# This file is the result of combining several RDB files, specifically # T0329.t06.dssp-ebghstl.rdb (weight 1.53986) # T0329.t06.stride-ebghtl.rdb (weight 1.24869) # T0329.t06.str2.rdb (weight 1.54758) # T0329.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 T0329.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0329 # 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 T0329.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 4931 # # ============================================ # Comments from T0329.t06.stride-ebghtl.rdb # ============================================ # TARGET T0329 # 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 T0329.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 4931 # # ============================================ # Comments from T0329.t06.str2.rdb # ============================================ # TARGET T0329 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0329.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 4931 # # ============================================ # Comments from T0329.t06.alpha.rdb # ============================================ # TARGET T0329 # 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 T0329.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 4931 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0766 0.0143 0.9091 2 K 0.1759 0.0147 0.8094 3 Y 0.4435 0.0061 0.5505 4 K 0.6306 0.0318 0.3376 5 A 0.9152 0.0035 0.0812 6 A 0.9306 0.0032 0.0662 7 I 0.9320 0.0032 0.0648 8 F 0.9050 0.0040 0.0910 9 D 0.5279 0.0075 0.4647 10 M 0.1247 0.0555 0.8198 11 D 0.0529 0.0362 0.9109 12 G 0.0875 0.0558 0.8567 13 T 0.3450 0.0509 0.6041 14 I 0.6787 0.0473 0.2740 15 L 0.5727 0.0550 0.3724 16 D 0.2504 0.0539 0.6956 17 T 0.0622 0.1688 0.7691 18 S 0.0422 0.3935 0.5644 19 A 0.0166 0.7507 0.2326 20 D 0.0245 0.7720 0.2034 21 L 0.0067 0.9293 0.0640 22 T 0.0053 0.9487 0.0460 23 S 0.0050 0.9553 0.0397 24 A 0.0047 0.9585 0.0368 25 L 0.0047 0.9596 0.0357 26 N 0.0047 0.9603 0.0351 27 Y 0.0047 0.9598 0.0355 28 A 0.0047 0.9598 0.0355 29 F 0.0047 0.9575 0.0378 30 E 0.0051 0.9499 0.0450 31 Q 0.0075 0.9051 0.0874 32 T 0.0448 0.6074 0.3478 33 G 0.0320 0.1204 0.8476 34 H 0.0524 0.0712 0.8765 35 R 0.0530 0.1132 0.8338 36 H 0.0655 0.1027 0.8318 37 D 0.1831 0.0619 0.7551 38 F 0.1878 0.0227 0.7895 39 T 0.0962 0.0246 0.8792 40 V 0.0071 0.9197 0.0732 41 E 0.0059 0.9385 0.0556 42 D 0.0071 0.9370 0.0559 43 I 0.0126 0.9241 0.0634 44 K 0.0128 0.8884 0.0988 45 N 0.0152 0.8285 0.1563 46 F 0.0264 0.7409 0.2327 47 F 0.0407 0.5989 0.3605 48 G 0.0355 0.3739 0.5906 49 S 