# This file is the result of combining several RDB files, specifically # T0182.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0182.t2k.stride-ebghtl.rdb (weight 1.24869) # T0182.t2k.str.rdb (weight 1.53983) # T0182.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 T0182.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0182 # 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 T0182.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 300 # # ============================================ # Comments from T0182.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0182 # 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 T0182.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 300 # # ============================================ # Comments from T0182.t2k.str.rdb # ============================================ # TARGET T0182 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0182.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 300 # # ============================================ # Comments from T0182.t2k.alpha.rdb # ============================================ # TARGET T0182 # 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 T0182.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 300 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0862 0.0243 0.8895 2 I 0.3174 0.0664 0.6163 3 R 0.3719 0.0712 0.5570 4 I 0.2256 0.0492 0.7252 5 K 0.0974 0.0297 0.8729 6 T 0.0492 0.0240 0.9268 7 P 0.0047 0.9247 0.0706 8 S 0.0045 0.9487 0.0468 9 E 0.0045 0.9539 0.0416 10 I 0.0043 0.9606 0.0351 11 E 0.0044 0.9586 0.0371 12 K 0.0044 0.9569 0.0387 13 M 0.0044 0.9576 0.0380 14 K 0.0045 0.9576 0.0379 15 K 0.0045 0.9553 0.0403 16 A 0.0045 0.9529 0.0426 17 G 0.0044 0.9553 0.0402 18 K 0.0044 0.9552 0.0404 19 A 0.0044 0.9551 0.0405 20 V 0.0044 0.9551 0.0405 21 A 0.0044 0.9562 0.0394 22 V 0.0044 0.9567 0.0388 23 A 0.0044 0.9551 0.0405 24 L 0.0044 0.9551 0.0405 25 R 0.0045 0.9525 0.0430 26 E 0.0045 0.9444 0.0511 27 V 0.0045 0.9342 0.0613 28 R 0.0056 0.9178 0.0765 29 K 0.0076 0.8556 0.1368 30 V 0.0109 0.7553 0.2338 31 I 0.0734 0.4753 0.4513 32 V 0.0752 0.1547 0.7701 33 P 0.0235 0.1028 0.8737 34 G 0.0244 0.0402 0.9354 35 K 0.1413 0.0261 0.8326 36 T 0.1702 0.0383 0.7915 37 A 0.0060 0.9317 0.0622 38 W 0.0044 0.9530 0.0426 39 D 0.0046 0.9553 0.0401 40 V 0.0044 0.9574 0.0382 41 E 0.0044 0.9594 0.0362 42 T 0.0044 0.9574 0.0381 43 L 0.0044 0.9571 0.0385 44 V 0.0044 0.9553 0.0403 45 L 0.0044 0.9547 0.0409 46 E 0.0045 0.9525 0.0431 47 I 0.0044 0.9534 0.0421 48 F 0.0045 0.9483 0.0471 49 K 0.0048 0.9383 0.0569 50 K 0.0077 0.8754 0.1169 51 L 0.0387 0.5154 0.4459 52 R 0.0402 0.1349 0.8249 53 V 0.0659 