# This file is the result of combining several RDB files, specifically # T0368.t06.dssp-ebghstl.rdb (weight 1.53986) # T0368.t06.stride-ebghtl.rdb (weight 1.24869) # T0368.t06.str2.rdb (weight 1.54758) # T0368.t06.alpha.rdb (weight 0.659012) # T0368.t04.dssp-ebghstl.rdb (weight 1.53986) # T0368.t04.stride-ebghtl.rdb (weight 1.24869) # T0368.t04.str2.rdb (weight 1.54758) # T0368.t04.alpha.rdb (weight 0.659012) # T0368.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0368.t2k.stride-ebghtl.rdb (weight 1.24869) # T0368.t2k.str2.rdb (weight 1.54758) # T0368.t2k.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 T0368.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0368 # 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 T0368.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 3.53726 # # ============================================ # Comments from T0368.t06.stride-ebghtl.rdb # ============================================ # TARGET T0368 # 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 T0368.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 3.53726 # # ============================================ # Comments from T0368.t06.str2.rdb # ============================================ # TARGET T0368 # 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 T0368.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 3.53726 # # ============================================ # Comments from T0368.t06.alpha.rdb # ============================================ # TARGET T0368 # 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 T0368.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 3.53726 # # ============================================ # Comments from T0368.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0368 # 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 T0368.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 3.53726 # # ============================================ # Comments from T0368.t04.stride-ebghtl.rdb # ============================================ # TARGET T0368 # 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 T0368.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 3.53726 # # ============================================ # Comments from T0368.t04.str2.rdb # ============================================ # TARGET T0368 # 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 T0368.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 3.53726 # # ============================================ # Comments from T0368.t04.alpha.rdb # ============================================ # TARGET T0368 # 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 T0368.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 3.53726 # # ============================================ # Comments from T0368.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0368 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0368.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 783 # # ============================================ # Comments from T0368.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0368 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0368.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 783 # # ============================================ # Comments from T0368.t2k.str2.rdb # ============================================ # TARGET T0368 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0368.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 783 # # ============================================ # Comments from T0368.t2k.alpha.rdb # ============================================ # TARGET T0368 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0368.