# This file is the result of combining several RDB files, specifically # T0487.t06.str2.rdb (weight 1.54425) # T0487.t06.str4.rdb (weight 0.924988) # T0487.t06.pb.rdb (weight 0.789901) # T0487.t06.bys.rdb (weight 0.748322) # T0487.t06.alpha.rdb (weight 0.678173) # T0487.t04.str2.rdb (weight 1.54425) # T0487.t04.str4.rdb (weight 0.924988) # T0487.t04.pb.rdb (weight 0.789901) # T0487.t04.bys.rdb (weight 0.748322) # T0487.t04.alpha.rdb (weight 0.678173) # T0487.t2k.str2.rdb (weight 1.54425) # T0487.t2k.str4.rdb (weight 0.924988) # T0487.t2k.pb.rdb (weight 0.789901) # T0487.t2k.bys.rdb (weight 0.748322) # T0487.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 T0487.t06.str2.rdb # ============================================ # TARGET T0487 # 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 T0487.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 428 # # ============================================ # Comments from T0487.t06.str4.rdb # ============================================ # TARGET T0487 # 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 T0487.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 428 # # ============================================ # Comments from T0487.t06.pb.rdb # ============================================ # TARGET T0487 # 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 T0487.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 428 # # ============================================ # Comments from T0487.t06.bys.rdb # ============================================ # TARGET T0487 # 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 T0487.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 428 # # ============================================ # Comments from T0487.t06.alpha.rdb # ============================================ # TARGET T0487 # 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 T0487.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 428 # # ============================================ # Comments from T0487.t04.str2.rdb # ============================================ # TARGET T0487 # 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 T0487.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 427 # # ============================================ # Comments from T0487.t04.str4.rdb # ============================================ # TARGET T0487 # 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 T0487.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 427 # # ============================================ # Comments from T0487.t04.pb.rdb # ============================================ # TARGET T0487 # 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 T0487.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 427 # # ============================================ # Comments from T0487.t04.bys.rdb # ============================================ # TARGET T0487 # 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 T0487.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 427 # # ============================================ # Comments from T0487.t04.alpha.rdb # ============================================ # TARGET T0487 # 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 T0487.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 427 # # ============================================ # Comments from T0487.t2k.str2.rdb # ============================================ # TARGET T0487 # 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 T0487.