# This file is the result of combining several RDB files, specifically # T0299.t06.dssp-ebghstl.rdb (weight 1.53986) # T0299.t06.stride-ebghtl.rdb (weight 1.24869) # T0299.t06.str2.rdb (weight 1.54758) # T0299.t06.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 T0299.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0299 # 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 T0299.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 50.2483 # # ============================================ # Comments from T0299.t06.stride-ebghtl.rdb # ============================================ # TARGET T0299 # 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 T0299.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 50.2483 # # ============================================ # Comments from T0299.t06.str2.rdb # ============================================ # TARGET T0299 # 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 T0299.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 50.2483 # # ============================================ # Comments from T0299.t06.alpha.rdb # ============================================ # TARGET T0299 # 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 T0299.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 50.2483 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0585 0.0392 0.9023 2 T 0.1708 0.1111 0.7182 3 R 0.5442 0.1501 0.3056 4 Y 0.7800 0.1102 0.1098 5 A 0.8373 0.0875 0.0752 6 L 0.8696 0.0601 0.0703 7 L 0.8690 0.0549 0.0761 8 V 0.7762 0.0742 0.1496 9 R 0.6126 0.1103 0.2771 10 G 0.5641 0.1128 0.3232 11 I 0.5729 0.1107 0.3163 12 N 0.4555 0.1009 0.4436 13 V 0.2176 0.1057 0.6767 14 G 0.0837 0.0693 0.8470 15 G 0.0578 0.0958 0.8464 16 K 0.0645 0.1560 0.7796 17 N 0.1055 0.1408 0.7537 18 K 0.2771 0.1079 0.6149 19 V 0.4573 0.0428 0.4999 20 V 0.2646 0.0455 0.6899 21 M 0.0168 0.8828 0.1004 22 A 0.0056 0.9459 0.0485 23 E 0.0051 0.9521 0.0427 24 L 0.0049 0.9540 0.0411 25 R 0.0047 0.9601 0.0353 26 Q 0.0047 0.9592 0.0362 27 E 0.0047 0.9585 0.0368 28 L 0.0047 0.9547 0.0406 29 T 0.0049 0.9415 0.0536 30 N 0.0056 0.8858 0.1086 31 L 0.0428 0.5136 0.4436 32 G 0.0380 0.0628 0.8992 33 L 0.0722 0.1815 0.7462 34 E 0.0507 0.3724 0.5768 35 K 0.1405 0.2943 0.5652 36 V 0.4005 0.1004 0.4991 37 E 0.5889 0.1117 0.2994 38 S 0.8139 0.0615 0.1246 39 Y 0.8032 0.0763 0.1205 40 I 0.7667 0.0748 0.1586 41 N 0.6681 0.0588 0.2731 42 S 0.4820 0.0436 0.4744 43 G 0.3617 0.0452 0.5931 44 N 0.4594 0.0446 0.4960 45 I 0.7396 0.0316 0.2287 46 F 0.8234 0.0298 0.1468 47 F 0.7442 0.0305 0.2253 48 T 0.4542 0.0431 0.5027 49 S 0.2209 0.0329 0.7463 50 I 0.0500 0.2171 0.7329 51 D 0.0568 0.1939 0.7493 52 S 0.0644 0.2574 0.6781 53 K 0.0048 0.9195 0.0757 54 A 0.0047 0.9466 0.0487 55 Q 0.0047 0.9543 0.0410 56 L 0.0047 0.9571 0.0382 57 V 0.0047 0.9605 0.0349 58 E 0.0047 0.9608 0.0345 59 K 0.0047 0.9598 0.0355 60 L 0.0047 0.9597 0.0356 61 E 0.0047 0.9604 0.0349 62 T 0.0048 0.9589 0.0363 63 F 0.0048 0.9551 0.0401 64 F 0.0049 0.9490 0.0461 65 A 0.0056 0.9301 0.0643 66 V 0.0079 0.8708 0.1213 67 H 