# This file is the result of combining several RDB files, specifically # T0274.t04.dssp-ebghstl.rdb (weight 1.53986) # T0274.t04.stride-ebghtl.rdb (weight 1.24869) # T0274.t04.str2.rdb (weight 1.54758) # T0274.t04.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 T0274.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0274 # 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 T0274.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 375 # # ============================================ # Comments from T0274.t04.stride-ebghtl.rdb # ============================================ # TARGET T0274 # 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 T0274.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 375 # # ============================================ # Comments from T0274.t04.str2.rdb # ============================================ # TARGET T0274 # 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 T0274.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 375 # # ============================================ # Comments from T0274.t04.alpha.rdb # ============================================ # TARGET T0274 # 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 T0274.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 375 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0626 0.0162 0.9211 2 N 0.0717 0.0221 0.9062 3 L 0.0088 0.7955 0.1957 4 E 0.0061 0.8764 0.1175 5 A 0.0071 0.8889 0.1040 6 K 0.0065 0.8884 0.1051 7 K 0.0055 0.9375 0.0570 8 K 0.0059 0.9385 0.0556 9 V 0.0068 0.9265 0.0668 10 L 0.0126 0.8896 0.0978 11 R 0.0176 0.7683 0.2142 12 S 0.0282 0.5511 0.4208 13 F 0.0697 0.1524 0.7780 14 T 0.0806 0.1106 0.8088 15 Y 0.1658 0.0630 0.7712 16 G 0.3581 0.0321 0.6098 17 L 0.7632 0.0063 0.2305 18 Y 0.9153 0.0036 0.0811 19 V 0.9294 0.0032 0.0674 20 L 0.9212 0.0035 0.0753 21 T 0.8786 0.0046 0.1168 22 A 0.6888 0.0099 0.3012 23 K 0.3128 0.0296 0.6576 24 D 0.1024 0.0381 0.8596 25 G 0.0432 0.0421 0.9147 26 D 0.0566 0.0467 0.8967 27 E 0.4744 0.0280 0.4977 28 V 0.6643 0.0217 0.3140 29 A 0.7155 0.0273 0.2572 30 A 0.7985 0.0284 0.1732 31 G 0.7737 0.0282 0.1981 32 T 0.7928 0.0347 0.1724 33 V 0.6730 0.1093 0.2177 34 N 0.6169 0.1335 0.2496 35 W 0.5853 0.1482 0.2665 36 V 0.5829 0.1257 0.2914 37 T 0.5252 0.1147 0.3600 38 Q 0.4187 0.1617 0.4196 39 A 0.3698 0.1424 0.4878 40 S 0.3167 0.0951 0.5882 41 F 0.2092 0.0783 0.7125 42 Q 0.1173 0.0386 0.8441 43 P 0.1224 0.0316 0.8460 44 P 0.2603 0.0264 0.7133 45 L 0.7665 0.0083 0.2252 46 V 0.9157 0.0035 0.0809 47 A 0.9317 0.0032 0.0650 48 V 0.9255 0.0040 0.0705 49 G 0.8923 0.0056 0.1021 50 L 0.6804 0.0133 0.3063 51 K 0.2680 0.0236 0.7084 52 R 0.0986 0.0782 0.8231 53 D 0.0555 0.1985 0.7460 54 S 0.0211 0.5055 0.4734 55 H 0.0333 0.6188 0.3479 56 L 0.0235 0.8213 