# This file is the result of combining several RDB files, specifically # T0379.t06.dssp-ebghstl.rdb (weight 1.53986) # T0379.t06.stride-ebghtl.rdb (weight 1.24869) # T0379.t06.str2.rdb (weight 1.54758) # T0379.t06.alpha.rdb (weight 0.659012) # T0379.t04.dssp-ebghstl.rdb (weight 1.53986) # T0379.t04.stride-ebghtl.rdb (weight 1.24869) # T0379.t04.str2.rdb (weight 1.54758) # T0379.t04.alpha.rdb (weight 0.659012) # T0379.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0379.t2k.stride-ebghtl.rdb (weight 1.24869) # T0379.t2k.str2.rdb (weight 1.54758) # T0379.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 T0379.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 4630 # # ============================================ # Comments from T0379.t06.stride-ebghtl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 4630 # # ============================================ # Comments from T0379.t06.str2.rdb # ============================================ # TARGET T0379 # 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 T0379.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 4630 # # ============================================ # Comments from T0379.t06.alpha.rdb # ============================================ # TARGET T0379 # 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 T0379.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 4630 # # ============================================ # Comments from T0379.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 2240 # # ============================================ # Comments from T0379.t04.stride-ebghtl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 2240 # # ============================================ # Comments from T0379.t04.str2.rdb # ============================================ # TARGET T0379 # 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 T0379.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 2240 # # ============================================ # Comments from T0379.t04.alpha.rdb # ============================================ # TARGET T0379 # 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 T0379.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 2240 # # ============================================ # Comments from T0379.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 926 # # ============================================ # Comments from T0379.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0379 # 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 T0379.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 926 # # ============================================ # Comments from T0379.t2k.str2.rdb # ============================================ # TARGET T0379 # 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 T0379.