# This file is the result of combining several RDB files, specifically # T0503.t04.dssp-ebghstl.rdb (weight 1.53986) # T0503.t04.stride-ebghtl.rdb (weight 1.24869) # T0503.t04.str2.rdb (weight 1.54758) # T0503.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 T0503.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0503 # 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 T0503.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 2115 # # ============================================ # Comments from T0503.t04.stride-ebghtl.rdb # ============================================ # TARGET T0503 # 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 T0503.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 2115 # # ============================================ # Comments from T0503.t04.str2.rdb # ============================================ # TARGET T0503 # 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 T0503.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 2115 # # ============================================ # Comments from T0503.t04.alpha.rdb # ============================================ # TARGET T0503 # 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 T0503.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 2115 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0358 0.1941 0.7701 2 H 0.0287 0.5077 0.4636 3 T 0.0103 0.8730 0.1167 4 A 0.0088 0.9010 0.0901 5 L 0.0079 0.9180 0.0741 6 I 0.0087 0.9092 0.0822 7 N 0.0069 0.8607 0.1324 8 H 0.0114 0.7763 0.2124 9 I 0.0335 0.5993 0.3672 10 R 0.0223 0.6524 0.3252 11 K 0.0274 0.6677 0.3048 12 F 0.0485 0.6262 0.3254 13 I 0.0585 0.4097 0.5318 14 F 0.0681 0.1433 0.7886 15 L 0.1053 0.0173 0.8774 16 T 0.0607 0.0133 0.9260 17 D 0.0050 0.9300 0.0650 18 E 0.0048 0.9426 0.0526 19 D 0.0052 0.9361 0.0587 20 A 0.0050 0.9405 0.0545 21 G 0.0050 0.9023 0.0926 22 T 0.0062 0.8944 0.0993 23 L 0.0093 0.8823 0.1085 24 S 0.0085 0.8728 0.1186 25 A 0.0092 0.8111 0.1797 26 F 0.0236 0.6539 0.3225 27 F 0.1776 0.3218 0.5005 28 Q 0.3854 0.1754 0.4392 29 L 0.6086 0.1288 0.2627 30 K 0.6237 0.0958 0.2805 31 K 0.7607 0.0390 0.2003 32 V 0.4409 0.0293 0.5298 33 R 0.1739 0.0231 0.8030 34 K 0.0444 0.1150 0.8406 35 K 0.0424 0.0653 0.8923 36 E 0.3529 0.0349 0.6123 37 T 0.7642 0.0155 0.2203 38 L 0.8479 0.0246 0.1274 39 L 0.7673 0.0443 0.1885 40 K 0.6130 0.0612 0.3259 41 T 0.1987 0.0921 0.7092 42 G 0.0865 0.0503 0.8632 43 E 0.2434 0.0506 0.7060 44 I 0.3377 0.1132 0.5491 45 C 0.3181 0.1181 0.5638 46 R 0.2505 0.1496 0.5998 47 I 0.6602 0.0578 0.2821 48 N 0.8494 0.0201 0.1305 49 Y 0.9184 0.0069 0.0747 50 F 0.9220 0.0051 0.0729 51 V 0.9196 0.0068 0.0736 52 V 0.8563 0.0278 0.1159 53 K 0.7177 0.0389 0.2434 54 G 0.6481 0.0168 0.3351 55 C 0.8734 0.0074 0.1192 56 L 0.9194 0.0037 0.0769 57 R 0.9215 0.0040 0.0745 58 L 0.9275 0.0030 0.0694 59 F 0.9100 0.0062 0.0838 60 F 0.9172 0.0040 0.0788 61 I 0.8739 0.0081 0.1180 62 D 0.4057 0.0133 0.5810 63 E 0.0176 0.1167 0.8658 64 K 0.0462 0.0285 0.9253 65 G 0.0764 0.0362 0.8874 66 I 0.3279 0.0574 0.6147 67 E 0.8517 0.0234 0.1249 68 Q 0.8765 0.0195 0.1040 69 T 0.8968 0.0211 0.0821 70 T 0.8800 0.0301 0.0898 71 Q 0.8437 0.0499 0.1064 72 F 0.7932 0.0629 0.1439 73 A 