0.1552 57 H 0.0073 0.9298 0.0629 58 A 0.0073 0.9455 0.0473 59 L 0.0097 0.9479 0.0424 60 V 0.0161 0.9327 0.0512 61 E 0.0092 0.9187 0.0721 62 R 0.0127 0.8011 0.1863 63 T 0.0494 0.2367 0.7139 64 G 0.0402 0.0356 0.9243 65 K 0.3347 0.0131 0.6523 66 L 0.8825 0.0036 0.1140 67 A 0.9241 0.0035 0.0724 68 L 0.9243 0.0039 0.0719 69 M 0.8709 0.0095 0.1195 70 T 0.5977 0.0157 0.3866 71 L 0.1755 0.0370 0.7875 72 A 0.0676 0.0981 0.8342 73 H 0.0101 0.6763 0.3136 74 D 0.0113 0.7696 0.2191 75 Q 0.0055 0.9205 0.0740 76 K 0.0053 0.9484 0.0463 77 A 0.0053 0.9467 0.0481 78 I 0.0053 0.9468 0.0480 79 A 0.0054 0.9452 0.0494 80 Q 0.0053 0.9306 0.0641 81 D 0.0071 0.8572 0.1357 82 F 0.0158 0.6952 0.2890 83 F 0.0517 0.3665 0.5818 84 K 0.0642 0.1410 0.7948 85 P 0.0721 0.1424 0.7855 86 T 0.1108 0.0758 0.8134 87 V 0.0768 0.0734 0.8498 88 R 0.0561 0.1196 0.8243 89 E 0.0588 0.2389 0.7022 90 G 0.0722 0.2434 0.6844 91 D 0.0990 0.2615 0.6394 92 R 0.1651 0.3816 0.4533 93 L 0.2298 0.3262 0.4440 94 N 0.1490 0.2538 0.5973 95 G 0.1248 0.1154 0.7598 96 H 0.1948 0.0290 0.7761 97 P 0.2292 0.0348 0.7361 98 F 0.2915 0.0273 0.6812 99 E 0.4089 0.0218 0.5693 100 P 0.3575 0.0272 0.6153 101 S 0.1592 0.0277 0.8131 102 P 0.0793 0.1288 0.7920 103 T 0.0758 0.1218 0.8024 104 F 0.1106 0.0772 0.8122 105 G 0.0835 0.0439 0.8726 106 L 0.1490 0.0700 0.7810 107 P 0.2102 0.1227 0.6671 108 L 0.3182 0.2922 0.3896 109 L 0.1846 0.4405 0.3749 110 T 0.1045 0.4362 0.4592 111 E 0.1196 0.2636 0.6168 112 L 0.2568 0.0928 0.6504 113 P 0.2761 0.1380 0.5858 114 Y 0.7195 0.0674 0.2131 115 W 0.8679 0.0363 0.0958 116 L 0.8894 0.0274 0.0832 117 E 0.8620 0.0271 0.1109 118 A 0.8041 0.0178 0.1781 119 E 0.8276 0.0186 0.1538 120 V 0.8276 0.0195 0.1529 121 R 0.7843 0.0440 0.1717 122 H 0.8272 0.0178 0.1550 123 L 0.8080 0.0226 0.1694 124 Y 0.6701 0.0158 0.3141 125 P 0.4429 0.0281 0.5290 126 G 0.1535 0.0664 0.7801 127 G 0.1378 0.0598 0.8025 128 D 0.1746 0.0531 0.7723 129 H 0.4461 0.0293 0.5245 130 S 0.7724 0.0113 0.2163 131 L 0.9198 0.0043 0.0759 132 V 0.9250 0.0035 0.0715 133 V 0.9154 0.0053 0.0793 134 A 0.8924 0.0058 0.1018 135 E 0.9030 0.0047 0.0923 136 V 0.9145 0.0044 0.0811 137 V 0.8536 0.0307 0.1157 138 E 0.8887 0.0117 0.0996 139 A 0.8151 0.0196 0.1653 140 G 0.7663 0.0213 0.2124 141 V 0.6451 0.0257 0.3292 142 R 0.3978 0.0399 0.5623 143 R 0.1406 0.1525 0.7070 144 E 0.0713 0.1526 0.7761 145 E 0.0914 0.0872 0.8214 146 K 0.1293 0.0247 0.8460 147 P 0.2666 0.0319 0.7015 148 L 0.6945 0.0269 0.2786 149 V 0.8517 0.0164 0.1319 150 M 0.8592 0.0143 0.1265 151 W 0.7382 0.0331 0.2287 152 D 0.3173 0.0488 0.6339 153 T 0.1271 0.0490 0.8239 154 G 0.2120 0.0601 0.7279 155 W 0.4974 0.0621 0.4405 156 F 0.5306 0.0499 0.4195 157 Y 0.3513 0.0524 0.5963 158 G 0.1638 0.0403 0.7959 159 G 0.0708 0.0296 0.8996