# This file is the result of combining several RDB files, specifically # T0284.t06.dssp-ebghstl.rdb (weight 1.53986) # T0284.t06.stride-ebghtl.rdb (weight 1.24869) # T0284.t06.str2.rdb (weight 1.54758) # T0284.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 T0284.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0284 # 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 T0284.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 694.638 # # ============================================ # Comments from T0284.t06.stride-ebghtl.rdb # ============================================ # TARGET T0284 # 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 T0284.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 694.638 # # ============================================ # Comments from T0284.t06.str2.rdb # ============================================ # TARGET T0284 # 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 T0284.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 694.638 # # ============================================ # Comments from T0284.t06.alpha.rdb # ============================================ # TARGET T0284 # 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 T0284.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 694.638 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0561 0.0429 0.9009 2 H 0.0534 0.1034 0.8432 3 R 0.0481 0.2077 0.7442 4 A 0.0408 0.2825 0.6767 5 S 0.0503 0.3226 0.6271 6 H 0.0151 0.6919 0.2930 7 H 0.0094 0.8321 0.1585 8 E 0.0108 0.8621 0.1271 9 L 0.0061 0.9119 0.0819 10 R 0.0048 0.9462 0.0490 11 A 0.0047 0.9558 0.0395 12 M 0.0047 0.9554 0.0399 13 F 0.0047 0.9562 0.0390 14 R 0.0047 0.9574 0.0379 15 A 0.0048 0.9534 0.0418 16 L 0.0052 0.9426 0.0522 17 L 0.0060 0.9166 0.0773 18 D 0.0092 0.7597 0.2311 19 S 0.0494 0.2691 0.6815 20 S 0.0297 0.0425 0.9277 21 R 0.0700 0.0286 0.9014 22 C 0.3387 0.0153 0.6460 23 Y 0.7520 0.0096 0.2384 24 H 0.8308 0.0112 0.1580 25 T 0.8030 0.0088 0.1883 26 A 0.6247 0.0433 0.3320 27 S 0.4017 0.0374 0.5609 28 V 0.2015 0.0873 0.7112 29 F 0.1378 0.0702 0.7920 30 D 0.0715 0.0623 0.8662 31 P 0.0081 0.9108 0.0811 32 M 0.0054 0.9418 0.0529 33 S 0.0048 0.9549 0.0403 34 A 0.0047 0.9594 0.0359 35 R 0.0049 0.9581 0.0370 36 I 0.0049 0.9578 0.0373 37 A 0.0050 0.9559 0.0391 38 A 0.0049 0.9485 0.0465 39 D 0.0054 0.9251 0.0695 40 L 0.0439 0.5148 0.4412 41 G 0.0437 0.0223 0.9340 42 F 0.1192 0.0076 0.8732 43 E 0.2667 0.0387 0.6946 44 C 0.9258 0.0034 0.0708 45 G 0.9312 0.0033 0.0655 46 I 0.9304 0.0035 0.0662 47 L 0.8357 0.0125 0.1518 48 G 0.2263 0.0316 0.7421 49 G 0.0575 0.1234 0.8191 50 S 0.0621 0.4423 0.4957 51 V 0.0481 0.7689 0.1830 52 A 0.0488 0.8202 0.1310 53 S 0.0579 0.8199 0.1222 54 L 0.0656 0.7905 0.1439 55 Q 0.0728 0.7552 0.1720 56 V 0.0871 0.6734 0.2395 57 L 0.0764 0.4584 0.4651 58 A 0.0892 0.1666 0.7442 59 A 0.0762 0.0545 0.8693 60 P 0.0583 0.1284 0.8133 61 D 0.0791 0.1131 0.8078 62 F 0.1334 0.1588 0.7078 63 A 0.2141 0.1125 0.6734 64 L 0.3681 0.0599 0.5720 65 I 0.3414 