# This file is the result of combining several RDB files, specifically # T0393.t04.dssp-ebghstl.rdb (weight 1.53986) # T0393.t04.stride-ebghtl.rdb (weight 1.24869) # T0393.t04.str2.rdb (weight 1.54758) # T0393.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 T0393.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0393 # 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 T0393.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 2001 # # ============================================ # Comments from T0393.t04.stride-ebghtl.rdb # ============================================ # TARGET T0393 # 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 T0393.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 2001 # # ============================================ # Comments from T0393.t04.str2.rdb # ============================================ # TARGET T0393 # 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 T0393.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 2001 # # ============================================ # Comments from T0393.t04.alpha.rdb # ============================================ # TARGET T0393 # 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 T0393.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 2001 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0861 0.0352 0.8788 2 K 0.1119 0.0478 0.8403 3 R 0.1116 0.0879 0.8005 4 S 0.1065 0.1027 0.7908 5 I 0.0643 0.3587 0.5770 6 E 0.0502 0.2992 0.6505 7 D 0.0887 0.1595 0.7518 8 T 0.1052 0.0192 0.8756 9 P 0.2323 0.0140 0.7536 10 I 0.8568 0.0075 0.1357 11 V 0.9264 0.0055 0.0681 12 L 0.9276 0.0069 0.0656 13 I 0.8431 0.0485 0.1084 14 G 0.4776 0.0566 0.4658 15 A 0.1422 0.1869 0.6709 16 G 0.0602 0.4472 0.4926 17 N 0.0236 0.7260 0.2504 18 L 0.0124 0.8238 0.1638 19 A 0.0068 0.9043 0.0889 20 T 0.0050 0.9534 0.0416 21 N 0.0047 0.9592 0.0362 22 L 0.0047 0.9587 0.0366 23 A 0.0047 0.9606 0.0347 24 K 0.0046 0.9604 0.0349 25 A 0.0046 0.9599 0.0355 26 L 0.0047 0.9585 0.0368 27 Y 0.0048 0.9499 0.0453 28 R 0.0053 0.9128 0.0819 29 K 0.0390 0.3833 0.5777 30 G 0.0368 0.0216 0.9416 31 F 0.0788 0.0083 0.9130 32 R 0.4540 0.0100 0.5360 33 I 0.8842 0.0050 0.1107 34 V 0.8909 0.0113 0.0978 35 Q 0.9092 0.0058 0.0850 36 V 0.8429 0.0086 0.1485 37 Y 0.6867 0.0230 0.2903 38 S 0.2668 0.0208 0.7124 39 R 0.0798 0.0444 0.8758 40 T 0.0644 0.0222 0.9134 41 E 0.0049 0.9330 0.0621 42 E 0.0047 0.9506 0.0447 43 S 0.0048 0.9525 0.0428 44 A 0.0047 0.9581 0.0372 45 R 0.0047 0.9603 0.0350 46 E 0.0047 0.9590 0.0364 47 L 0.0047 0.9572 0.0381 48 A 0.0050 0.9561 0.0389 49 Q 0.0051 0.9349 0.0599 50 K 0.0075 0.8754 0.1171 51 V 0.0497 0.5294 0.4209 52 E 0.0625 0.0571 0.8804 53 A 0.1613 0.0237 0.8150 54 E 0.4831 0.0355 0.4815 55 Y 0.5854 0.0396 0.3750 56 T 0.4828 0.0318 0.4853 57 T 0.2197 