# This file is the result of combining several RDB files, specifically # T0248.t04.dssp-ebghstl.rdb (weight 1.53986) # T0248.t04.stride-ebghtl.rdb (weight 1.24869) # T0248.t04.str2.rdb (weight 1.54758) # T0248.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 T0248.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0248 # 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 T0248.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 10 # # ============================================ # Comments from T0248.t04.stride-ebghtl.rdb # ============================================ # TARGET T0248 # 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 T0248.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 10 # # ============================================ # Comments from T0248.t04.str2.rdb # ============================================ # TARGET T0248 # 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 T0248.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 10 # # ============================================ # Comments from T0248.t04.alpha.rdb # ============================================ # TARGET T0248 # 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 T0248.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 10 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1398 0.3152 0.5450 2 I 0.1587 0.2572 0.5842 3 N 0.0888 0.1931 0.7181 4 K 0.0834 0.1125 0.8041 5 P 0.0367 0.4841 0.4792 6 N 0.0288 0.6037 0.3675 7 Q 0.0525 0.7350 0.2126 8 F 0.0513 0.8451 0.1036 9 V 0.0300 0.8797 0.0903 10 N 0.0318 0.8425 0.1257 11 H 0.0111 0.8910 0.0979 12 L 0.0050 0.9468 0.0482 13 S 0.0047 0.9569 0.0384 14 A 0.0047 0.9571 0.0382 15 L 0.0048 0.9551 0.0402 16 K 0.0048 0.9509 0.0443 17 K 0.0052 0.9314 0.0633 18 H 0.0069 0.8932 0.0999 19 F 0.0160 0.8076 0.1764 20 A 0.0142 0.7755 0.2103 21 S 0.0168 0.8004 0.1828 22 Y 0.0071 0.9269 0.0660 23 K 0.0055 0.9460 0.0485 24 E 0.0071 0.9423 0.0506 25 L 0.0075 0.9349 0.0576 26 R 0.0084 0.9363 0.0553 27 E 0.0060 0.9347 0.0593 28 A 0.0063 0.9197 0.0740 29 F 0.0105 0.8873 0.1022 30 N 0.0101 0.8334 0.1565 31 D 0.0140 0.7919 0.1941 32 Y 0.0294 0.7495 0.2212 33 H 0.0677 0.5923 0.3399 34 K 0.0499 0.3849 0.5652 35 H 0.0429 0.2133 0.7438 36 N 0.0546 0.1261 0.8193 37 G 0.0346 0.1694 0.7960 38 D 0.0297 0.4540 0.5164 39 E 0.0571 0.7222 0.2207 40 L 0.0350 0.7917 0.1733 41 T 0.0256 0.8310 0.1434 42 T 0.0208 0.8745 0.1046 43 F 0.0137 0.9096 0.0767 44 F 0.0065 0.9353 0.0582 45 L 0.0049 0.9538 0.0413 46 H 0.0048 0.9566 0.0386 47 Q 0.0048 0.9555 0.0396 48 F 0.0047 0.9599 0.0354 49 D 0.0046 0.9615 0.0339 50 K 0.0046 0.9615 0.0338 51 V 0.0047 0.9601 0.0352 52 M 0.0047 0.9607 0.0346 53 E 0.0046 0.9617 0.0337 54 L 0.0047 0.9596 0.0357 55 V 0.0048 0.9480 0.0473 56 K 0.0050 0.8942 0.1009 57 Q 0.0165 0.7554 0.2281 58 K 0.0362 0.4792 0.4846 59 D 0.0453 0.3107 0.6440 60 F 0.0085 0.8252 0.1663 61 K 0.0055 0.9280 0.0666 62 T 0.0062 0.9369 0.0569 63 A 0.0060 0.9413 0.0527 64 Q 0.0060 0.9455 0.0486 65 S 0.0053 0.9356 0.0591 66 R 0.0057 0.9249 0.0695 67 C 0.0057 0.9367 0.0577 68 E 0.0061 