0.0189 0.6397 66 T 0.1604 0.0141 0.8255 67 L 0.0049 0.9404 0.0547 68 S 0.0047 0.9533 0.0420 69 E 0.0047 0.9572 0.0381 70 F 0.0047 0.9596 0.0358 71 V 0.0047 0.9603 0.0351 72 E 0.0047 0.9581 0.0372 73 Q 0.0047 0.9528 0.0424 74 A 0.0058 0.9454 0.0489 75 T 0.0063 0.9313 0.0624 76 R 0.0087 0.9068 0.0846 77 I 0.0152 0.8595 0.1253 78 G 0.0245 0.7502 0.2253 79 R 0.0370 0.5564 0.4066 80 V 0.0779 0.3840 0.5381 81 A 0.1223 0.1885 0.6893 82 R 0.1313 0.0813 0.7874 83 L 0.1964 0.0145 0.7890 84 P 0.3622 0.0104 0.6274 85 V 0.8793 0.0052 0.1155 86 I 0.9134 0.0062 0.0804 87 A 0.8911 0.0120 0.0969 88 D 0.6795 0.0130 0.3076 89 A 0.2121 0.0422 0.7457 90 D 0.0923 0.1060 0.8018 91 H 0.0709 0.1522 0.7769 92 G 0.0662 0.1053 0.8285 93 Y 0.1209 0.0913 0.7878 94 G 0.1006 0.0878 0.8116 95 N 0.0746 0.1302 0.7952 96 A 0.0053 0.9336 0.0611 97 L 0.0049 0.9528 0.0423 98 N 0.0048 0.9532 0.0420 99 V 0.0047 0.9571 0.0382 100 M 0.0047 0.9583 0.0370 101 R 0.0047 0.9587 0.0367 102 T 0.0047 0.9587 0.0367 103 V 0.0046 0.9615 0.0339 104 V 0.0047 0.9611 0.0342 105 E 0.0046 0.9614 0.0339 106 L 0.0046 0.9608 0.0345 107 E 0.0048 0.9541 0.0411 108 R 0.0049 0.8927 0.1024 109 A 0.0406 0.3792 0.5802 110 G 0.0392 0.0319 0.9289 111 I 0.1448 0.0246 0.8305 112 A 0.3470 0.0388 0.6142 113 A 0.8733 0.0122 0.1144 114 L 0.9093 0.0099 0.0808 115 T 0.9075 0.0102 0.0823 116 I 0.8293 0.0267 0.1441 117 E 0.5620 0.0414 0.3966 118 D 0.2697 0.0581 0.6722 119 T 0.2058 0.0845 0.7097 120 L 0.2384 0.0933 0.6683 121 L 0.1408 0.0843 0.7749 122 P 0.1010 0.1981 0.7008 123 A 0.0837 0.4279 0.4883 124 Q 0.1170 0.4418 0.4412 125 F 0.1459 0.3067 0.5474 126 G 0.1584 0.1412 0.7004 127 R 0.1478 0.1252 0.7270 128 K 0.1260 0.1243 0.7498 129 S 0.1494 0.0843 0.7663 130 T 0.2337 0.0744 0.6918 131 D 0.5224 0.0606 0.4170 132 L 0.7172 0.0533 0.2295 133 I 0.7419 0.0404 0.2177 134 C 0.6345 0.0402 0.3253 135 V 0.2317 0.3312 0.4371 136 E 0.1170 0.4011 0.4819 137 E 0.1000 0.4368 0.4632 138 G 0.0977 0.4477 0.4546 139 V 0.1014 0.5760 0.3226 140 G 0.0934 0.6769 0.2297 141 K 0.1453 0.7378 0.1169 142 I 0.1748 0.7367 0.0885 143 R 0.1687 0.7417 0.0896 144 A 0.2041 0.6778 0.1181 145 A 0.1346 0.7215 0.1438 146 L 0.1184 0.7478 0.1338 147 E 0.1128 0.7185 0.1687 148 A 0.1396 0.6234 0.2370 149 R 0.1377 0.4590 0.4032 150 V 0.1343 0.1734 0.6923 151 D 0.0889 0.0232 0.8879 152 P 0.0298 0.1358 0.8344 153 A 0.0648 0.0868 0.8484 154 L 0.5790 0.0245 0.3965 155 T 0.8596 0.0095 0.1309 156 I 0.9161 0.0067 0.0772 157 I 0.8949 0.0130 0.0921 158 A 0.8418 0.0133 0.1449 159 R 0.5764 0.0358 0.3877 160 T 0.3043 0.0950 0.6007 161 N 0.1051 0.3024 0.5925 162 A 0.0297 0.6787 0.2916 163 E 0.0326 0.6517 0.3157 164 L 0.0413 0.5144 0.4442 165 I 0.0760 0.1674 0.7566 166 D 0.0703 0.0737 0.8559 167 V 0.0049 0.9286 0.0665 168 D 0.0047 0.9557 0.0396 169 A 0.0047 0.9581 0.0372 170 V 0.0047 0.9601 0.0352 171 I 0.0047 0.9604 0.0350 172 Q 0.0047 0.9594 0.0360 173 R 0.0047 0.9562 0.0391 174 T 0.0047 0.9562 0.0391 175 L 0.0047 0.9543 0.0410 176 A 0.0048 0.9511 0.0441 177 Y 0.0049 