# This file is the result of combining several RDB files, specifically # T0379.t06.dssp-ebghstl.rdb (weight 1.53986) # T0379.t06.stride-ebghtl.rdb (weight 1.24869) # T0379.t06.str2.rdb (weight 1.54758) # T0379.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 T0379.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 4630 # # ============================================ # Comments from T0379.t06.stride-ebghtl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 4630 # # ============================================ # Comments from T0379.t06.str2.rdb # ============================================ # TARGET T0379 # 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 T0379.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 4630 # # ============================================ # Comments from T0379.t06.alpha.rdb # ============================================ # TARGET T0379 # 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 T0379.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 4630 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0768 0.0166 0.9066 2 I 0.2902 0.0064 0.7035 3 R 0.3732 0.0283 0.5984 4 N 0.9010 0.0040 0.0950 5 I 0.9283 0.0032 0.0685 6 V 0.9306 0.0034 0.0660 7 F 0.9105 0.0052 0.0842 8 D 0.7026 0.0076 0.2898 9 L 0.2371 0.0755 0.6874 10 G 0.0623 0.0589 0.8789 11 G 0.0881 0.0767 0.8352 12 V 0.4101 0.1103 0.4796 13 L 0.6856 0.1004 0.2140 14 I 0.6049 0.0951 0.3000 15 H 0.4151 0.0921 0.4928 16 L 0.1029 0.1827 0.7143 17 N 0.0709 0.1830 0.7461 18 R 0.0253 0.5322 0.4426 19 E 0.0065 0.9145 0.0789 20 E 0.0063 0.9373 0.0564 21 S 0.0054 0.9499 0.0447 22 I 0.0047 0.9579 0.0374 23 R 0.0047 0.9588 0.0365 24 R 0.0047 0.9594 0.0359 25 F 0.0047 0.9587 0.0366 26 K 0.0048 0.9530 0.0422 27 A 0.0055 0.9281 0.0665 28 I 0.0434 0.5192 0.4373 29 G 0.0385 0.0374 0.9241 30 V 0.0719 0.0525 0.8756 31 A 0.1746 0.1830 0.6425 32 D 0.1784 0.3454 0.4763 33 I 0.0908 0.5683 0.3409 34 E 0.0729 0.6891 0.2380 35 E 0.0653 0.6628 0.2720 36 M 0.0693 0.5757 0.3551 37 L 0.0756 0.3880 0.5364 38 D 0.1029 0.2619 0.6352 39 P 0.0339 0.4807 0.4854 40 Y 0.0451 0.4843 0.4706 41 L 0.0782 0.4109 0.5108 42 Q 0.0606 0.3398 0.5996 43 K 0.0418 0.3800 0.5782 44 G 0.0474 0.3145 0.6381 45 L 0.1173 0.4290 0.4537 46 F 0.1837 0.5146 0.3017 47 L 0.2007 0.5345 0.2648 48 D 0.2284 0.5284 0.2433 49 L 0.1140 0.6528 0.2332 50 E 0.0762 0.6357 0.2881 51 S 0.0646 0.3492 0.5862 52 G 0.0381 0.1063 0.8556 53 R 0.0787 0.1038 0.8174 54 K 0.1009 0.1197 0.7793 55 S 0.0777 0.1846 0.7378 56 E 0.0092 0.8843 0.1065 57 E 0.0053 0.9428 0.0519 58 E 0.0050 0.9500 0.0451 59 F 0.0048 0.9523 0.0430 60 R 0.0047 0.9545 0.0408 61 T 0.0048 0.9505 0.0446 62 E 0.0049 0.9442 0.0509 63 L 0.0057 0.9320 0.0623 64 S 0.0076 0.9148 0.0776 65 R 0.0076 0.8798 0.1126 66 Y 0.0130 0.8003 0.1867 67 I 0.0434 0.6001 0.3565 68 G 0.0343 0.2805 0.6852 69 K 0.0500 0.2316 0.7184 70 E 0.0811 0.1783 0.7406 71 L 0.1211 0.0978 0.7811 72 T 0.0931 0.0725 0.8344 73 Y 0.0053 0.9369 0.0578 74 Q 0.0047 0.9560 0.0393 75 Q 0.0047 0.9580 0.0373 76 V 0.0047 0.9582 0.0371 77 Y 0.0047 0.9576 0.0377 78 D 0.0051 0.9535 0.0415 79 A 0.0050 0.9480 0.0470 80 L 0.0058 0.9362 0.0580 81 L 0.0080 0.9006 0.0914 82 G 0.0095 0.7934 0.1971 83 F 0.0156 0.7057 0.2787 84 L 0.0546 0.5319 0.4136 85 E 0.0446 0.4189 0.5365 86 E 0.0810 0.3688 0.5502 