0.9288 0.0652 69 E 0.0060 0.9164 0.0776 70 E 0.0083 0.8684 0.1233 71 L 0.0270 0.7445 0.2285 72 A 0.0273 0.3779 0.5947 73 A 0.0503 0.0480 0.9017 74 P 0.0412 0.0980 0.8608 75 Y 0.0908 0.0863 0.8229 76 L 0.1096 0.0157 0.8747 77 P 0.0731 0.0211 0.9057 78 K 0.0218 0.7813 0.1969 79 P 0.0112 0.8589 0.1299 80 L 0.0055 0.9298 0.0646 81 V 0.0048 0.9509 0.0443 82 S 0.0047 0.9555 0.0398 83 F 0.0048 0.9529 0.0423 84 F 0.0047 0.9568 0.0385 85 Q 0.0047 0.9613 0.0341 86 S 0.0046 0.9613 0.0341 87 L 0.0047 0.9593 0.0361 88 L 0.0047 0.9565 0.0388 89 Q 0.0047 0.9415 0.0538 90 L 0.0049 0.9163 0.0789 91 V 0.0072 0.8508 0.1420 92 N 0.0088 0.7269 0.2642 93 H 0.0074 0.8692 0.1234 94 D 0.0072 0.8772 0.1155 95 L 0.0080 0.8771 0.1149 96 L 0.0084 0.8889 0.1028 97 E 0.0074 0.9295 0.0631 98 Q 0.0081 0.8947 0.0971 99 Q 0.0081 0.8785 0.1133 100 N 0.0142 0.8537 0.1321 101 A 0.0075 0.8970 0.0955 102 A 0.0091 0.8957 0.0952 103 L 0.0110 0.8624 0.1266 104 A 0.0101 0.7058 0.2841 105 S 0.0156 0.2908 0.6936 106 L 0.0611 0.0341 0.9048 107 P 0.0529 0.0233 0.9237 108 A 0.0053 0.8938 0.1009 109 A 0.0048 0.9471 0.0481 110 K 0.0049 0.9493 0.0458 111 I 0.0050 0.9531 0.0419 112 I 0.0050 0.9561 0.0388 113 E 0.0053 0.9573 0.0374 114 L 0.0057 0.9511 0.0432 115 V 0.0071 0.9368 0.0561 116 L 0.0136 0.8971 0.0892 117 Q 0.0256 0.7151 0.2594 118 D 0.0610 0.3140 0.6250 119 Y 0.0530 0.1690 0.7779 120 P 0.0141 0.3796 0.6063 121 N 0.0273 0.3814 0.5913 122 K 0.0527 0.4668 0.4805 123 L 0.1210 0.5859 0.2931 124 N 0.1825 0.5536 0.2639 125 M 0.1453 0.7380 0.1167 126 I 0.1004 0.8157 0.0838 127 H 0.0652 0.8389 0.0960 128 Y 0.0543 0.8242 0.1215 129 L 0.0529 0.7629 0.1843 130 L 0.0389 0.6784 0.2827 131 P 0.0228 0.6983 0.2788 132 K 0.0222 0.7159 0.2618 133 T 0.0293 0.6638 0.3069 134 K 0.0257 0.6481 0.3261 135 A 0.0372 0.5114 0.4514 136 F 0.0749 0.2424 0.6827 137 V 0.1446 0.0832 0.7722 138 K 0.1312 0.0282 0.8406 139 P 0.0271 0.7024 0.2704 140 H 0.0126 0.7728 0.2146 141 L 0.0105 0.8331 0.1563 142 L 0.0139 0.8043 0.1818 143 Q 0.0106 0.7896 0.1998 144 R 0.0149 0.7973 0.1878 145 L 0.0489 0.7817 0.1694 146 Q 0.0331 0.7772 0.1897 147 F 0.0733 0.7629 0.1638 148 V 0.1214 0.6982 0.1804 149 L 0.1696 0.5145 0.3158 150 T 0.1092 0.3118 0.5790 151 D 0.0513 0.3983 0.5503 152 S 0.0080 0.8583 0.1337 153 E 0.0112 0.8710 0.1178 154 L 0.0163 0.8621 0.1215 155 L 0.0157 0.8055 0.1788 156 E 0.0160 0.7025 0.2815 157 L 0.0293 0.7236 0.2471 158 K 0.0272 0.6903 0.2824 159 R 0.0247 0.8594 0.1159 160 F 0.0279 0.8874 0.0846 161 S 0.0106 0.9285 0.0610 162 F 0.0071 0.9486 0.0443 163 F 0.0058 0.9537 0.0405 164 Q 0.0054 0.9535 0.0411 165 A 0.0062 0.9410 0.0528 166 L 0.0101 0.8780 0.1119 167 N 0.0144 0.6262 0.3594 168 Q 0.0227 0.3447 0.6327 169 I 0.0664 0.0676 0.8660 170 P 0.0328 0.1737 0.7936 171 G 0.0447 0.2289 0.7264 172 F 0.0874 0.2556 0.6570 173 Q 0.0827 0.1371 0.7802 174 G 0.0551 0.0875 0.8574 175 E 0.1494 0.0913 0.7592 176 Q 0.4083 0.1012 0.4905 177 V 0.5984 0.1485 0.2531 178 E 0.6547 0.1812 0.1641 179 Y 0.6456 0.2074 0.1470 180 F 0.5130 0.2779 0.2090 181 N 0.2612 0.3276 0.4112 182 S 