# This file is the result of combining several RDB files, specifically # T0336.t06.dssp-ebghstl.rdb (weight 1.53986) # T0336.t06.stride-ebghtl.rdb (weight 1.24869) # T0336.t06.str2.rdb (weight 1.54758) # T0336.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 T0336.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0336 # 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 T0336.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 35.1964 # # ============================================ # Comments from T0336.t06.stride-ebghtl.rdb # ============================================ # TARGET T0336 # 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 T0336.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 35.1964 # # ============================================ # Comments from T0336.t06.str2.rdb # ============================================ # TARGET T0336 # 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 T0336.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 35.1964 # # ============================================ # Comments from T0336.t06.alpha.rdb # ============================================ # TARGET T0336 # 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 T0336.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 35.1964 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0649 0.0235 0.9115 2 S 0.0956 0.0330 0.8714 3 M 0.1035 0.3197 0.5768 4 E 0.1084 0.3481 0.5435 5 E 0.0459 0.7663 0.1878 6 E 0.0661 0.7283 0.2055 7 E 0.0586 0.7797 0.1617 8 F 0.0452 0.7919 0.1629 9 D 0.0516 0.7057 0.2427 10 I 0.0080 0.9140 0.0779 11 R 0.0069 0.9276 0.0655 12 E 0.0065 0.9371 0.0564 13 A 0.0071 0.9332 0.0596 14 L 0.0119 0.8930 0.0951 15 A 0.0128 0.7489 0.2383 16 N 0.0433 0.4247 0.5320 17 G 0.0307 0.1698 0.7995 18 E 0.0376 0.3249 0.6376 19 H 0.0669 0.4350 0.4981 20 L 0.0292 0.7477 0.2231 21 E 0.0239 0.8028 0.1734 22 K 0.0364 0.8274 0.1362 23 I 0.0475 0.8289 0.1236 24 L 0.0565 0.8163 0.1272 25 I 0.0533 0.7980 0.1487 26 M 0.0315 0.7837 0.1848 27 A 0.0350 0.7157 0.2493 28 K 0.0249 0.7091 0.2660 29 Y 0.0376 0.6029 0.3595 30 D 0.0420 0.6610 0.2970 31 E 0.0064 0.9087 0.0849 32 S 0.0058 0.9185 0.0757 33 V 0.0060 0.9143 0.0797 34 L 0.0048 0.9442 0.0510 35 K 0.0047 0.9489 0.0463 36 K 0.0048 0.9440 0.0512 37 L 0.0049 0.9340 0.0610 38 I 0.0051 0.9255 0.0694 39 E 0.0071 0.8792 0.1137 40 L 0.0103 0.7181 0.2716 41 L 0.0623 0.3023 0.6353 42 D 0.0424 0.1168 0.8408 43 D 0.0224 0.2560 0.7216 44 D 0.0423 0.2151 0.7425 45 L 0.0608 0.3728 0.5664 46 W 0.0778 0.4930 0.4292 47 T 0.0599 0.6600 0.2800 48 V 0.0062 0.9413 0.0525 49 V 0.0051 0.9539 0.0410 50 K 0.0047 0.9588 0.0365 51 N 0.0047 0.9571 0.0382 52 A 0.0047 0.9589 0.0364 53 I 0.0047 0.9608 