# This file is the result of combining several RDB files, specifically # T0386.t06.dssp-ebghstl.rdb (weight 1.53986) # T0386.t06.stride-ebghtl.rdb (weight 1.24869) # T0386.t06.str2.rdb (weight 1.54758) # T0386.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 T0386.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 543 # # ============================================ # Comments from T0386.t06.stride-ebghtl.rdb # ============================================ # TARGET T0386 # 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 T0386.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 543 # # ============================================ # Comments from T0386.t06.str2.rdb # ============================================ # TARGET T0386 # 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 T0386.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 543 # # ============================================ # Comments from T0386.t06.alpha.rdb # ============================================ # TARGET T0386 # 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 T0386.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 543 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 A 0.0165 0.8347 0.1488 2 M 0.0103 0.9182 0.0715 3 I 0.0101 0.9235 0.0664 4 N 0.0112 0.9189 0.0698 5 L 0.0081 0.9185 0.0735 6 R 0.0093 0.8992 0.0915 7 E 0.0120 0.8733 0.1147 8 E 0.0149 0.7655 0.2196 9 S 0.0252 0.5970 0.3778 10 L 0.0576 0.1825 0.7599 11 P 0.0333 0.1943 0.7724 12 E 0.0445 0.1777 0.7778 13 Y 0.0722 0.1182 0.8096 14 F 0.1107 0.0284 0.8609 15 D 0.0661 0.0220 0.9119 16 T 0.0048 0.9524 0.0428 17 A 0.0047 0.9587 0.0366 18 Y 0.0047 0.9599 0.0354 19 L 0.0047 0.9608 0.0346 20 C 0.0046 0.9609 0.0344 21 H 0.0046 0.9608 0.0345 22 I 0.0046 0.9607 0.0346 23 H 0.0047 0.9586 0.0367 24 Q 0.0048 0.9540 0.0412 25 Q 0.0052 0.9343 0.0606 26 L 0.0066 0.9012 0.0922 27 F 0.0125 0.8020 0.1855 28 K 0.0179 0.6426 0.3395 29 N 0.0298 0.3831 0.5871 30 T 0.0716 0.3049 0.6235 31 F 0.1184 0.2427 0.6389 32 E 0.1041 0.2810 0.6149 33 W 0.1398 0.2455 0.6147 34 A 0.1363 0.2196 0.6440 35 G 0.2147 0.1103 0.6750 36 Y 0.5907 0.0615 0.3478 37 L 0.7456 0.0301 0.2242 38 R 0.7056 0.0208 0.2736 39 H 0.6153 0.0189 0.3658 40 I 0.5188 0.0175 0.4638 41 P 0.5200 0.0280 0.4520 42 F 0.5567 0.0356 0.4078 43 T 0.6363 0.0333 0.3305 44 F 0.5311 0.0620 0.4069 45 A 0.3517 0.0733 0.5749 46 D 0.1700 0.0634 0.7666 47 G 0.1875 0.0563 0.7562 48 T 0.2933 0.0736 0.6330 49 T 0.3783 0.1578 0.4639 50 A 0.4574 0.1353 0.4073 51 A 0.5187 0.1250 0.3563 52 M 0.3293 0.1265 0.5443 53 P 0.2304 0.2096 0.5599 54 E 0.1859 0.2466 0.5675 55 M 0.2159 0.2066 0.5775 56 K 0.1968 0.1921 0.6110 57 R 0.1760 0.2450 0.5790 58 T 0.0930 0.1430 0.7640 59 G 0.1595 0.0558 0.7847 60 W 0.4869 0.0419 0.4712 61 K 0.6749 0.0625 0.2626 62 N 0.7002 0.0399 0.2598 63 A 0.5870 0.0462 0.3668 64 F 0.3484 0.0449 0.6067 65 A 0.1786 0.0412 0.7802 66 I 0.0886 0.0801 0.8313 67 G 0.0124 0.7014 0.2862 68 D 0.0065 0.8041 0.1895 69 E 0.0081 0.8380 0.1539 70 I 0.0076 0.8649 0.1276 71 Q 0.0054 0.9291 0.0655 72 E 0.0048 0.9250 0.0702 73 G 0.0048 0.9113 0.0839 74 L 0.0048 0.9288 0.0664 75 Q 0.0047 0.9413 0.0540 76 R 0.0048 0.9366 0.0587 77 L 0.0048 0.9421 0.0531 78 D 0.0047 0.9506 0.0447 79 Q 0.0047 0.9448 0.0504 80 T 0.0048 0.9351 