0.0878 0.4933 0.4190 183 K 0.1280 0.4893 0.3827 184 L 0.2730 0.4066 0.3204 185 K 0.3822 0.2511 0.3667 186 Q 0.6161 0.1523 0.2316 187 K 0.6483 0.1461 0.2057 188 F 0.7553 0.0811 0.1636 189 T 0.8150 0.0311 0.1539 190 L 0.7841 0.0176 0.1983 191 T 0.5331 0.0163 0.4506 192 L 0.1731 0.1383 0.6886 193 G 0.1257 0.1026 0.7717 194 E 0.1522 0.2127 0.6351 195 F 0.2225 0.1921 0.5854 196 E 0.3947 0.1794 0.4259 197 I 0.3869 0.2751 0.3380 198 A 0.3233 0.2221 0.4546 199 Q 0.2275 0.1852 0.5874 200 Q 0.1098 0.0736 0.8166 201 P 0.0291 0.3272 0.6437 202 D 0.0381 0.3189 0.6430 203 A 0.0161 0.7508 0.2330 204 K 0.0055 0.9345 0.0601 205 A 0.0053 0.9484 0.0463 206 Y 0.0047 0.9531 0.0422 207 F 0.0046 0.9609 0.0345 208 E 0.0046 0.9617 0.0337 209 Q 0.0046 0.9617 0.0337 210 L 0.0047 0.9605 0.0348 211 I 0.0046 0.9613 0.0341 212 T 0.0047 0.9610 0.0343 213 Q 0.0047 0.9602 0.0351 214 I 0.0047 0.9588 0.0365 215 Q 0.0048 0.9529 0.0423 216 Q 0.0052 0.9472 0.0477 217 L 0.0080 0.9099 0.0820 218 F 0.0144 0.8261 0.1596 219 L 0.0340 0.6219 0.3441 220 K 0.0355 0.4909 0.4736 221 E 0.0682 0.1451 0.7867 222 P 0.0241 0.4408 0.5351 223 V 0.0386 0.5211 0.4402 224 N 0.0239 0.7460 0.2301 225 A 0.0073 0.9238 0.0689 226 E 0.0059 0.9374 0.0567 227 F 0.0049 0.9465 0.0486 228 A 0.0047 0.9597 0.0356 229 N 0.0047 0.9595 0.0358 230 E 0.0047 0.9580 0.0374 231 I 0.0047 0.9567 0.0386 232 I 0.0047 0.9563 0.0390 233 D 0.0048 0.9545 0.0407 234 A 0.0051 0.9328 0.0621 235 F 0.0058 0.8823 0.1119 236 L 0.0167 0.8614 0.1219 237 V 0.0316 0.8251 0.1433 238 S 0.0444 0.7216 0.2339 239 Y 0.0922 0.5551 0.3527 240 F 0.1492 0.1298 0.7211 241 P 0.0870 0.1465 0.7665 242 L 0.0844 0.1046 0.8110 243 H 0.0819 0.0342 0.8838 244 P 0.0590 0.0401 0.9008 245 P 0.0766 0.0667 0.8568 246 V 0.1091 0.0213 0.8696 247 P 0.1041 0.0322 0.8638 248 L 0.0052 0.9252 0.0696 249 A 0.0047 0.9575 0.0378 250 Q 0.0047 0.9605 0.0348 251 L 0.0047 0.9601 0.0353 252 A 0.0047 0.9607 0.0346 253 A 0.0046 0.9605 0.0348 254 K 0.0047 0.9584 0.0369 255 I 0.0047 0.9580 0.0373 256 Y 0.0047 0.9601 0.0352 257 E 0.0047 0.9609 0.0344 258 Y 0.0047 0.9602 0.0352 259 V 0.0047 0.9576 0.0377 260 S 0.0048 0.9557 0.0395 261 Q 0.0050 0.9507 0.0443 262 I 0.0076 0.9301 0.0624 263 V 0.0111 0.8968 0.0921 264 L 0.0271 0.7508 0.2221 265 N 0.0319 0.4692 0.4989 266 E 0.0593 0.4398 0.5008 267 A 0.1381 0.4235 0.4383 268 V 0.1732 0.4002 0.4266 269 N 0.1657 0.3567 0.4776 270 L 0.1194 0.3474 0.5332 271 K 0.0833 0.2959 0.6208 272 D 0.0637 0.3095 0.6268 273 E 0.0106 0.7554 0.2340 274 L 0.0222 0.7671 0.2107 275 I 0.0490 0.8236 0.1274 276 K 0.0739 0.8371 0.0889 277 L 0.1460 0.8039 0.0500 278 I 0.1203 0.8334 0.0463 279 V 0.0855 0.8670 0.0475 280 H 0.0350 0.9109 0.0541 281 T 0.0322 0.9038 0.0641 282 L 0.0178 0.9039 0.0783 283 Y 0.0104 0.9131 0.0764 284 E 0.0115 0.9017 0.0868 285 Q 0.0161 0.8394 0.1445 286 L 0.0481 0.6981 0.2537 287 D 0.0665 0.4706 0.4629 288 R 0.0726 0.3046 0.6227 289 P 0.0809 0.3455 0.5737 290 V 0.0762 0.3929 0.5309 291 G 0.0648 0.2367 0.6985 292 D 0.0626 0.2130 0.7244 293 E 0.0784 0.1820 0.7395 294 N 0.0596 0.0526 0.8878