# This file is the result of combining several RDB files, specifically # T0365.t06.dssp-ebghstl.rdb (weight 1.53986) # T0365.t06.stride-ebghtl.rdb (weight 1.24869) # T0365.t06.str2.rdb (weight 1.54758) # T0365.t06.alpha.rdb (weight 0.659012) # T0365.t04.dssp-ebghstl.rdb (weight 1.53986) # T0365.t04.stride-ebghtl.rdb (weight 1.24869) # T0365.t04.str2.rdb (weight 1.54758) # T0365.t04.alpha.rdb (weight 0.659012) # T0365.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0365.t2k.stride-ebghtl.rdb (weight 1.24869) # T0365.t2k.str2.rdb (weight 1.54758) # T0365.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 T0365.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0365 # Using neural net t06-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 T0365.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 170 # # ============================================ # Comments from T0365.t06.stride-ebghtl.rdb # ============================================ # TARGET T0365 # Using neural net t06-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 T0365.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 170 # # ============================================ # Comments from T0365.t06.str2.rdb # ============================================ # TARGET T0365 # Using neural net 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 T0365.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 170 # # ============================================ # Comments from T0365.t06.alpha.rdb # ============================================ # TARGET T0365 # Using neural net 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 T0365.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 170 # # ============================================ # Comments from T0365.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0365 # Using neural net t06-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 T0365.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 164 # # ============================================ # Comments from T0365.t04.stride-ebghtl.rdb # ============================================ # TARGET T0365 # 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 T0365.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 164 # # ============================================ # Comments from T0365.t04.str2.rdb # ============================================ # TARGET T0365 # Using neural net t04-2621-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 T0365.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 164 # # ============================================ # Comments from T0365.t04.alpha.rdb # ============================================ # TARGET T0365 # 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 T0365.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 164 # # ============================================ # Comments from T0365.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0365 # 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 T0365.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 91 # # ============================================ # Comments from T0365.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0365 # 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 T0365.