87 I 0.1116 0.2429 0.6454 88 S 0.0645 0.1424 0.7931 89 A 0.0067 0.8143 0.1790 90 E 0.0085 0.7232 0.2683 91 K 0.0066 0.8962 0.0972 92 F 0.0068 0.9289 0.0644 93 D 0.0054 0.9384 0.0562 94 Y 0.0049 0.9414 0.0537 95 I 0.0060 0.9309 0.0631 96 D 0.0066 0.8692 0.1243 97 S 0.0091 0.7183 0.2726 98 L 0.0413 0.4616 0.4970 99 R 0.0597 0.0870 0.8533 100 P 0.0214 0.2170 0.7616 101 D 0.0263 0.0815 0.8922 102 Y 0.3656 0.0134 0.6210 103 R 0.6907 0.0141 0.2952 104 L 0.9310 0.0033 0.0657 105 F 0.9329 0.0033 0.0638 106 L 0.9322 0.0032 0.0646 107 L 0.9030 0.0046 0.0924 108 S 0.5538 0.0125 0.4337 109 N 0.1130 0.0362 0.8507 110 T 0.0583 0.0453 0.8964 111 N 0.0901 0.0460 0.8640 112 P 0.0136 0.7872 0.1992 113 Y 0.0159 0.8572 0.1269 114 V 0.0228 0.8832 0.0941 115 L 0.0325 0.8744 0.0930 116 D 0.0376 0.8569 0.1056 117 L 0.0306 0.8528 0.1166 118 A 0.0307 0.7854 0.1839 119 M 0.0615 0.6102 0.3283 120 S 0.0674 0.3746 0.5580 121 P 0.0370 0.4547 0.5082 122 R 0.0510 0.3655 0.5835 123 F 0.0642 0.1728 0.7630 124 L 0.0784 0.1312 0.7905 125 P 0.0497 0.1937 0.7566 126 S 0.0484 0.2035 0.7481 127 G 0.0601 0.2066 0.7333 128 R 0.1082 0.1620 0.7298 129 T 0.1617 0.1572 0.6812 130 L 0.0420 0.5830 0.3750 131 D 0.0224 0.7280 0.2496 132 S 0.0227 0.7431 0.2342 133 F 0.0451 0.6918 0.2631 134 F 0.1463 0.4609 0.3928 135 D 0.1387 0.4351 0.4262 136 K 0.3584 0.3897 0.2520 137 V 0.5636 0.3045 0.1318 138 Y 0.6607 0.1939 0.1454 139 A 0.5961 0.1279 0.2760 140 S 0.3777 0.1373 0.4850 141 C 0.2176 0.1716 0.6108 142 Q 0.2025 0.2011 0.5964 143 M 0.1319 0.1812 0.6869 144 G 0.0813 0.1273 0.7914 145 K 0.0983 0.0932 0.8085 146 Y 0.1292 0.0595 0.8113 147 K 0.0964 0.0262 0.8774 148 P 0.0781 0.0347 0.8872 149 N 0.0771 0.0354 0.8875 150 E 0.0058 0.9237 0.0705 151 D 0.0052 0.9455 0.0493 152 I 0.0047 0.9561 0.0392 153 F 0.0047 0.9606 0.0348 154 L 0.0046 0.9612 0.0341 155 E 0.0046 0.9612 0.0342 156 M 0.0046 0.9615 0.0339 157 I 0.0047 0.9605 0.0348 158 A 0.0048 0.9524 0.0428 159 D 0.0058 0.9010 0.0931 160 S 0.0437 0.4082 0.5481 161 G 0.0391 0.0166 0.9444 162 M 0.0665 0.0077 0.9258 163 K 0.0800 0.0099 0.9101 164 P 0.0418 0.5970 0.3613 165 E 0.0608 0.5886 0.3506 166 E 0.1630 0.4609 0.3761 167 T 0.8217 0.0186 0.1598 168 L 0.8889 0.0086 0.1025 169 F 0.9025 0.0054 0.0921 170 I 0.8068 0.0405 0.1527 171 D 0.4952 0.0168 0.4880 172 D 0.1814 0.0312 0.7875 173 G 0.0791 0.0450 0.8759 174 P 0.0136 0.6170 0.3693 175 A 0.0147 0.6899 0.2954 176 N 0.0221 0.7276 0.2503 177 V 0.0076 0.9335 0.0590 178 A 0.0055 0.9477 0.0468 179 T 0.0047 0.9561 0.0391 180 A 0.0047 0.9564 0.0389 181 E 0.0049 0.9486 0.0465 182 R 0.0054 0.9145 0.0801 183 L 0.0444 0.3643 0.5913 184 G 0.0425 0.0147 0.9428 185 F 0.1005 0.0070 0.8925 186 H 0.3928 0.0321 0.5751 187 T 0.8318 0.0070 0.1612 188 Y 0.8501 0.0078 0.1421 189 C 0.7807 0.0071 0.2122 190 P 0.4277 0.0190 0.5533 191 D 0.1689 0.0449 0.7862 192 N 0.0902 0.0631 0.8467 193 G 0.0531 0.1354 0.8115 194 E 0.0651 0.2411 0.6938 195 N 0.0907 0.2582 0.6511 196 W 0.1026 0.3043 0.5931 197 I 0.0945 0.3305 0.5750 198 P 0.0510 0.5486 0.4003 199 A 0.0597 0.6015 0.3388 200 I 0.0784 0.5704 0.3512 201 T 0.0776 0.6418 0.2806 202 R 0.0504 0.7447 0.2049 203 L 0.0726 0.7720 0.1554 204 L 0.0723 0.7761 0.1516 205 R 0.0732 0.7226 0.2042 206 E 0.0524 0.5814 0.3662 207 Q 0.0570 0.2987 0.6443 208 K 0.0364 0.0634 0.9002