# This file is the result of combining several RDB files, specifically # T0279.t04.dssp-ebghstl.rdb (weight 1.53986) # T0279.t04.stride-ebghtl.rdb (weight 1.24869) # T0279.t04.str2.rdb (weight 1.54758) # T0279.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 T0279.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0279 # 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 T0279.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 208 # # ============================================ # Comments from T0279.t04.stride-ebghtl.rdb # ============================================ # TARGET T0279 # 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 T0279.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 208 # # ============================================ # Comments from T0279.t04.str2.rdb # ============================================ # TARGET T0279 # 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 T0279.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 208 # # ============================================ # Comments from T0279.t04.alpha.rdb # ============================================ # TARGET T0279 # 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 T0279.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 208 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0605 0.0870 0.8524 2 R 0.0697 0.1666 0.7637 3 R 0.0846 0.2010 0.7144 4 L 0.0838 0.1844 0.7318 5 E 0.0560 0.3305 0.6135 6 E 0.0474 0.3658 0.5868 7 D 0.0888 0.2131 0.6981 8 A 0.1593 0.0598 0.7809 9 V 0.4959 0.0150 0.4891 10 R 0.8939 0.0065 0.0996 11 V 0.9208 0.0048 0.0744 12 A 0.9141 0.0053 0.0807 13 Y 0.7999 0.0115 0.1886 14 A 0.3472 0.0218 0.6310 15 G 0.0940 0.0568 0.8492 16 L 0.0493 0.2406 0.7101 17 R 0.0562 0.3267 0.6171 18 R 0.0316 0.4468 0.5216 19 K 0.0144 0.7226 0.2630 20 E 0.0059 0.9048 0.0893 21 A 0.0048 0.9482 0.0470 22 F 0.0047 0.9580 0.0373 23 K 0.0046 0.9614 0.0339 24 A 0.0046 0.9611 0.0342 25 L 0.0046 0.9614 0.0340 26 A 0.0047 0.9611 0.0342 27 E 0.0048 0.9536 0.0416 28 K 0.0056 0.9228 0.0716 29 L 0.0407 0.4186 0.5407 30 G 0.0375 0.0180 0.9446 31 F 0.0657 0.0091 0.9252 32 T 0.2257 0.0117 0.7626 33 P 0.6291 0.0167 0.3541 34 L 0.7758 0.0226 0.2016 35 L 0.8471 0.0134 0.1395 36 F 0.7287 0.0130 0.2582 37 P 0.6353 0.0174 0.3474 38 V 0.6015 0.0562 0.3424 39 Q 0.7042 0.0408 0.2550 40 A 0.7685 0.0331 0.1984 41 T 0.7829 0.0262 0.1908 42 E 0.7166 0.0172 0.2661 43 K 0.6285 0.0210 0.3505 44 V 0.2235 0.0127 0.7637 45 P 0.1053 0.0153 0.8793 46 V 0.0584 0.0564 0.8852 47 P 0.0143 0.7485 0.2372 48 E 0.0100 0.8590 0.1310 49 Y 0.0099 0.8751 0.1149 50 R 0.0056 0.9380 0.0563 51 D 0.0048 0.9519 0.0432 52 Q 0.0048 0.9515 0.0437 53 V 0.0049 0.9468 0.0483 54 R 0.0051 0.9355 0.0594 55 A 0.0057 0.8872 0.1071 56 L 0.0090 0.8153 0.1756 