# This file is the result of combining several RDB files, specifically # T0627.t06.str2.rdb (weight 1.54425) # T0627.t06.str4.rdb (weight 0.924988) # T0627.t06.pb.rdb (weight 0.789901) # T0627.t06.bys.rdb (weight 0.748322) # T0627.t06.alpha.rdb (weight 0.678173) # T0627.t04.str2.rdb (weight 1.54425) # T0627.t04.str4.rdb (weight 0.924988) # T0627.t04.pb.rdb (weight 0.789901) # T0627.t04.bys.rdb (weight 0.748322) # T0627.t04.alpha.rdb (weight 0.678173) # T0627.t2k.str2.rdb (weight 1.54425) # T0627.t2k.str4.rdb (weight 0.924988) # T0627.t2k.pb.rdb (weight 0.789901) # T0627.t2k.bys.rdb (weight 0.748322) # T0627.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 T0627.t06.str2.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1077 # # ============================================ # Comments from T0627.t06.str4.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1077 # # ============================================ # Comments from T0627.t06.pb.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1077 # # ============================================ # Comments from T0627.t06.bys.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1077 # # ============================================ # Comments from T0627.t06.alpha.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1077 # # ============================================ # Comments from T0627.t04.str2.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1052 # # ============================================ # Comments from T0627.t04.str4.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1052 # # ============================================ # Comments from T0627.t04.pb.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1052 # # ============================================ # Comments from T0627.t04.bys.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1052 # # ============================================ # Comments from T0627.t04.alpha.rdb # ============================================ # TARGET T0627 # 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 T0627.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 1052 # # ============================================ # Comments from T0627.t2k.str2.rdb # ============================================ # TARGET T0627 # 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 T0627.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 28.3949 # # ============================================ # Comments from T0627.t2k.str4.rdb # ============================================ # TARGET T0627 # 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 T0627.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 28.3949 # # ============================================ # Comments from T0627.t2k.pb.rdb # ============================================ # TARGET T0627 # 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 T0627.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 28.3949 # # ============================================ # Comments from T0627.t2k.bys.rdb # ============================================ # TARGET T0627 # 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 T0627.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 28.3949 # # ============================================ # Comments from T0627.t2k.alpha.rdb # ============================================ # TARGET T0627 # 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 T0627.