# This file is the result of combining several RDB files, specifically # T0393.t2k.str2.rdb (weight 1.54425) # T0393.t2k.str4.rdb (weight 0.924988) # T0393.t2k.pb.rdb (weight 0.789901) # T0393.t2k.bys.rdb (weight 0.748322) # T0393.t2k.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.t2k.str2.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 511 # # ============================================ # Comments from T0393.t2k.str4.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 511 # # ============================================ # Comments from T0393.t2k.pb.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 511 # # ============================================ # Comments from T0393.t2k.bys.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 511 # # ============================================ # Comments from T0393.t2k.alpha.rdb # ============================================ # TARGET T0393 # Using neural net dunbrack-40pc-3157-t2k-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.t2k-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 511 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3693 0.1697 0.4611 2 K 0.2852 0.1718 0.5430 3 R 0.2424 0.2085 0.5491 4 S 0.2163 0.1473 0.6364 5 I 0.0903 0.4103 0.4995 6 E 0.0735 0.3334 0.5932 7 D 0.0749 0.1572 0.7678 8 T 0.2948 0.0197 0.6855 9 P 0.4859 0.0166 0.4975 10 I 0.7930 0.0068 0.2002 11 V 0.8190 0.0047 0.1763 12 L 0.7764 0.0053 0.2183 13 I 0.7452 0.0176 0.2373 14 G 0.5872 0.0257 0.3872 15 A 0.2118 0.2122 0.5759 16 G 0.0765 0.4057 0.5178 17 N 0.0253 0.7702 0.2044 18 L 0.0130 0.8831 0.1039 19 A 0.0084 0.9196 0.0720 20 T 0.0083 0.9212 0.0705 21 N 0.0083 0.9251 0.0667 22 L 0.0083 0.9229 0.0688 23 A 0.0083 0.9227 0.0690 24 K 0.0083 0.9239 0.0679 25 A 0.0083 0.9243 0.0675 26 L 0.0083 0.9199 0.0718 27 Y 0.0088 0.8888 0.1025 28 R 0.0115 0.8202 0.1683 29 K 0.0539 0.2125 0.7335 30 G 0.0487 0.0633 0.8880 31 F 0.2199 0.0230 0.7571 32 R 0.4676 0.0293 0.5031 33 I 0.7558 0.0123 0.2319 34 V 0.7946 0.0084 0.1970 35 Q 0.7990 0.0062 0.1948 36 V 0.7815 0.0101 0.2084 37 Y 0.6905 0.0355 0.2740 38 S 0.4296 0.0528 0.5176 39 R 0.2154 0.1265 0.6580 40 T 0.1639 0.0441 0.7921 41 E 0.0120 0.7372 0.2508 42 E 0.0093 0.8663 0.1243 43 S 0.0090 0.9107 0.0802 44 A 0.0086 0.9148 0.0766 45 R 0.0083 0.9241 0.0676 46 E 0.0083 0.9236 0.0681 47 L 0.0084 0.9181 0.0734 48 A 0.0087 0.9036 0.0877 49 Q 0.0091 0.8851 0.1057 50 K 0.0193 0.7297 0.2511 51 V 0.0715 0.4234 0.5051 52 E 0.0709 0.1462 0.7829 53 A 0.1845 0.1225 0.6930 54 E 0.2710 0.1293 0.5997 55 Y 0.3483 0.1536 0.4981 56 T 0.2731 0.2241 0.5028 57 T 0.2145 0.2650 0.5205 58 D 0.1766 0.1850 0.6384 59 L 0.0315 0.6776 0.2909 60 A 0.0146 0.7894 0.1961 61 E 0.0207 0.7453 0.2340 62 V 