# This file is the result of combining several RDB files, specifically # T0632.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0632.t2k.stride-ebghtl.rdb (weight 1.24869) # T0632.t2k.str2.rdb (weight 1.54758) # T0632.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 T0632.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0632 # 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 T0632.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 1934 # # ============================================ # Comments from T0632.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0632 # 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 T0632.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 1934 # # ============================================ # Comments from T0632.t2k.str2.rdb # ============================================ # TARGET T0632 # 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 T0632.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 1934 # # ============================================ # Comments from T0632.t2k.alpha.rdb # ============================================ # TARGET T0632 # 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 T0632.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 1934 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0304 0.1323 0.8373 2 D 0.0614 0.3977 0.5408 3 K 0.0678 0.5521 0.3801 4 R 0.0735 0.6073 0.3192 5 L 0.0683 0.5362 0.3955 6 Q 0.0665 0.3841 0.5494 7 Q 0.0497 0.3442 0.6061 8 D 0.0660 0.2515 0.6825 9 R 0.0386 0.5364 0.4250 10 I 0.0500 0.6830 0.2669 11 V 0.0469 0.7295 0.2236 12 D 0.0494 0.7162 0.2345 13 K 0.0418 0.7062 0.2521 14 M 0.0456 0.6717 0.2827 15 E 0.0432 0.5685 0.3883 16 R 0.0388 0.4338 0.5274 17 F 0.0736 0.1234 0.8030 18 L 0.0225 0.3250 0.6525 19 S 0.0265 0.3822 0.5912 20 T 0.0508 0.5133 0.4359 21 A 0.0581 0.5487 0.3932 22 N 0.0880 0.5109 0.4011 23 E 0.0808 0.5072 0.4119 24 E 0.0981 0.4355 0.4664 25 E 0.0608 0.5652 0.3740 26 K 0.0449 0.5998 0.3552 27 D 0.0410 0.4648 0.4941 28 V 0.0488 0.3189 0.6323 29 L 0.0695 0.1011 0.8294 30 S 0.0551 0.0856 0.8593 31 S 0.0186 0.5622 0.4193 32 I 0.0120 0.6890 0.2990 33 V 0.0151 0.7118 0.2732 34 D 0.0176 0.7734 0.2090 35 G 0.0129 0.8447 0.1424 36 L 0.0134 0.8512 0.1354 37 L 0.0170 0.8303 0.1527 38 A 0.0218 0.8328 0.1454 39 K 0.0219 0.7980 0.1800 40 Q 0.0298 0.6781 0.2922 41 E 0.0512 0.5086 0.4402 42 R 0.0770 0.4353 0.4877 43 R 0.0892 0.3392 0.5717 44 Y 0.0634 0.2764 0.6602 45 A 0.0527 0.2273 0.7200 46 T 0.0584 0.2716 0.6700 47 Y 0.0522 0.4149 0.5329 48 L 0.0588 0.5370 0.4042 49 A 0.0782 0.5707 0.3511 50 S 0.1013 0.5078 0.3909 51 L 0.1504 0.3728 0.4768 52 T 0.1717 0.1380 0.6903 53 Q 0.2023 0.0322 0.7655 54 I 0.6218 0.0092 0.3690 55 E 0.8536 0.0061 0.1402 56 S 0.9049 0.0032 0.0919 57 Q 0.8805 0.0133 0.1062 58 E 0.8817 0.0047 0.1137 59 R 0.7258 0.0220 0.2522 60 E 0.3936 0.0285 0.5779 61 D 0.0438 0.0493 