# This file is the result of combining several RDB files, specifically # T0329.t06.dssp-ebghstl.rdb (weight 1.53986) # T0329.t06.stride-ebghtl.rdb (weight 1.24869) # T0329.t06.str2.rdb (weight 1.54758) # T0329.t06.alpha.rdb (weight 0.659012) # T0329.t04.dssp-ebghstl.rdb (weight 1.53986) # T0329.t04.stride-ebghtl.rdb (weight 1.24869) # T0329.t04.str2.rdb (weight 1.54758) # T0329.t04.alpha.rdb (weight 0.659012) # T0329.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0329.t2k.stride-ebghtl.rdb (weight 1.24869) # T0329.t2k.str2.rdb (weight 1.54758) # T0329.t2k.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 T0329.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0329 # 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 T0329.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 4931 # # ============================================ # Comments from T0329.t06.stride-ebghtl.rdb # ============================================ # TARGET T0329 # 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 T0329.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 4931 # # ============================================ # Comments from T0329.t06.str2.rdb # ============================================ # TARGET T0329 # 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 T0329.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 4931 # # ============================================ # Comments from T0329.t06.alpha.rdb # ============================================ # TARGET T0329 # 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 T0329.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 4931 # # ============================================ # Comments from T0329.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0329 # 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 T0329.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 2251 # # ============================================ # Comments from T0329.t04.stride-ebghtl.rdb # ============================================ # TARGET T0329 # 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 T0329.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 2251 # # ============================================ # Comments from T0329.t04.str2.rdb # ============================================ # TARGET T0329 # 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 T0329.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 2251 # # ============================================ # Comments from T0329.t04.alpha.rdb # ============================================ # TARGET T0329 # 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 T0329.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 2251 # # ============================================ # Comments from T0329.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0329 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0329.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1744 # # ============================================ # Comments from T0329.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0329 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0329.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1744 # # ============================================ # Comments from T0329.t2k.str2.rdb # ============================================ # TARGET T0329 # 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 T0329.