# This file is the result of combining several RDB files, specifically # T0443.t06.str2.rdb (weight 1.54425) # T0443.t06.str4.rdb (weight 0.924988) # T0443.t06.pb.rdb (weight 0.789901) # T0443.t06.bys.rdb (weight 0.748322) # T0443.t06.alpha.rdb (weight 0.678173) # 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 T0443.t06.str2.rdb # ============================================ # TARGET T0443 # Using neural net dunbrack-40pc-3157-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 T0443.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 209 # # ============================================ # Comments from T0443.t06.str4.rdb # ============================================ # TARGET T0443 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-str4-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 21 (1 str4 ) # The input amino acid frequencies were determined from # alignment T0443.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 209 # # ============================================ # Comments from T0443.t06.pb.rdb # ============================================ # TARGET T0443 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-pb-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 16 (1 pb ) # The input amino acid frequencies were determined from # alignment T0443.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 209 # # ============================================ # Comments from T0443.t06.bys.rdb # ============================================ # TARGET T0443 # Using neural net dunbrack-40pc-3157-t06-IDGaaH13-3-13-7-13-9-13-11-bys-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 11 (1 Bystroff ) # The input amino acid frequencies were determined from # alignment T0443.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 209 # # ============================================ # Comments from T0443.t06.alpha.rdb # ============================================ # TARGET T0443 # Using neural net dunbrack-40pc-3157-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 T0443.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 209 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1863 0.0926 0.7211 2 Q 0.1786 0.0367 0.7846 3 P 0.1158 0.4006 0.4837 4 E 0.0214 0.6438 0.3348 5 T 0.0325 0.7131 0.2544 6 S 0.0120 0.8531 0.1349 7 A 0.0086 0.9064 0.0850 8 Q 0.0083 0.9208 0.0709 9 Y 0.0083 0.9219 0.0698 10 Q 0.0083 0.9215 0.0702 11 H 0.0083 0.9222 0.0695 12 R 0.0084 0.9162 0.0754 13 F 0.0085 0.9157 0.0758 14 S 0.0085 0.9126 0.0789 15 Q 0.0086 0.9085 0.0829 16 A 0.0101 0.8728 0.1171 17 I 0.0305 0.7357 0.2338 18 R 0.0465 0.5317 0.4218 19 G 0.0722 0.2284 0.6994 20 G 0.0949 0.2026 0.7025 21 E 0.1298 0.2019 0.6683 22 A 0.1536 0.2130 0.6334 23 A 0.1009 0.4017 0.4974 24 D 0.0762 0.2917 0.6322 25 G 0.0574 0.1723 0.7702 26 L 0.1865 0.0573 0.7563 27 P 0.1502 0.1355 0.7143 28 Q 0.0498 0.6255 0.3247 29 D 0.0334 0.7502 0.2164 30 R 0.0506 0.7868 0.1626 31 L 