# This file is the result of combining several RDB files, specifically # T0245.t04.dssp-ebghstl.rdb (weight 1.53986) # T0245.t04.stride-ebghtl.rdb (weight 1.24869) # T0245.t04.str2.rdb (weight 1.54758) # T0245.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 T0245.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0245 # 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 T0245.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 18.5039 # # ============================================ # Comments from T0245.t04.stride-ebghtl.rdb # ============================================ # TARGET T0245 # 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 T0245.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 18.5039 # # ============================================ # Comments from T0245.t04.str2.rdb # ============================================ # TARGET T0245 # 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 T0245.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 18.5039 # # ============================================ # Comments from T0245.t04.alpha.rdb # ============================================ # TARGET T0245 # 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 T0245.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 18.5039 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0478 0.1307 0.8215 2 M 0.0636 0.4805 0.4559 3 W 0.0130 0.8776 0.1094 4 E 0.0064 0.9380 0.0557 5 Q 0.0058 0.9500 0.0442 6 F 0.0052 0.9423 0.0525 7 K 0.0053 0.9497 0.0450 8 K 0.0051 0.9561 0.0388 9 E 0.0052 0.9503 0.0446 10 K 0.0052 0.9448 0.0500 11 L 0.0061 0.9208 0.0731 12 R 0.0057 0.8695 0.1248 13 G 0.0069 0.6807 0.3124 14 Y 0.0102 0.6481 0.3417 15 L 0.0182 0.6231 0.3587 16 E 0.0212 0.6853 0.2935 17 A 0.0234 0.6665 0.3101 18 K 0.0470 0.4738 0.4792 19 N 0.0300 0.4352 0.5348 20 Q 0.0515 0.2650 0.6835 21 R 0.0809 0.1097 0.8094 22 K 0.1999 0.0731 0.7270 23 V 0.2463 0.0742 0.6795 24 D 0.0788 0.0940 0.8271 25 F 0.0066 0.8128 0.1805 26 D 0.0070 0.8394 0.1536 27 I 0.0059 0.9202 0.0738 28 V 0.0063 0.9398 0.0540 29 E 0.0060 0.9397 0.0543 30 L 0.0055 0.9469 0.0476 31 L 0.0050 0.9546 0.0404 32 D 0.0054 0.9485 0.0461 33 L 0.0061 0.9266 0.0674 34 I 0.0136 0.8421 0.1443 35 N 0.0423 0.5108 0.4469 36 S 0.0555 0.1982 0.7462 37 F 0.0644 0.1503 0.7853 38 D 0.0276 0.1985 0.7739 39 D 0.0627 0.1559 0.7815 40 F 0.4673 0.0684 0.4643 41 V 0.7162 0.0272 0.2567 42 T 0.7359 0.0256 0.2385 43 L 0.5823 0.0498 0.3679 44 S 0.3992 0.0630 0.5379 45 S 0.2042 0.1728 0.6230 46 C 0.1914 0.1608 0.6478 47 S 0.2422 0.0959 0.6619 48 G 0.3715 0.0483 0.5803 49 R 0.6628 0.0185 0.3188 50 I 0.8925 0.0053 0.1021 51 A 0.9174 0.0044 0.0782 52 V 0.9215 0.0051 0.0734 53 V 0.8790 0.0103 0.1107 54 D 0.7605 0.0074 0.2321 55 L 0.4192 0.0337 0.5471 56 E 0.2288 0.0425 0.7287 57 K 0.1335 0.0363 0.8302 58 P 0.0680 0.0790 0.8530 59 G 0.0522 0.0738 0.8740 60 D 0.0980 0.0935 0.8085 61 K 0.1270 0.1413 0.7317 62 A 0.1415 0.1668 0.6918 63 S 0.1654 0.1279 0.7067 64 S 0.4548 0.0658 0.4794 65 L 0.7031 0.0463 0.2506 66 F 0.8480 0.0328 0.1192 67 L 0.8408 0.0522 0.1070 68 G 0.8196 0.0487 0.1317 69 K 0.7968 0.0492 0.1540 70 W 0.6298 0.0581 0.3121 71 H 0.2556 0.0702 0.6742 72 E 0.0843 0.0771 0.8386 73 G 0.0655 0.0660 0.8686 74 V 0.1570 0.0287 0.8143 75 E 0.1625 0.0294 