# This file is the result of combining several RDB files, specifically # T0356.t06.dssp-ebghstl.rdb (weight 1.53986) # T0356.t06.stride-ebghtl.rdb (weight 1.24869) # T0356.t06.str2.rdb (weight 1.54758) # T0356.t06.alpha.rdb (weight 0.659012) # T0356.t04.dssp-ebghstl.rdb (weight 1.53986) # T0356.t04.stride-ebghtl.rdb (weight 1.24869) # T0356.t04.str2.rdb (weight 1.54758) # T0356.t04.alpha.rdb (weight 0.659012) # T0356.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0356.t2k.stride-ebghtl.rdb (weight 1.24869) # T0356.t2k.str2.rdb (weight 1.54758) # T0356.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 T0356.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.1135 # # ============================================ # Comments from T0356.t06.stride-ebghtl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.1135 # # ============================================ # Comments from T0356.t06.str2.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.1135 # # ============================================ # Comments from T0356.t06.alpha.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.1135 # # ============================================ # Comments from T0356.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.3343 # # ============================================ # Comments from T0356.t04.stride-ebghtl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.3343 # # ============================================ # Comments from T0356.t04.str2.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.3343 # # ============================================ # Comments from T0356.t04.alpha.rdb # ============================================ # TARGET T0356 # 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 T0356.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 32.3343 # # ============================================ # Comments from T0356.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 209 # # ============================================ # Comments from T0356.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0356 # 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 T0356.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 209 # # ============================================ # Comments from T0356.t2k.str2.rdb # ============================================ # TARGET T0356 # 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 T0356.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 209 # # ============================================ # Comments from T0356.t2k.alpha.rdb # ============================================ # TARGET T0356 # 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 T0356.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 209 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 T 0.3999 0.0460 0.5541 2 W 0.5396 0.0316 0.4289 3 G 0.7243 0.0184 0.2573 4 L 0.8670 0.0088 0.1243 5 T 0.9023 0.0061 0.0916 6 V 0.9086 0.0051 0.0862 7 T 0.8695 0.0145 0.1160 8 R 0.7925 0.0122 0.1953 9 G 0.3561 0.0148 0.6291 10 P 0.0234 0.1394 0.8372 11 H 0.0268 0.1071 0.8661 12 K 0.0786 0.0503 0.8711 13 E 0.1252 0.0347 0.8401 14 R 0.6337 0.0200 0.3463 15 Q 0.7841 0.0200 0.1959 16 N 0.7765 0.0279 0.1957 17 L 0.7347 0.0340 0.2313 18 G 0.7390 0.0446 0.2164 19 I 0.8175 0.0410 0.1414 20 Y 0.8384 0.0359 0.1257 21 R 0.8025 0.0579 0.1396 22 Q 0.8264 0.0412 0.1324 23 Q 0.8375 0.0359 0.1266 24 L 0.8261 0.0342 0.1397 25 I 0.6678 0.0458 0.2864 26 G 0.2675 0.0320 0.7005 27 K 0.0243 0.0897 0.8860 28 N 0.0784 0.0581 0.8636 29 K 0.7101 0.0127 0.2772 30 L 0.8936 0.0039 0.1025 31 I 0.9212 0.0040 0.0748 32 M 0.9211 0.0041 0.0748 33 R 0.9105 0.0039 0.0856 34 W 0.8698 0.0071 0.1231 35 L 0.6943 0.0106 0.2951 36 S 0.3985 0.0404 0.5611 37 H 0.1142 0.0677 0.8181 38 R 0.0494 0.1593 0.7913 39 G 0.0534 0.2970 0.6496 40 G 