57 A 0.0392 0.5566 0.4042 58 Q 0.0247 0.3148 0.6605 59 G 0.0410 0.0689 0.8901 60 V 0.1213 0.0137 0.8650 61 D 0.2256 0.0399 0.7345 62 L 0.8966 0.0050 0.0984 63 F 0.9308 0.0039 0.0653 64 L 0.9327 0.0035 0.0638 65 A 0.8939 0.0058 0.1003 66 T 0.4506 0.0244 0.5251 67 T 0.0797 0.0560 0.8643 68 G 0.0071 0.7705 0.2224 69 V 0.0055 0.9280 0.0665 70 G 0.0050 0.9488 0.0461 71 V 0.0049 0.9585 0.0366 72 R 0.0049 0.9593 0.0358 73 D 0.0049 0.9580 0.0371 74 L 0.0047 0.9563 0.0390 75 L 0.0047 0.9581 0.0372 76 E 0.0048 0.9540 0.0412 77 A 0.0051 0.9508 0.0441 78 G 0.0052 0.9448 0.0500 79 K 0.0055 0.9216 0.0730 80 A 0.0062 0.8768 0.1170 81 L 0.0446 0.4729 0.4825 82 G 0.0426 0.0400 0.9174 83 L 0.0665 0.0276 0.9059 84 D 0.1099 0.0381 0.8520 85 L 0.0581 0.2807 0.6612 86 E 0.0328 0.3763 0.5909 87 G 0.0216 0.5299 0.4485 88 P 0.0190 0.6393 0.3417 89 L 0.0273 0.6396 0.3331 90 A 0.0234 0.5067 0.4699 91 K 0.0371 0.2868 0.6761 92 A 0.1394 0.0966 0.7640 93 F 0.3181 0.0751 0.6067 94 R 0.7674 0.0556 0.1771 95 L 0.8367 0.0693 0.0940 96 A 0.8172 0.0656 0.1172 97 R 0.5928 0.0889 0.3183 98 G 0.1297 0.0800 0.7903 99 A 0.0092 0.8900 0.1008 100 K 0.0063 0.9391 0.0546 101 A 0.0053 0.9510 0.0437 102 A 0.0047 0.9608 0.0345 103 R 0.0046 0.9614 0.0340 104 A 0.0046 0.9617 0.0337 105 L 0.0047 0.9607 0.0346 106 K 0.0048 0.9547 0.0405 107 E 0.0058 0.9315 0.0627 108 A 0.0408 0.5113 0.4479 109 G 0.0367 0.0221 0.9412 110 L 0.0566 0.0086 0.9348 111 P 0.0799 0.0103 0.9099 112 P 0.1512 0.2499 0.5989 113 H 0.2365 0.2861 0.4774 114 A 0.3706 0.2097 0.4197 115 V 0.2560 0.0511 0.6929 116 G 0.0962 0.0519 0.8518 117 D 0.0619 0.0796 0.8585 118 G 0.0642 0.1069 0.8289 119 T 0.0944 0.1569 0.7487 120 S 0.0235 0.7817 0.1948 121 K 0.0096 0.8805 0.1099 122 S 0.0084 0.8917 0.0999 123 L 0.0095 0.8823 0.1082 124 L 0.0108 0.8725 0.1167 125 P 0.0099 0.8221 0.1680 126 L 0.0175 0.6926 0.2899 127 L 0.0848 0.1399 0.7754 128 P 0.0559 0.1152 0.8289 129 Q 0.0360 0.1621 0.8019 130 G 0.0356 0.1325 0.8320 131 R 0.0625 0.0576 0.8800 132 G 0.1800 0.0202 0.7998 133 V 0.6145 0.0095 0.3760 134 A 0.8886 0.0045 0.1069 135 A 0.9188 0.0040 0.0772 136 L 0.9084 0.0053 0.0863 137 Q 0.8132 0.0117 0.1751 138 L 0.4685 0.0376 0.4939 139 Y 0.1731 0.0516 0.7752 140 G 0.0580 0.0634 0.8785 141 K 0.0799 0.0489 0.8711 142 P 0.0887 0.1015 0.8097 143 L 0.0322 0.5496 0.4182 144 P 0.0061 0.8712 0.1227 145 L 0.0057 0.9265 0.0678 146 L 0.0049 0.9392 0.0558 147 E 0.0048 0.9538 0.0415 148 N 0.0048 0.9536 0.0416 149 A 0.0047 0.9581 0.0372 150 L 0.0047 0.9576 0.0377 151 A 0.0049 0.9376 0.0575 152 E 0.0057 0.8738 0.1205 153 R 0.0418 0.3433 0.6148 154 G 0.0378 0.0177 0.9445 155 Y 0.1096 0.0077 0.8828 156 R 0.7342 0.0064 0.2593 157 V 0.8442 0.0042 0.1516 158 L 0.8228 0.0127 0.1645 159 P 0.8236 0.0052 0.1712 160 L 