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 783 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1395 0.2315 0.6290 2 K 0.1541 0.3802 0.4658 3 P 0.1940 0.4053 0.4007 4 L 0.1782 0.3439 0.4779 5 K 0.1161 0.2139 0.6700 6 E 0.0915 0.0518 0.8566 7 V 0.0225 0.3906 0.5869 8 V 0.0193 0.3865 0.5942 9 G 0.0358 0.4636 0.5006 10 A 0.0064 0.8874 0.1061 11 Y 0.0057 0.9205 0.0738 12 L 0.0055 0.9283 0.0662 13 A 0.0061 0.9299 0.0640 14 L 0.0061 0.9360 0.0579 15 S 0.0058 0.9384 0.0557 16 D 0.0061 0.9346 0.0594 17 A 0.0059 0.9294 0.0647 18 Q 0.0051 0.9405 0.0544 19 R 0.0052 0.9470 0.0478 20 Q 0.0050 0.9441 0.0508 21 L 0.0056 0.9126 0.0818 22 V 0.0064 0.8361 0.1575 23 A 0.0436 0.4093 0.5471 24 G 0.0351 0.1438 0.8211 25 E 0.0468 0.1941 0.7591 26 Y 0.0141 0.7755 0.2104 27 D 0.0068 0.9187 0.0745 28 E 0.0056 0.9372 0.0572 29 A 0.0056 0.9458 0.0485 30 A 0.0049 0.9554 0.0397 31 A 0.0049 0.9555 0.0396 32 N 0.0049 0.9517 0.0434 33 C 0.0049 0.9524 0.0426 34 R 0.0048 0.9516 0.0436 35 R 0.0050 0.9428 0.0522 36 A 0.0051 0.9356 0.0593 37 M 0.0079 0.9026 0.0896 38 E 0.0096 0.8143 0.1761 39 I 0.0269 0.6491 0.3241 40 S 0.0738 0.1742 0.7520 41 H 0.0200 0.2841 0.6959 42 T 0.0274 0.2527 0.7199 43 M 0.0594 0.2347 0.7059 44 P 0.0429 0.4137 0.5434 45 P 0.0189 0.6523 0.3288 46 E 0.0170 0.7120 0.2710 47 E 0.0244 0.7084 0.2672 48 A 0.0305 0.6584 0.3111 49 F 0.0322 0.5907 0.3771 50 D 0.0305 0.4702 0.4993 51 H 0.0407 0.3958 0.5636 52 A 0.0422 0.3367 0.6211 53 G 0.0188 0.4920 0.4893 54 F 0.0205 0.5369 0.4426 55 D 0.0220 0.6238 0.3542 56 A 0.0076 0.9107 0.0817 57 F 0.0074 0.9294 0.0632 58 C 0.0057 0.9415 0.0528 59 H 0.0057 0.9425 0.0517 60 A 0.0056 0.9449 0.0495 61 G 0.0055 0.9448 0.0497 62 L 0.0051 0.9485 0.0464 63 A 0.0052 0.9465 0.0484 64 E 0.0053 0.9504 0.0443 65 A 0.0052 0.9518 0.0430 66 L 0.0050 0.9473 0.0476 67 A 0.0053 0.9076 0.0871 68 G 0.0062 0.8088 0.1851 69 L 0.0447 0.3691 0.5862 70 R 0.0364 0.1035 0.8601 71 S 0.0532 0.1255 0.8212 72 F 0.0128 0.8064 0.1808 73 D 0.0064 0.9231 0.0705 74 E 0.0055 0.9396 0.0548 75 A 0.0051 0.9489 0.0460 76 L 0.0049 0.9559 0.0392 77 H 0.0049 0.9553 0.0398 78 S 0.0049 0.9519 0.0432 79 A 0.0048 0.9541 0.0411 80 D 0.0048 0.9539 0.0413 81 K 0.0049 0.9484 0.0466 82 A 0.0050 0.9387 0.0562 83 L 0.0071 0.9046 0.0883 84 H 0.0082 0.8197 0.1721 85 Y 0.0258 0.6440 0.3302 86 F 0.0745 0.1429 0.7827 87 N 0.0153 0.3530 0.6318 88 R 0.0212 0.3410 0.6377 89 R 0.0566 0.3479 0.5955 90 G 0.0511 0.3835 0.5654 91 E 0.0559 0.3889 0.5553 92 L 0.0684 0.3536 0.5780 93 N 0.0696 0.2988 0.6315 94 Q 0.0509 0.3016 0.6475 95 D 0.0353 0.3600 0.6048 96 E 0.0386 0.3972 0.5643 97 G 0.0484 0.4204 0.5312 98 K 0.0413 0.6620 0.2967 99 L 0.0543 0.7486 0.1972 100 W 0.0482 0.8025 0.1493 101 I 0.0481 0.8437 0.1082 102 S 0.0373 0.8679 0.0949 103 A 0.0233 0.8985 0.0782 104 V 0.0125 0.9193 0.0682 105 Y 0.0093 0.9281 0.0626 106 S 0.0083 0.9322 0.0595 107 R 0.0054 0.9475 0.0471 108 A 0.0059 0.9495 0.0447 109 L 0.0056 0.9518 0.0427 110 A 0.0052 0.9546 0.0402 111 L 0.0050 0.9500 0.0450 112 D 0.0050 0.9211 0.0738 113 G 0.0059 0.8449 0.1492 114 L 0.0444 0.3753 0.5804 115 G 0.0376 0.0886 0.8737 116 R 0.0531 0.1332 0.8137 117 G 0.0157 0.7551 0.2291 118 A 0.0070 0.9088 0.0841 119 E 0.0057 0.9314 0.0629 120 A 0.0053 0.9423 0.0525 121 M 0.0051 0.9540 0.0408 122 P 0.0049 0.9542 0.0409 123 E 0.0051 0.9505 0.0443 124 F 0.0049 0.9531 0.0421 125 K 0.0048 0.9536 0.0416 126 K 0.0050 0.9472 0.0478 127 V 0.0051 0.9358 0.0591 128 V 0.0066 0.8970 0.0964 129 E 0.0085 0.7698 0.2217 130 M 0.0270 0.5420 0.4310 131 I 0.0752 0.0868 0.8380 132 E 0.0104 0.3425 0.6472 133 E 0.0145 0.3069 0.6786 134 R 0.0404 0.4093 0.5503 135 K 0.0076 0.8111 0.1813 136 G 0.0079 0.8333 0.1588 137 E 0.0083 0.8567 0.1350 138 T 0.0088 0.8786 0.1126 139 P 0.0092 0.8731 0.1177 140 G 0.0095 0.8703 0.1202 141 K 0.0078 0.9063 0.0859 142 E 0.0074 0.9129 0.0797 143 R 0.0069 0.9349 0.0582 144 M 0.0067 0.9436 0.0496 145 M 0.0060 0.9442 0.0497 146 E 0.0058 0.9203 0.0740 147 V 0.0062 0.8736 0.1202 148 A 0.0436 0.4988 0.4575 149 I 0.0343 0.1650 0.8007 150 D 0.0449 0.2128 0.7423 151 R 0.0116 0.8216 0.1668 152 I 0.0066 0.9184 0.0751 153 A 0.0055 0.9357 0.0589 154 Q 0.0052 0.9437 0.0511 155 L 0.0049 0.9542 0.0408 156 G 0.0048 0.9538 0.0414 157 A 0.0048 0.9513 0.0439 158 S 0.0048 0.9509 0.0442 159 N 0.0048 0.9494 0.0458 160 Q 0.0049 0.9437 0.0514 161 Q 0.0052 0.9279 0.0669 162 K 0.0091 0.8943 0.0967 163 K 0.0111 0.8035 0.1854 164 P 0.0357 0.6286 0.3357 165 G 0.0819 0.1157 0.8025 166 Y 0.0144 0.3447 0.6409 167 K 0.0139 0.3520 0.6341 168 A 0.0516 0.4042 0.5443 169 W 0.0915 0.4504 0.4581 170 W 0.1002 0.4659 0.4339 171 E 0.1085 0.4285 0.4630 172 F 0.0989 0.3115 0.5896 173 W 0.1029 0.1563 0.7408 174 S 0.0511 0.0551 0.8938