0.0600 81 L 0.0061 0.9003 0.0935 82 A 0.0073 0.7772 0.2155 83 E 0.0103 0.6289 0.3608 84 K 0.0154 0.6410 0.3436 85 N 0.0252 0.5147 0.4602 86 N 0.0318 0.4877 0.4805 87 L 0.0440 0.5118 0.4442 88 Q 0.0310 0.4203 0.5487 89 G 0.0324 0.2882 0.6794 90 L 0.0837 0.1887 0.7276 91 T 0.0691 0.1755 0.7554 92 R 0.0370 0.5792 0.3838 93 E 0.0263 0.7406 0.2331 94 E 0.0205 0.8268 0.1527 95 F 0.0064 0.9212 0.0724 96 N 0.0055 0.9423 0.0522 97 S 0.0047 0.9560 0.0393 98 E 0.0047 0.9581 0.0371 99 A 0.0047 0.9601 0.0352 100 I 0.0047 0.9596 0.0357 101 E 0.0047 0.9603 0.0350 102 L 0.0048 0.9569 0.0383 103 F 0.0051 0.9541 0.0408 104 N 0.0067 0.9408 0.0526 105 S 0.0084 0.9149 0.0767 106 L 0.0132 0.8771 0.1097 107 N 0.0245 0.8159 0.1596 108 Q 0.0795 0.7111 0.2094 109 L 0.1418 0.5531 0.3050 110 H 0.1578 0.1227 0.7194 111 P 0.0852 0.1219 0.7929 112 F 0.1064 0.1148 0.7787 113 R 0.0942 0.1560 0.7498 114 E 0.0568 0.1410 0.8022 115 G 0.0461 0.1216 0.8323 116 N 0.0463 0.1328 0.8209 117 G 0.0275 0.3244 0.6480 118 R 0.0099 0.8952 0.0949 119 T 0.0094 0.9449 0.0458 120 Q 0.0047 0.9581 0.0372 121 R 0.0047 0.9611 0.0342 122 L 0.0047 0.9609 0.0345 123 F 0.0047 0.9604 0.0349 124 F 0.0047 0.9608 0.0346 125 E 0.0046 0.9606 0.0348 126 N 0.0047 0.9594 0.0360 127 L 0.0047 0.9590 0.0364 128 A 0.0047 0.9595 0.0358 129 K 0.0049 0.9541 0.0410 130 A 0.0064 0.9176 0.0761 131 A 0.0441 0.3953 0.5606 132 G 0.0326 0.0198 0.9476 133 H 0.0637 0.0108 0.9256 134 Q 0.1864 0.0143 0.7993 135 L 0.3491 0.0122 0.6387 136 N 0.3629 0.0143 0.6228 137 F 0.2606 0.2107 0.5287 138 S 0.2641 0.2033 0.5326 139 L 0.2412 0.2634 0.4954 140 I 0.1913 0.0988 0.7099 141 T 0.1110 0.0555 0.8335 142 K 0.0068 0.9412 0.0520 143 E 0.0052 0.9548 0.0400 144 R 0.0047 0.9575 0.0378 145 M 0.0047 0.9602 0.0352 146 M 0.0047 0.9606 0.0348 147 V 0.0047 0.9587 0.0367 148 A 0.0047 0.9555 0.0397 149 S 0.0049 0.9484 0.0467 150 V 0.0054 0.9340 0.0606 151 A 0.0078 0.9156 0.0766 152 V 0.0199 0.8523 0.1278 153 A 0.0265 0.7051 0.2684 154 E 0.0225 0.5164 0.4611 155 N 0.0485 0.1610 0.7905 156 G 0.0278 0.0592 0.9130 157 D 0.0888 0.0442 0.8670 158 L 0.0655 0.4686 0.4659 159 E 0.0171 0.8297 0.1533 160 P 0.0113 0.9182 0.0705 161 M 0.0049 0.9491 0.0460 162 Q 0.0050 0.9554 0.0395 163 H 0.0048 0.9527 0.0425 164 L 0.0048 0.9483 0.0469 165 F 0.0049 0.9426 0.0525 166 E 0.0057 0.9256 0.0687 167 D 0.0079 0.8502 0.1419 168 I 0.0143 0.7085 0.2772 169 S 0.0289 0.4938 0.4773 170 N 0.0477 0.3192 0.6330 171 P 0.0051 0.8844 0.1104 172 E 0.0051 0.9215 0.0734 173 K 0.0048 0.9455 0.0497 174 I 0.0047 0.9531 0.0422 175 R 0.0048 0.9483 0.0469 176 L 0.0048 0.9442 0.0510 177 L 0.0047 0.9536 0.0417 178 K 0.0047 0.9575 0.0377 179 E 0.0048 0.9557 0.0395 180 F 0.0048 0.9541 0.0411 181 M 0.0048 0.9542 0.0410 182 H 0.0049 0.9486 0.0465 183 T 0.0053 0.9415 0.0532 184 M 0.0078 0.9291 0.0631 185 K 0.0098 0.8625 0.1277 186 N 0.0146 0.7512 0.2343 187 T 0.0472 0.4582 0.4946 188 G 0.0390 0.1937 0.7674 189 R 0.0766 0.1938 0.7296 190 N 0.1509 0.2114 0.6376 191 V 0.1494 0.3084 0.5422 192 N 0.1169 0.2510 0.6321 193 D 0.1230 0.2143 0.6627 194 R 0.1617 0.1932 0.6451 195 P 0.2077 0.2393 0.5530 196 V 0.3864 0.2911 0.3226 197 M 0.4822 0.2797 0.2381 198 V 0.4467 0.2511 0.3022 199 A 0.3572 0.2125 0.4303 200 K 0.1802 0.1463 0.6735 201 E 0.0477 0.0534 0.8989