# This file is the result of combining several RDB files, specifically # T0301.t06.dssp-ebghstl.rdb (weight 1.53986) # T0301.t06.stride-ebghtl.rdb (weight 1.24869) # T0301.t06.str2.rdb (weight 1.54758) # T0301.t06.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 T0301.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0301 # 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 T0301.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 9.35855 # # ============================================ # Comments from T0301.t06.stride-ebghtl.rdb # ============================================ # TARGET T0301 # 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 T0301.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 9.35855 # # ============================================ # Comments from T0301.t06.str2.rdb # ============================================ # TARGET T0301 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0301.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 9.35855 # # ============================================ # Comments from T0301.t06.alpha.rdb # ============================================ # TARGET T0301 # 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 T0301.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 9.35855 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0837 0.0402 0.8761 2 A 0.1106 0.0421 0.8473 3 H 0.1031 0.0279 0.8690 4 P 0.0776 0.0393 0.8830 5 P 0.1027 0.1128 0.7845 6 Q 0.2320 0.1583 0.6097 7 I 0.3876 0.0907 0.5218 8 R 0.4630 0.0482 0.4888 9 I 0.3963 0.0249 0.5787 10 P 0.4008 0.0318 0.5675 11 A 0.6744 0.0591 0.2665 12 T 0.7479 0.0798 0.1723 13 Y 0.7495 0.1021 0.1484 14 L 0.6675 0.0913 0.2413 15 R 0.4949 0.0620 0.4431 16 G 0.2823 0.0620 0.6557 17 G 0.1444 0.0720 0.7836 18 T 0.1614 0.0848 0.7538 19 S 0.1707 0.0937 0.7356 20 K 0.1399 0.1644 0.6958 21 G 0.2399 0.1936 0.5665 22 V 0.4823 0.2309 0.2868 23 F 0.6087 0.1666 0.2246 24 F 0.6282 0.1238 0.2480 25 R 0.4898 0.1127 0.3975 26 L 0.0616 0.5937 0.3446 27 E 0.0210 0.5759 0.4031 28 D 0.0288 0.5281 0.4430 29 L 0.0810 0.1303 0.7888 30 P 0.0573 0.1862 0.7564 31 E 0.0296 0.5139 0.4565 32 S 0.0378 0.4275 0.5347 33 C 0.0851 0.2646 0.6503 34 R 0.0809 0.1228 0.7963 35 V 0.0609 0.0485 0.8906 36 P 0.0465 0.0971 0.8564 37 G 0.0276 0.2709 0.7015 38 E 0.0201 0.5351 0.4448 39 A 0.0210 0.7077 0.2713 40 R 0.0138 0.8216 0.1646 41 D 0.0117 0.8460 0.1423 42 R 0.0069 0.9244 0.0687 43 L 0.0085 0.9205 0.0710 44 F 0.0102 0.9282 0.0615 45 M 0.0119 0.9351 0.0529 46 R 0.0163 0.9192 0.0646 47 V 0.0240 0.8692 0.1069 48 I 0.0530 0.5507 0.3962 49 G 0.0840 0.1691 0.7469 50 S 0.1126 0.0528 0.8346 51 P 0.0767 0.0810 0.8424 52 D 0.0878 0.0574 0.8548 53 P 0.0154 0.3617 0.6230 54 Y 0.0216 0.3561 0.6223 55 A 0.0500 0.3938 0.5563 56 A 0.0910 0.2302 0.6788 57 H 0.2891 0.1695 0.5414 58 I 0.4319 0.1183 0.4498 59 D 0.2893 0.1169 0.5938 60 G 0.2267 0.1011 0.6722 61 M 0.2257 0.0969 0.6775 62 G 0.1871 0.0721 0.7408 63 G 0.1283 0.0657 0.8060 64 A 0.1624 0.0704 0.7672 65 T 0.1258 0.0625 0.8118 66 S 0.0932 0.1428 0.7640 67 S 0.0935 0.1463 0.7601 68 T 0.1991 0.0961 0.7048 