0.0992 0.8348 54 K 0.1157 0.1578 0.7264 55 P 0.0988 0.2238 0.6773 56 A 0.0693 0.2568 0.6739 57 F 0.0630 0.2762 0.6608 58 K 0.0682 0.2635 0.6683 59 G 0.0761 0.2045 0.7193 60 Y 0.1097 0.1529 0.7374 61 G 0.1392 0.1188 0.7420 62 G 0.1635 0.1001 0.7364 63 Y 0.1894 0.0844 0.7263 64 K 0.1944 0.1113 0.6943 65 Y 0.3253 0.1353 0.5394 66 A 0.5983 0.1104 0.2913 67 T 0.6786 0.0828 0.2387 68 C 0.6436 0.0654 0.2910 69 V 0.4298 0.0577 0.5125 70 S 0.2241 0.0535 0.7224 71 V 0.0770 0.2550 0.6680 72 N 0.0778 0.2375 0.6847 73 E 0.1135 0.2748 0.6117 74 E 0.2220 0.2395 0.5385 75 V 0.3055 0.1709 0.5235 76 V 0.3061 0.1391 0.5548 77 H 0.2542 0.0985 0.6473 78 G 0.2163 0.0580 0.7257 79 L 0.1790 0.0439 0.7771 80 P 0.0984 0.0773 0.8243 81 L 0.0584 0.1161 0.8254 82 K 0.0638 0.1007 0.8356 83 E 0.1595 0.0716 0.7689 84 K 0.3663 0.0271 0.6066 85 V 0.5792 0.0174 0.4034 86 F 0.4171 0.0183 0.5645 87 K 0.1815 0.0240 0.7945 88 E 0.0518 0.0727 0.8756 89 G 0.0352 0.0356 0.9292 90 D 0.2551 0.0143 0.7306 91 I 0.8192 0.0038 0.1770 92 V 0.8989 0.0046 0.0965 93 S 0.9151 0.0036 0.0813 94 V 0.8856 0.0044 0.1099 95 D 0.7607 0.0102 0.2290 96 V 0.6614 0.0338 0.3047 97 G 0.5574 0.0394 0.4032 98 A 0.6838 0.0366 0.2796 99 V 0.6967 0.0399 0.2634 100 Y 0.6139 0.0665 0.3196 101 Q 0.1329 0.0714 0.7957 102 G 0.1122 0.0656 0.8222 103 L 0.4773 0.0555 0.4672 104 Y 0.6210 0.0489 0.3300 105 G 0.5594 0.0497 0.3910 106 D 0.4909 0.0659 0.4432 107 A 0.5639 0.0742 0.3619 108 A 0.6290 0.0641 0.3068 109 V 0.6743 0.0386 0.2871 110 T 0.7298 0.0326 0.2376 111 Y 0.7189 0.0282 0.2529 112 I 0.6210 0.0369 0.3421 113 V 0.2910 0.0652 0.6437 114 G 0.1229 0.0398 0.8373 115 E 0.0908 0.0234 0.8858 116 T 0.0708 0.0230 0.9062 117 D 0.0509 0.0234 0.9257 118 E 0.0060 0.9099 0.0842 119 R 0.0047 0.9376 0.0577 120 G 0.0046 0.9505 0.0449 121 K 0.0044 0.9571 0.0385 122 E 0.0046 0.9556 0.0398 123 L 0.0044 0.9582 0.0374 124 V 0.0044 0.9600 0.0357 125 R 0.0044 0.9599 0.0357 126 V 0.0044 0.9600 0.0356 127 T 0.0044 0.9597 0.0359 128 R 0.0045 0.9586 0.0369 129 E 0.0045 0.9574 0.0381 130 V 0.0044 0.9555 0.0401 131 L 0.0046 0.9567 0.0387 132 E 0.0046 0.9544 0.0409 133 K 0.0047 0.9506 0.0447 134 A 0.0046 0.9461 0.0492 135 I 0.0053 0.9305 0.0642 136 K 0.0076 0.8613 0.1311 137 M 0.0120 0.6894 0.2986 138 I 0.0746 0.3805 0.5449 139 K 0.0648 0.1042 0.8310 140 P 0.0242 0.1220 0.8537 141 G 0.0224 0.0569 0.9208 142 I 0.1660 0.0366 0.7974 143 R 0.2216 0.0473 0.7311 144 L 0.0453 0.7009 0.2538 145 G 0.0134 0.7850 0.2017 146 D 0.0204 0.8259 0.1537 147 V 0.0052 0.9253 0.0695 148 S 0.0047 0.9458 0.0494 149 H 0.0045 0.9571 0.0385 150 C 0.0044 0.9580 0.0377 151 I 0.0044 0.9574 0.0382 152 Q 0.0044 0.9583 0.0373 153 