0.0583 0.7220 58 D 0.1483 0.0361 0.8155 59 L 0.0089 0.8580 0.1331 60 A 0.0069 0.8543 0.1388 61 E 0.0082 0.8825 0.1093 62 V 0.0210 0.8020 0.1770 63 N 0.0328 0.5657 0.4015 64 P 0.0093 0.5305 0.4602 65 Y 0.0220 0.2864 0.6916 66 A 0.1587 0.0621 0.7793 67 K 0.1887 0.0462 0.7651 68 L 0.9121 0.0036 0.0843 69 Y 0.9329 0.0033 0.0638 70 I 0.9328 0.0031 0.0641 71 V 0.9139 0.0067 0.0794 72 S 0.7907 0.0107 0.1986 73 L 0.3907 0.0104 0.5989 74 K 0.1198 0.0123 0.8679 75 D 0.0144 0.6184 0.3672 76 S 0.0087 0.8037 0.1876 77 A 0.0081 0.8595 0.1324 78 F 0.0052 0.9431 0.0517 79 A 0.0052 0.9532 0.0416 80 E 0.0055 0.9527 0.0419 81 L 0.0053 0.9518 0.0429 82 L 0.0050 0.9454 0.0496 83 Q 0.0056 0.9091 0.0853 84 G 0.0064 0.8315 0.1620 85 I 0.0135 0.7514 0.2351 86 V 0.0233 0.6425 0.3342 87 E 0.0210 0.5350 0.4440 88 G 0.0263 0.3236 0.6500 89 K 0.1043 0.1417 0.7540 90 R 0.0775 0.0985 0.8240 91 E 0.0326 0.1802 0.7872 92 E 0.0437 0.0892 0.8671 93 A 0.5027 0.0190 0.4783 94 L 0.8985 0.0036 0.0979 95 M 0.9295 0.0037 0.0668 96 V 0.9286 0.0034 0.0680 97 H 0.8918 0.0111 0.0971 98 T 0.7015 0.0240 0.2745 99 A 0.4421 0.0629 0.4950 100 G 0.2887 0.0807 0.6307 101 S 0.1724 0.1070 0.7206 102 I 0.1176 0.1062 0.7762 103 P 0.0900 0.2650 0.6450 104 M 0.0164 0.8004 0.1832 105 N 0.0123 0.8740 0.1137 106 V 0.0159 0.9036 0.0804 107 W 0.0158 0.8797 0.1045 108 E 0.0173 0.8626 0.1202 109 G 0.0147 0.7399 0.2454 110 H 0.0215 0.6445 0.3340 111 V 0.0874 0.2019 0.7106 112 P 0.0219 0.3366 0.6415 113 H 0.0288 0.3069 0.6643 114 Y 0.0635 0.1476 0.7889 115 G 0.1049 0.0462 0.8490 116 V 0.4084 0.0207 0.5709 117 F 0.7244 0.0197 0.2560 118 Y 0.7509 0.0210 0.2281 119 P 0.6627 0.0383 0.2991 120 M 0.5442 0.0733 0.3825 121 Q 0.3962 0.1130 0.4909 122 T 0.3073 0.1343 0.5584 123 F 0.2166 0.1308 0.6526 124 S 0.1303 0.0683 0.8013 125 K 0.0366 0.1593 0.8041 126 Q 0.0421 0.1219 0.8360 127 R 0.0842 0.2398 0.6759 128 E 0.0745 0.5838 0.3417 129 V 0.0762 0.6574 0.2664 130 D 0.1049 0.6066 0.2885 131 F 0.0975 0.5670 0.3355 132 K 0.0645 0.2497 0.6858 133 E 0.0890 0.0896 0.8214 134 I 0.2013 0.0213 0.7773 135 P 0.4725 0.0190 0.5085 136 F 0.8511 0.0175 0.1314 137 F 0.9069 0.0126 0.0806 138 I 0.8931 0.0144 0.0926 139 E 0.7586 0.0226 0.2188 140 A 0.2808 0.0288 0.6904 141 S 0.0788 0.0184 0.9027 142 S 0.0586 0.0187 0.9228 143 T 0.0051 0.9286 0.0663 144 E 0.0049 0.9383 0.0569 145 D 0.0052 0.9403 0.0545 146 A 0.0047 0.9539 0.0414 147 A 0.0048 0.9479 0.0473 148 F 0.0048 0.9401 0.0551 149 L 0.0049 0.9506 0.0445 150 K 0.0047 0.9557 0.0396 151 A 0.0047 0.9571 0.0382 152 I 0.0047 0.9555 0.0398 153 A 0.0048 0.9538 0.0414 154 S 0.0048 0.9446 0.0505 155 T 0.0061 0.9067 0.0872 156 L 0.0112 0.7857 0.2031 157 S 0.0321 0.5972 0.3707 158 N 0.0414 0.4904 0.4683 159 R 0.1518 0.3574 0.4908 160 V 0.5069 0.1642 0.3288 161 Y 0.7011 