0.0613 0.6063 0.3324 63 N 0.1292 0.3707 0.5002 64 P 0.0421 0.4772 0.4807 65 Y 0.0805 0.2511 0.6684 66 A 0.2296 0.1462 0.6242 67 K 0.4066 0.0706 0.5228 68 L 0.7656 0.0107 0.2236 69 Y 0.7728 0.0070 0.2201 70 I 0.8030 0.0055 0.1915 71 V 0.7995 0.0101 0.1904 72 S 0.7483 0.0129 0.2388 73 L 0.4071 0.0286 0.5644 74 K 0.2156 0.0518 0.7326 75 D 0.0815 0.3415 0.5771 76 S 0.0258 0.6278 0.3464 77 A 0.0299 0.7517 0.2184 78 F 0.0153 0.8764 0.1083 79 A 0.0094 0.9104 0.0802 80 E 0.0087 0.9193 0.0721 81 L 0.0087 0.9159 0.0754 82 L 0.0091 0.9046 0.0863 83 Q 0.0092 0.8720 0.1189 84 G 0.0129 0.7551 0.2320 85 I 0.0306 0.7078 0.2616 86 V 0.0499 0.5642 0.3859 87 E 0.0535 0.4671 0.4794 88 G 0.0590 0.2909 0.6500 89 K 0.1574 0.2036 0.6390 90 R 0.1864 0.1088 0.7048 91 E 0.1432 0.2338 0.6230 92 E 0.1753 0.1402 0.6845 93 A 0.4936 0.0257 0.4807 94 L 0.7362 0.0084 0.2554 95 M 0.8007 0.0058 0.1935 96 V 0.8053 0.0070 0.1877 97 H 0.7154 0.0117 0.2729 98 T 0.5571 0.0604 0.3825 99 A 0.3061 0.0889 0.6051 100 G 0.2061 0.0905 0.7035 101 S 0.2369 0.1062 0.6569 102 I 0.2679 0.0524 0.6797 103 P 0.2046 0.1167 0.6787 104 M 0.1207 0.4733 0.4060 105 N 0.1116 0.5435 0.3449 106 V 0.0942 0.6231 0.2828 107 W 0.0985 0.5934 0.3081 108 E 0.0729 0.5852 0.3419 109 G 0.0513 0.4729 0.4758 110 H 0.0988 0.3586 0.5426 111 V 0.1722 0.1877 0.6401 112 P 0.0991 0.3705 0.5304 113 H 0.1104 0.3161 0.5735 114 Y 0.1811 0.1861 0.6328 115 G 0.2909 0.0916 0.6175 116 V 0.5282 0.0494 0.4224 117 F 0.5863 0.0402 0.3735 118 Y 0.5150 0.0296 0.4555 119 P 0.3709 0.1298 0.4994 120 M 0.2731 0.1543 0.5726 121 Q 0.2822 0.1012 0.6166 122 T 0.1985 0.1792 0.6223 123 F 0.1841 0.1788 0.6372 124 S 0.1578 0.1449 0.6972 125 K 0.0752 0.4293 0.4954 126 Q 0.0987 0.4592 0.4421 127 R 0.1384 0.4898 0.3719 128 E 0.1495 0.5323 0.3181 129 V 0.1687 0.5476 0.2837 130 D 0.1382 0.4800 0.3817 131 F 0.1514 0.3644 0.4842 132 K 0.1659 0.2675 0.5666 133 E 0.2094 0.1881 0.6025 134 I 0.3496 0.0852 0.5652 135 P 0.4195 0.1294 0.4511 136 F 0.5661 0.1339 0.3000 137 F 0.5963 0.1328 0.2708 138 I 0.4964 0.1791 0.3245 139 E 0.3365 0.2476 0.4158 140 A 0.2030 0.2054 0.5916 141 S 0.1575 0.1441 0.6984 142 S 0.1576 0.1497 0.6927 143 T 0.0148 0.7312 0.2540 144 E 0.0104 0.8578 0.1319 145 D 0.0102 0.9045 0.0853 146 A 0.0085 0.9153 0.0762 147 A 0.0083 0.9213 0.0704 148 F 0.0083 0.9233 0.0684 149 L 0.0083 0.9209 0.0707 150 K 0.0083 0.9230 0.0687 151 A 0.0083 0.9242 0.0676 152 I 0.0084 0.9174 0.0742 153 A 0.0086 0.9071 0.0844 154 S 0.0090 0.8789 0.1121 155 T 0.0177 0.7505 0.2318 156 L 0.0621 0.4723 0.4656 157 S 0.0828 0.2463 0.6710 158 N 0.1471 0.1739 0.6791 159 R 0.3491 0.0740 0.5769 160 V 0.5295 0.0580 0.4125 161 Y 0.6132 0.0397 0.3471 162 D 0.5678 0.0345 0.3977 163 A 0.3869 0.0537 