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 28.3949 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2362 0.2165 0.5473 2 I 0.2323 0.2757 0.4920 3 D 0.1980 0.3760 0.4260 4 T 0.1565 0.5202 0.3233 5 F 0.1192 0.6038 0.2770 6 E 0.1142 0.5733 0.3125 7 R 0.1527 0.4052 0.4420 8 T 0.1674 0.2146 0.6181 9 G 0.1300 0.1789 0.6911 10 P 0.1147 0.3472 0.5381 11 L 0.1547 0.3657 0.4796 12 M 0.2464 0.3271 0.4266 13 E 0.2826 0.2212 0.4962 14 A 0.2548 0.2158 0.5294 15 S 0.2013 0.1481 0.6506 16 S 0.1222 0.2855 0.5923 17 Y 0.1448 0.1813 0.6739 18 P 0.0411 0.6412 0.3177 19 A 0.0109 0.8304 0.1588 20 W 0.0088 0.9008 0.0905 21 A 0.0084 0.9175 0.0740 22 Q 0.0084 0.9152 0.0764 23 Q 0.0083 0.9132 0.0784 24 L 0.0087 0.9009 0.0904 25 I 0.0091 0.8648 0.1261 26 N 0.0098 0.7754 0.2148 27 D 0.0180 0.5593 0.4227 28 C 0.0654 0.4093 0.5253 29 S 0.0601 0.3794 0.5604 30 P 0.0214 0.7153 0.2633 31 A 0.0159 0.8271 0.1570 32 K 0.0155 0.8787 0.1059 33 A 0.0198 0.8481 0.1321 34 R 0.0432 0.7756 0.1811 35 V 0.0713 0.6882 0.2405 36 V 0.1026 0.5763 0.3210 37 E 0.1095 0.4781 0.4124 38 H 0.1188 0.4776 0.4036 39 E 0.0260 0.7760 0.1979 40 L 0.0223 0.8421 0.1356 41 Y 0.0182 0.8960 0.0857 42 Q 0.0169 0.8990 0.0841 43 Q 0.0242 0.8487 0.1271 44 M 0.0373 0.7759 0.1869 45 R 0.0451 0.6119 0.3430 46 D 0.0530 0.3063 0.6407 47 A 0.0572 0.2008 0.7420 48 K 0.1650 0.1188 0.7162 49 L 0.2219 0.0668 0.7113 50 S 0.1532 0.0384 0.8084 51 P 0.0108 0.7528 0.2364 52 Q 0.0091 0.8745 0.1164 53 I 0.0083 0.9230 0.0687 54 M 0.0083 0.9217 0.0700 55 R 0.0083 0.9242 0.0675 56 Q 0.0083 0.9232 0.0685 57 Y 0.0084 0.9182 0.0734 58 L 0.0097 0.8745 0.1158 59 I 0.0187 0.7611 0.2202 60 G 0.0375 0.3804 0.5821 61 G 0.0458 0.2529 0.7014 62 W 0.1321 0.3553 0.5125 63 P 0.1039 0.5793 0.3167 64 V 0.0809 0.7279 0.1912 65 V 0.0347 0.8381 0.1273 66 E 0.0172 0.8604 0.1224 67 Q 0.0151 0.8595 0.1255 68 F 0.0173 0.8716 0.1112 69 A 0.0096 0.9022 0.0882 70 V 0.0085 0.9164 0.0752 71 Y 0.0085 0.9177 0.0738 72 M 0.0088 0.9124 0.0787 73 A 0.0091 0.9064 0.0845 74 K 0.0094 0.8968 0.0937 75 N 0.0132 0.8427 0.1441 76 L 0.0255 0.7823 0.1923 77 T 0.0469 0.6655 0.2876 78 K 0.0876 0.4439 0.4685 79 T 0.1405 0.3083 0.5512 80 R 0.0946 0.3792 0.5262 81 F 0.0946 0.3159 0.5895 82 G 0.1029 0.2400 0.6570 83 R 0.1797 0.1834 0.6369 84 H 0.1937 0.0654 0.7409 85 P 0.1065 0.2348 0.6587 86 G 0.0675 0.2932 0.6393 87 E 0.0387 0.6608 0.3005 88 D 0.0213 0.8386 0.1401 89 M 0.0123 0.8892 0.0985 90 A 0.0104 0.9084 0.0812 91 R 0.0096 0.9104 0.0800 92 R 0.0087 0.9142 0.0770 93 W 0.0092 0.9069 0.0839 94 L 0.0106 0.8809 0.1085 95 M 0.0140 0.8556 0.1304 96 R 0.0220 0.7597 0.2183 97 N 0.0524 0.5693 0.3783 98 I 0.1436 0.4579 0.3986 99 R 0.2451 0.3424 0.4125 100 V 0.3614 0.2797 0.3588 101 E 0.3071 0.3020 0.3909 102 L 0.1907 0.4629 0.3464 103 N 0.1138 0.4080 0.4782 104 H 0.1192 0.4511 0.4297 105 A 0.0770 0.6683 0.2548 106 D 0.0419 0.8142 0.1439 107 Y 0.0256 0.8705 0.1038 108 W 0.0169 0.8920 0.0910 109 V 0.0103 0.9113 0.0784 110 N 0.0092 0.9165 0.0743 111 W 0.0105 0.9053 0.0842 112 C 0.0112 0.8907 0.0982 113 A 0.0136 0.8350 0.1514 114 A 0.0210 0.7490 0.2300 115 H 0.0562 0.2786 0.6652 116 D 0.0560 0.0923 0.8517 117 V 0.1825 0.0536 0.7639 118 T 0.1817 0.0281 0.7901 119 L 0.0232 0.7126 0.2642 120 E 0.0131 0.8326 0.1543 121 D 0.0227 0.8395 0.1378 122 L 0.0284 0.8237 0.1479 123 H 0.0274 0.7290 0.2436 124 D 0.0301 0.5496 0.4203 125 Q 0.0837 0.3480 0.5683 126 R 0.1387 0.2096 0.6517 127 V 0.1712 0.1499 0.6788 128 A 0.1224 0.1988 0.6788 129 P 0.0114 0.7854 0.2032 130 E 0.0103 0.8624 0.1273 131 L 0.0105 0.9074 0.0821 132 H 0.0087 0.9137 0.0775 