0.9069 62 G 0.0525 0.0417 0.9058 63 R 0.7230 0.0081 0.2689 64 F 0.9135 0.0033 0.0832 65 E 0.9270 0.0040 0.0690 66 V 0.9197 0.0042 0.0761 67 R 0.9085 0.0045 0.0870 68 L 0.7970 0.0063 0.1967 69 P 0.5459 0.0080 0.4461 70 I 0.2560 0.0282 0.7158 71 G 0.0966 0.0401 0.8632 72 P 0.0226 0.4811 0.4963 73 L 0.0235 0.5616 0.4149 74 V 0.0596 0.5761 0.3644 75 N 0.0758 0.3575 0.5667 76 N 0.0714 0.1511 0.7775 77 P 0.0701 0.1541 0.7759 78 L 0.0647 0.2449 0.6904 79 N 0.0912 0.2824 0.6264 80 M 0.2202 0.4163 0.3635 81 V 0.2417 0.5311 0.2272 82 H 0.1141 0.6859 0.2000 83 G 0.0219 0.8229 0.1553 84 G 0.0076 0.9227 0.0697 85 I 0.0048 0.9537 0.0415 86 T 0.0047 0.9578 0.0374 87 A 0.0047 0.9567 0.0386 88 T 0.0048 0.9539 0.0413 89 L 0.0048 0.9557 0.0395 90 L 0.0048 0.9512 0.0439 91 D 0.0051 0.9461 0.0488 92 T 0.0053 0.9464 0.0482 93 A 0.0052 0.9420 0.0528 94 M 0.0053 0.9414 0.0533 95 G 0.0050 0.9354 0.0596 96 Q 0.0062 0.9347 0.0591 97 M 0.0078 0.9346 0.0576 98 V 0.0103 0.9041 0.0856 99 N 0.0184 0.8361 0.1456 100 R 0.0309 0.6830 0.2861 101 Q 0.0702 0.4153 0.5145 102 L 0.1098 0.0776 0.8126 103 P 0.0618 0.0665 0.8717 104 D 0.0292 0.1154 0.8554 105 G 0.0356 0.0734 0.8910 106 Q 0.2117 0.0328 0.7555 107 S 0.5615 0.0147 0.4239 108 A 0.7998 0.0088 0.1914 109 V 0.8512 0.0070 0.1418 110 T 0.8749 0.0054 0.1198 111 S 0.8746 0.0082 0.1172 112 E 0.9087 0.0040 0.0873 113 L 0.8977 0.0054 0.0970 114 N 0.9055 0.0035 0.0910 115 I 0.8924 0.0062 0.1014 116 H 0.8630 0.0132 0.1238 117 Y 0.8553 0.0151 0.1296 118 V 0.7711 0.0254 0.2034 119 K 0.7151 0.0207 0.2643 120 P 0.5771 0.0294 0.3935 121 G 0.3005 0.0337 0.6658 122 M 0.1121 0.0576 0.8303 123 G 0.0506 0.0379 0.9115 124 T 0.1502 0.0335 0.8162 125 Y 0.6875 0.0055 0.3070 126 L 0.9044 0.0034 0.0922 127 R 0.9225 0.0041 0.0733 128 A 0.9227 0.0041 0.0731 129 V 0.9163 0.0055 0.0782 130 A 0.9002 0.0052 0.0946 131 S 0.8960 0.0055 0.0985 132 I 0.9078 0.0030 0.0893 133 V 0.8378 0.0167 0.1455 134 H 0.7935 0.0081 0.1985 135 Q 0.3618 0.0501 0.5881 136 G 0.1786 0.0308 0.7906 137 K 0.2693 0.0300 0.7007 138 Q 0.7060 0.0070 0.2870 139 R 0.8960 0.0036 0.1004 140 I 0.9201 0.0035 0.0764 141 V 0.9300 0.0030 0.0670 142 V 0.9230 0.0038 0.0731 143 E 0.9268 0.0031 0.0701 144 G 0.9116 0.0045 0.0839 145 K 0.9225 0.0036 0.0739 146 V 0.9085 0.0036 0.0880 147 Y 0.8729 0.0067 0.1203 148 T 0.4280 0.0132 0.5588 149 D 0.0193 0.1064 0.8742 150 Q 0.0469 0.0175 0.9355 151 G 0.0839 0.0256 0.8905 152 E 0.4593 0.0081 0.5326 153 T 0.9078 0.0030 0.0892 154 V 0.8884 0.0102 0.1014 155 A 0.9253 0.0035 0.0712 156 M 0.9228 0.0043 0.0730 157 G 0.9203 0.0039 0.0758 158 T 0.9195 0.0048 0.0757 159 G 0.9078 0.0049 0.0872 160 S 0.9164 0.0050 0.0786 161 F 0.9133 0.0046 0.0821 162 F 0.9042 0.0044 0.0915 163 V 0.8697 0.0052 0.1251 164 L 0.6407 0.0122 0.3471 165 R 0.3379 0.0194 0.6427 166 S 0.1121 0.0645 0.8234 167 R 0.0671 0.0577 0.8752 168 G 0.0378 0.0386 0.9236