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 926 # # ============================================ # Comments from T0379.t2k.alpha.rdb # ============================================ # TARGET T0379 # 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 T0379.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 926 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0847 0.0242 0.8911 2 I 0.3023 0.0118 0.6859 3 R 0.5752 0.0398 0.3850 4 N 0.8734 0.0063 0.1203 5 I 0.9203 0.0033 0.0764 6 V 0.9189 0.0038 0.0774 7 F 0.8917 0.0052 0.1031 8 D 0.5907 0.0066 0.4028 9 L 0.0987 0.0850 0.8163 10 G 0.0509 0.0402 0.9088 11 G 0.0810 0.0593 0.8597 12 V 0.4384 0.0333 0.5284 13 L 0.7547 0.0217 0.2236 14 I 0.6724 0.0323 0.2953 15 H 0.3773 0.0353 0.5874 16 L 0.0700 0.1853 0.7447 17 N 0.0521 0.4507 0.4972 18 R 0.0133 0.8168 0.1699 19 E 0.0114 0.8681 0.1205 20 E 0.0085 0.9000 0.0915 21 S 0.0071 0.9236 0.0693 22 I 0.0071 0.9353 0.0576 23 R 0.0062 0.9392 0.0546 24 R 0.0059 0.9386 0.0555 25 F 0.0059 0.9351 0.0590 26 K 0.0061 0.9285 0.0655 27 A 0.0066 0.9162 0.0772 28 I 0.0079 0.8788 0.1133 29 G 0.0094 0.8304 0.1602 30 V 0.0134 0.7593 0.2274 31 A 0.0408 0.5369 0.4223 32 D 0.0392 0.2574 0.7034 33 I 0.0537 0.2948 0.6514 34 E 0.0569 0.3661 0.5769 35 E 0.0542 0.4625 0.4833 36 M 0.0517 0.4991 0.4492 37 L 0.0266 0.7228 0.2506 38 D 0.0173 0.8381 0.1446 39 P 0.0146 0.8746 0.1109 40 Y 0.0142 0.8855 0.1003 41 L 0.0152 0.8785 0.1064 42 Q 0.0155 0.8635 0.1209 43 K 0.0198 0.8271 0.1531 44 G 0.0263 0.7657 0.2080 45 L 0.0342 0.7017 0.2642 46 F 0.0407 0.6411 0.3182 47 L 0.0448 0.6333 0.3219 48 D 0.0380 0.7007 0.2613 49 L 0.0340 0.7664 0.1996 50 E 0.0355 0.7837 0.1808 51 S 0.0361 0.7850 0.1789 52 G 0.0404 0.7525 0.2072 53 R 0.0543 0.7493 0.1964 54 K 0.0578 0.7467 0.1955 55 S 0.0588 0.7105 0.2308 56 E 0.0419 0.7529 0.2052 57 E 0.0336 0.7673 0.1991 58 E 0.0312 0.7557 0.2132 59 F 0.0339 0.7179 0.2482 60 R 0.0375 0.6721 0.2904 61 T 0.0380 0.6435 0.3185 62 E 0.0424 0.6225 0.3350 63 L 0.0435 0.5936 0.3629 64 S 0.0418 0.5758 0.3824 65 R 0.0301 0.5806 0.3894 66 Y 0.0368 0.5532 0.4100 67 I 0.0274 0.5974 0.3752 68 G 0.0262 0.6041 0.3697 69 K 0.0231 0.6412 0.3358 70 E 0.0170 0.7348 0.2481 71 L 0.0115 0.8030 0.1856 72 T 0.0101 0.8482 0.1417 73 Y 0.0085 0.8874 0.1041 74 Q 0.0079 0.9140 0.0781 75 Q 0.0072 0.9280 0.0648 76 V 0.0075 0.9279 0.0646 77 Y 0.0073 0.9249 0.0678 78 D 0.0071 0.9199 0.0730 79 A 0.0076 0.9061 0.0863 80 L 0.0091 0.8679 0.1230 81 L 0.0118 0.7984 0.1899 82 G 0.0145 0.7156 0.2699 83 F 0.0182 0.5812 0.4006 84 L 0.0314 0.3804 0.5882 85 E 0.0743 0.1751 0.7506 86 E 0.0828 0.1191 0.7981 87 I 0.1208 0.0824 0.7968 88 S 0.0699 0.0611 0.8689 89 A 0.0112 0.4595 0.5293 90 E 0.0186 0.4482 0.5332 91 K 0.0093 0.8532 0.1375 92 F 0.0051 0.9438 0.0511 93 D 0.0051 0.9437 0.0512 94 Y 0.0048 0.9498 0.0454 95 I 0.0053 0.9386 0.0561 96 D 0.0059 0.9120 0.0821 97 S 0.0065 0.8647 0.1288 98 L 0.0162 0.7471 0.2367 99 R 0.0259 0.5391 0.4350 100 P 0.0327 0.1861 0.7812 101 D 0.0256 0.0478 0.9266 102 Y 