0.0346 54 S 0.0046 0.9609 0.0344 55 I 0.0046 0.9611 0.0343 56 I 0.0047 0.9607 0.0347 57 M 0.0046 0.9606 0.0347 58 V 0.0047 0.9582 0.0371 59 I 0.0048 0.9505 0.0447 60 A 0.0052 0.9326 0.0623 61 K 0.0062 0.8791 0.1147 62 T 0.0134 0.7719 0.2147 63 R 0.0314 0.6761 0.2925 64 E 0.0147 0.6526 0.3328 65 D 0.0174 0.6519 0.3308 66 L 0.0364 0.6543 0.3093 67 Y 0.0763 0.6104 0.3133 68 E 0.0530 0.6820 0.2649 69 P 0.0460 0.7342 0.2198 70 M 0.0462 0.7739 0.1798 71 L 0.0409 0.7983 0.1608 72 K 0.0186 0.8555 0.1260 73 K 0.0157 0.8577 0.1266 74 L 0.0189 0.8556 0.1255 75 F 0.0195 0.8839 0.0966 76 S 0.0168 0.9073 0.0759 77 L 0.0200 0.9074 0.0725 78 L 0.0351 0.8580 0.1069 79 K 0.0328 0.8120 0.1553 80 K 0.0296 0.6761 0.2943 81 S 0.0624 0.3365 0.6011 82 E 0.0291 0.2665 0.7044 83 A 0.0307 0.2324 0.7369 84 I 0.0742 0.1054 0.8204 85 P 0.0234 0.5940 0.3825 86 L 0.0344 0.7390 0.2266 87 T 0.0232 0.8560 0.1209 88 Q 0.0109 0.9284 0.0606 89 E 0.0115 0.9310 0.0574 90 I 0.0101 0.9373 0.0526 91 A 0.0125 0.9309 0.0566 92 K 0.0104 0.9131 0.0764 93 A 0.0125 0.8782 0.1093 94 F 0.0133 0.8670 0.1197 95 G 0.0188 0.7672 0.2140 96 Q 0.0161 0.8046 0.1793 97 M 0.0235 0.8141 0.1624 98 A 0.0288 0.7152 0.2560 99 K 0.0210 0.5367 0.4423 100 E 0.0287 0.4501 0.5212 101 K 0.0773 0.1896 0.7331 102 P 0.0206 0.6571 0.3223 103 E 0.0194 0.7570 0.2236 104 L 0.0188 0.8347 0.1466 105 V 0.0276 0.8570 0.1155 106 K 0.0194 0.8366 0.1440 107 S 0.0232 0.8209 0.1559 108 M 0.0312 0.8412 0.1276 109 I 0.0334 0.8543 0.1123 110 P 0.0340 0.8750 0.0911 111 V 0.0379 0.8842 0.0779 112 L 0.0349 0.8875 0.0776 113 F 0.0351 0.8700 0.0949 114 A 0.0339 0.7925 0.1736 115 N 0.0447 0.6248 0.3305 116 Y 0.1234 0.1407 0.7359 117 R 0.1106 0.0646 0.8249 118 I 0.0796 0.1499 0.7706 119 G 0.0783 0.0858 0.8360 120 D 0.0922 0.0393 0.8685 121 E 0.0453 0.2149 0.7397 122 K 0.0901 0.1852 0.7247 123 T 0.1960 0.2038 0.6002 124 K 0.4844 0.1756 0.3400 125 I 0.6252 0.1384 0.2364 126 N 0.4616 0.2241 0.3142 127 V 0.2143 0.5951 0.1906 128 S 0.1433 0.6791 0.1776 129 Y 0.1307 0.7493 0.1200 130 A 0.1003 0.7911 0.1086 131 L 0.0439 0.8660 0.0901 132 E 0.0174 0.9162 0.0665 133 E 0.0125 0.9250 0.0625 134 I 0.0117 0.9072 0.0810 135 A 0.0155 0.8577 0.1269 136 K 0.0165 0.6998 0.2836 137 A 0.0386 0.4486 0.5128 138 N 0.0781 0.1592 0.7628 139 P 0.0088 0.7044 0.2868 140 M 0.0103 0.7742 0.2155 141 L 0.0123 0.8142 0.1735 142 M 0.0074 0.8883 0.1043 143 A 0.0050 0.9375 0.0575 144 S 0.0048 0.9428 0.0524 145 I 0.0048 0.9462 0.0489 146 V 0.0047 0.9554 0.0399 147 R 0.0047 0.9571 0.0382 148 D 0.0047 0.9552 0.0401 149 F 0.0047 0.9539 0.0415 150 M 0.0047 0.9517 0.0436 151 S 0.0049 0.9322 0.0629 152 M 0.0052 0.8880 0.1068 153 L 0.0093 0.7652 0.2255 154 S 0.0179 0.4548 