# This file is the result of combining several RDB files, specifically # T0276.t04.dssp-ebghstl.rdb (weight 1.53986) # T0276.t04.stride-ebghtl.rdb (weight 1.24869) # T0276.t04.str2.rdb (weight 1.54758) # T0276.t04.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 T0276.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0276 # 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 T0276.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 187.973 # # ============================================ # Comments from T0276.t04.stride-ebghtl.rdb # ============================================ # TARGET T0276 # 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 T0276.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 187.973 # # ============================================ # Comments from T0276.t04.str2.rdb # ============================================ # TARGET T0276 # 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 T0276.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 187.973 # # ============================================ # Comments from T0276.t04.alpha.rdb # ============================================ # TARGET T0276 # 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 T0276.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 187.973 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0693 0.0340 0.8967 2 T 0.0792 0.1117 0.8091 3 K 0.0049 0.9424 0.0527 4 A 0.0047 0.9584 0.0369 5 E 0.0047 0.9607 0.0346 6 L 0.0046 0.9606 0.0347 7 R 0.0046 0.9609 0.0344 8 R 0.0046 0.9612 0.0342 9 R 0.0046 0.9596 0.0358 10 A 0.0047 0.9582 0.0371 11 R 0.0047 0.9603 0.0350 12 A 0.0047 0.9602 0.0352 13 A 0.0047 0.9557 0.0396 14 W 0.0048 0.9318 0.0633 15 R 0.0051 0.8166 0.1783 16 R 0.0078 0.5903 0.4019 17 L 0.0534 0.2292 0.7174 18 D 0.0662 0.1253 0.8085 19 L 0.0078 0.8079 0.1843 20 K 0.0054 0.9127 0.0819 21 A 0.0052 0.9328 0.0619 22 L 0.0051 0.9281 0.0668 23 S 0.0048 0.9370 0.0583 24 R 0.0047 0.9553 0.0400 25 A 0.0047 0.9553 0.0399 26 V 0.0047 0.9506 0.0446 27 G 0.0049 0.9450 0.0501 28 A 0.0051 0.9156 0.0793 29 A 0.0056 0.8762 0.1183 30 L 0.0065 0.8362 0.1573 31 L 0.0086 0.7689 0.2226 32 P 0.0065 0.8138 0.1797 33 W 0.0076 0.8823 0.1102 34 L 0.0083 0.9053 0.0864 35 R 0.0099 0.8853 0.1048 36 E 0.0175 0.7949 0.1876 37 R 0.0510 0.3459 0.6031 38 G 0.0502 0.0380 0.9118 39 F 0.1375 0.0236 0.8390 40 R 0.3653 0.0541 0.5806 41 H 0.8918 0.0052 0.1030 42 I 0.9242 0.0036 0.0722 43 L 0.9293 0.0038 0.0668 44 L 0.9165 0.0043 0.0791 45 Y 0.8186 0.0104 0.1710 46 H 0.4503 0.0098 0.5399 47 P 0.1894 0.0201 0.7905 48 L 0.0883 0.0309 0.8808 49 P 0.0249 0.1695 0.8056 50 H 0.0240 0.1803 0.7957 51 E 0.1218 0.2953 0.5830 52 L 0.2414 0.2487 0.5099 53 N 0.1952 0.1935 0.6113 54 L 0.0595 0.6269 0.3136 55 L 0.0157 0.9006 0.0838 56 P 0.0079 0.9310 0.0611 57 L 0.0061 0.9380 0.0559 58 M 0.0073 0.9181 0.0746 59 E 0.0069 0.8237 0.1694 60 A 0.0127 0.5068 0.4805 61 Y 0.0660 0.0657 0.8683 62 P 0.0357 0.0758 0.8885 63 A 0.1610 0.0399 0.7991 64 R 0.5906 0.0261 0.3832 65 Y 0.8976 0.0047 0.0977 66 Y 0.9105 0.0040 0.0856 67 L 0.8807 0.0049 0.1145 68 P 0.7849 0.0056 0.2095 69 K 0.7757 