# This file is the result of combining several RDB files, specifically # T0289.t04.dssp-ebghstl.rdb (weight 1.53986) # T0289.t04.stride-ebghtl.rdb (weight 1.24869) # T0289.t04.str2.rdb (weight 1.54758) # T0289.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 T0289.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 959 # # ============================================ # Comments from T0289.t04.stride-ebghtl.rdb # ============================================ # TARGET T0289 # 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 T0289.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 959 # # ============================================ # Comments from T0289.t04.str2.rdb # ============================================ # TARGET T0289 # 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 T0289.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 959 # # ============================================ # Comments from T0289.t04.alpha.rdb # ============================================ # TARGET T0289 # 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 T0289.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 959 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 S 0.1480 0.0285 0.8235 2 T 0.4421 0.0177 0.5402 3 S 0.7024 0.0150 0.2826 4 C 0.7427 0.0192 0.2381 5 V 0.6093 0.0285 0.3622 6 A 0.2925 0.0550 0.6525 7 E 0.1048 0.0568 0.8384 8 E 0.0841 0.0443 0.8716 9 P 0.1056 0.0615 0.8329 10 I 0.1739 0.0176 0.8085 11 K 0.2893 0.0105 0.7002 12 K 0.7974 0.0054 0.1972 13 I 0.9278 0.0033 0.0689 14 A 0.9329 0.0032 0.0638 15 I 0.9290 0.0033 0.0677 16 F 0.8858 0.0055 0.1088 17 G 0.6248 0.0194 0.3558 18 G 0.3078 0.0311 0.6612 19 T 0.3011 0.0503 0.6486 20 H 0.1862 0.0611 0.7528 21 G 0.0506 0.2157 0.7337 22 N 0.0467 0.2251 0.7283 23 E 0.0673 0.4645 0.4682 24 L 0.0559 0.6754 0.2687 25 T 0.0278 0.7717 0.2005 26 G 0.0061 0.9413 0.0527 27 V 0.0047 0.9594 0.0359 28 F 0.0046 0.9613 0.0341 29 L 0.0046 0.9614 0.0340 30 V 0.0046 0.9613 0.0341 31 T 0.0046 0.9614 0.0339 32 H 0.0046 0.9607 0.0347 33 W 0.0047 0.9586 0.0368 34 L 0.0048 0.9512 0.0440 35 K 0.0055 0.8841 0.1104 36 N 0.0246 0.6143 0.3611 37 G 0.0224 0.3193 0.6583 38 A 0.0295 0.2945 0.6760 39 E 0.0400 0.5218 0.4382 40 V 0.0879 0.5655 0.3466 41 H 0.0925 0.6142 0.2933 42 R 0.1144 0.4999 0.3856 43 A 0.0413 0.2842 0.6745 44 G 0.0473 0.0626 0.8900 45 L 0.2722 0.0093 0.7184 46 E 0.7934 0.0066 0.2001 47 V 0.8782 0.0044 0.1174 48 K 0.8428 0.0060 0.1512 49 P 0.7936 0.0080 0.1984 50 F 0.6550 0.0318 0.3133 51 I 0.5814 0.0225 0.3960 52 T 0.3078 0.0377 0.6544 53 N 0.1921 0.0341 0.7738 54 P 0.0570 0.4824 0.4606 55 R 0.0360 0.6212 0.3428 56 A 0.0660 0.7678 0.1662 57 V 0.1282 0.7405 0.1312 58 E 0.1286 0.7056 0.1658 59 K 0.1289 0.5800 0.2911 60 C 0.1814 0.3394 0.4792 61 T 0.2072 0.1914 0.6014 62 R 0.2403 0.1564 0.6033 63 Y 0.2591 0.1260 0.6149 64 I 0.1596 0.1116 0.7288 65 D 0.1389 0.0619 0.7992 66 C 0.2118 0.0750 0.7132 67 D 0.3358 0.0722 0.5920 68 L 0.1353 0.3449 0.5197 69 N 0.1363 0.3659 0.4978 70 R 0.1665 0.3859 0.4476 71 V 0.1889 0.1910 0.6201 72 F 0.1811 0.0869 0.7320 73 D 0.1360 0.0843 0.7797 74 L 0.0400 0.5739 0.3861 75 E 0.0218 0.6546 0.3236 76 N 0.0423 0.6286 0.3291 77 L 0.0515 0.5105 0.4380 78 S 0.0571 0.4127 0.5301 79 K 0.0858 0.3586 0.5555 80 E 0.0974 0.2569 0.6457 81 M 0.1009 0.2299 0.6693 82 S 0.0844 0.1545 0.7611 83 E 0.0451 0.2123 0.7426 84 D 0.0660 0.1395 0.7945 85 L 0.0702 0.1925 0.7374 86 P 0.0497 0.3143 0.6360 87 Y 0.0437 