0.0392 0.4722 0.4886 50 G 0.0453 0.5283 0.4263 51 V 0.0409 0.7714 0.1877 52 V 0.0302 0.8760 0.0938 53 V 0.0224 0.9213 0.0563 54 A 0.0217 0.9275 0.0508 55 V 0.0177 0.9332 0.0491 56 T 0.0137 0.9390 0.0473 57 R 0.0125 0.9247 0.0628 58 A 0.0142 0.8995 0.0863 59 L 0.0248 0.8343 0.1410 60 A 0.0305 0.7336 0.2359 61 Y 0.0336 0.6432 0.3232 62 E 0.0497 0.5419 0.4084 63 A 0.0716 0.4408 0.4876 64 G 0.0741 0.2618 0.6642 65 S 0.0786 0.1904 0.7310 66 S 0.0400 0.4729 0.4871 67 R 0.0292 0.6401 0.3306 68 E 0.0267 0.8197 0.1536 69 S 0.0378 0.8543 0.1079 70 L 0.0480 0.8739 0.0781 71 V 0.0496 0.8670 0.0833 72 A 0.0453 0.8272 0.1276 73 F 0.0543 0.7085 0.2372 74 G 0.0605 0.4638 0.4756 75 T 0.0686 0.3811 0.5504 76 K 0.0587 0.4144 0.5269 77 D 0.0594 0.4776 0.4630 78 E 0.0660 0.4552 0.4789 79 Q 0.1150 0.3742 0.5108 80 I 0.1111 0.1802 0.7087 81 P 0.0574 0.2276 0.7150 82 E 0.0391 0.1873 0.7736 83 A 0.0600 0.0826 0.8573 84 V 0.1129 0.0221 0.8650 85 T 0.0629 0.0171 0.9200 86 Q 0.0049 0.9414 0.0538 87 T 0.0047 0.9524 0.0429 88 E 0.0047 0.9578 0.0375 89 V 0.0047 0.9606 0.0347 90 N 0.0047 0.9596 0.0357 91 R 0.0047 0.9557 0.0395 92 V 0.0048 0.9540 0.0412 93 L 0.0050 0.9509 0.0441 94 E 0.0058 0.9311 0.0631 95 V 0.0074 0.8805 0.1121 96 F 0.0169 0.7894 0.1938 97 K 0.0227 0.6855 0.2917 98 P 0.0070 0.8441 0.1489 99 Y 0.0116 0.7830 0.2053 100 Y 0.0232 0.7754 0.2014 101 A 0.0203 0.7684 0.2114 102 D 0.0180 0.7159 0.2660 103 H 0.0528 0.6385 0.3088 104 C 0.1212 0.4228 0.4560 105 Q 0.1338 0.3540 0.5122 106 I 0.1394 0.3380 0.5226 107 K 0.1169 0.2474 0.6357 108 T 0.1051 0.1076 0.7873 109 G 0.0839 0.0652 0.8509 110 P 0.0829 0.0818 0.8353 111 F 0.0591 0.0518 0.8891 112 P 0.0153 0.4144 0.5703 113 G 0.0188 0.4572 0.5240 114 I 0.0067 0.9007 0.0926 115 L 0.0058 0.9495 0.0447 116 D 0.0061 0.9525 0.0414 117 L 0.0057 0.9559 0.0385 118 M 0.0047 0.9604 0.0349 119 K 0.0046 0.9598 0.0355 120 N 0.0047 0.9599 0.0355 121 L 0.0047 0.9591 0.0363 122 R 0.0048 0.9507 0.0445 123 Q 0.0054 0.9158 0.0788 124 K 0.0412 0.3003 0.6586 125 G 0.0394 0.0139 0.9467 126 V 0.0947 0.0077 0.8975 127 K 0.6757 0.0055 0.3187 128 L 0.9299 0.0035 0.0666 129 A 0.9324 0.0034 0.0642 130 V 0.9327 0.0032 0.0641 131 V 0.8883 0.0056 0.1062 132 S 0.5186 0.0134 0.4680 133 N 0.0730 0.0397 0.8873 134 K 0.0651 0.0252 0.9097 135 P 0.0466 0.1844 0.7690 136 N 0.0144 0.7202 0.2654 137 E 0.0076 0.9120 0.0804 138 A 0.0054 0.9458 0.0488 139 V 0.0052 0.9565 0.0383 140 Q 0.0059 0.9584 0.0357 141 V 0.0052 0.9575 0.0374 142 L 0.0049 0.9572 0.0379 143 V 0.0048 0.9525 0.0427 144 E 0.0054 0.9306 0.0640 145 E 0.0069 