# This file is the result of combining several RDB files, specifically # T0199.t04.dssp-ebghstl.rdb (weight 1.53986) # T0199.t04.stride-ebghtl.rdb (weight 1.24869) # T0199.t04.str2.rdb (weight 1.54758) # T0199.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 T0199.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0199 # 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 T0199.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 82.279 # # ============================================ # Comments from T0199.t04.stride-ebghtl.rdb # ============================================ # TARGET T0199 # 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 T0199.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 82.279 # # ============================================ # Comments from T0199.t04.str2.rdb # ============================================ # TARGET T0199 # 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 T0199.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 82.279 # # ============================================ # Comments from T0199.t04.alpha.rdb # ============================================ # TARGET T0199 # 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 T0199.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 82.279 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 D 0.0862 0.0196 0.8941 2 P 0.0049 0.9438 0.0513 3 E 0.0047 0.9591 0.0362 4 K 0.0047 0.9610 0.0343 5 V 0.0047 0.9611 0.0342 6 L 0.0047 0.9604 0.0350 7 F 0.0046 0.9610 0.0343 8 L 0.0046 0.9607 0.0347 9 A 0.0047 0.9601 0.0352 10 G 0.0047 0.9602 0.0351 11 N 0.0046 0.9612 0.0342 12 L 0.0047 0.9563 0.0390 13 L 0.0048 0.9437 0.0515 14 A 0.0050 0.8979 0.0971 15 R 0.0058 0.7296 0.2646 16 L 0.0174 0.5794 0.4033 17 T 0.0609 0.2705 0.6686 18 E 0.0503 0.1765 0.7731 19 G 0.1843 0.1110 0.7047 20 Y 0.5040 0.0828 0.4132 21 V 0.8366 0.0394 0.1241 22 L 0.8934 0.0213 0.0853 23 I 0.8850 0.0134 0.1017 24 E 0.7396 0.0211 0.2393 25 R 0.3031 0.0118 0.6851 26 P 0.0963 0.0682 0.8355 27 N 0.0839 0.0636 0.8525 28 T 0.0800 0.1215 0.7986 29 R 0.0882 0.1724 0.7394 30 D 0.1756 0.1528 0.6716 31 L 0.4142 0.0679 0.5179 32 K 0.7168 0.0334 0.2498 33 I 0.8277 0.0122 0.1600 34 L 0.7831 0.0355 0.1814 35 R 0.8880 0.0054 0.1067 36 V 0.9062 0.0034 0.0903 37 M 0.9199 0.0039 0.0762 38 L 0.9073 0.0035 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0.0047 0.9539 0.0414 78 N 0.0051 0.9527 0.0422 79 F 0.0058 0.9446 0.0497 80 L 0.0065 0.9309 0.0626 81 L 0.0133 0.8366 0.1501 82 R 0.0365 0.3374 0.6261 83 G 0.0237 0.0535 0.9227 84 R 0.1163 0.0181 0.8656 85 T 0.1763 0.0156 0.8080 86 V 0.0305 0.7814 0.1881 87 G 0.0302 0.7798 0.1900 88 E 0.0341 0.8055 0.1603 89 V 0.0943 0.5780 0.3277 90 L 0.0781 0.3809 0.5410 91 M 0.0289 0.7443 0.2268 92 G 0.0278 0.6650 0.3072 93 K 0.0310 0.7104 0.2586 94 I 0.0247 0.8185 0.1568 95 E 0.0149 0.8607 0.1244 96 S 0.0111 0.8852 0.1037 97 L 0.0118 0.8684 0.1198 98 K 0.0129 0.8635 0.1237 99 G 0.0099 0.8426 0.1474 100 S 0.0090 0.8861 0.1049 101 G 0.0075 0.9234 0.0691 102 F 0.0050 0.9543 0.0407 103 L 0.0052 0.9570 0.0377 104 R 0.0052 0.9568 0.0379 105 L 0.0047 0.9558 0.0395 106 I 0.0048 0.9541 0.0411 107 E 0.0052 0.9510 0.0438 