0.4186 0.5377 88 E 0.0258 0.5939 0.3803 89 V 0.0216 0.7660 0.2123 90 R 0.0467 0.7753 0.1780 91 R 0.0145 0.9206 0.0649 92 A 0.0067 0.9536 0.0397 93 Q 0.0052 0.9561 0.0387 94 E 0.0050 0.9566 0.0384 95 I 0.0049 0.9519 0.0431 96 N 0.0056 0.9436 0.0508 97 H 0.0067 0.8834 0.1099 98 L 0.0134 0.8009 0.1857 99 F 0.0554 0.4744 0.4702 100 G 0.0446 0.1017 0.8537 101 P 0.0348 0.2454 0.7198 102 K 0.0352 0.2902 0.6746 103 N 0.0500 0.2633 0.6868 104 S 0.0562 0.2039 0.7400 105 D 0.0527 0.1933 0.7540 106 D 0.0847 0.1305 0.7848 107 A 0.2127 0.0448 0.7425 108 Y 0.5009 0.0093 0.4899 109 D 0.7038 0.0101 0.2862 110 V 0.9252 0.0034 0.0714 111 V 0.9324 0.0032 0.0644 112 F 0.9261 0.0040 0.0698 113 D 0.8853 0.0037 0.1111 114 L 0.5335 0.0355 0.4310 115 H 0.2491 0.0602 0.6907 116 N 0.1417 0.1023 0.7560 117 T 0.1061 0.1331 0.7609 118 T 0.1043 0.1781 0.7176 119 S 0.0634 0.2904 0.6461 120 N 0.0904 0.2773 0.6323 121 M 0.1436 0.1942 0.6622 122 G 0.1742 0.0856 0.7402 123 C 0.2969 0.0592 0.6438 124 T 0.5004 0.0790 0.4206 125 L 0.6452 0.0839 0.2710 126 I 0.6658 0.0831 0.2512 127 L 0.5827 0.1004 0.3169 128 E 0.4049 0.0969 0.4982 129 D 0.1636 0.1210 0.7154 130 S 0.0771 0.1709 0.7520 131 R 0.0582 0.1562 0.7856 132 N 0.0660 0.1572 0.7769 133 D 0.0136 0.6607 0.3257 134 F 0.0129 0.7496 0.2375 135 L 0.0085 0.8711 0.1204 136 I 0.0060 0.9187 0.0753 137 Q 0.0060 0.9246 0.0694 138 M 0.0052 0.9307 0.0641 139 F 0.0053 0.9263 0.0684 140 H 0.0048 0.9403 0.0549 141 Y 0.0050 0.9360 0.0590 142 I 0.0074 0.9256 0.0670 143 K 0.0070 0.9243 0.0687 144 T 0.0103 0.8863 0.1034 145 C 0.0179 0.7791 0.2030 146 M 0.0493 0.5106 0.4402 147 A 0.0476 0.1926 0.7598 148 P 0.0481 0.0893 0.8627 149 L 0.0934 0.0374 0.8692 150 P 0.1400 0.0698 0.7902 151 C 0.3130 0.1007 0.5862 152 S 0.4482 0.0981 0.4537 153 V 0.5034 0.1236 0.3729 154 Y 0.4822 0.1203 0.3975 155 L 0.3654 0.1388 0.4958 156 I 0.2360 0.1556 0.6084 157 E 0.1522 0.1085 0.7392 158 H 0.1027 0.0671 0.8302 159 P 0.0367 0.2133 0.7500 160 S 0.0619 0.2160 0.7221 161 L 0.1069 0.3498 0.5433 162 K 0.0866 0.4487 0.4647 163 Y 0.0925 0.5586 0.3489 164 A 0.0835 0.6830 0.2336 165 T 0.1015 0.6880 0.2105 166 T 0.0974 0.7009 0.2017 167 R 0.0771 0.6891 0.2338 168 S 0.0812 0.5691 0.3497 169 I 0.0895 0.3317 0.5788 170 A 0.1228 0.1183 0.7589 171 K 0.1762 0.0589 0.7650 172 Y 0.2345 0.0183 0.7472 173 P 0.5336 0.0255 0.4409 174 V 0.8365 0.0209 0.1426 175 G 0.9008 0.0124 0.0868 176 I 0.9055 0.0106 0.0839 177 E 0.8626 0.0097 0.1277 178 V 0.5102 0.0258 0.4641 179 G 0.2105 0.0177 0.7719 180 P 0.1192 0.0503 0.8305 181 Q 0.0960 0.0396 0.8644 182 P 0.0607 0.0973 0.8420 183 H 0.0615 0.1108 0.8277 184 G 0.0587 0.1047 0.8366 185 V 0.1224 0.1227 0.7549 186 L 0.1197 0.0526 0.8277 187 R 0.0633 0.0974 0.8393 188 A 0.0051 0.9068 0.0881 189 D 0.0050 0.9233 0.0717 190 I 0.0053 0.9381 0.0566 191 L 0.0054 0.9481 0.0465 192 D 0.0047 0.9533 0.0421 193 Q 0.0047 0.9474 0.0480 194 M 0.0047 0.9521 0.0432 195 R 0.0047 0.9579 0.0374 196 R 0.0047 0.9580 0.0373 197 M 0.0047 0.9528 0.0425 198 L 0.0047 0.9573 0.0380 199 K 0.0047 0.9590 0.0364 200 H 0.0047 0.9524 0.0429 201 A 0.0048 0.9539 0.0413 202 L 0.0047 0.9528 0.0425 203 D 0.0048 0.9459 0.0493 204 F 0.0049 0.9410 0.0540 205 I 0.0063 0.9300 0.0636 206 Q 0.0068 0.8919 0.1013 207 R 0.0124 0.8554 0.1321 208 F 0.0454 0.6925 0.2621 209 N 0.0417 0.5146 0.4437 210 E 0.0309 0.2791 0.6900 211 G 0.0319 0.0868 0.8813 212 K 0.0835 0.0609 0.8556 213 E 0.1358 0.0400 0.8241 214 F 0.0711 0.0393 0.8896