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 1744 # # ============================================ # Comments from T0329.t2k.alpha.rdb # ============================================ # TARGET T0329 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0329.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 1744 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0905 0.0238 0.8857 2 K 0.2312 0.0125 0.7563 3 Y 0.5247 0.0065 0.4688 4 K 0.7400 0.0222 0.2379 5 A 0.9166 0.0040 0.0795 6 A 0.9282 0.0033 0.0685 7 I 0.9213 0.0041 0.0746 8 F 0.8758 0.0057 0.1185 9 D 0.4792 0.0106 0.5102 10 M 0.0952 0.1052 0.7996 11 D 0.0707 0.0366 0.8928 12 G 0.1072 0.0589 0.8339 13 T 0.4098 0.0540 0.5362 14 I 0.6515 0.0567 0.2918 15 L 0.5545 0.0820 0.3635 16 D 0.2447 0.0847 0.6706 17 T 0.0649 0.1883 0.7468 18 S 0.0385 0.6450 0.3166 19 A 0.0083 0.8460 0.1457 20 D 0.0103 0.8589 0.1307 21 L 0.0057 0.9293 0.0650 22 T 0.0050 0.9410 0.0540 23 S 0.0049 0.9498 0.0453 24 A 0.0050 0.9526 0.0424 25 L 0.0048 0.9539 0.0413 26 N 0.0048 0.9535 0.0417 27 Y 0.0048 0.9545 0.0408 28 A 0.0047 0.9542 0.0410 29 F 0.0050 0.9458 0.0493 30 E 0.0054 0.9266 0.0681 31 Q 0.0077 0.8756 0.1167 32 T 0.0432 0.5445 0.4124 33 G 0.0346 0.0676 0.8978 34 H 0.0582 0.0576 0.8842 35 R 0.0778 0.0718 0.8504 36 H 0.0783 0.1274 0.7943 37 D 0.0712 0.1800 0.7488 38 F 0.0416 0.5782 0.3801 39 T 0.0211 0.7321 0.2468 40 V 0.0191 0.8346 0.1463 41 E 0.0250 0.8443 0.1307 42 D 0.0327 0.8329 0.1345 43 I 0.0334 0.8156 0.1510 44 K 0.0382 0.7579 0.2039 45 N 0.0454 0.6561 0.2985 46 F 0.0525 0.5035 0.4440 47 F 0.0598 0.3447 0.5955 48 G 0.0538 0.3224 0.6238 49 S 0.0449 0.4088 0.5464 50 G 0.0403 0.5927 0.3671 51 V 0.0624 0.6946 0.2429 52 V 0.0664 0.7567 0.1769 53 V 0.0703 0.7793 0.1503 54 A 0.0741 0.7849 0.1409 55 V 0.0625 0.7708 0.1667 56 T 0.0508 0.7044 0.2448 57 R 0.0557 0.5856 0.3587 58 A 0.0545 0.5434 0.4022 59 L 0.0512 0.5242 0.4246 60 A 0.0568 0.4840 0.4592 61 Y 0.0662 0.5055 0.4283 62 E 0.0630 0.5310 0.4059 63 A 0.0699 0.4772 0.4529 64 G 0.0743 0.4091 0.5166 65 S 0.0729 0.4514 0.4757 66 S 0.0632 0.5009 0.4360 67 R 0.0703 0.5588 0.3709 68 E 0.0867 0.5818 0.3316 69 S 0.1017 0.5949 0.3034 70 L 0.0894 0.6362 0.2744 71 V 0.0797 0.6587 0.2616 72 A 0.0709 0.6835 0.2456 73 F 0.0595 0.6842 0.2563 74 G 0.0579 0.6328 0.3093 75 T 0.0538 0.6274 0.3188 76 K 0.0457 0.6920 0.2624 77 D 0.0388 0.7261 0.2350 78 E 0.0408 0.6935 0.2657 79 Q 0.0532 0.6334 0.3134 80 I 0.0403 0.5396 0.4201 81 P 0.0317 0.5991 0.3692 82 E 0.0286 0.6071 0.3643 83 A 0.0340 0.5453 0.4207 84 V 0.0344 0.4699 0.4958 85 T 0.0372 0.4243 0.5385 86 Q 0.0228 0.6826 0.2946 87 T 0.0167 0.7389 0.2444 88 E 0.0162 0.7713 0.2125 89 V 0.0113 0.8416 0.1471 90 N 0.0090 0.8787 0.1123 91 R 0.0078 0.8934 0.0988 92 V 0.0076 0.8913 0.1011 93 L 0.0070 0.9031 0.0899 94 E 0.0064 0.9070 0.0866 95 V 0.0064 0.8889 0.1048 96 F 0.0075 0.8487 0.1438 97 K 0.0070 0.7860 0.2070 98 P 0.0060 0.9208 0.0732 99 Y 0.0064 0.9129 0.0808 100 Y 0.0100 0.9048 0.0851 101 A 0.0095 0.8931 0.0974 102 D 0.0108 0.8597 0.1295 103 H 0.0204 0.7778 0.2018 104 C 0.0402 0.5744 0.3854 105 Q 0.0439 0.4651 0.4910 106 I 0.0398 0.4122 0.5480 107 K 0.0520 0.2912 0.6567 108 T 0.0943 0.1263 0.7795 109 G 0.0974 0.0951 0.8075 110 P 0.1062 0.1117 0.7820 111 F 0.0707 0.0811 0.8482 112 P 0.0170 0.3746 0.6084 113 G 0.0284 0.3242 0.6474 114 I 0.0092 0.8971 0.0937 115 L 0.0048 