0.9469 0.0482 178 Q 0.0057 0.9386 0.0557 179 E 0.0063 0.8932 0.1005 180 A 0.0410 0.4822 0.4768 181 G 0.0508 0.0353 0.9139 182 A 0.1099 0.0087 0.8813 183 D 0.1921 0.0448 0.7631 184 G 0.9109 0.0044 0.0847 185 I 0.9306 0.0032 0.0662 186 C 0.9265 0.0035 0.0700 187 L 0.8759 0.0045 0.1195 188 V 0.6233 0.0303 0.3465 189 G 0.3749 0.0231 0.6020 190 V 0.1696 0.0248 0.8057 191 R 0.0854 0.0513 0.8632 192 D 0.0764 0.0326 0.8910 193 F 0.0051 0.9394 0.0555 194 A 0.0048 0.9543 0.0410 195 H 0.0048 0.9557 0.0395 196 L 0.0047 0.9578 0.0374 197 E 0.0047 0.9594 0.0360 198 A 0.0047 0.9568 0.0386 199 I 0.0048 0.9519 0.0433 200 A 0.0049 0.9460 0.0491 201 E 0.0060 0.9017 0.0923 202 H 0.0096 0.7131 0.2773 203 L 0.0712 0.2896 0.6392 204 H 0.0510 0.0826 0.8664 205 I 0.1684 0.0255 0.8061 206 P 0.3806 0.0279 0.5915 207 L 0.8361 0.0209 0.1430 208 M 0.8744 0.0175 0.1081 209 L 0.8781 0.0230 0.0989 210 V 0.7984 0.0472 0.1544 211 T 0.5962 0.0476 0.3562 212 Y 0.3038 0.0513 0.6449 213 G 0.1115 0.0465 0.8420 214 N 0.0879 0.0443 0.8678 215 P 0.0744 0.1212 0.8044 216 Q 0.0656 0.1852 0.7492 217 L 0.0663 0.2608 0.6729 218 R 0.0494 0.3717 0.5789 219 D 0.0640 0.5496 0.3864 220 D 0.0083 0.9144 0.0773 221 A 0.0060 0.9428 0.0511 222 R 0.0059 0.9521 0.0420 223 L 0.0065 0.9520 0.0415 224 A 0.0073 0.9413 0.0514 225 R 0.0067 0.9122 0.0811 226 L 0.0434 0.4825 0.4741 227 G 0.0448 0.0286 0.9266 228 V 0.1778 0.0196 0.8026 229 R 0.6079 0.0354 0.3567 230 V 0.8148 0.0389 0.1464 231 V 0.8071 0.0509 0.1420 232 V 0.7211 0.0829 0.1961 233 N 0.3120 0.1095 0.5785 234 G 0.0768 0.2929 0.6303 235 H 0.0222 0.7015 0.2764 236 A 0.0087 0.9146 0.0766 237 A 0.0065 0.9395 0.0540 238 Y 0.0057 0.9534 0.0409 239 F 0.0049 0.9575 0.0375 240 A 0.0047 0.9568 0.0385 241 A 0.0047 0.9558 0.0395 242 I 0.0048 0.9573 0.0380 243 K 0.0048 0.9549 0.0403 244 A 0.0048 0.9511 0.0441 245 T 0.0047 0.9553 0.0399 246 Y 0.0047 0.9596 0.0357 247 D 0.0047 0.9591 0.0362 248 C 0.0047 0.9581 0.0373 249 L 0.0047 0.9579 0.0373 250 R 0.0047 0.9576 0.0377 251 E 0.0050 0.9516 0.0434 252 E 0.0056 0.9377 0.0567 253 R 0.0117 0.8968 0.0915 254 G 0.0107 0.7426 0.2467 255 A 0.0187 0.5622 0.4191 256 V 0.0490 0.3889 0.5621 257 A 0.0640 0.2835 0.6526 258 S 0.0685 0.2542 0.6773 259 D 0.0839 0.1254 0.7907 260 L 0.1320 0.0314 0.8366 261 T 0.0982 0.0236 0.8782 262 A 0.0055 0.9204 0.0741 263 S 0.0048 0.9391 0.0562 264 E 0.0058 0.9339 0.0603 265 L 0.0112 0.9120 0.0768 266 S 0.0159 0.8539 0.1302 267 K 0.0162 0.7452 0.2386 268 K 0.0297 0.6290 0.3413 269 Y 0.0965 0.3234 0.5800 270 T 0.0600 0.1189 0.8211 271 F 0.0492 0.2750 0.6758 272 P 0.0225 0.7404 0.2371 273 E 0.0090 0.9054 0.0856 274 E 0.0094 0.9214 0.0692 275 Y 0.0115 0.9174 0.0711 276 Q 0.0142 0.9077 0.0781 277 A 0.0136 0.8835 0.1030 278 W 0.0141 0.8463 0.1396 279 A 0.0170 0.8172 0.1658 280 R 0.0166 0.8298 0.1536 281 D 0.0239 0.7771 0.1989 282 Y 0.0338 0.7649 0.2014 283 M 0.0592 0.6888 0.2520 284 E 0.0812 0.5699 0.3489 285 V 0.0741 0.4623 0.4636 286 K 0.0668 0.2675 0.6657 287 E 0.0396 0.0702 0.8902