0.8408 0.1522 146 L 0.0214 0.6220 0.3566 147 F 0.0457 0.0863 0.8679 148 P 0.0302 0.1999 0.7699 149 G 0.0285 0.1993 0.7722 150 S 0.1153 0.2448 0.6399 151 F 0.2918 0.1177 0.5905 152 D 0.2656 0.1087 0.6256 153 F 0.6980 0.0645 0.2374 154 A 0.8338 0.0333 0.1330 155 L 0.8434 0.0266 0.1300 156 G 0.6693 0.0272 0.3035 157 E 0.3133 0.0639 0.6228 158 K 0.1413 0.0975 0.7612 159 S 0.0871 0.1360 0.7769 160 G 0.0950 0.1383 0.7668 161 I 0.1471 0.1695 0.6834 162 R 0.1526 0.1588 0.6886 163 R 0.1391 0.0760 0.7849 164 K 0.1001 0.0219 0.8780 165 P 0.0860 0.0238 0.8902 166 A 0.0741 0.0570 0.8689 167 P 0.0111 0.8298 0.1592 168 D 0.0077 0.9144 0.0779 169 M 0.0052 0.9461 0.0486 170 T 0.0047 0.9577 0.0375 171 S 0.0046 0.9609 0.0344 172 E 0.0046 0.9610 0.0343 173 C 0.0047 0.9612 0.0342 174 V 0.0047 0.9598 0.0355 175 K 0.0049 0.9554 0.0397 176 V 0.0067 0.9288 0.0645 177 L 0.0459 0.5255 0.4286 178 G 0.0393 0.0202 0.9405 179 V 0.0647 0.0088 0.9264 180 P 0.0755 0.0114 0.9132 181 R 0.0214 0.6667 0.3119 182 D 0.0258 0.6418 0.3324 183 K 0.2098 0.4605 0.3298 184 C 0.8303 0.0212 0.1486 185 V 0.8820 0.0139 0.1041 186 Y 0.9092 0.0069 0.0840 187 I 0.7947 0.0242 0.1810 188 G 0.3505 0.0220 0.6275 189 D 0.1409 0.0269 0.8322 190 S 0.0677 0.1619 0.7704 191 E 0.0175 0.6979 0.2846 192 I 0.0283 0.7357 0.2360 193 D 0.0350 0.7209 0.2441 194 I 0.0056 0.9463 0.0481 195 Q 0.0048 0.9560 0.0393 196 T 0.0048 0.9578 0.0374 197 A 0.0049 0.9546 0.0405 198 R 0.0051 0.9322 0.0627 199 N 0.0066 0.8008 0.1926 200 S 0.0465 0.3368 0.6167 201 E 0.0502 0.0259 0.9239 202 M 0.1031 0.0089 0.8879 203 D 0.2928 0.0436 0.6635 204 E 0.8957 0.0054 0.0989 205 I 0.9253 0.0037 0.0710 206 A 0.9265 0.0038 0.0697 207 V 0.8791 0.0087 0.1122 208 N 0.5869 0.0126 0.4006 209 W 0.1794 0.0497 0.7709 210 G 0.0783 0.0535 0.8682 211 F 0.0796 0.1045 0.8159 212 R 0.0763 0.1029 0.8207 213 S 0.0777 0.1392 0.7831 214 V 0.0475 0.4623 0.4902 215 P 0.0142 0.8610 0.1247 216 F 0.0117 0.8985 0.0897 217 L 0.0133 0.9087 0.0780 218 Q 0.0113 0.8952 0.0935 219 K 0.0135 0.7956 0.1909 220 H 0.0470 0.3821 0.5709 221 G 0.0631 0.0289 0.9080 222 A 0.1258 0.0181 0.8561 223 T 0.4614 0.0437 0.4949 224 V 0.8322 0.0135 0.1544 225 I 0.8647 0.0179 0.1174 226 V 0.7797 0.0278 0.1925 227 D 0.3436 0.0757 0.5806 228 T 0.1159 0.0875 0.7966 229 A 0.0118 0.7974 0.1907 230 E 0.0054 0.9202 0.0743 231 K 0.0055 0.9232 0.0714 232 L 0.0053 0.9429 0.0518 233 E 0.0048 0.9510 0.0442 234 E 0.0049 0.9439 0.0512 235 A 0.0059 0.9270 0.0671 236 I 0.0115 0.8619 0.1267 237 L 0.0163 0.5456 0.4382 238 G 0.0215 0.1921 0.7864 239 E 0.0454 0.1335 0.8212