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 91 # # ============================================ # Comments from T0365.t2k.str2.rdb # ============================================ # TARGET T0365 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0365.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 91 # # ============================================ # Comments from T0365.t2k.alpha.rdb # ============================================ # TARGET T0365 # 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 T0365.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 91 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0772 0.0606 0.8622 2 P 0.1342 0.0965 0.7692 3 V 0.1429 0.2442 0.6129 4 N 0.1346 0.2894 0.5760 5 S 0.1196 0.3628 0.5176 6 I 0.1237 0.3791 0.4972 7 L 0.1189 0.3400 0.5411 8 G 0.1062 0.2305 0.6633 9 V 0.0720 0.3034 0.6246 10 F 0.0719 0.3230 0.6051 11 A 0.0506 0.2698 0.6795 12 K 0.0365 0.2538 0.7097 13 S 0.0754 0.1931 0.7315 14 P 0.0295 0.5311 0.4394 15 I 0.0152 0.7516 0.2331 16 K 0.0105 0.9014 0.0881 17 P 0.0066 0.9227 0.0707 18 L 0.0051 0.9438 0.0511 19 Q 0.0047 0.9566 0.0386 20 E 0.0048 0.9562 0.0391 21 H 0.0048 0.9551 0.0401 22 M 0.0047 0.9592 0.0361 23 D 0.0047 0.9600 0.0353 24 K 0.0048 0.9585 0.0368 25 V 0.0047 0.9598 0.0355 26 Y 0.0047 0.9595 0.0357 27 D 0.0048 0.9564 0.0388 28 C 0.0048 0.9517 0.0435 29 A 0.0048 0.9537 0.0416 30 S 0.0050 0.9460 0.0490 31 L 0.0050 0.9279 0.0671 32 L 0.0051 0.9388 0.0561 33 V 0.0048 0.9556 0.0396 34 P 0.0047 0.9577 0.0376 35 F 0.0048 0.9554 0.0398 36 F 0.0048 0.9528 0.0424 37 E 0.0048 0.9480 0.0472 38 A 0.0050 0.9370 0.0579 39 T 0.0063 0.9013 0.0924 40 I 0.0111 0.7775 0.2115 41 T 0.0363 0.3762 0.5875 42 G 0.0313 0.1054 0.8632 43 N 0.0619 0.0439 0.8942 44 W 0.0235 0.6331 0.3434 45 D 0.0096 0.7822 0.2082 46 D 0.0082 0.8407 0.1511 47 A 0.0055 0.9323 0.0623 48 V 0.0054 0.9400 0.0545 49 Q 0.0051 0.9449 0.0500 50 I 0.0051 0.9466 0.0483 51 R 0.0048 0.9507 0.0444 52 K 0.0049 0.9433 0.0519 53 Q 0.0051 0.9336 0.0613 54 I 0.0055 0.9440 0.0505 55 S 0.0052 0.9441 0.0507 56 L 0.0057 0.9426 0.0517 57 A 0.0064 0.9403 0.0533 58 E 0.0081 0.9384 0.0535 59 K 0.0079 0.9236 0.0685 60 Q 0.0101 0.9108 0.0792 61 G 0.0078 0.9253 0.0669 62 D 0.0070 0.9297 0.0633 63 S 0.0049 0.9476 0.0476 64 L 0.0048 0.9523 0.0429 65 K 0.0047 0.9581 0.0372 66 R 0.0047 0.9570 0.0383 67 E 0.0047 0.9543 0.0410 68 I 0.0047 0.9528 0.0425 69 R 0.0049 0.9442 0.0510 70 L 0.0053 0.9057 0.0890 71 T 0.0103 0.7694 0.2203 72 L 0.0519 0.3938 0.5543 73 P 0.0268 0.3017 0.6715 74 S 0.0371 0.3021 0.6608 75 G 0.1688 0.2590 0.5722 76 L 0.4252 0.1330 0.4418 77 F 0.5514 0.0561 0.3925 78 M 0.5165 0.0297 0.4538 79 P 0.4014 0.0341 0.5645 80 V 0.1772 0.0421 0.7807 81 E 0.1099 0.0349 0.8552 82 R 0.0114 0.7834 0.2052 83 T 0.0072 0.8268 0.1660 84 D 0.0072 0.8867 0.1061 85 L 0.0048 0.9467 0.0485 86 L 0.0047 0.9547 0.0406 87 E 0.0048 0.9521 0.0431 88 L 0.0048 0.9499 0.0453 89 L 0.0049 0.9505 0.0446 90 T 0.0050 0.9360 0.0590 91 Q 0.0053 0.9374 0.0573 92 Q 0.0049 0.9492 0.0459 93 D 0.0053 0.9483 0.0464 94 K 0.0050 0.9484 0.0466 95 I 0.0048 0.9546 0.0406 96 A 0.0049 0.9578 0.0373 97 N 0.0050 0.9531 0.0419 98 K 0.0049 0.9482 0.0468 99 A 0.0048 0.9526 0.0426 100 K 0.0049 0.9503 0.0448 101 D 0.0051 0.9374 0.0575 102 I 0.0051 0.9305 0.0645 103 S 0.0087 0.9102 0.0811 104 G 0.0141 0.8641 0.1219 105 R 