0.9543 0.0409 116 D 0.0048 0.9563 0.0390 117 L 0.0048 0.9573 0.0379 118 M 0.0049 0.9567 0.0384 119 K 0.0049 0.9576 0.0374 120 N 0.0050 0.9576 0.0374 121 L 0.0049 0.9558 0.0393 122 R 0.0050 0.9447 0.0502 123 Q 0.0058 0.9016 0.0926 124 K 0.0439 0.3018 0.6543 125 G 0.0395 0.0156 0.9449 126 V 0.0985 0.0081 0.8933 127 K 0.4844 0.0084 0.5072 128 L 0.9225 0.0038 0.0737 129 A 0.9294 0.0035 0.0672 130 V 0.9297 0.0033 0.0670 131 V 0.8691 0.0067 0.1242 132 S 0.4329 0.0227 0.5444 133 N 0.0918 0.0317 0.8765 134 K 0.0644 0.0521 0.8834 135 P 0.0617 0.2583 0.6800 136 N 0.0172 0.7348 0.2480 137 E 0.0114 0.8710 0.1175 138 A 0.0118 0.8975 0.0907 139 V 0.0109 0.9166 0.0724 140 Q 0.0161 0.9204 0.0635 141 V 0.0122 0.9158 0.0719 142 L 0.0103 0.8984 0.0912 143 V 0.0129 0.8434 0.1436 144 E 0.0191 0.7027 0.2782 145 E 0.0446 0.4167 0.5387 146 L 0.0462 0.1674 0.7864 147 F 0.0573 0.2703 0.6724 148 P 0.0458 0.4051 0.5491 149 G 0.0469 0.4227 0.5305 150 S 0.1662 0.3562 0.4776 151 F 0.3839 0.1507 0.4654 152 D 0.4533 0.1197 0.4270 153 F 0.8127 0.0527 0.1347 154 A 0.8552 0.0352 0.1097 155 L 0.8386 0.0310 0.1304 156 G 0.5480 0.0462 0.4058 157 E 0.1731 0.1717 0.6552 158 K 0.0877 0.2541 0.6582 159 S 0.0722 0.3062 0.6216 160 G 0.0989 0.2293 0.6718 161 I 0.0931 0.1927 0.7143 162 R 0.0780 0.1468 0.7752 163 R 0.0706 0.0645 0.8650 164 K 0.0962 0.0392 0.8646 165 P 0.0880 0.0504 0.8616 166 A 0.0744 0.0472 0.8784 167 P 0.0194 0.7110 0.2696 168 D 0.0108 0.8936 0.0956 169 M 0.0053 0.9466 0.0481 170 T 0.0048 0.9572 0.0381 171 S 0.0049 0.9584 0.0366 172 E 0.0048 0.9596 0.0356 173 C 0.0047 0.9598 0.0355 174 V 0.0048 0.9587 0.0366 175 K 0.0053 0.9511 0.0436 176 V 0.0064 0.9175 0.0761 177 L 0.0457 0.4747 0.4797 178 G 0.0390 0.0217 0.9392 179 V 0.0692 0.0078 0.9229 180 P 0.0762 0.0117 0.9121 181 R 0.0310 0.5942 0.3748 182 D 0.0291 0.6120 0.3589 183 K 0.1886 0.4973 0.3141 184 C 0.7963 0.0207 0.1830 185 V 0.8763 0.0098 0.1139 186 Y 0.9039 0.0062 0.0899 187 I 0.7917 0.0416 0.1667 188 G 0.3990 0.0298 0.5712 189 D 0.1109 0.0229 0.8661 190 S 0.0593 0.0564 0.8843 191 E 0.0158 0.6295 0.3547 192 I 0.0186 0.7513 0.2301 193 D 0.0227 0.7863 0.1910 194 I 0.0071 0.9461 0.0468 195 Q 0.0055 0.9537 0.0408 196 T 0.0051 0.9564 0.0385 197 A 0.0054 0.9530 0.0417 198 R 0.0049 0.9402 0.0548 199 N 0.0067 0.8576 0.1357 200 S 0.0417 0.3845 0.5738 201 E 0.0480 0.0231 0.9289 202 M 0.0993 0.0091 0.8916 203 D 0.3813 0.0258 0.5930 204 E 0.9112 0.0042 0.0846 205 I 0.9238 0.0045 0.0717 206 A 0.9238 0.0037 0.0725 207 V 0.8775 0.0069 0.1156 208 N 0.6130 0.0218 0.3652 209 W 0.1735 0.0498 0.7767 210 G 0.0663 0.0778 0.8558 211 F 0.0679 0.1144 0.8178 212 R 0.0819 0.1202 0.7979 213 S 0.0687 0.1954 0.7359 214 V 0.0297 0.5143 0.4560 215 P 0.0182 0.7693 0.2125 216 F 0.0122 0.8196 0.1682 217 L 0.0130 0.8193 0.1677 218 Q 0.0151 0.8098 0.1751 219 K 0.0212 0.6976 0.2813 220 H 0.0526 0.4046 0.5428 221 G 0.0838 0.1064 0.8098 222 A 0.1044 0.0568 0.8389 223 T 0.3411 0.0911 0.5678 224 V 0.8210 0.0295 0.1496 225 I 0.8713 0.0147 0.1140 226 V 0.7591 0.0202 0.2208 227 D 0.2222 0.0808 0.6969 228 T 0.0987 0.0382 0.8630 229 A 0.0101 0.8117 0.1782 230 E 0.0054 0.9271 0.0675 231 K 0.0075 0.9114 0.0812 232 L 0.0053 0.9410 0.0537 233 E 0.0053 0.9407 0.0540 234 E 0.0052 0.9258 0.0690 235 A 0.0068 0.9032 0.0900 236 I 0.0180 0.8139 0.1682 237 L 0.0138 0.4791 0.5072 238 G 0.0268 0.1565 0.8167 239 E 0.0319 0.1157 0.8524