69 S 0.2874 0.0416 0.6711 70 K 0.6288 0.0184 0.3528 71 C 0.8816 0.0054 0.1130 72 V 0.9192 0.0041 0.0767 73 I 0.9218 0.0034 0.0749 74 L 0.8710 0.0075 0.1215 75 S 0.5851 0.0123 0.4025 76 K 0.1825 0.0881 0.7294 77 S 0.0823 0.0798 0.8380 78 S 0.0858 0.0743 0.8400 79 Q 0.0629 0.0261 0.9110 80 P 0.0319 0.0949 0.8732 81 G 0.0393 0.1327 0.8280 82 H 0.1470 0.0959 0.7570 83 D 0.3288 0.0612 0.6100 84 V 0.5463 0.0736 0.3800 85 D 0.5830 0.0893 0.3277 86 Y 0.7927 0.0415 0.1658 87 L 0.8439 0.0288 0.1273 88 Y 0.8452 0.0283 0.1265 89 G 0.8144 0.0253 0.1603 90 Q 0.8291 0.0200 0.1509 91 V 0.8205 0.0276 0.1520 92 S 0.7970 0.0126 0.1903 93 I 0.5795 0.0401 0.3805 94 D 0.2310 0.0532 0.7157 95 K 0.1514 0.0645 0.7841 96 P 0.1811 0.1226 0.6963 97 F 0.4885 0.1067 0.4047 98 V 0.6595 0.0425 0.2980 99 D 0.4635 0.0357 0.5008 100 W 0.1880 0.1282 0.6838 101 S 0.1292 0.0902 0.7806 102 G 0.0794 0.1123 0.8083 103 N 0.0895 0.1155 0.7950 104 C 0.1605 0.1691 0.6704 105 G 0.1237 0.2084 0.6679 106 N 0.1500 0.3244 0.5256 107 L 0.1589 0.5409 0.3001 108 S 0.1839 0.5604 0.2557 109 T 0.1487 0.5885 0.2628 110 G 0.1278 0.5827 0.2895 111 A 0.1147 0.6154 0.2699 112 G 0.0533 0.6743 0.2725 113 A 0.0219 0.8517 0.1265 114 F 0.0484 0.8402 0.1114 115 A 0.0815 0.8069 0.1116 116 L 0.0965 0.7635 0.1400 117 H 0.0625 0.6781 0.2595 118 A 0.0622 0.3429 0.5948 119 G 0.0554 0.0665 0.8780 120 L 0.1469 0.0354 0.8177 121 V 0.3529 0.0225 0.6246 122 D 0.1389 0.0243 0.8368 123 P 0.0250 0.6057 0.3693 124 A 0.0322 0.5548 0.4130 125 R 0.1724 0.3914 0.4362 126 I 0.2520 0.0435 0.7045 127 P 0.1268 0.0597 0.8135 128 E 0.0508 0.1225 0.8267 129 D 0.0627 0.0685 0.8688 130 G 0.1272 0.0462 0.8266 131 I 0.6621 0.0159 0.3219 132 C 0.8621 0.0065 0.1314 133 E 0.9177 0.0044 0.0779 134 V 0.9235 0.0038 0.0727 135 R 0.9250 0.0047 0.0703 136 I 0.9186 0.0072 0.0741 137 W 0.8636 0.0209 0.1155 138 Q 0.7632 0.0315 0.2053 139 A 0.4421 0.1400 0.4179 140 N 0.2211 0.1295 0.6494 141 I 0.1174 0.1050 0.7777 142 G 0.1323 0.0860 0.7817 143 K 0.5434 0.0537 0.4029 144 T 0.8490 0.0230 0.1280 145 I 0.8991 0.0144 0.0865 146 I 0.9034 0.0123 0.0843 147 A 0.8846 0.0119 0.1035 148 H 0.8564 0.0106 0.1329 149 V 0.8358 0.0065 0.1577 150 P 0.8112 0.0047 0.1840 151 V 0.5119 0.0183 0.4698 152 S 0.2228 0.0534 0.7238 153 G 0.0598 0.0358 0.9044 154 G 0.1491 0.0331 0.8178 155 Q 0.6159 0.0168 0.3672 156 V 0.8515 0.0084 0.1402 157 Q 0.8054 0.0186 0.1760 158 E 0.7795 0.0273 0.1932 159 T 0.5566 0.0316 0.4117 160 G 0.4023 0.0283 0.5694 161 D 0.5379 0.0252 0.4369 162 F 0.7597 0.0187 0.2215 163 E 0.7766 0.0183 0.2050 164 L 0.7590 0.0222 0.2188 165 D 0.4315 0.0550 0.5135 166 G 0.1840 0.0349 0.7810 167 V 0.3981 0.0236 0.5783 168 T 0.4042 0.0251 0.5707 169 F 0.2135 0.0356 0.7509 170 P 0.1553 0.0849 0.7597 171 A 0.1318 0.2335 0.6347 172 A 0.2462 0.1442 0.6095 173 E 0.5014 0.0919 0.4067 174 I 0.7926 0.0287 0.1787 175 V 0.8374 0.0281 0.1344 176 L 0.8501 0.0247 0.1252 177 E 0.7715 0.0285 0.2000 178 F 0.6657 0.0293 0.3050 179 L 0.3877 0.0392 0.5732 180 D 0.1459 0.0233 0.8308 181 P 0.0422 0.1206 0.8372 182 S 0.0585 0.0859 0.8556 183 D 0.0471 0.0480 0.9049