0.5594 164 D 0.2122 0.0439 0.7440 165 S 0.0328 0.4955 0.4717 166 E 0.0330 0.5065 0.4605 167 Q 0.0711 0.5435 0.3854 168 R 0.0790 0.6058 0.3152 169 K 0.0990 0.6604 0.2406 170 S 0.1203 0.6988 0.1810 171 L 0.1378 0.7123 0.1499 172 H 0.2025 0.6749 0.1226 173 L 0.1670 0.7204 0.1126 174 A 0.1213 0.7574 0.1213 175 A 0.0770 0.7972 0.1258 176 V 0.0634 0.7786 0.1580 177 F 0.0628 0.7284 0.2088 178 T 0.0377 0.7839 0.1784 179 C 0.0146 0.8546 0.1308 180 N 0.0114 0.8838 0.1047 181 F 0.0097 0.9039 0.0864 182 T 0.0084 0.9180 0.0736 183 N 0.0083 0.9220 0.0697 184 H 0.0083 0.9234 0.0684 185 M 0.0083 0.9244 0.0674 186 Y 0.0083 0.9244 0.0673 187 A 0.0083 0.9240 0.0677 188 L 0.0083 0.9245 0.0673 189 A 0.0083 0.9203 0.0714 190 A 0.0083 0.9213 0.0704 191 E 0.0083 0.9241 0.0676 192 L 0.0083 0.9228 0.0688 193 L 0.0084 0.9186 0.0730 194 K 0.0087 0.8959 0.0954 195 K 0.0137 0.8020 0.1843 196 Y 0.0572 0.3020 0.6408 197 N 0.0485 0.0683 0.8832 198 L 0.1530 0.0213 0.8257 199 P 0.1583 0.0468 0.7949 200 F 0.0248 0.6976 0.2776 201 D 0.0153 0.8267 0.1580 202 V 0.0247 0.8470 0.1283 203 M 0.0225 0.8520 0.1254 204 L 0.0147 0.8849 0.1004 205 P 0.0086 0.9113 0.0801 206 L 0.0087 0.9116 0.0798 207 I 0.0085 0.9140 0.0774 208 D 0.0084 0.9150 0.0766 209 E 0.0085 0.9106 0.0809 210 T 0.0094 0.9044 0.0862 211 A 0.0093 0.8847 0.1060 212 R 0.0095 0.8654 0.1251 213 K 0.0120 0.8102 0.1778 214 V 0.0231 0.7990 0.1780 215 H 0.0318 0.7403 0.2279 216 E 0.0502 0.5864 0.3634 217 L 0.1191 0.3551 0.5258 218 E 0.1846 0.1341 0.6813 219 P 0.0998 0.4481 0.4521 220 K 0.0763 0.5514 0.3723 221 T 0.0938 0.5323 0.3739 222 A 0.1043 0.4603 0.4354 223 Q 0.1403 0.3406 0.5191 224 T 0.1584 0.1970 0.6446 225 G 0.1333 0.2132 0.6535 226 P 0.1395 0.3825 0.4780 227 A 0.1668 0.4784 0.3548 228 I 0.1969 0.4798 0.3233 229 R 0.1796 0.4271 0.3933 230 Y 0.1192 0.3686 0.5123 231 D 0.1322 0.3411 0.5267 232 E 0.0198 0.7520 0.2282 233 N 0.0183 0.8190 0.1628 234 V 0.0240 0.8639 0.1121 235 I 0.0120 0.8958 0.0922 236 G 0.0096 0.9096 0.0808 237 N 0.0094 0.9089 0.0817 238 H 0.0112 0.9052 0.0836 239 L 0.0094 0.9107 0.0799 240 R 0.0091 0.9078 0.0831 241 M 0.0132 0.8294 0.1574 242 L 0.0283 0.7076 0.2641 243 A 0.0290 0.5694 0.4016 244 D 0.0486 0.3513 0.6001 245 D 0.1181 0.1819 0.7000 246 P 0.0409 0.5177 0.4414 247 A 0.0133 0.7901 0.1967 248 M 0.0105 0.8816 0.1079 249 Q 0.0116 0.8976 0.0909 250 R 0.0117 0.9072 0.0812 251 L 0.0102 0.9147 0.0751 252 Y 0.0097 0.9149 0.0754 253 E 0.0091 0.9130 0.0778 254 L 0.0108 0.8962 0.0930 255 L 0.0185 0.8609 0.1206 256 S 0.0243 0.8364 0.1394 257 R 0.0228 0.8391 0.1381 258 S 0.0424 0.7837 0.1739 259 I 0.0433 0.7821 0.1746 260 H 0.0461 0.7472 0.2067 261 E 0.0624 0.6170 0.3206 262 R 0.1075 0.4275 0.4650 263 Q 0.1677 0.2901 0.5422