0.8080 76 V 0.0079 0.9212 0.0709 77 S 0.0054 0.9472 0.0474 78 E 0.0054 0.9506 0.0440 79 V 0.0062 0.9521 0.0417 80 A 0.0065 0.9524 0.0412 81 E 0.0063 0.9521 0.0416 82 A 0.0075 0.9406 0.0519 83 A 0.0095 0.9065 0.0840 84 L 0.0136 0.8075 0.1789 85 R 0.0193 0.5974 0.3834 86 S 0.0345 0.3495 0.6160 87 R 0.0529 0.1561 0.7910 88 K 0.1200 0.1148 0.7652 89 V 0.3910 0.0867 0.5223 90 A 0.6503 0.0516 0.2981 91 W 0.8161 0.0438 0.1401 92 L 0.8528 0.0398 0.1074 93 I 0.8246 0.0370 0.1384 94 Q 0.7397 0.0267 0.2336 95 Y 0.4662 0.0174 0.5164 96 P 0.2315 0.0236 0.7449 97 P 0.3255 0.0194 0.6550 98 I 0.8161 0.0110 0.1729 99 I 0.9033 0.0082 0.0885 100 H 0.9223 0.0069 0.0708 101 V 0.8997 0.0094 0.0909 102 A 0.8265 0.0118 0.1617 103 C 0.5021 0.0534 0.4444 104 R 0.1527 0.0840 0.7634 105 N 0.1000 0.0513 0.8487 106 I 0.0064 0.8944 0.0992 107 G 0.0049 0.9388 0.0563 108 A 0.0049 0.9452 0.0500 109 A 0.0047 0.9580 0.0373 110 K 0.0046 0.9614 0.0339 111 L 0.0046 0.9610 0.0343 112 L 0.0047 0.9601 0.0353 113 M 0.0047 0.9605 0.0349 114 N 0.0047 0.9601 0.0352 115 A 0.0047 0.9585 0.0368 116 A 0.0048 0.9520 0.0432 117 N 0.0053 0.9333 0.0614 118 T 0.0075 0.8818 0.1107 119 A 0.0456 0.5916 0.3628 120 G 0.0449 0.2232 0.7319 121 F 0.1431 0.2646 0.5923 122 R 0.2082 0.3486 0.4432 123 R 0.2641 0.2845 0.4514 124 S 0.2338 0.1548 0.6114 125 G 0.3192 0.0818 0.5991 126 V 0.4844 0.0855 0.4301 127 I 0.5925 0.0873 0.3202 128 S 0.5559 0.0640 0.3801 129 L 0.3360 0.1198 0.5442 130 S 0.1746 0.0894 0.7360 131 N 0.1903 0.0601 0.7496 132 Y 0.6620 0.0173 0.3206 133 V 0.9143 0.0055 0.0802 134 V 0.9218 0.0071 0.0711 135 E 0.9266 0.0052 0.0683 136 I 0.9076 0.0073 0.0851 137 A 0.7678 0.0139 0.2184 138 S 0.4622 0.0252 0.5126 139 L 0.3145 0.0806 0.6049 140 E 0.4284 0.0794 0.4922 141 R 0.6051 0.0705 0.3244 142 I 0.7451 0.0307 0.2242 143 E 0.7305 0.0272 0.2423 144 L 0.6810 0.0263 0.2927 145 P 0.6383 0.0259 0.3358 146 V 0.4865 0.1346 0.3790 147 A 0.2490 0.1751 0.5759 148 E 0.1554 0.2026 0.6421 149 K 0.0623 0.0687 0.8691 150 G 0.0942 0.0428 0.8631 151 L 0.4294 0.0250 0.5456 152 M 0.8103 0.0117 0.1780 153 L 0.7514 0.0130 0.2355 154 V 0.5425 0.0154 0.4422 155 D 0.1444 0.0131 0.8426 156 D 0.0053 0.9081 0.0866 157 A 0.0053 0.9432 0.0515 158 Y 0.0053 0.9483 0.0464 159 L 0.0047 0.9592 0.0361 160 S 0.0047 0.9611 0.0343 161 Y 0.0047 0.9611 0.0343 162 V 0.0047 0.9611 0.0342 163 V 0.0047 0.9611 0.0343 164 R 0.0046 0.9617 0.0336 165 W 0.0047 0.9596 0.0357 166 A 0.0047 0.9551 0.0402 167 N 0.0049 0.9572 0.0379 168 E 0.0048 0.9593 0.0359 169 K 0.0049 0.9566 0.0385 170 L 0.0053 0.9486 0.0461 171 L 0.0061 0.9257 0.0682 172 K 0.0144 0.7917 0.1939 173 G 0.0177 0.6011 0.3812 174 K 0.0128 0.7314 0.2558 175 E 0.0206 0.8019 0.1775 176 K 0.0092 0.8836 0.1072 177 L 0.0053 0.9249 0.0699 178 G 0.0048 0.9410 0.0542 179 R 0.0047 0.9456 0.0496 180 L 0.0048 0.9537 0.0415 181 Q 0.0047 0.9599 0.0354 182 E 0.0047 0.9609 0.0344 183 A 0.0047 0.9592 0.0361 184 L 0.0047 0.9565 0.0387 185 E 0.0048 0.9511 0.0441 186 S 0.0049 0.9382 0.0569 187 L 0.0055 0.9112 0.0833 188 Q 0.0087 0.8648 0.1264 189 R 0.0129 0.7726 0.2145 190 E 0.0287 0.5715 0.3997 191 N 0.0449 0.2812 0.6738 192 A 0.0671 0.2301 0.7028 193 Y 0.1156 0.1780 0.7064 194 C 0.1158 0.1219 0.7623 195 S 0.0758 0.0802 0.8441 196 D 0.0485 0.0519 0.8997