E 0.0044 0.9575 0.0381 154 T 0.0044 0.9574 0.0382 155 V 0.0045 0.9534 0.0421 156 E 0.0048 0.9421 0.0531 157 S 0.0074 0.8693 0.1233 158 V 0.0410 0.4397 0.5193 159 G 0.0425 0.0375 0.9200 160 F 0.0739 0.0259 0.9002 161 N 0.1638 0.0427 0.7935 162 V 0.3052 0.0794 0.6154 163 I 0.3588 0.0657 0.5754 164 R 0.3454 0.0914 0.5633 165 D 0.2711 0.1014 0.6275 166 Y 0.2952 0.0966 0.6082 167 V 0.3113 0.0767 0.6120 168 G 0.3009 0.0797 0.6194 169 H 0.2856 0.0919 0.6226 170 G 0.3000 0.0910 0.6091 171 V 0.3136 0.0914 0.5950 172 G 0.2885 0.0783 0.6332 173 R 0.3829 0.1102 0.5070 174 E 0.4801 0.1014 0.4185 175 L 0.4133 0.1419 0.4448 176 H 0.2607 0.1358 0.6034 177 E 0.1413 0.1428 0.7159 178 D 0.1286 0.0864 0.7849 179 P 0.1429 0.1022 0.7549 180 Q 0.2484 0.1193 0.6323 181 I 0.3609 0.1101 0.5290 182 P 0.2973 0.1487 0.5540 183 N 0.2528 0.1630 0.5842 184 Y 0.2134 0.1535 0.6331 185 G 0.1568 0.1087 0.7345 186 T 0.1141 0.0747 0.8112 187 P 0.0746 0.1399 0.7856 188 G 0.0704 0.1120 0.8176 189 T 0.1091 0.0859 0.8050 190 G 0.1934 0.0725 0.7341 191 V 0.3488 0.0245 0.6267 192 V 0.5556 0.0123 0.4320 193 L 0.5410 0.0129 0.4461 194 R 0.2528 0.0171 0.7302 195 K 0.0477 0.0671 0.8852 196 G 0.0419 0.0342 0.9239 197 M 0.3927 0.0112 0.5961 198 T 0.8394 0.0049 0.1557 199 L 0.8856 0.0064 0.1080 200 A 0.8836 0.0056 0.1108 201 I 0.8337 0.0100 0.1563 202 E 0.6554 0.0112 0.3334 203 P 0.5687 0.0330 0.3982 204 M 0.6286 0.0376 0.3339 205 V 0.6680 0.0506 0.2813 206 S 0.6165 0.0433 0.3402 207 E 0.4189 0.0453 0.5358 208 G 0.1793 0.0828 0.7379 209 D 0.1041 0.1242 0.7717 210 W 0.1370 0.1191 0.7439 211 R 0.3327 0.0960 0.5712 212 V 0.5532 0.0804 0.3664 213 V 0.5854 0.0827 0.3319 214 V 0.5460 0.0819 0.3721 215 K 0.2927 0.0705 0.6368 216 E 0.1324 0.1225 0.7451 217 D 0.0999 0.0843 0.8158 218 G 0.1900 0.0571 0.7529 219 W 0.4293 0.0359 0.5348 220 T 0.6806 0.0259 0.2935 221 A 0.7551 0.0200 0.2249 222 V 0.7381 0.0200 0.2419 223 T 0.6039 0.0369 0.3591 224 V 0.3483 0.0835 0.5682 225 D 0.1321 0.0683 0.7996 226 G 0.1204 0.0534 0.8262 227 S 0.4077 0.0266 0.5657 228 R 0.7021 0.0123 0.2857 229 C 0.8216 0.0080 0.1704 230 A 0.8967 0.0044 0.0989 231 H 0.9102 0.0040 0.0858 232 F 0.8968 0.0052 0.0981 233 E 0.8409 0.0158 0.1433 234 H 0.7875 0.0128 0.1998 235 T 0.8598 0.0063 0.1339 236 I 0.9169 0.0038 0.0793 237 L 0.9226 0.0036 0.0738 238 I 0.8882 0.0079 0.1039 239 T 0.6014 0.0077 0.3909 240 E 0.0716 0.1101 0.8183 241 N 0.0538 0.0369 0.9093 242 G 0.1177 0.0399 0.8424 243 A 0.4366 0.0214 0.5420 244 E 0.7675 0.0153 0.2172 245 I 0.7980 0.0218 0.1802 246 L 0.6062 0.0498 0.3441 247 T 0.3461 0.0592 0.5947 248 K 0.2086 0.0450 0.7464 249 E 0.1081 0.0202 0.8717 250 G 0.0468 0.0282 0.9249