# This file is the result of combining several RDB files, specifically # T0393.t04.str2.rdb (weight 1.54425) # T0393.t04.str4.rdb (weight 0.924988) # T0393.t04.pb.rdb (weight 0.789901) # T0393.t04.bys.rdb (weight 0.748322) # T0393.t04.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 T0393.t04.str2.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t04-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 T0393.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 2003 # # ============================================ # Comments from T0393.t04.str4.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t04-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 T0393.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 2003 # # ============================================ # Comments from T0393.t04.pb.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t04-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 T0393.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 2003 # # ============================================ # Comments from T0393.t04.bys.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t04-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 T0393.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 2003 # # ============================================ # Comments from T0393.t04.alpha.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t04-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 T0393.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 2003 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.2423 0.1273 0.6304 2 K 0.2252 0.1231 0.6517 3 R 0.2454 0.2033 0.5513 4 S 0.2174 0.1548 0.6278 5 I 0.1401 0.3665 0.4934 6 E 0.1298 0.2755 0.5948 7 D 0.1776 0.1322 0.6901 8 T 0.3088 0.0416 0.6496 9 P 0.4504 0.0517 0.4979 10 I 0.7737 0.0177 0.2086 11 V 0.7836 0.0162 0.2003 12 L 0.7953 0.0097 0.1950 13 I 0.7097 0.0346 0.2557 14 G 0.5294 0.0528 0.4178 15 A 0.2514 0.1872 0.5613 16 G 0.1392 0.3136 0.5473 17 N 0.0780 0.5179 0.4041 18 L 0.0512 0.5765 0.3723 19 A 0.0280 0.7391 0.2329 20 T 0.0094 0.8666 0.1240 21 N 0.0085 0.9038 0.0877 22 L 0.0084 0.9171 0.0745 23 A 0.0085 0.9103 0.0812 24 K 0.0083 0.9152 0.0764 25 A 0.0084 0.9115 0.0801 26 L 0.0089 0.8980 0.0932 27 Y 0.0092 0.8884 0.1024 28 R 0.0114 0.8264 0.1622 29 K 0.0513 0.2811 0.6676 30 G 0.0462 0.0667 0.8872 31 F 0.2135 0.0198 0.7667 32 R 0.4203 0.0310 0.5488 33 I 0.6836 0.0170 0.2993 34 V 0.6973 0.0208 0.2819 35 Q 0.7625 0.0092 0.2283 36 V 0.7390 0.0178 0.2432 37 Y 0.6218 0.0323 0.3459 38 S 0.3255 0.0373 0.6372 39 R 0.1643 0.1666 0.6691 40 T 0.1625 0.0845 0.7530 41 E 0.0148 0.7239 0.2613 42 E 0.0101 0.8457 0.1441 43 S 0.0118 0.8885 0.0998 44 A 0.0086 0.9111 0.0803 45 R 0.0084 0.9152 0.0765 46 E 0.0083 0.9194 0.0723 47 L 0.0085 0.9156 0.0759 48 A 0.0085 0.9068 0.0847 49 Q 0.0091 0.8749 0.1160 50 K 0.0163 0.7720 0.2117 51 V 