0.6881 0.0076 0.3043 161 M 0.6868 0.0070 0.3062 162 P 0.5750 0.0180 0.4071 163 Y 0.6000 0.0409 0.3591 164 R 0.6704 0.0350 0.2947 165 H 0.6765 0.0230 0.3005 166 L 0.4489 0.0139 0.5371 167 P 0.2350 0.0137 0.7513 168 D 0.0616 0.0134 0.9250 169 P 0.0296 0.3737 0.5967 170 E 0.0267 0.5143 0.4589 171 G 0.0301 0.5872 0.3827 172 I 0.0145 0.8712 0.1143 173 L 0.0082 0.9354 0.0564 174 R 0.0081 0.9404 0.0516 175 L 0.0053 0.9518 0.0430 176 E 0.0047 0.9589 0.0364 177 E 0.0047 0.9598 0.0355 178 A 0.0050 0.9568 0.0382 179 L 0.0057 0.9419 0.0523 180 L 0.0079 0.8454 0.1467 181 R 0.0395 0.3949 0.5656 182 G 0.0311 0.0590 0.9099 183 E 0.0590 0.0380 0.9030 184 V 0.1894 0.0089 0.8017 185 D 0.3723 0.0325 0.5952 186 A 0.9204 0.0038 0.0758 187 L 0.9322 0.0032 0.0645 188 A 0.9326 0.0032 0.0642 189 F 0.8929 0.0054 0.1016 190 V 0.4461 0.0171 0.5368 191 A 0.0799 0.0214 0.8987 192 A 0.0056 0.8775 0.1169 193 I 0.0049 0.9502 0.0449 194 Q 0.0048 0.9571 0.0381 195 V 0.0047 0.9581 0.0372 196 E 0.0047 0.9601 0.0352 197 F 0.0048 0.9560 0.0393 198 L 0.0048 0.9515 0.0437 199 F 0.0051 0.9403 0.0546 200 E 0.0076 0.8909 0.1015 201 G 0.0101 0.7420 0.2479 202 A 0.0452 0.3962 0.5586 203 K 0.0387 0.1935 0.7678 204 D 0.0733 0.0503 0.8765 205 P 0.0118 0.4944 0.4938 206 K 0.0080 0.7147 0.2773 207 A 0.0102 0.8158 0.1740 208 L 0.0077 0.8594 0.1330 209 R 0.0054 0.9179 0.0767 210 E 0.0052 0.9246 0.0702 211 A 0.0055 0.9186 0.0759 212 L 0.0085 0.8657 0.1258 213 N 0.0113 0.7378 0.2509 214 T 0.0278 0.3340 0.6382 215 R 0.0630 0.0419 0.8951 216 V 0.2172 0.0068 0.7760 217 K 0.6698 0.0087 0.3214 218 A 0.9244 0.0034 0.0721 219 L 0.9286 0.0036 0.0679 220 A 0.9126 0.0042 0.0832 221 V 0.6534 0.0239 0.3226 222 G 0.1308 0.0637 0.8055 223 R 0.0377 0.5436 0.4187 224 V 0.0328 0.7076 0.2595 225 T 0.0238 0.8250 0.1512 226 A 0.0047 0.9585 0.0368 227 D 0.0046 0.9607 0.0346 228 A 0.0046 0.9617 0.0337 229 L 0.0047 0.9609 0.0344 230 R 0.0048 0.9529 0.0423 231 E 0.0056 0.9241 0.0703 232 W 0.0401 0.3923 0.5676 233 G 0.0345 0.0202 0.9454 234 V 0.0682 0.0092 0.9226 235 K 0.1609 0.0145 0.8246 236 P 0.4073 0.0357 0.5570 237 F 0.6316 0.0544 0.3140 238 Y 0.7748 0.0321 0.1931 239 V 0.6187 0.0446 0.3368 240 D 0.2868 0.0635 0.6498 241 E 0.1191 0.1362 0.7447 242 T 0.0860 0.1519 0.7621 243 E 0.0671 0.2162 0.7167 244 R 0.0668 0.2229 0.7102 245 L 0.0056 0.9124 0.0820 246 G 0.0048 0.9527 0.0425 247 S 0.0047 0.9558 0.0395 248 L 0.0047 0.9592 0.0361 249 L 0.0047 0.9601 0.0352 250 Q 0.0047 0.9604 0.0350 251 G 0.0047 0.9594 0.0359 252 F 0.0047 0.9572 0.0381 253 K 0.0047 0.9586 0.0367 254 R 0.0048 0.9572 0.0380 255 A 0.0053 0.9440 0.0506 256 L 0.0064 0.9184 0.0752 257 Q 0.0085 0.8567 0.1348 258 K 0.0170 0.6964 0.2867 259 E 0.0232 0.4628 0.5140 260 V 0.0330 0.1674 0.7996 261 A 0.0340 0.0490 0.9170