133 A 0.0091 0.9091 0.0818 134 L 0.0143 0.8913 0.0944 135 S 0.0197 0.8672 0.1131 136 H 0.0210 0.8613 0.1177 137 W 0.0402 0.8261 0.1337 138 C 0.0648 0.7769 0.1583 139 W 0.0846 0.7291 0.1863 140 Q 0.1206 0.5796 0.2998 141 T 0.1444 0.4061 0.4495 142 S 0.1450 0.2463 0.6086 143 S 0.1096 0.2421 0.6484 144 S 0.0686 0.3781 0.5534 145 D 0.0452 0.5607 0.3941 146 S 0.0532 0.6911 0.2557 147 L 0.0195 0.8239 0.1566 148 A 0.0121 0.8795 0.1084 149 V 0.0104 0.9112 0.0784 150 A 0.0110 0.9128 0.0762 151 M 0.0118 0.9115 0.0767 152 A 0.0118 0.8955 0.0927 153 A 0.0186 0.8492 0.1322 154 T 0.0377 0.7348 0.2275 155 N 0.0601 0.6786 0.2613 156 Y 0.0517 0.7210 0.2272 157 A 0.0797 0.7279 0.1924 158 I 0.1234 0.6497 0.2270 159 E 0.1241 0.5719 0.3039 160 G 0.1175 0.4384 0.4441 161 A 0.1221 0.4210 0.4568 162 T 0.1151 0.3619 0.5229 163 G 0.0894 0.4715 0.4391 164 E 0.1274 0.5710 0.3016 165 W 0.1299 0.6599 0.2102 166 S 0.1487 0.6516 0.1997 167 A 0.2052 0.6222 0.1726 168 V 0.2870 0.5008 0.2123 169 V 0.3423 0.4168 0.2409 170 C 0.2835 0.3517 0.3648 171 S 0.1572 0.3311 0.5117 172 T 0.0955 0.2330 0.6715 173 G 0.1070 0.2679 0.6250 174 V 0.2478 0.3292 0.4230 175 Y 0.3058 0.3974 0.2968 176 A 0.2501 0.4625 0.2874 177 E 0.2019 0.4618 0.3362 178 A 0.1909 0.3253 0.4837 179 F 0.2281 0.1895 0.5824 180 A 0.1530 0.3163 0.5307 181 E 0.0476 0.6638 0.2886 182 E 0.0576 0.6300 0.3125 183 T 0.0868 0.5283 0.3848 184 R 0.0865 0.4959 0.4176 185 K 0.0351 0.7403 0.2247 186 K 0.0185 0.8200 0.1615 187 S 0.0192 0.8629 0.1179 188 M 0.0153 0.8963 0.0884 189 K 0.0128 0.9063 0.0809 190 W 0.0146 0.9016 0.0837 191 L 0.0171 0.8990 0.0839 192 K 0.0175 0.8912 0.0913 193 M 0.0332 0.8410 0.1259 194 H 0.0549 0.7711 0.1739 195 A 0.0556 0.7589 0.1855 196 Q 0.0674 0.6858 0.2467 197 Y 0.1022 0.5692 0.3286 198 D 0.0918 0.4629 0.4453 199 D 0.0385 0.5556 0.4059 200 A 0.0585 0.4385 0.5029 201 H 0.1261 0.2468 0.6271 202 P 0.0235 0.7379 0.2386 203 W 0.0096 0.8614 0.1290 204 E 0.0085 0.9148 0.0767 205 A 0.0084 0.9187 0.0730 206 L 0.0083 0.9220 0.0697 207 E 0.0083 0.9247 0.0670 208 I 0.0083 0.9239 0.0678 209 I 0.0083 0.9238 0.0679 210 C 0.0083 0.9227 0.0690 211 T 0.0085 0.9154 0.0762 212 L 0.0123 0.8277 0.1600 213 V 0.0403 0.5362 0.4235 214 G 0.0426 0.2476 0.7098 215 N 0.0903 0.1802 0.7294 216 K 0.1611 0.0903 0.7485 217 P 0.0793 0.2819 0.6388 218 S 0.1077 0.2501 0.6421 219 L 0.0210 0.7259 0.2531 220 Q 0.0152 0.8344 0.1504 221 L 0.0127 0.8952 0.0921 222 Q 0.0085 0.9204 0.0710 223 A 0.0083 0.9208 0.0709 224 E 0.0083 0.9249 0.0668 225 L 0.0083 0.9221 0.0695 226 R 0.0083 0.9230 0.0687 227 Q 0.0083 0.9237 0.0680 228 A 0.0083 0.9219 0.0698 229 V 0.0084 0.9181 0.0735 230 T 0.0085 0.9124 0.0791 231 K 0.0086 0.9078 0.0836 232 S 0.0091 0.8994 0.0915 233 Y 0.0086 0.9074 0.0840 234 D 0.0084 0.9176 0.0740 235 Y 0.0083 0.9204 0.0713 236 M 0.0083 0.9209 0.0707 237 Y 0.0084 0.9184 0.0732 238 L 0.0084 0.9141 0.0775 239 F 0.0087 0.8936 0.0976 240 L 0.0095 0.8824 0.1082 241 E 0.0096 0.8678 0.1226 242 R 0.0136 0.8151 0.1713 243 C 0.0352 0.7299 0.2349 244 I 0.0877 0.6300 0.2823 245 Q 0.1200 0.4946 0.3854 246 L 0.0755 0.5732 0.3513 247 D 0.0883 0.4504 0.4613 248 K 0.1332 0.3105 0.5562 249 V 0.2253 0.1897 0.5851 250 K 0.2819 0.1045 0.6136 251 S 0.2157 0.0425 0.7418 252 P 0.0904 0.3361 0.5735 253 R 0.1359 0.2471 0.6169 254 G 0.2506 0.1415 0.6079 255 R 0.4695 0.0975 0.4330 256 V 0.6207 0.0933 0.2860 257 A 0.6571 0.0973 0.2457 258 A 0.6719 0.0881 0.2400 259 L 0.6368 0.0853 0.2778 260 E 0.5615 0.0839 0.3546 261 M 0.3772 0.0980 0.5248