0.0622 0.3237 0.6141 52 E 0.0541 0.1245 0.8214 53 A 0.2429 0.0779 0.6792 54 E 0.3760 0.1217 0.5023 55 Y 0.5243 0.1060 0.3698 56 T 0.3918 0.1112 0.4970 57 T 0.3245 0.0794 0.5961 58 D 0.1940 0.0323 0.7737 59 L 0.0224 0.6864 0.2912 60 A 0.0132 0.7498 0.2370 61 E 0.0165 0.8288 0.1547 62 V 0.0368 0.6763 0.2869 63 N 0.0915 0.4778 0.4308 64 P 0.0377 0.5105 0.4518 65 Y 0.0781 0.2422 0.6798 66 A 0.2506 0.1267 0.6227 67 K 0.4570 0.0594 0.4836 68 L 0.7971 0.0047 0.1982 69 Y 0.7662 0.0066 0.2272 70 I 0.8065 0.0042 0.1893 71 V 0.8068 0.0069 0.1862 72 S 0.7504 0.0077 0.2420 73 L 0.4579 0.0271 0.5151 74 K 0.1969 0.0346 0.7685 75 D 0.0713 0.4187 0.5100 76 S 0.0226 0.6900 0.2874 77 A 0.0246 0.7634 0.2120 78 F 0.0133 0.8703 0.1164 79 A 0.0092 0.9038 0.0870 80 E 0.0087 0.9148 0.0765 81 L 0.0093 0.9084 0.0824 82 L 0.0114 0.8604 0.1282 83 Q 0.0216 0.8196 0.1588 84 G 0.0215 0.7108 0.2678 85 I 0.0370 0.7365 0.2265 86 V 0.0537 0.6300 0.3163 87 E 0.0609 0.4889 0.4502 88 G 0.0707 0.3105 0.6188 89 K 0.1631 0.1919 0.6451 90 R 0.1859 0.0818 0.7323 91 E 0.0936 0.3075 0.5989 92 E 0.1063 0.1367 0.7570 93 A 0.4385 0.0244 0.5371 94 L 0.7239 0.0110 0.2651 95 M 0.8013 0.0064 0.1924 96 V 0.7983 0.0076 0.1941 97 H 0.7007 0.0175 0.2817 98 T 0.5250 0.0806 0.3944 99 A 0.3468 0.1342 0.5189 100 G 0.2503 0.1486 0.6011 101 S 0.2179 0.1487 0.6334 102 I 0.2289 0.1033 0.6678 103 P 0.1506 0.2003 0.6491 104 M 0.0421 0.6362 0.3216 105 N 0.0260 0.7920 0.1820 106 V 0.0205 0.8606 0.1189 107 W 0.0200 0.8303 0.1497 108 E 0.0203 0.8199 0.1598 109 G 0.0210 0.7576 0.2214 110 H 0.0461 0.5952 0.3587 111 V 0.1270 0.3170 0.5560 112 P 0.0635 0.4310 0.5055 113 H 0.0693 0.4065 0.5242 114 Y 0.1058 0.2057 0.6886 115 G 0.1489 0.0959 0.7553 116 V 0.4065 0.0487 0.5447 117 F 0.5529 0.0343 0.4128 118 Y 0.4879 0.0260 0.4861 119 P 0.3607 0.1963 0.4430 120 M 0.2990 0.1271 0.5739 121 Q 0.3863 0.0425 0.5713 122 T 0.4111 0.0601 0.5288 123 F 0.3915 0.0790 0.5294 124 S 0.2078 0.0773 0.7150 125 K 0.1163 0.2060 0.6777 126 Q 0.1254 0.1452 0.7294 127 R 0.2019 0.1281 0.6700 128 E 0.1743 0.3679 0.4579 129 V 0.1451 0.5826 0.2724 130 D 0.1415 0.5842 0.2743 131 F 0.1775 0.4786 0.3439 132 K 0.1751 0.2987 0.5262 133 E 0.2016 0.1385 0.6599 134 I 0.3374 0.0411 0.6215 135 P 0.4703 0.0646 0.4652 136 F 0.7373 0.0256 0.2372 137 F 0.7670 0.0167 0.2163 138 I 0.7368 0.0263 0.2369 139 E 0.6245 0.0433 0.3322 140 A 0.3375 0.0742 0.5883 141 S 0.1798 0.0647 0.7555 142 S 0.1519 0.0899 0.7583 143 T 0.0149 0.7132 0.2719 144 E 0.0102 0.8373 0.1525 145 D 0.0098 0.8929 0.0973 146 A 0.0085 0.9116 0.0800 147 A 0.0084 0.9077 0.0839 148 F 0.0086 0.9059 0.0855 149 L 0.0088 0.9024 0.0888 150 K 0.0084 0.9181 0.0735 151 A 0.0084 0.9157 0.0759 152 I 0.0086 0.9125 0.0789 153 A 0.0085 0.9133 0.0782 154 S 0.0088 0.8973 0.0939 155 T 0.0114 0.8320 0.1566 156 L 0.0336 0.6488 0.3176 157 S 0.0566 0.5076 0.4358 158 N 0.0892 