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 79 # # ============================================ # Comments from T0487.t2k.str4.rdb # ============================================ # TARGET T0487 # 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 T0487.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 79 # # ============================================ # Comments from T0487.t2k.pb.rdb # ============================================ # TARGET T0487 # 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 T0487.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 79 # # ============================================ # Comments from T0487.t2k.bys.rdb # ============================================ # TARGET T0487 # 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 T0487.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 79 # # ============================================ # Comments from T0487.t2k.alpha.rdb # ============================================ # TARGET T0487 # 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 T0487.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 79 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.1114 0.0701 0.8185 2 L 0.2861 0.0440 0.6699 3 Q 0.4499 0.0314 0.5187 4 V 0.5984 0.0473 0.3542 5 V 0.6577 0.0306 0.3117 6 A 0.5634 0.0494 0.3872 7 L 0.4394 0.0798 0.4807 8 S 0.2442 0.1085 0.6473 9 G 0.1538 0.0967 0.7495 10 A 0.1993 0.1097 0.6909 11 Y 0.2528 0.0405 0.7066 12 P 0.2222 0.1439 0.6339 13 A 0.2908 0.2250 0.4842 14 E 0.5907 0.0967 0.3126 15 L 0.7507 0.0199 0.2295 16 A 0.7614 0.0159 0.2227 17 V 0.7470 0.0269 0.2261 18 G 0.7093 0.0226 0.2681 19 F 0.6679 0.0365 0.2956 20 D 0.5573 0.0399 0.4028 21 A 0.4021 0.1556 0.4423 22 G 0.2929 0.1292 0.5779 23 G 0.2387 0.0949 0.6664 24 R 0.2280 0.1134 0.6585 25 E 0.1651 0.2025 0.6324 26 S 0.1376 0.2024 0.6601 27 F 0.1506 0.2042 0.6452 28 R 0.2452 0.1934 0.5614 29 F 0.3929 0.1248 0.4823 30 G 0.4869 0.0823 0.4308 31 G 0.6474 0.0555 0.2972 32 A 0.7256 0.0436 0.2308 33 A 0.7654 0.0376 0.1970 34 C 0.7889 0.0286 0.1825 35 A 0.7642 0.0332 0.2025 36 V 0.7355 0.0378 0.2267 37 G 0.5649 0.0686 0.3665 38 G 0.3507 0.1065 0.5427 39 D 0.1780 0.1653 0.6566 40 G 0.1199 0.1549 0.7252 41 G 0.1657 0.1430 0.6913 42 H 0.3314 0.1153 0.5534 43 L 0.4648 0.1000 0.4352 44 L 0.5917 0.0819 0.3264 45 W 0.6431 0.0675 0.2894 46 T 0.6708 0.0502 0.2790 47 L 0.5963 0.0356 0.3681 48 P 0.4582 0.1026 0.4392 49 E 0.4049 0.1856 0.4095 50 A 0.2779 0.2809 0.4413 51 Q 0.2413 0.2631 0.4956 52 A 0.1554 0.1639 0.6807 53 G 0.1044 0.1132 0.7824 54 E 0.1609 0.1562 0.6828 55 R 0.2703 0.1302 0.5995 56 I 0.2971 0.0488 0.6541 57 P 0.1738 0.1274 0.6988 58 Q 0.0233 0.7423 0.2344 59 E 0.0115 0.8554 0.1331 60 V 0.0107 0.9069 0.0824 61 V 0.0087 0.9141 0.0772 62 W 0.0083 0.9210 0.0707 63 D 0.0083 0.9239 0.0679 64 L 0.0083 0.9235 0.0682 65 L 0.0083 0.9228 0.0689 66 E 0.0083 0.9233 0.0684 67 E 0.0083 0.9245 0.0673 68 T 0.0083 0.9239 0.0679 69 L 0.0083 0.9228 0.0689 70 W 0.0083 0.9225 0.0692 71 A 0.0083 0.9224 0.0693 72 F 0.0086 0.9196 0.0718 73 R 0.0085 0.9162 0.0752 74 R 0.0091 0.8956 0.0952 75 K 0.0152 0.7870 0.1977 76 A 0.0549 0.3184 0.6267 77 G 0.0492 0.0884 0.8624 78 R 0.1641 0.0652 0.7707 79 L 0.2342 0.0266 0.7392 80 P 0.2585 0.0700 0.6715 81 S 0.3190 0.0860 0.5950 82 R 0.6723 0.0135 0.3142 83 V 0.7554 0.0057 0.2388 84 L 0.8201 0.0043 0.1756 85 L 0.8040 0.0046 0.1914 86 L 0.7570 0.0083 0.2348 87 R 0.5512 0.0395 0.4093 88 D 0.3035 0.0586 0.6379 89 G 0.2247 0.0637 0.7117 90 R 0.3228 0.0520 0.6251 91 V 0.2257 0.0262 0.7481 92 P 0.1254 0.2172 0.6574 93 Q 0.0640 0.3488 0.5872 94 D 0.0870 0.4438 0.4692 95 E 0.1126 0.6290 0.2584 96 F 0.0612 