0.0272 0.8433 0.1295 106 V 0.1012 0.7481 0.1507 107 I 0.2115 0.6088 0.1797 108 G 0.2715 0.4783 0.2502 109 R 0.2483 0.3438 0.4078 110 Q 0.2556 0.1540 0.5904 111 L 0.1863 0.1225 0.6912 112 L 0.1572 0.0947 0.7482 113 I 0.0976 0.0610 0.8414 114 P 0.0564 0.0801 0.8635 115 Q 0.0149 0.6675 0.3176 116 A 0.0088 0.8017 0.1895 117 L 0.0074 0.8522 0.1404 118 Q 0.0054 0.9297 0.0649 119 V 0.0051 0.9448 0.0501 120 P 0.0052 0.9502 0.0446 121 F 0.0048 0.9553 0.0399 122 I 0.0047 0.9599 0.0354 123 A 0.0047 0.9601 0.0352 124 Y 0.0047 0.9586 0.0367 125 L 0.0047 0.9593 0.0360 126 Q 0.0047 0.9582 0.0370 127 R 0.0048 0.9538 0.0415 128 C 0.0047 0.9539 0.0414 129 I 0.0047 0.9581 0.0372 130 D 0.0047 0.9578 0.0375 131 A 0.0047 0.9562 0.0391 132 V 0.0047 0.9571 0.0382 133 G 0.0048 0.9548 0.0404 134 L 0.0048 0.9490 0.0462 135 A 0.0048 0.9503 0.0449 136 Q 0.0048 0.9556 0.0397 137 Q 0.0048 0.9509 0.0443 138 V 0.0048 0.9510 0.0442 139 I 0.0048 0.9492 0.0460 140 N 0.0049 0.9401 0.0550 141 E 0.0061 0.9114 0.0825 142 L 0.0060 0.9194 0.0746 143 D 0.0050 0.9331 0.0619 144 D 0.0058 0.9293 0.0649 145 L 0.0078 0.9200 0.0722 146 L 0.0135 0.8903 0.0962 147 E 0.0131 0.7828 0.2041 148 A 0.0391 0.5074 0.4535 149 G 0.0409 0.1700 0.7891 150 F 0.0481 0.1190 0.8330 151 R 0.0429 0.1705 0.7867 152 G 0.0246 0.3860 0.5894 153 R 0.0294 0.5356 0.4350 154 E 0.0299 0.7214 0.2486 155 V 0.0098 0.8916 0.0985 156 D 0.0088 0.9247 0.0665 157 F 0.0074 0.9354 0.0572 158 V 0.0063 0.9457 0.0480 159 A 0.0060 0.9522 0.0419 160 K 0.0058 0.9496 0.0446 161 M 0.0051 0.9502 0.0447 162 I 0.0048 0.9544 0.0408 163 N 0.0048 0.9534 0.0418 164 E 0.0049 0.9474 0.0477 165 L 0.0054 0.9510 0.0435 166 D 0.0052 0.9508 0.0440 167 I 0.0055 0.9433 0.0512 168 I 0.0064 0.9408 0.0528 169 E 0.0070 0.9377 0.0554 170 E 0.0066 0.9253 0.0681 171 D 0.0087 0.9098 0.0815 172 T 0.0064 0.9277 0.0658 173 D 0.0056 0.9330 0.0614 174 D 0.0048 0.9502 0.0451 175 L 0.0048 0.9539 0.0414 176 Q 0.0047 0.9561 0.0392 177 I 0.0047 0.9577 0.0376 178 Q 0.0047 0.9583 0.0370 179 L 0.0047 0.9585 0.0368 180 R 0.0047 0.9561 0.0391 181 R 0.0048 0.9524 0.0428 182 Q 0.0051 0.9399 0.0550 183 L 0.0069 0.9073 0.0857 184 F 0.0126 0.8140 0.1733 185 A 0.0174 0.7168 0.2658 186 L 0.0249 0.5597 0.4154 187 E 0.0329 0.4220 0.5451 188 S 0.0222 0.3275 0.6504 189 E 0.0339 0.2351 0.7309 190 L 0.0729 0.1055 0.8217 191 N 0.0687 0.0435 0.8878 192 P 0.0212 0.8837 0.0951 193 V 0.0124 0.9245 0.0631 194 D 0.0086 0.9439 0.0475 195 V 0.0106 0.9459 0.0435 196 M 0.0076 0.9493 0.0431 197 F 0.0066 0.9505 0.0429 198 L 0.0047 0.9560 0.0392 199 Y 0.0047 0.9584 0.0369 200 K 0.0048 0.9570 0.0382 201 T 0.0047 0.9577 0.0376 202 I 0.0048 0.9564 0.0388 203 E 0.0049 0.9520 0.0431 204 W 0.0050 0.9470 0.0481 205 V 0.0049 0.9486 0.0465 206 G 0.0048 0.9518 0.0433 207 G 0.0050 0.9417 0.0532 208 L 0.0051 0.9429 0.0521 209 A 0.0055 0.9441 0.0504 210 D 0.0055 0.9182 0.0762 211 L 0.0058 0.9130 0.0811 212 A 0.0057 0.9272 0.0671 213 E 0.0054 0.9288 0.0658 214 R 0.0054 0.9156 0.0790 215 V 0.0058 0.9285 0.0657 216 G 0.0069 0.9450 0.0481 217 S 0.0065 0.9365 0.0570 218 R 0.0063 0.9353 0.0583 219 L 0.0103 0.9360 0.0537 220 E 0.0127 0.9218 0.0655 221 L 0.0344 0.8947 0.0709 222 M 0.0485 0.8770 0.0745 223 L 0.1000 0.7966 0.1035 224 A 0.1462 0.6176 0.2362 225 R 0.1720 0.3434 0.4847 226 V 0.0566 0.0383 0.9052