0.3798 0.5311 159 R 0.2403 0.2253 0.5343 160 V 0.4456 0.1030 0.4514 161 Y 0.5512 0.0756 0.3732 162 D 0.5307 0.0557 0.4136 163 A 0.3442 0.1231 0.5328 164 D 0.1941 0.0824 0.7235 165 S 0.0379 0.4914 0.4707 166 E 0.0349 0.6064 0.3588 167 Q 0.0469 0.6282 0.3248 168 R 0.0294 0.7783 0.1923 169 K 0.0186 0.8379 0.1435 170 S 0.0236 0.8679 0.1085 171 L 0.0238 0.8785 0.0977 172 H 0.0230 0.8879 0.0891 173 L 0.0261 0.8833 0.0906 174 A 0.0372 0.8335 0.1294 175 A 0.0595 0.7473 0.1932 176 V 0.0507 0.6360 0.3134 177 F 0.0541 0.5208 0.4252 178 T 0.0521 0.5866 0.3613 179 C 0.0173 0.7689 0.2138 180 N 0.0112 0.8761 0.1127 181 F 0.0100 0.9131 0.0769 182 T 0.0085 0.9209 0.0706 183 N 0.0083 0.9243 0.0674 184 H 0.0083 0.9251 0.0666 185 M 0.0083 0.9251 0.0667 186 Y 0.0083 0.9249 0.0668 187 A 0.0083 0.9252 0.0666 188 L 0.0083 0.9249 0.0668 189 A 0.0083 0.9247 0.0671 190 A 0.0083 0.9235 0.0682 191 E 0.0083 0.9230 0.0688 192 L 0.0083 0.9158 0.0759 193 L 0.0085 0.9152 0.0762 194 K 0.0088 0.9108 0.0805 195 K 0.0129 0.8225 0.1645 196 Y 0.0564 0.2157 0.7280 197 N 0.0459 0.0676 0.8865 198 L 0.1557 0.0239 0.8204 199 P 0.1622 0.0200 0.8178 200 F 0.0160 0.7118 0.2722 201 D 0.0125 0.8227 0.1648 202 V 0.0117 0.8736 0.1148 203 M 0.0118 0.8725 0.1157 204 L 0.0101 0.9025 0.0875 205 P 0.0085 0.9171 0.0744 206 L 0.0086 0.9125 0.0789 207 I 0.0092 0.9054 0.0854 208 D 0.0103 0.8966 0.0931 209 E 0.0130 0.8522 0.1348 210 T 0.0303 0.7872 0.1825 211 A 0.0237 0.7353 0.2410 212 R 0.0337 0.6724 0.2939 213 K 0.0396 0.5298 0.4306 214 V 0.0876 0.5264 0.3860 215 H 0.0981 0.5720 0.3298 216 E 0.1420 0.5081 0.3498 217 L 0.2007 0.3212 0.4780 218 E 0.2497 0.1132 0.6371 219 P 0.1729 0.2061 0.6210 220 K 0.1502 0.2594 0.5904 221 T 0.1948 0.1571 0.6480 222 A 0.1902 0.2481 0.5617 223 Q 0.2193 0.1819 0.5988 224 T 0.2176 0.1026 0.6798 225 G 0.1732 0.0782 0.7486 226 P 0.1620 0.1980 0.6400 227 A 0.2301 0.2053 0.5646 228 I 0.2868 0.1288 0.5844 229 R 0.2540 0.1327 0.6134 230 Y 0.2187 0.1136 0.6677 231 D 0.1310 0.3095 0.5595 232 E 0.0482 0.6316 0.3202 233 N 0.0432 0.6776 0.2793 234 V 0.0583 0.7697 0.1720 235 I 0.0368 0.8227 0.1404 236 G 0.0169 0.8828 0.1003 237 N 0.0103 0.8929 0.0968 238 H 0.0121 0.8816 0.1063 239 L 0.0117 0.8940 0.0943 240 R 0.0100 0.8915 0.0985 241 M 0.0105 0.8727 0.1168 242 L 0.0176 0.8447 0.1376 243 A 0.0230 0.7251 0.2518 244 D 0.0305 0.5815 0.3880 245 D 0.0614 0.5001 0.4385 246 P 0.0167 0.7512 0.2320 247 A 0.0136 0.8018 0.1846 248 M 0.0140 0.8319 0.1541 249 Q 0.0136 0.8279 0.1585 250 R 0.0190 0.7785 0.2025 251 L 0.0222 0.8119 0.1659 252 Y 0.0132 0.8827 0.1041 253 E 0.0105 0.9092 0.0803 254 L 0.0097 0.9133 0.0770 255 L 0.0087 0.9142 0.0771 256 S 0.0087 0.9146 0.0767 257 R 0.0086 0.9074 0.0840 258 S 0.0091 0.8944 0.0965 259 I 0.0124 0.8455 0.1421 260 H 0.0159 0.8199 0.1642 261 E 0.0401 0.5961 0.3638 262 R 0.0686 0.3354 0.5959 263 Q 0.0976 0.2191 0.6833