0.0059 0.2184 70 V 0.6996 0.0116 0.2887 71 A 0.3743 0.0422 0.5835 72 G 0.1415 0.0503 0.8082 73 K 0.0820 0.0423 0.8757 74 G 0.2351 0.0324 0.7324 75 L 0.5650 0.0090 0.4260 76 T 0.8502 0.0056 0.1442 77 V 0.8868 0.0054 0.1078 78 H 0.8375 0.0072 0.1553 79 P 0.7966 0.0075 0.1959 80 F 0.4323 0.0351 0.5326 81 G 0.1939 0.0226 0.7835 82 P 0.1057 0.0317 0.8626 83 L 0.0961 0.0246 0.8794 84 A 0.1058 0.0150 0.8792 85 P 0.1367 0.0532 0.8101 86 G 0.0928 0.0362 0.8709 87 P 0.0921 0.1280 0.7800 88 F 0.1159 0.1167 0.7674 89 G 0.1302 0.0825 0.7872 90 L 0.1811 0.0398 0.7791 91 L 0.3739 0.0248 0.6013 92 E 0.2096 0.0187 0.7717 93 P 0.1552 0.0241 0.8207 94 T 0.1361 0.0351 0.8288 95 T 0.0855 0.0187 0.8958 96 P 0.0662 0.0218 0.9120 97 P 0.0614 0.0655 0.8731 98 E 0.0615 0.0661 0.8724 99 D 0.0943 0.0275 0.8782 100 P 0.0273 0.3916 0.5810 101 R 0.0483 0.3710 0.5807 102 V 0.2257 0.2520 0.5223 103 L 0.3956 0.0218 0.5826 104 D 0.5124 0.0573 0.4303 105 L 0.9115 0.0068 0.0817 106 V 0.9306 0.0036 0.0658 107 V 0.9251 0.0032 0.0717 108 V 0.8434 0.0136 0.1431 109 P 0.5557 0.0215 0.4228 110 G 0.5605 0.0343 0.4052 111 L 0.7315 0.0338 0.2347 112 A 0.8732 0.0123 0.1145 113 F 0.8659 0.0177 0.1164 114 D 0.4821 0.0151 0.5028 115 R 0.0286 0.1250 0.8464 116 E 0.0390 0.0425 0.9185 117 G 0.0913 0.0579 0.8508 118 Y 0.3251 0.0414 0.6335 119 R 0.7236 0.0407 0.2357 120 L 0.5799 0.0699 0.3502 121 G 0.3216 0.0583 0.6201 122 H 0.2063 0.0555 0.7382 123 G 0.1345 0.0540 0.8116 124 Q 0.1117 0.1212 0.7670 125 G 0.1737 0.1668 0.6595 126 F 0.1692 0.4397 0.3911 127 Y 0.1017 0.6436 0.2547 128 D 0.0453 0.7661 0.1885 129 R 0.0145 0.8756 0.1100 130 F 0.0180 0.8626 0.1194 131 L 0.0166 0.8243 0.1591 132 K 0.0143 0.7523 0.2334 133 E 0.0193 0.4911 0.4896 134 V 0.0791 0.1460 0.7749 135 R 0.0664 0.0554 0.8782 136 A 0.1292 0.0482 0.8226 137 A 0.3205 0.0257 0.6538 138 T 0.8576 0.0087 0.1336 139 V 0.9136 0.0093 0.0770 140 G 0.9246 0.0052 0.0703 141 V 0.9126 0.0068 0.0806 142 V 0.7184 0.0171 0.2645 143 P 0.2955 0.0660 0.6385 144 Q 0.1045 0.3648 0.5307 145 A 0.0837 0.5370 0.3793 146 L 0.1596 0.3823 0.4581 147 L 0.2241 0.2905 0.4854 148 F 0.1420 0.1742 0.6838 149 P 0.0640 0.2500 0.6859 150 A 0.0918 0.1841 0.7240 151 L 0.0997 0.0327 0.8676 152 P 0.0884 0.0288 0.8827 153 R 0.1381 0.0390 0.8230 154 D 0.0886 0.0292 0.8822 155 P 0.0201 0.3527 0.6273 156 W 0.0370 0.3222 0.6408 157 D 0.0916 0.2548 0.6536 158 V 0.2016 0.0482 0.7502 159 P 0.2669 0.0273 0.7059 160 V 0.2135 0.1591 0.6274 161 D 0.1743 0.1860 0.6398 162 H 0.6302 0.1704 0.1994 163 L 0.8767 0.0202 0.1031 164 A 0.8499 0.0129 0.1372 165 T 0.5369 0.0130 0.4501 166 E 0.0692 0.2951 0.6357 167 A 0.0596 0.1521 0.7882 168 G 0.0841 0.1531 0.7628 169 V 0.5474 0.0540 0.3986 170 E 0.7584 0.0428 0.1988 171 A 0.7707 0.0522 0.1770 172 V 0.5415 0.0613 0.3972 173 K 0.2802 0.0471 0.6728 174 R 0.1488 0.0209 0.8304 175 P 0.1334 0.0406 0.8260 176 A 0.1019 0.0220 0.8761 177 P 0.0961 0.0340 0.8699 178 G 0.0860 0.0180 0.8960 179 P 0.0966 0.0599 0.8436 180 G 0.0868 0.0808 0.8324 181 G 0.1885 0.0687 0.7428 182 L 0.2550 0.0528 0.6922 183 L 0.2069 0.0368 0.7563 184 D 0.0912 0.0232 0.8857