108 S 0.0079 0.9249 0.0672 109 L 0.0122 0.8579 0.1298 110 I 0.0308 0.6628 0.3065 111 G 0.0337 0.3930 0.5732 112 E 0.0394 0.3701 0.5905 113 T 0.0474 0.4331 0.5195 114 V 0.0438 0.6577 0.2985 115 E 0.0520 0.7297 0.2183 116 R 0.1099 0.7224 0.1678 117 Y 0.2240 0.6530 0.1231 118 L 0.1923 0.6793 0.1284 119 D 0.1108 0.7393 0.1499 120 A 0.0499 0.6196 0.3305 121 G 0.0558 0.3980 0.5462 122 L 0.0697 0.6556 0.2747 123 E 0.0462 0.8226 0.1312 124 N 0.0311 0.8161 0.1527 125 L 0.0335 0.7506 0.2159 126 L 0.0506 0.5153 0.4342 127 K 0.0441 0.3101 0.6458 128 D 0.0684 0.0831 0.8485 129 E 0.0198 0.1945 0.7856 130 T 0.0485 0.1328 0.8188 131 L 0.1275 0.0352 0.8373 132 T 0.0740 0.0159 0.9102 133 L 0.0053 0.9298 0.0650 134 E 0.0047 0.9495 0.0458 135 D 0.0047 0.9523 0.0430 136 I 0.0047 0.9561 0.0392 137 R 0.0047 0.9592 0.0361 138 N 0.0047 0.9563 0.0390 139 L 0.0047 0.9565 0.0388 140 L 0.0047 0.9588 0.0364 141 E 0.0047 0.9600 0.0353 142 E 0.0048 0.9562 0.0391 143 V 0.0049 0.9449 0.0502 144 K 0.0059 0.8576 0.1366 145 D 0.0180 0.6741 0.3079 146 Q 0.0311 0.7304 0.2385 147 K 0.0090 0.8310 0.1600 148 F 0.0131 0.8716 0.1153 149 L 0.0124 0.9180 0.0696 150 E 0.0133 0.9236 0.0631 151 S 0.0119 0.9081 0.0800 152 L 0.0168 0.8587 0.1245 153 V 0.0341 0.6999 0.2660 154 G 0.0440 0.2876 0.6684 155 E 0.0404 0.0658 0.8938 156 G 0.0743 0.0283 0.8974 157 I 0.4924 0.0070 0.5007 158 T 0.8755 0.0037 0.1208 159 V 0.9165 0.0034 0.0801 160 R 0.9008 0.0046 0.0946 161 I 0.7683 0.0228 0.2089 162 G 0.3582 0.0397 0.6020 163 R 0.2322 0.1988 0.5690 164 E 0.1897 0.2872 0.5232 165 I 0.1405 0.2049 0.6546 166 G 0.0742 0.1362 0.7896 167 R 0.0859 0.3025 0.6116 168 K 0.0894 0.4530 0.4575 169 K 0.0915 0.4516 0.4570 170 L 0.1160 0.4408 0.4432 171 E 0.0842 0.4729 0.4429 172 K 0.1393 0.2932 0.5675 173 F 0.5020 0.0982 0.3997 174 A 0.8062 0.0246 0.1692 175 V 0.9039 0.0093 0.0868 176 F 0.9068 0.0072 0.0860 177 S 0.8334 0.0158 0.1508 178 G 0.6926 0.0209 0.2865 179 K 0.6445 0.0299 0.3257 180 Y 0.5779 0.0466 0.3755 181 F 0.3859 0.0566 0.5575 182 K 0.1537 0.0603 0.7860 183 G 0.0556 0.0344 0.9099 184 E 0.0855 0.0402 0.8743 185 S 0.2532 0.0167 0.7301 186 P 0.4738 0.0240 0.5022 187 I 0.6461 0.0274 0.3265 188 G 0.7899 0.0093 0.2008 189 S 0.8762 0.0062 0.1175 190 V 0.9281 0.0032 0.0687 191 Y 0.9301 0.0035 0.0664 192 L 0.9299 0.0031 0.0670 193 F 0.8551 0.0099 0.1350 194 T 0.5352 0.0108 0.4539 195 S 0.3539 0.0434 0.6027 196 K 0.3642 0.0908 0.5450 197 V 0.3945 0.0970 0.5084 198 T 0.2163 0.1101 0.6736 199 K 0.1729 0.1497 0.6774 200 Y 0.0438 0.5379 0.4183 201 D 0.0110 0.7656 0.2233 202 R 0.0089 0.7341 0.2570 203 N 0.0109 0.8172 0.1719 204 H 0.0078 0.8711 0.1211 205 R 0.0078 0.9272 0.0650 206 V 0.0050 0.9534 0.0416 207 F 0.0047 0.9601 0.0352 208 E 0.0046 0.9615 0.0338 209 Y 0.0046 0.9617 0.0337 210 I 0.0047 0.9607 0.0347 211 L 0.0047 0.9604 0.0350 212 N 0.0047 0.9581 0.0372 213 R 0.0048 0.9485 0.0467 214 L 0.0049 0.9441 0.0510 215 S 0.0050 0.9422 0.0528 216 E 0.0052 0.9242 0.0706 217 Y 0.0068 0.8946 0.0986 218 F 0.0176 0.7861 0.1963 219 T 0.0215 0.6408 0.3376 220 S 0.0196 0.5872 0.3932 221 T 0.0285 0.5282 0.4433 222 S 0.0527 0.3741 0.5733 223 R 0.0535 0.1514 0.7951 224 R 0.0508 0.0500 0.8992