0.0550 0.8340 0.1109 32 N 0.0334 0.8763 0.0902 33 V 0.0241 0.8972 0.0787 34 Y 0.0129 0.9151 0.0720 35 I 0.0085 0.9222 0.0693 36 R 0.0083 0.9209 0.0707 37 L 0.0083 0.9226 0.0691 38 I 0.0084 0.9211 0.0706 39 R 0.0086 0.9190 0.0724 40 N 0.0088 0.9063 0.0849 41 N 0.0099 0.8984 0.0917 42 I 0.0088 0.9091 0.0822 43 H 0.0084 0.9157 0.0759 44 S 0.0084 0.9195 0.0721 45 F 0.0085 0.9177 0.0738 46 I 0.0087 0.9104 0.0809 47 D 0.0090 0.8877 0.1032 48 R 0.0108 0.8318 0.1574 49 C 0.0216 0.7356 0.2428 50 Y 0.0309 0.7299 0.2392 51 T 0.0125 0.8499 0.1377 52 E 0.0104 0.9018 0.0877 53 T 0.0102 0.9085 0.0813 54 R 0.0097 0.8957 0.0946 55 Q 0.0142 0.8447 0.1411 56 Y 0.0343 0.7061 0.2596 57 F 0.0841 0.4583 0.4575 58 D 0.0981 0.3004 0.6015 59 S 0.0206 0.7168 0.2626 60 K 0.0123 0.8346 0.1530 61 E 0.0141 0.8743 0.1115 62 W 0.0099 0.9062 0.0839 63 S 0.0084 0.9176 0.0740 64 R 0.0084 0.9208 0.0708 65 L 0.0086 0.9191 0.0723 66 K 0.0085 0.9168 0.0747 67 E 0.0084 0.9172 0.0743 68 G 0.0090 0.9052 0.0858 69 F 0.0108 0.8925 0.0967 70 V 0.0125 0.8689 0.1186 71 R 0.0180 0.7984 0.1836 72 D 0.0385 0.5633 0.3982 73 A 0.1123 0.2771 0.6106 74 R 0.0962 0.3049 0.5989 75 A 0.0735 0.3607 0.5658 76 Q 0.0842 0.2720 0.6439 77 T 0.1736 0.1977 0.6287 78 P 0.0816 0.4688 0.4496 79 Y 0.0977 0.5110 0.3912 80 F 0.0806 0.6474 0.2720 81 Q 0.0448 0.7159 0.2394 82 E 0.0608 0.6180 0.3212 83 I 0.1301 0.4440 0.4259 84 P 0.0313 0.6812 0.2875 85 G 0.0146 0.7929 0.1924 86 E 0.0170 0.8276 0.1554 87 F 0.0187 0.8745 0.1069 88 L 0.0103 0.8909 0.0988 89 Q 0.0111 0.8811 0.1078 90 Y 0.0158 0.8302 0.1540 91 C 0.0338 0.7363 0.2299 92 Q 0.0463 0.5339 0.4198 93 S 0.1223 0.2014 0.6764 94 P 0.1445 0.1275 0.7280 95 P 0.1121 0.2004 0.6875 96 L 0.1112 0.1824 0.7064 97 S 0.1064 0.2784 0.6152 98 D 0.0324 0.6193 0.3483 99 G 0.0300 0.6962 0.2737 100 I 0.0209 0.8222 0.1569 101 L 0.0120 0.8919 0.0961 102 A 0.0136 0.8948 0.0916 103 L 0.0187 0.8839 0.0974 104 M 0.0332 0.8541 0.1126 105 D 0.0292 0.8675 0.1033 106 F 0.0235 0.8812 0.0953 107 E 0.0152 0.8964 0.0884 108 Y 0.0136 0.9044 0.0820 109 T 0.0109 0.9066 0.0826 110 Q 0.0142 0.8934 0.0925 111 L 0.0216 0.8542 0.1242 112 L 0.0252 0.8180 0.1568 113 A 0.0302 0.7739 0.1959 114 E 0.0415 0.6834 0.2751 115 V 0.0650 0.6115 0.3235 116 A 0.0574 0.5000 0.4426 117 Q 0.0743 0.3057 0.6199 118 I 0.1884 0.0935 0.7181 119 P 0.1482 0.1645 0.6872 120 D 0.1834 0.1333 0.6833 121 I 0.2283 0.0590 0.7127 122 P 0.1687 0.1237 0.7076 123 D 0.0640 0.5386 0.3974 124 I 0.0593 0.6269 0.3138 125 H 0.0976 0.5304 0.3720 126 Y 0.1213 0.4280 0.4508 127 S 0.1118 0.3300 0.5583 128 N 0.1035 0.3128 0.5837 129 D 0.1350 0.1929 0.6722 130 S 0.2152 0.1469 0.6380 131 K 0.3362 0.1020 0.5618 132 Y 0.4316 0.0574 0.5109 133 T 0.3911 0.0308 0.5781 134 P 0.2845 0.0836 0.6318 135 S 0.2415 0.0642 0.6943 136 P 0.1165 0.3518 0.5317 137 A 0.1660 0.3950 0.4391 138 A 0.4215 0.2859 0.2926 139 F 0.5481 0.2142 0.2377 140 I 0.5835 0.1983 0.2182 141 R 0.5021 