0.0843 0.2146 162 D 0.6749 0.0514 0.2737 163 A 0.2665 0.0628 0.6707 164 D 0.0870 0.0461 0.8670 165 S 0.0107 0.6701 0.3192 166 E 0.0122 0.7399 0.2479 167 Q 0.0125 0.7570 0.2306 168 R 0.0102 0.8723 0.1175 169 K 0.0090 0.9099 0.0810 170 S 0.0084 0.9408 0.0508 171 L 0.0085 0.9514 0.0400 172 H 0.0070 0.9545 0.0385 173 L 0.0066 0.9526 0.0408 174 A 0.0072 0.9395 0.0533 175 A 0.0082 0.9065 0.0853 176 V 0.0161 0.7877 0.1962 177 F 0.0154 0.7609 0.2237 178 T 0.0077 0.8651 0.1272 179 C 0.0051 0.9283 0.0665 180 N 0.0047 0.9469 0.0484 181 F 0.0047 0.9578 0.0375 182 T 0.0047 0.9606 0.0348 183 N 0.0046 0.9612 0.0342 184 H 0.0046 0.9615 0.0338 185 M 0.0046 0.9614 0.0340 186 Y 0.0046 0.9613 0.0341 187 A 0.0046 0.9617 0.0337 188 L 0.0046 0.9606 0.0348 189 A 0.0047 0.9580 0.0374 190 A 0.0046 0.9605 0.0348 191 E 0.0046 0.9612 0.0342 192 L 0.0046 0.9617 0.0336 193 L 0.0047 0.9602 0.0351 194 K 0.0048 0.9547 0.0406 195 K 0.0060 0.9222 0.0718 196 Y 0.0435 0.3982 0.5582 197 N 0.0457 0.0200 0.9343 198 L 0.0604 0.0122 0.9274 199 P 0.0688 0.0154 0.9158 200 F 0.0052 0.9179 0.0768 201 D 0.0048 0.9505 0.0447 202 V 0.0051 0.9479 0.0470 203 M 0.0049 0.9525 0.0426 204 L 0.0047 0.9593 0.0361 205 P 0.0047 0.9592 0.0361 206 L 0.0047 0.9589 0.0364 207 I 0.0048 0.9543 0.0409 208 D 0.0047 0.9494 0.0459 209 E 0.0049 0.9170 0.0781 210 T 0.0053 0.8884 0.1064 211 A 0.0080 0.8530 0.1389 212 R 0.0090 0.7856 0.2054 213 K 0.0115 0.6873 0.3012 214 V 0.0157 0.7309 0.2534 215 H 0.0214 0.6858 0.2928 216 E 0.0345 0.5693 0.3962 217 L 0.0795 0.3690 0.5515 218 E 0.1005 0.1105 0.7890 219 P 0.0589 0.2659 0.6752 220 K 0.0613 0.3393 0.5994 221 T 0.0987 0.3279 0.5734 222 A 0.0956 0.2462 0.6582 223 Q 0.1267 0.1584 0.7149 224 T 0.1177 0.0867 0.7956 225 G 0.0721 0.0461 0.8818 226 P 0.0709 0.1049 0.8242 227 A 0.1570 0.1325 0.7105 228 I 0.2485 0.0806 0.6709 229 R 0.1786 0.0781 0.7433 230 Y 0.0929 0.0634 0.8437 231 D 0.0468 0.2246 0.7286 232 E 0.0217 0.6171 0.3613 233 N 0.0344 0.6504 0.3152 234 V 0.0542 0.7487 0.1971 235 I 0.0222 0.8690 0.1089 236 G 0.0063 0.9176 0.0761 237 N 0.0059 0.9168 0.0772 238 H 0.0048 0.9386 0.0567 239 L 0.0047 0.9552 0.0400 240 R 0.0047 0.9547 0.0406 241 M 0.0049 0.9471 0.0480 242 L 0.0061 0.9090 0.0849 243 A 0.0082 0.7499 0.2420 244 D 0.0167 0.5589 0.4244 245 D 0.0526 0.4886 0.4588 246 P 0.0068 0.8175 0.1757 247 A 0.0068 0.8364 0.1568 248 M 0.0066 0.8996 0.0938 249 Q 0.0063 0.8872 0.1064 250 R 0.0076 0.8644 0.1280 251 L 0.0069 0.9032 0.0900 252 Y 0.0056 0.9472 0.0472 253 E 0.0052 0.9557 0.0391 254 L 0.0047 0.9580 0.0373 255 L 0.0047 0.9570 0.0383 256 S 0.0047 0.9553 0.0400 257 R 0.0048 0.9540 0.0413 258 S 0.0049 0.9444 0.0507 259 I 0.0053 0.9217 0.0730 260 H 0.0095 0.8332 0.1573 261 E 0.0159 0.6295 0.3546 262 R 0.0373 0.2043 0.7584 263 Q 0.0312 0.0656 0.9032