0.5273 155 S 0.0352 0.2656 0.6992 156 K 0.0349 0.1665 0.7986 157 N 0.0609 0.1169 0.8222 158 R 0.0427 0.3141 0.6431 159 E 0.0458 0.4977 0.4565 160 D 0.0488 0.5400 0.4112 161 K 0.0851 0.5513 0.3636 162 L 0.1774 0.6116 0.2110 163 T 0.1887 0.6012 0.2101 164 A 0.1110 0.7542 0.1347 165 L 0.0771 0.8141 0.1088 166 N 0.0481 0.8627 0.0892 167 F 0.0143 0.9304 0.0553 168 I 0.0076 0.9445 0.0480 169 E 0.0066 0.9435 0.0499 170 A 0.0065 0.9190 0.0745 171 M 0.0109 0.8098 0.1793 172 G 0.0162 0.6161 0.3677 173 E 0.0206 0.5797 0.3997 174 N 0.0323 0.4258 0.5419 175 S 0.0375 0.3989 0.5636 176 F 0.0478 0.3269 0.6252 177 K 0.0720 0.3502 0.5778 178 Y 0.1121 0.3683 0.5196 179 V 0.1098 0.3536 0.5366 180 N 0.0624 0.3371 0.6005 181 P 0.0157 0.5891 0.3952 182 F 0.0168 0.5859 0.3974 183 L 0.0113 0.7709 0.2178 184 P 0.0049 0.9278 0.0673 185 R 0.0051 0.9411 0.0538 186 I 0.0051 0.9455 0.0494 187 I 0.0050 0.9487 0.0463 188 N 0.0055 0.9322 0.0623 189 L 0.0066 0.8977 0.0957 190 L 0.0106 0.8412 0.1482 191 H 0.0193 0.6914 0.2893 192 D 0.0358 0.4920 0.4722 193 G 0.0347 0.3663 0.5989 194 D 0.0469 0.2706 0.6826 195 E 0.1246 0.3073 0.5681 196 I 0.3222 0.3308 0.3470 197 V 0.4076 0.2721 0.3203 198 R 0.3780 0.1895 0.4325 199 A 0.2078 0.3483 0.4439 200 S 0.1075 0.2934 0.5992 201 A 0.0493 0.5727 0.3781 202 V 0.0600 0.6275 0.3126 203 E 0.0748 0.6445 0.2807 204 A 0.0574 0.6635 0.2791 205 L 0.0885 0.5187 0.3927 206 V 0.2010 0.4213 0.3778 207 H 0.2275 0.4161 0.3564 208 L 0.2450 0.3798 0.3752 209 A 0.1745 0.2124 0.6131 210 T 0.1749 0.2339 0.5912 211 L 0.0071 0.8994 0.0934 212 N 0.0057 0.9329 0.0614 213 D 0.0048 0.9481 0.0471 214 K 0.0048 0.9499 0.0453 215 L 0.0048 0.9527 0.0425 216 R 0.0047 0.9566 0.0387 217 K 0.0047 0.9572 0.0381 218 V 0.0047 0.9543 0.0410 219 V 0.0051 0.9489 0.0460 220 I 0.0057 0.9304 0.0639 221 K 0.0070 0.8796 0.1134 222 R 0.0110 0.8123 0.1768 223 L 0.0117 0.8176 0.1706 224 E 0.0081 0.8340 0.1579 225 E 0.0111 0.8194 0.1695 226 L 0.0144 0.8099 0.1757 227 N 0.0160 0.7348 0.2493 228 D 0.0237 0.6264 0.3499 229 T 0.0249 0.6615 0.3136 230 S 0.0120 0.8510 0.1370 231 S 0.0058 0.9334 0.0608 232 L 0.0055 0.9472 0.0473 233 V 0.0054 0.9453 0.0493 234 N 0.0055 0.9417 0.0528 235 K 0.0064 0.9210 0.0726 236 T 0.0078 0.9029 0.0893 237 V 0.0126 0.9003 0.0871 238 K 0.0087 0.9294 0.0620 239 E 0.0080 0.9363 0.0557 240 G 0.0072 0.9293 0.0635 241 I 0.0085 0.9254 0.0660 242 S 0.0102 0.8982 0.0916 243 R 0.0125 0.8819 0.1056 244 L 0.0281 0.8457 0.1262 245 L 0.0455 0.7593 0.1953 246 L 0.0903 0.6303 0.2794 247 L 0.1233 0.3705 0.5062 248 E 0.0800 0.3141 0.6059 249 G 0.0592 0.2267 0.7141 250 H 0.0709 0.1309 0.7982 251 S 0.0733 0.0740 0.8527 252 S 0.0517 0.0477 0.9006 253 S 0.0425 0.0362 0.9213