0.0438 0.6795 0.2768 41 A 0.0343 0.8132 0.1525 42 L 0.0363 0.8380 0.1256 43 D 0.0378 0.8280 0.1342 44 Y 0.0346 0.8441 0.1213 45 Q 0.0356 0.8216 0.1428 46 E 0.0134 0.8764 0.1102 47 W 0.0116 0.8982 0.0902 48 C 0.0112 0.8982 0.0906 49 A 0.0113 0.9027 0.0860 50 A 0.0096 0.8841 0.1063 51 H 0.0154 0.7910 0.1935 52 P 0.0446 0.2548 0.7006 53 G 0.0320 0.0273 0.9407 54 E 0.0914 0.0171 0.8915 55 R 0.2569 0.0124 0.7308 56 F 0.3462 0.0094 0.6444 57 P 0.5057 0.0085 0.4858 58 V 0.8865 0.0088 0.1048 59 S 0.9159 0.0074 0.0767 60 V 0.9225 0.0057 0.0718 61 A 0.8972 0.0068 0.0960 62 L 0.6148 0.0404 0.3448 63 G 0.2217 0.0360 0.7423 64 A 0.1073 0.0392 0.8535 65 D 0.0823 0.0638 0.8540 66 P 0.0132 0.8203 0.1665 67 A 0.0128 0.8885 0.0987 68 T 0.0223 0.8871 0.0905 69 I 0.0599 0.8406 0.0994 70 L 0.0833 0.7866 0.1301 71 G 0.1088 0.7279 0.1633 72 A 0.1160 0.6376 0.2464 73 V 0.1392 0.4093 0.4515 74 T 0.1476 0.0868 0.7656 75 P 0.1663 0.0334 0.8002 76 V 0.1824 0.0294 0.7881 77 P 0.0971 0.0283 0.8746 78 D 0.0307 0.1087 0.8606 79 T 0.0385 0.0731 0.8884 80 L 0.1108 0.1840 0.7052 81 S 0.1303 0.2740 0.5956 82 E 0.0303 0.8490 0.1207 83 Y 0.0323 0.8770 0.0908 84 A 0.0338 0.8872 0.0791 85 F 0.0573 0.8664 0.0763 86 A 0.0566 0.8624 0.0810 87 G 0.0791 0.8129 0.1080 88 L 0.0774 0.7531 0.1695 89 L 0.0804 0.6088 0.3108 90 R 0.0536 0.2188 0.7277 91 G 0.0429 0.0367 0.9204 92 T 0.1667 0.0151 0.8182 93 K 0.4131 0.0109 0.5760 94 T 0.6148 0.0091 0.3761 95 E 0.6949 0.0065 0.2986 96 V 0.8104 0.0067 0.1829 97 V 0.8033 0.0103 0.1864 98 K 0.7517 0.0169 0.2314 99 C 0.4617 0.0309 0.5074 100 I 0.2652 0.0765 0.6583 101 S 0.1818 0.0699 0.7483 102 N 0.1431 0.0606 0.7964 103 D 0.1238 0.0424 0.8338 104 L 0.2810 0.0216 0.6974 105 E 0.4194 0.0198 0.5608 106 V 0.4605 0.0167 0.5228 107 P 0.3342 0.0207 0.6451 108 A 0.2485 0.0673 0.6842 109 S 0.3409 0.0306 0.6285 110 A 0.7038 0.0078 0.2884 111 E 0.8769 0.0044 0.1187 112 I 0.9155 0.0035 0.0809 113 V 0.9209 0.0033 0.0757 114 L 0.9152 0.0035 0.0813 115 E 0.8531 0.0149 0.1320 116 G 0.7785 0.0080 0.2135 117 Y 0.7797 0.0070 0.2133 118 I 0.5841 0.0076 0.4083 119 E 0.1827 0.0150 0.8022 120 Q 0.0185 0.1638 0.8177 121 G 0.0249 0.1433 0.8317 122 E 0.1447 0.1486 0.7067 123 T 0.3281 0.1076 0.5643 124 A 0.3738 0.0823 0.5439 125 P 0.2598 0.1215 0.6186 126 E 0.2150 0.0956 0.6894 127 G 0.1248 0.0483 0.8269 128 P 0.1264 0.0825 0.7912 129 Y 0.1252 0.1144 0.7604 130 G 0.1592 0.1544 0.6864 131 D 0.1828 0.1916 0.6255 132 H 0.2429 0.1790 0.5781 133 T 0.2340 0.1291 0.6369 134 G 0.2462 0.0881 0.6657 135 Y 0.3485 0.0731 0.5784 136 Y 0.3361 0.0616 0.6023 137 N 0.1693 0.0507 0.7800 138 E 0.1021 0.1243 0.7736 139 V 0.0869 0.1503 0.7628 140 D 0.1090 0.0875 0.8035 141 S 0.1342 0.0705 0.7952 142 F 0.2184 0.0210 0.7606 143 P 0.3367 0.0125 0.6508 144 V 0.8576 0.0061 0.1363 145 F 0.9095 0.0035 0.0870 146 T 0.9232 0.0034 0.0734 147 V 0.9118 0.0032 0.0849 148 T 0.8605 0.0258 0.1138 149 H 0.8880 0.0051 0.1069 150 I 0.8789 0.0055 0.1156 151 T 0.8412 0.0113 0.1474 152 Q 0.7146 0.0220 0.2635 153 R 0.4471 0.0616 0.4913 154 E 0.1843 0.0841 0.7316 155 D 0.1235 0.0357 0.8408 156 A 0.2378 0.0659 0.6963 157 I 0.4723 0.0656 0.4621 158 Y 0.5545 0.0754 0.3701 159 H 0.5619 0.0936 0.3445 160 S 0.5301 0.0931 0.3768 161 T 0.5510 0.0672 0.3818 162 Y 0.4390 0.0461 0.5149 163 T 0.1938 0.0529 0.7532 164 G 0.0953 0.0282 0.8765 165 R 0.0768 0.0286 0.8947 166 P 0.0659 0.0362 0.8978 167 P 0.0287 0.2524 0.7188 168 D 0.0294 0.2994 0.6711 169 E 0.0381 0.4817 0.4802 170 P 0.0213 0.6855 0.2932 171 A 0.0274 0.7891 0.1835 172 V 0.0226 0.8717 0.1058 173 L 0.0098 0.9164 0.0738 174 G 0.0071 0.9234 0.0695 175 V 0.0077 0.9370 0.0553 176 A 0.0067 0.9393 0.0540 177 L 0.0075 0.9264 0.0661 178 N 0.0089 0.8622 0.1289 179 E 0.0133 0.7404 0.2464 180 V 0.0270 0.5089 0.4641 181 F 0.0238 0.0927 0.8835