0.6319 0.0817 0.2864 74 I 0.2789 0.0808 0.6402 75 E 0.0437 0.1459 0.8104 76 N 0.0274 0.0872 0.8854 77 W 0.1801 0.1123 0.7076 78 W 0.3646 0.1990 0.4364 79 L 0.3127 0.3597 0.3276 80 S 0.2256 0.4014 0.3729 81 D 0.1381 0.5689 0.2930 82 Y 0.0826 0.7272 0.1902 83 M 0.0461 0.8107 0.1433 84 A 0.0332 0.8490 0.1177 85 F 0.0293 0.8253 0.1454 86 Q 0.0478 0.7193 0.2329 87 K 0.0359 0.4291 0.5350 88 Q 0.0313 0.1550 0.8137 89 Q 0.0737 0.0210 0.9053 90 P 0.0937 0.0304 0.8759 91 A 0.1779 0.0553 0.7668 92 D 0.3712 0.0635 0.5653 93 F 0.6571 0.0269 0.3160 94 Y 0.8442 0.0152 0.1405 95 I 0.8875 0.0120 0.1005 96 Q 0.8973 0.0093 0.0934 97 S 0.8805 0.0100 0.1094 98 V 0.7927 0.0220 0.1853 99 E 0.6622 0.0338 0.3039 100 N 0.4102 0.0412 0.5485 101 C 0.6505 0.0121 0.3374 102 E 0.8538 0.0074 0.1388 103 L 0.9203 0.0035 0.0761 104 L 0.9148 0.0051 0.0800 105 S 0.9075 0.0042 0.0883 106 I 0.7760 0.0075 0.2166 107 T 0.2978 0.0105 0.6917 108 Y 0.0080 0.8448 0.1472 109 T 0.0048 0.9232 0.0720 110 E 0.0052 0.9279 0.0670 111 Q 0.0048 0.9525 0.0428 112 E 0.0048 0.9565 0.0387 113 N 0.0049 0.9558 0.0393 114 L 0.0050 0.9480 0.0471 115 F 0.0052 0.9208 0.0740 116 E 0.0056 0.8260 0.1683 117 R 0.0127 0.6227 0.3646 118 I 0.0788 0.2032 0.7180 119 P 0.0051 0.8568 0.1381 120 A 0.0050 0.9320 0.0630 121 L 0.0048 0.9535 0.0417 122 E 0.0047 0.9590 0.0363 123 R 0.0047 0.9609 0.0344 124 Y 0.0047 0.9611 0.0343 125 F 0.0047 0.9609 0.0344 126 R 0.0047 0.9611 0.0343 127 L 0.0046 0.9613 0.0341 128 V 0.0047 0.9607 0.0346 129 Y 0.0047 0.9582 0.0371 130 Q 0.0047 0.9586 0.0367 131 K 0.0047 0.9582 0.0371 132 S 0.0047 0.9579 0.0374 133 F 0.0047 0.9583 0.0370 134 A 0.0047 0.9576 0.0377 135 A 0.0047 0.9572 0.0381 136 A 0.0047 0.9560 0.0393 137 Q 0.0048 0.9490 0.0462 138 L 0.0053 0.9350 0.0597 139 R 0.0065 0.9234 0.0701 140 S 0.0111 0.8998 0.0892 141 K 0.0099 0.8857 0.1044 142 F 0.0172 0.8171 0.1658 143 Q 0.0232 0.7054 0.2713 144 H 0.0312 0.5423 0.4265 145 M 0.0578 0.3002 0.6420 146 Y 0.0785 0.0906 0.8308 147 S 0.0590 0.0378 0.9032 148 K 0.0049 0.9465 0.0486 149 E 0.0047 0.9592 0.0361 150 E 0.0047 0.9596 0.0357 151 Q 0.0047 0.9607 0.0346 152 Y 0.0047 0.9586 0.0366 153 H 0.0047 0.9561 0.0392 154 N 0.0047 0.9479 0.0473 155 F 0.0053 0.9229 0.0717 156 S 0.0061 0.8940 0.0999 157 S 0.0079 0.7797 0.2124 158 R 0.0154 0.5945 0.3901 159 F 0.0550 0.2896 0.6554 160 P 0.0151 0.6692 0.3156 161 E 0.0128 0.7097 0.2775 162 F 0.0217 0.6728 0.3055 163 I 0.0694 0.4238 0.5067 164 Q 0.0460 0.1884 0.7656 165 R 0.0595 0.0656 0.8749 166 V 0.0857 0.0317 0.8827 167 P 0.0747 0.0505 0.8747 168 Q 0.0061 0.9381 0.0558 169 Y 0.0050 0.9556 0.0394 170 L 0.0048 0.9565 0.0388 171 L 0.0047 0.9596 0.0358 172 A 0.0047 0.9573 0.0380 173 S 0.0052 0.9437 0.0512 174 Y 0.0064 0.9053 0.0883 175 L 0.0477 0.4959 0.4564 176 G 0.0384 0.0631 0.8985 177 F 0.0796 0.0313 0.8891 178 T 0.0716 0.0288 0.8996 179 P 0.0089 0.8948 0.0963 180 E 0.0063 0.9304 0.0633 181 Y 0.0074 0.9443 0.0483 182 L 0.0056 0.9553 0.0392 183 S 0.0053 0.9562 0.0385 184 E 0.0050 0.9585 0.0364 185 I 0.0059 0.9528 0.0413 186 R 0.0085 0.9259 0.0656 187 K 0.0094 0.8426 0.1479 188 K 0.0366 0.4693 0.4941 189 Y 0.0351 0.1075 0.8574 190 I 0.0839 0.0355 0.8806 191 S 0.0805 0.0330 0.8865