0.0199 0.7053 0.2748 68 Y 0.0758 0.1845 0.7397 69 P 0.0435 0.1309 0.8256 70 F 0.1250 0.1149 0.7601 71 I 0.2845 0.0565 0.6590 72 Q 0.4219 0.0321 0.5460 73 S 0.5582 0.0315 0.4103 74 F 0.8799 0.0077 0.1124 75 S 0.9179 0.0049 0.0772 76 L 0.9035 0.0044 0.0921 77 L 0.7124 0.0151 0.2725 78 S 0.2347 0.0083 0.7570 79 L 0.0054 0.9108 0.0838 80 E 0.0047 0.9434 0.0518 81 D 0.0047 0.9501 0.0451 82 F 0.0047 0.9566 0.0387 83 E 0.0047 0.9583 0.0371 84 A 0.0047 0.9569 0.0383 85 E 0.0049 0.9515 0.0436 86 L 0.0051 0.9372 0.0577 87 E 0.0061 0.8612 0.1327 88 N 0.0106 0.6018 0.3876 89 L 0.0729 0.0842 0.8429 90 P 0.0278 0.2524 0.7198 91 A 0.0440 0.3244 0.6316 92 W 0.0763 0.4149 0.5088 93 W 0.1044 0.3564 0.5392 94 S 0.0996 0.2788 0.6216 95 R 0.0810 0.2169 0.7022 96 D 0.1103 0.1466 0.7432 97 L 0.0738 0.2789 0.6473 98 A 0.1104 0.2050 0.6846 99 R 0.3117 0.1251 0.5632 100 K 0.5184 0.0381 0.4435 101 D 0.8004 0.0147 0.1848 102 F 0.9123 0.0056 0.0821 103 L 0.9176 0.0078 0.0746 104 F 0.9045 0.0075 0.0879 105 Y 0.7800 0.0157 0.2043 106 T 0.3638 0.0475 0.5887 107 E 0.1033 0.0801 0.8166 108 G 0.0670 0.0564 0.8766 109 L 0.1150 0.0187 0.8664 110 D 0.0840 0.0163 0.8998 111 V 0.0059 0.8868 0.1073 112 D 0.0052 0.9322 0.0626 113 Q 0.0051 0.9432 0.0517 114 V 0.0061 0.9434 0.0505 115 I 0.0071 0.9359 0.0570 116 A 0.0069 0.9015 0.0916 117 T 0.0086 0.8533 0.1381 118 V 0.0181 0.8020 0.1798 119 E 0.0153 0.7316 0.2531 120 S 0.0226 0.6572 0.3203 121 L 0.0452 0.5107 0.4441 122 E 0.0673 0.3037 0.6290 123 L 0.0720 0.2024 0.7257 124 K 0.0799 0.1150 0.8050 125 D 0.1566 0.0830 0.7603 126 E 0.4964 0.0461 0.4575 127 V 0.8434 0.0216 0.1350 128 L 0.8920 0.0127 0.0952 129 Y 0.8940 0.0112 0.0948 130 F 0.8299 0.0227 0.1474 131 G 0.5130 0.0196 0.4674 132 K 0.2371 0.0621 0.7008 133 L 0.4959 0.0442 0.4599 134 G 0.8702 0.0084 0.1214 135 I 0.9144 0.0048 0.0808 136 F 0.9137 0.0057 0.0805 137 W 0.8009 0.0231 0.1760 138 G 0.5228 0.0366 0.4406 139 K 0.4334 0.0712 0.4954 140 F 0.3823 0.0634 0.5543 141 S 0.1997 0.0482 0.7521 142 E 0.0415 0.2650 0.6936 143 E 0.0392 0.2112 0.7496 144 S 0.0613 0.2037 0.7350 145 Y 0.0971 0.2465 0.6564 146 S 0.1221 0.2234 0.6545 147 K 0.1072 0.2745 0.6183 148 T 0.0949 0.3259 0.5792 149 A 0.0432 0.7053 0.2516 150 Y 0.0394 0.7851 0.1755 151 H 0.0376 0.7922 0.1702 152 K 0.0285 0.8361 0.1354 153 Y 0.0356 0.8122 0.1522 154 L 0.0507 0.7148 0.2345 155 L 0.1041 0.4952 0.4007 156 K 0.1479 0.3295 0.5226 157 V 0.1429 0.1415 0.7156 158 P 0.1517 0.1597 0.6887 159 F 0.1250 0.1833 0.6917 160 Y 0.1373 0.1023 0.7604 161 R 0.2564 0.0687 0.6749 162 H 0.3778 0.0782 0.5440 163 I 0.4938 0.1158 0.3904 164 T 0.5645 0.1384 0.2972 165 I 0.4268 0.3132 0.2600 166 R 0.3104 0.3813 0.3083 167 N 0.1318 0.4108 0.4574 168 A 0.0225 0.7488 0.2287 169 K 0.0217 0.7848 0.1935 170 T 0.0124 0.8941 0.0935 171 F 0.0049 0.9519 0.0432 172 D 0.0047 0.9588 0.0365 173 K 0.0047 0.9586 0.0367 174 I 0.0047 0.9568 0.0385 175 G 0.0047 0.9544 0.0409 176 Q 0.0048 0.9407 0.0545 177 M 0.0053 0.9040 0.0907 178 L 0.0102 0.7775 0.2123 179 K 0.0126 0.4345 0.5529 180 K 0.0255 0.0774 0.8971