# This file is the result of combining several RDB files, specifically # T0554.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0554.t2k.stride-ebghtl.rdb (weight 1.24869) # T0554.t2k.str.rdb (weight 1.53983) # 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 T0554.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0554 # 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 T0554.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 295 # # ============================================ # Comments from T0554.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0554 # 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 T0554.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 295 # # ============================================ # Comments from T0554.t2k.str.rdb # ============================================ # TARGET T0554 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0554.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 295 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0324 0.0092 0.9584 2 P 0.1519 0.0088 0.8393 3 V 0.6350 0.0124 0.3526 4 E 0.7446 0.0170 0.2384 5 L 0.6870 0.0119 0.3011 6 R 0.3085 0.0177 0.6738 7 A 0.0957 0.0200 0.8843 8 N 0.0294 0.0178 0.9527 9 W 0.0355 0.0133 0.9512 10 S 0.0151 0.0122 0.9728 11 E 0.0039 0.9090 0.0871 12 E 0.0038 0.9447 0.0516 13 D 0.0037 0.9609 0.0354 14 L 0.0037 0.9692 0.0271 15 E 0.0037 0.9727 0.0236 16 T 0.0037 0.9734 0.0229 17 V 0.0037 0.9727 0.0236 18 I 0.0037 0.9734 0.0229 19 R 0.0037 0.9755 0.0207 20 A 0.0037 0.9759 0.0204 21 V 0.0037 0.9752 0.0211 22 Y 0.0037 0.9741 0.0222 23 R 0.0037 0.9707 0.0256 24 Q 0.0037 0.9639 0.0324 25 V 0.0038 0.9362 0.0600 26 L 0.0043 0.8310 0.1647 27 G 0.0094 0.4830 0.5076 28 N 0.0232 0.2937 0.6831 29 D 0.0709 0.2072 0.7219 30 Y 0.1359 0.2433 0.6208 31 V 0.1402 0.2693 0.5904 32 M 0.1239 0.3172 0.5589 33 A 0.0860 0.4295 0.4845 34 S 0.0516 0.4727 0.4758 35 E 0.0554 0.4338 0.5107 36 R 0.0707 0.4021 0.5273 37 L 0.0620 0.5182 0.4198 38 V 0.0345 0.6649 0.3006 39 S 0.0258 0.7043 0.2699 40 A 0.0075 0.9104 0.0821 41 E 0.0059 0.9401 0.0540 42 S 0.0054 0.9480 0.0465 43 L 0.0048 0.9434 0.0518 44 L 0.0077 0.9175 0.0749 45 R 0.0070 0.8203 0.1727 46 N 0.0065 0.3982 0.5953 47 G 0.0151 0.0713 0.9136 48 K 0.1068 0.0370 0.8561 49 I 0.5250 0.0293 0.4457 50 T 0.4325 0.0337 0.5338 51 V 0.0098 0.9236 0.0666 52 R 0.0041 0.9625 0.0334 53 E 0.0037 0.9744 0.0219 54 F 0.0037 0.9742 0.0221 55 V 0.0037 0.9720 0.0243 56 R 0.0041 0.9659 0.0300 57 A 0.0038 0.9464 0.0498 58 V 0.0049 0.9007 0.0944 59 A 0.0104 0.6505 0.3391 60 K 0.0074 0.5077 0.4848 61 S 0.0081 0.3513 0.6405 62 E 0.0039 0.9245 0.0716 63 L 0.0038 0.9308 0.0654 64 Y 0.0042 0.9441 0.0517 65 K 0.0056 0.9359 0.0585 66 E 0.0098 0.8993 0.0909 67 K 0.0100 0.8383 0.1517 68 F 0.0303 0.6902 0.2795 69 L 0.0775 0.4535 0.4691 70 Y 0.0655 0.3522 0.5823 71 G 0.0278 0.3246 0.6475 72 N 0.0218 0.2745 0.7037 73 F 0.0189 0.2986 0.6825 74 Q 0.0118 0.6378 0.3505 75 T 0.0151 0.8617 0.1232 76 R 0.0112 0.9417 0.0471 77 V 0.0126 0.9570 0.0304 78 I 0.0066 0.9705 0.0229 79 E 0.0055 0.9730 0.0215 80 L 0.0044 0.9752 0.0204 81 N 0.0037 0.9752 0.0211 82 Y 0.0037 0.9730 0.0232 83 K 0.0037 0.9634 0.0329 84 H 0.0037 0.9375 0.0588 85 L 0.0056 0.8822 0.1122 86 L 0.0102 0.5909 0.3989 87 G 0.0153 0.0715 0.9131 88 R 0.0290 0.0440 0.9270 89 A 0.0315 0.0401 0.9284 90 P 0.0358 0.0620 0.9022 91 Y 0.0317 0.0364 0.9319 92 D 0.0140 0.0493 0.9367 93 E 0.0038 0.9489 0.0474 94 S 0.0038 0.9658 0.0304 95 E 0.0038 0.9694 0.0268 96 V 0.0037 0.9737 0.0226 97 I 0.0037 0.9723 0.0239 98 F 0.0037 0.9667 0.0296 99 H 0.0037 0.9692 0.0270 100 L 0.0037 0.9709 0.0254 101 D 0.0037 0.9716 0.0246 102 L 0.0037 0.9728 0.0235 103 Y 0.0038 0.9689 0.0274 104 E 0.0037 0.9534 0.0428 105 N 0.0041 0.8973 0.0986 106 E 0.0042 0.7019 0.2939 107 G 0.0123 0.3092 0.6785 108 F 0.0274 0.5136 0.4590 109 D 0.0575 0.7227 0.2198 110 A 0.1054 0.7800 0.1146 111 D 0.1245 0.8032 0.0722 112 I 0.1336 0.8084 0.0580 113 D 0.0929 0.8184 0.0887 114 S 0.0496 0.8306 0.1198 115 Y 0.0542 0.7921 0.1537 116 I 0.0802 0.6123 0.3075 117 D 0.0386 0.3327 0.6287 118 S 0.0071 0.5619 0.4310 119 P 0.0038 0.9576 0.0387 120 E 0.0037 0.9697 0.0266 121 Y 0.0037 0.9719 0.0244 122 T 0.0037 0.9637 0.0326 123 N 0.0045 0.9292 0.0663 124 S 0.0049 0.8506 0.1445 125 F 0.0097 0.5590 0.4313 126 G 0.0187 0.1577 0.8235 127 D 0.0296 0.2037 0.7667 128 W 0.1012 0.2162 0.6826 129 V 0.2358 0.1776 0.5866 130 V 0.2886 0.0795 0.6319 131 P 0.2798 0.1072 0.6129 132 Y 0.2757 0.1598 0.5645 133 Y 0.2197 0.1423 0.6381 134 R 0.0990 0.0705 0.8305 135 G 0.0132 0.0109 0.9759