0.1204 0.0141 0.8655 103 R 0.4969 0.0069 0.4962 104 L 0.9217 0.0038 0.0745 105 F 0.9294 0.0034 0.0672 106 L 0.9287 0.0033 0.0679 107 L 0.8817 0.0078 0.1105 108 S 0.5182 0.0220 0.4598 109 N 0.0911 0.0337 0.8751 110 T 0.0596 0.0477 0.8927 111 N 0.0643 0.1161 0.8196 112 P 0.0194 0.7122 0.2684 113 Y 0.0120 0.8142 0.1738 114 V 0.0145 0.8512 0.1343 115 L 0.0163 0.8748 0.1089 116 D 0.0213 0.8713 0.1074 117 L 0.0262 0.8348 0.1390 118 A 0.0276 0.7631 0.2093 119 M 0.0312 0.6609 0.3079 120 S 0.0262 0.3915 0.5823 121 P 0.0229 0.6214 0.3557 122 R 0.0251 0.6343 0.3407 123 F 0.0197 0.6613 0.3190 124 L 0.0192 0.6401 0.3407 125 P 0.0126 0.6165 0.3709 126 S 0.0177 0.6238 0.3586 127 G 0.0340 0.4926 0.4733 128 R 0.0519 0.4121 0.5360 129 T 0.0610 0.2995 0.6395 130 L 0.0474 0.5214 0.4313 131 D 0.0386 0.5898 0.3716 132 S 0.0403 0.5540 0.4057 133 F 0.0995 0.4309 0.4696 134 F 0.1826 0.1363 0.6811 135 D 0.2068 0.1318 0.6613 136 K 0.7957 0.0592 0.1451 137 V 0.8867 0.0303 0.0830 138 Y 0.8726 0.0291 0.0983 139 A 0.6238 0.0525 0.3236 140 S 0.1432 0.2218 0.6351 141 C 0.0429 0.4153 0.5418 142 Q 0.0633 0.5246 0.4121 143 M 0.0878 0.3943 0.5179 144 G 0.0643 0.1835 0.7522 145 K 0.1005 0.1484 0.7511 146 Y 0.1361 0.0979 0.7660 147 K 0.1111 0.0930 0.7959 148 P 0.0882 0.0779 0.8339 149 N 0.0748 0.0713 0.8538 150 E 0.0118 0.7651 0.2231 151 D 0.0074 0.8851 0.1075 152 I 0.0049 0.9438 0.0513 153 F 0.0047 0.9575 0.0378 154 L 0.0047 0.9592 0.0361 155 E 0.0047 0.9601 0.0353 156 M 0.0047 0.9599 0.0354 157 I 0.0048 0.9582 0.0371 158 A 0.0054 0.9447 0.0500 159 D 0.0066 0.8913 0.1021 160 S 0.0457 0.4828 0.4715 161 G 0.0383 0.0289 0.9328 162 M 0.0702 0.0086 0.9212 163 K 0.0757 0.0108 0.9135 164 P 0.0440 0.5735 0.3826 165 E 0.0333 0.6337 0.3329 166 E 0.1886 0.4909 0.3204 167 T 0.7846 0.0235 0.1919 168 L 0.8858 0.0089 0.1052 169 F 0.9032 0.0065 0.0903 170 I 0.7998 0.0432 0.1570 171 D 0.4288 0.0357 0.5354 172 D 0.1208 0.0373 0.8420 173 G 0.0601 0.0479 0.8920 174 P 0.0156 0.5419 0.4425 175 A 0.0130 0.6875 0.2995 176 N 0.0146 0.7414 0.2439 177 V 0.0130 0.9078 0.0792 178 A 0.0089 0.9292 0.0618 179 T 0.0096 0.9410 0.0494 180 A 0.0097 0.9393 0.0510 181 E 0.0082 0.9276 0.0642 182 R 0.0099 0.8774 0.1128 183 L 0.0444 0.3552 0.6004 184 G 0.0511 0.0187 0.9301 185 F 0.1290 0.0090 0.8620 186 H 0.5398 0.0264 0.4338 187 T 0.9098 0.0041 0.0861 188 Y 0.9196 0.0044 0.0760 189 C 0.9181 0.0036 0.0782 190 P 0.8163 0.0084 0.1753 191 D 0.3360 0.0254 0.6385 192 N 0.0866 0.0352 0.8782 193 G 0.0400 0.1936 0.7664 194 E 0.0295 0.3633 0.6072 195 N 0.0430 0.4459 0.5111 196 W 0.0316 0.5649 0.4035 197 I 0.0169 0.7443 0.2388 198 P 0.0136 0.7982 0.1882 199 A 0.0142 0.8343 0.1515 200 I 0.0131 0.8256 0.1613 201 T 0.0115 0.7940 0.1946 202 R 0.0189 0.6434 0.3377 203 L 0.0461 0.3920 0.5620 204 L 0.0480 0.1254 0.8266 205 R 0.0181 0.5300 0.4519 206 E 0.0237 0.4761 0.5002 207 Q 0.0527 0.3690 0.5783 208 K 0.0391 0.1324 0.8285