0.8020 0.1368 97 A 0.0377 0.8594 0.1029 98 L 0.0236 0.8877 0.0887 99 A 0.0147 0.9008 0.0844 100 L 0.0087 0.9094 0.0819 101 E 0.0085 0.9178 0.0737 102 A 0.0107 0.9007 0.0885 103 L 0.0128 0.8811 0.1061 104 A 0.0142 0.8204 0.1655 105 R 0.0275 0.6941 0.2784 106 E 0.0683 0.2712 0.6605 107 G 0.0704 0.0769 0.8527 108 I 0.2360 0.0337 0.7303 109 A 0.4531 0.0258 0.5211 110 Y 0.6597 0.0113 0.3290 111 D 0.6829 0.0139 0.3033 112 L 0.7954 0.0057 0.1989 113 V 0.7944 0.0062 0.1993 114 S 0.8068 0.0050 0.1881 115 V 0.7791 0.0071 0.2138 116 R 0.6862 0.0164 0.2973 117 K 0.5613 0.0407 0.3981 118 S 0.3680 0.0626 0.5694 119 G 0.2285 0.0716 0.6999 120 G 0.2225 0.0759 0.7016 121 G 0.4235 0.0476 0.5288 122 R 0.6048 0.0322 0.3629 123 V 0.6885 0.0250 0.2865 124 Y 0.6272 0.0186 0.3542 125 P 0.4975 0.0544 0.4481 126 V 0.3063 0.1282 0.5655 127 Q 0.2378 0.0928 0.6694 128 G 0.1995 0.1063 0.6942 129 R 0.3444 0.0876 0.5679 130 L 0.4233 0.0667 0.5100 131 A 0.4080 0.0885 0.5034 132 D 0.2730 0.0960 0.6310 133 G 0.1904 0.0664 0.7432 134 L 0.3834 0.0433 0.5733 135 Y 0.6282 0.0267 0.3451 136 V 0.6699 0.0138 0.3163 137 P 0.5508 0.0129 0.4363 138 L 0.3468 0.0671 0.5861 139 E 0.1590 0.2675 0.5735 140 D 0.1193 0.2030 0.6776 141 K 0.2113 0.2195 0.5692 142 T 0.3785 0.1790 0.4425 143 F 0.5877 0.0911 0.3212 144 L 0.7422 0.0364 0.2214 145 L 0.7688 0.0247 0.2065 146 L 0.7616 0.0224 0.2160 147 T 0.7156 0.0309 0.2535 148 V 0.5428 0.0567 0.4005 149 H 0.3598 0.0765 0.5637 150 R 0.2850 0.1398 0.5752 151 D 0.2361 0.1545 0.6095 152 F 0.2475 0.1524 0.6001 153 R 0.2276 0.1080 0.6644 154 G 0.2289 0.0723 0.6987 155 T 0.3097 0.0336 0.6568 156 P 0.3572 0.0970 0.5458 157 R 0.4251 0.0425 0.5324 158 P 0.4175 0.0699 0.5126 159 L 0.4958 0.0630 0.4412 160 K 0.7017 0.0264 0.2719 161 L 0.7620 0.0141 0.2239 162 V 0.7793 0.0112 0.2095 163 H 0.7517 0.0133 0.2349 164 E 0.6328 0.0377 0.3295 165 A 0.3372 0.0895 0.5733 166 G 0.1188 0.1061 0.7751 167 D 0.1329 0.1185 0.7486 168 T 0.1965 0.0497 0.7538 169 P 0.1593 0.1009 0.7398 170 L 0.0290 0.6983 0.2727 171 E 0.0132 0.8483 0.1385 172 A 0.0099 0.9086 0.0815 173 L 0.0084 0.9213 0.0703 174 A 0.0084 0.9195 0.0721 175 H 0.0083 0.9225 0.0692 176 Q 0.0083 0.9214 0.0702 177 I 0.0086 0.9163 0.0751 178 F 0.0089 0.9147 0.0764 179 H 0.0099 0.9012 0.0888 180 L 0.0230 0.8555 0.1215 181 T 0.0315 0.7847 0.1837 182 R 0.0644 0.6231 0.3125 183 L 0.1575 0.4546 0.3879 184 Y 0.2197 0.1831 0.5972 185 P 0.0917 0.4530 0.4553 186 A 0.0952 0.3123 0.5926 187 S 0.1195 0.2430 0.6375 188 G 0.1134 0.1735 0.7131 189 F 0.2112 0.1441 0.6447 190 A 0.2565 0.1393 0.6042 191 F 0.3290 0.0865 0.5846 192 P 0.2595 0.1387 0.6018 193 R 0.3017 0.1176 0.5807 194 L 0.3508 0.0580 0.5912 195 P 0.3607 0.1200 0.5194 196 A 0.3485 0.1338 0.5177 197 P 0.2645 0.3456 0.3899 198 L 0.1534 0.6240 0.2226 199 H 0.0670 0.7846 0.1483 200 L 0.0316 0.8511 0.1173 201 A 0.0126 0.8986 0.0888 202 D 0.0093 0.9130 0.0778 203 R 0.0087 0.9139 0.0774 204 L 0.0095 0.9161 0.0744 205 V 0.0097 0.9148 0.0755 206 K 0.0088 0.9167 0.0746 207 E 0.0121 0.8844 0.1035 208 V 0.0289 0.7735 0.1976 209 G 0.0349 0.6732 0.2918 210 R 0.0670 0.5983 0.3348 211 L 0.1000 0.3606 0.5394 212 G 0.1123 0.2582 0.6295 213 I 0.1670 0.2402 0.5927 214 R 0.1812 0.2563 0.5624 215 H 0.1989 0.1866 0.6145 216 L 0.1573 0.3627 0.4801 217 K 0.1588 0.3999 0.4413 218 E 0.1699 0.3943 0.4358 219 V 0.1819 0.3308 0.4873 220 D 0.1670 0.2992 0.5338 221 R 0.1526 0.3531 0.4944 222 E 0.2202 0.2572 0.5226 223 K 0.4520 0.1243 0.4237 224 L 0.6784 0.0407 0.2809 225 F 0.7666 0.0195 0.2139 226 F 0.7555 0.0178 0.2267 227 V 0.6379 0.0341 0.3280