0.4387 45 V 0.3606 0.1349 0.5045 46 H 0.4470 0.1326 0.4204 47 F 0.5800 0.1511 0.2690 48 V 0.4176 0.3395 0.2430 49 E 0.3361 0.3721 0.2919 50 H 0.2439 0.3156 0.4405 51 A 0.1494 0.3923 0.4583 52 K 0.1263 0.3319 0.5418 53 Y 0.1396 0.2168 0.6436 54 C 0.2193 0.0669 0.7139 55 P 0.1558 0.2523 0.5920 56 R 0.1909 0.2070 0.6021 57 G 0.5437 0.0820 0.3743 58 L 0.7223 0.0258 0.2519 59 V 0.7942 0.0165 0.1893 60 M 0.7742 0.0189 0.2070 61 S 0.7043 0.0380 0.2577 62 A 0.5179 0.1521 0.3300 63 N 0.3724 0.1560 0.4716 64 C 0.2743 0.1834 0.5423 65 V 0.2149 0.2236 0.5615 66 K 0.1687 0.2004 0.6309 67 D 0.1892 0.1207 0.6901 68 T 0.2951 0.0505 0.6543 69 P 0.3473 0.1486 0.5041 70 F 0.5138 0.1409 0.3453 71 H 0.6208 0.1181 0.2611 72 F 0.6479 0.0931 0.2591 73 F 0.5866 0.1009 0.3125 74 K 0.4393 0.1532 0.4074 75 Q 0.2381 0.1921 0.5698 76 N 0.2092 0.1301 0.6607 77 V 0.3953 0.0812 0.5235 78 M 0.5078 0.0839 0.4083 79 T 0.4368 0.0799 0.4833 80 T 0.3076 0.1003 0.5921 81 D 0.2005 0.0584 0.7411 82 A 0.0170 0.7030 0.2800 83 E 0.0130 0.8171 0.1699 84 K 0.0160 0.8657 0.1183 85 S 0.0178 0.8618 0.1204 86 F 0.0159 0.8785 0.1056 87 H 0.0193 0.8657 0.1151 88 D 0.0347 0.8195 0.1457 89 I 0.0676 0.7638 0.1686 90 R 0.0897 0.6467 0.2636 91 L 0.1510 0.3978 0.4512 92 N 0.1631 0.1323 0.7046 93 R 0.0501 0.3570 0.5929 94 D 0.0934 0.1957 0.7109 95 E 0.1688 0.2223 0.6088 96 D 0.3304 0.1177 0.5519 97 I 0.6607 0.0347 0.3046 98 Y 0.7710 0.0122 0.2168 99 I 0.8156 0.0069 0.1775 100 Q 0.8134 0.0072 0.1793 101 L 0.8016 0.0082 0.1902 102 N 0.7394 0.0164 0.2443 103 F 0.5594 0.0529 0.3876 104 K 0.2297 0.1954 0.5749 105 S 0.1407 0.3080 0.5512 106 S 0.1044 0.3770 0.5186 107 F 0.1203 0.3645 0.5152 108 Q 0.1400 0.2972 0.5628 109 N 0.1376 0.2611 0.6012 110 A 0.0253 0.7031 0.2716 111 N 0.0226 0.7786 0.1989 112 Y 0.0229 0.8595 0.1177 113 V 0.0187 0.8878 0.0935 114 A 0.0212 0.8851 0.0938 115 V 0.0304 0.8621 0.1075 116 L 0.0391 0.8012 0.1597 117 E 0.0396 0.6504 0.3101 118 E 0.0734 0.4565 0.4701 119 N 0.1586 0.1500 0.6914 120 P 0.0524 0.3698 0.5778 121 Y 0.0856 0.2448 0.6696 122 L 0.1922 0.1078 0.7000 123 P 0.1824 0.2048 0.6128 124 K 0.1730 0.3166 0.5104 125 H 0.2208 0.3101 0.4691 126 I 0.2106 0.4020 0.3874 127 E 0.2206 0.4580 0.3214 128 V 0.1804 0.5221 0.2975 129 N 0.0978 0.5933 0.3088 130 E 0.0351 0.7244 0.2405 131 K 0.0257 0.8001 0.1742 132 D 0.0159 0.8687 0.1154 133 R 0.0091 0.9058 0.0852 134 L 0.0086 0.9161 0.0753 135 L 0.0085 0.9197 0.0718 136 A 0.0084 0.9195 0.0721 137 E 0.0084 0.9192 0.0725 138 R 0.0084 0.9190 0.0726 139 F 0.0086 0.9160 0.0755 140 L 0.0087 0.9122 0.0791 141 E 0.0085 0.9116 0.0799 142 E 0.0089 0.9039 0.0872 143 S 0.0100 0.8991 0.0910 144 V 0.0098 0.9001 0.0901 145 F 0.0099 0.9049 0.0852 146 S 0.0099 0.9048 0.0853 147 F 0.0097 0.9067 0.0836 148 R 0.0094 0.9107 0.0799 149 R 0.0087 0.9138 0.0775 150 E 0.0085 0.9190 0.0726 151 R 0.0085 0.9160 0.0754 152 L 0.0090 0.9101 0.0809 153 L 0.0088 0.9091 0.0821 154 K 0.0085 0.9123 0.0791 155 Q 0.0088 0.8993 0.0919 156 I 0.0123 0.8795 0.1083 157 D 0.0099 0.8960 0.0941 158 E 0.0088 0.8894 0.1018 159 A 0.0093 0.8820 0.1088 160 L 0.0135 0.8435 0.1429 161 D 0.0187 0.7631 0.2182 162 K 0.0219 0.7298 0.2483 163 Q 0.0403 0.5528 0.4069 164 D 0.0687 0.5647 0.3666 165 K 0.0100 0.8688 0.1212 166 E 0.0088 0.8979 0.0933 167 A 0.0086 0.9152 0.0762 168 F 0.0085 0.9202 0.0713 169 H 0.0084 0.9165 0.0751 170 R 0.0086 0.9195 0.0719 171 L 0.0091 0.9113 0.0796 172 T 0.0086 0.9142 0.0771 173 A 0.0084 0.9115 0.0801 174 E 0.0086 0.9119 0.0795 175 L 0.0117 0.8946 0.0938 176 K 0.0099 0.8222 0.1679 177 M 0.0232 0.6689 0.3079 178 L 0.0724 0.4023 0.5254