0.2300 0.2679 142 Q 0.4915 0.1803 0.3282 143 Y 0.3994 0.1359 0.4648 144 R 0.2665 0.1376 0.5959 145 Y 0.3095 0.0902 0.6004 146 D 0.2278 0.1327 0.6396 147 V 0.2159 0.2762 0.5078 148 T 0.2013 0.2489 0.5498 149 H 0.2104 0.1764 0.6133 150 D 0.1849 0.1175 0.6977 151 L 0.1494 0.2148 0.6357 152 Q 0.0993 0.3741 0.5266 153 E 0.1054 0.3350 0.5595 154 A 0.1879 0.2204 0.5917 155 E 0.2031 0.2648 0.5322 156 T 0.4052 0.1409 0.4539 157 A 0.7093 0.0505 0.2403 158 L 0.7667 0.0214 0.2119 159 L 0.8073 0.0133 0.1794 160 I 0.7894 0.0153 0.1953 161 W 0.7438 0.0165 0.2397 162 R 0.6155 0.0274 0.3571 163 N 0.3286 0.0208 0.6506 164 A 0.0758 0.3909 0.5333 165 E 0.0670 0.2949 0.6381 166 D 0.1099 0.1932 0.6969 167 D 0.2943 0.0962 0.6095 168 V 0.6028 0.0382 0.3590 169 M 0.6435 0.0481 0.3084 170 Y 0.7124 0.0331 0.2546 171 Q 0.6310 0.0571 0.3119 172 T 0.5592 0.0577 0.3831 173 L 0.3989 0.0592 0.5420 174 D 0.1791 0.0492 0.7717 175 G 0.0156 0.7311 0.2533 176 F 0.0127 0.8340 0.1533 177 D 0.0103 0.9057 0.0840 178 M 0.0089 0.9191 0.0720 179 M 0.0083 0.9228 0.0689 180 L 0.0083 0.9239 0.0678 181 L 0.0083 0.9221 0.0695 182 E 0.0083 0.9206 0.0711 183 I 0.0087 0.9093 0.0820 184 M 0.0109 0.8868 0.1023 185 G 0.0138 0.7539 0.2323 186 S 0.0312 0.4521 0.5167 187 S 0.0524 0.2966 0.6510 188 A 0.0906 0.2495 0.6599 189 L 0.1815 0.1406 0.6779 190 S 0.1635 0.0655 0.7711 191 F 0.0141 0.7440 0.2419 192 D 0.0093 0.8645 0.1262 193 T 0.0084 0.9198 0.0718 194 L 0.0084 0.9202 0.0714 195 A 0.0084 0.9180 0.0736 196 Q 0.0083 0.9226 0.0691 197 T 0.0084 0.9202 0.0715 198 L 0.0085 0.9148 0.0767 199 V 0.0088 0.8819 0.1093 200 E 0.0104 0.7848 0.2048 201 F 0.0242 0.6068 0.3689 202 M 0.1078 0.2733 0.6189 203 P 0.0385 0.4465 0.5149 204 K 0.0347 0.5109 0.4544 205 A 0.0392 0.6439 0.3170 206 D 0.0249 0.7468 0.2283 207 N 0.0162 0.8350 0.1488 208 W 0.0103 0.8976 0.0922 209 K 0.0085 0.9163 0.0752 210 N 0.0084 0.9187 0.0729 211 I 0.0085 0.9190 0.0725 212 L 0.0084 0.9174 0.0742 213 L 0.0088 0.9090 0.0821 214 G 0.0093 0.8994 0.0913 215 K 0.0104 0.8965 0.0930 216 W 0.0112 0.8836 0.1052 217 S 0.0106 0.8394 0.1499 218 G 0.0119 0.7761 0.2120 219 W 0.0170 0.8252 0.1578 220 I 0.0232 0.8051 0.1718 221 E 0.0412 0.6587 0.3002 222 Q 0.0720 0.4182 0.5098 223 R 0.1278 0.2451 0.6271 224 I 0.4302 0.1139 0.4560 225 I 0.5187 0.0813 0.4000 226 I 0.4270 0.0631 0.5099 227 P 0.3201 0.1552 0.5247 228 S 0.2569 0.2341 0.5091 229 L 0.2547 0.2356 0.5097 230 S 0.2196 0.2543 0.5261 231 A 0.1939 0.2857 0.5205 232 I 0.1810 0.3256 0.4934 233 S 0.1734 0.3204 0.5062 234 E 0.1385 0.3240 0.5375 235 N 0.1431 0.2259 0.6310 236 M 0.1304 0.2874 0.5822 237 E 0.1108 0.2792 0.6100 238 G 0.0888 0.2214 0.6899 239 N 0.1245 0.1519 0.7236 240 S 0.2036 0.0988 0.6976 241 P 0.1220 0.3474 0.5306 242 S 0.1298 0.4224 0.4478 243 Q 0.1178 0.5760 0.3063 244 N 0.1092 0.5412 0.3496 245 H 0.1448 0.4482 0.4071 246 L 0.1777 0.3506 0.4717 247 S 0.1852 0.1960 0.6187 248 A 0.0632 0.4284 0.5084