# This file is the result of combining several RDB files, specifically # T0407.t2k.str2.rdb (weight 1.54425) # T0407.t2k.str4.rdb (weight 0.924988) # T0407.t2k.pb.rdb (weight 0.789901) # T0407.t2k.bys.rdb (weight 0.748322) # T0407.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 T0407.t2k.str2.rdb # ============================================ # TARGET T0407 # 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 T0407.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 458 # # ============================================ # Comments from T0407.t2k.str4.rdb # ============================================ # TARGET T0407 # 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 T0407.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 458 # # ============================================ # Comments from T0407.t2k.pb.rdb # ============================================ # TARGET T0407 # 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 T0407.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 458 # # ============================================ # Comments from T0407.t2k.bys.rdb # ============================================ # TARGET T0407 # 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 T0407.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 458 # # ============================================ # Comments from T0407.t2k.alpha.rdb # ============================================ # TARGET T0407 # 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 T0407.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 458 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 P 0.2463 0.1129 0.6408 2 D 0.2299 0.0955 0.6747 3 L 0.2337 0.1918 0.5744 4 D 0.1720 0.1706 0.6574 5 G 0.1644 0.1395 0.6961 6 Y 0.2971 0.1012 0.6017 7 T 0.3921 0.0734 0.5345 8 T 0.4630 0.0700 0.4670 9 L 0.5494 0.0563 0.3944 10 K 0.6088 0.0445 0.3467 11 C 0.6276 0.0444 0.3281 12 D 0.5825 0.0535 0.3640 13 F 0.6041 0.0956 0.3003 14 H 0.5915 0.0906 0.3179 15 M 0.5816 0.0980 0.3204 16 H 0.5032 0.0908 0.4060 17 S 0.4525 0.1197 0.4278 18 V 0.3701 0.1814 0.4485 19 F 0.3196 0.1663 0.5141 20 S 0.2333 0.1822 0.5844 21 D 0.1194 0.2068 0.6738 22 G 0.0874 0.1467 0.7659 23 L 0.1788 0.1373 0.6839 24 V 0.2238 0.1248 0.6514 25 W 0.1683 0.0813 0.7505 26 P 0.0227 0.6831 0.2942 27 T 0.0119 0.8312 0.1569 28 V 0.0090 0.9093 0.0817 29 R 0.0086 0.9195 0.0719 30 V 0.0084 0.9169 0.0747 31 D 0.0083 0.9239 0.0678 32 E 0.0083 0.9246 0.0671 33 A 0.0083 0.9231 0.0686 34 Y 0.0085 0.9065 0.0850 35 R 0.0107 0.8359 0.1534 36 D 0.0516 0.2490 0.6994 37 G 0.0489 0.0675 0.8835 38 L 0.2122 0.0400 0.7478 39 D 0.3804 0.0790 0.5406 40 A 0.7434 0.0335 0.2231 41 I 0.7539 0.0191 0.2270 42 S 0.7775 0.0152 0.2074 43 L 0.7453 0.0288 0.2258 44 T 0.6202 0.0343 0.3455 45 E 0.3361 0.1375 0.5263 46 H 0.2299 0.1924 0.5777 47 I 0.1437 0.3426 0.5136 48 E 0.1382 0.3264 0.5354 49 Y 0.1647 0.2284 0.6069 50 R 0.1693 0.1735 0.6572 51 P 0.1249 0.3205 0.5546 52 H 0.1342 0.3756 0.4902 53 K 0.0871 0.5950 0.3179 54 Q 0.0702 0.6401 0.2898 55 D 0.0960 0.5467 0.3573 56 V 0.1386 0.4629 0.3985 57 V 0.1381 0.3762 0.4857 58 S 0.0633 0.5838 0.3528 59 D 0.0388 0.6250 0.3362 60 H 0.0467 0.6312 0.3220 61 N 0.0460 0.6478 0.3062 62 R 0.0463 0.7081 0.2456 63 S 0.0455 0.7380 0.2166 64 F 0.0256 0.8443 0.1301 65 D 0.0117 0.8989 0.0894 66 L 0.0097 0.9101 0.0802 67 C 0.0094 0.9153 0.0753 68 R 0.0086 0.9151 0.0763 69 E 0.0086 0.9160 0.0755 70 Q 0.0102 0.8971 0.0927 71 A 0.0114 0.8816 0.1070 72 E 0.0140 0.8218 0.1642 73 K 0.0302 0.7166 0.2533 74 L 0.0686 0.2357 0.6957 75 G 0.0607 0.0679 0.8714 76 I 0.3093 0.0169 0.6738 77 L 0.5741 0.0200 0.4058 78 L 0.7112 0.0137 0.2752 79 I 0.6317 0.0167 0.3515 80 K 0.5089 0.0349 0.4562 81 G 0.3996 0.0464 0.5540 82 S 0.5590 0.0458 0.3952 83 E 0.6830 0.0239 0.2931 84 I 0.7070 0.0251 0.2679 85 T 0.6109 0.0363 0.3528 86 R 0.4985 0.1065 0.3950 87 A 0.3589 0.1148 0.5263 88 M 0.2515 0.1221 0.6264 89 A 0.1975 0.0919 0.7106 90 P 0.1246 0.2026 0.6728 91 G 0.1529 0.1597 0.6874 92 H 0.3448 0.1263 0.5290 93 F 0.4841 0.1090 0.4069 94 N 0.5371 0.0952 0.3677 95 A 0.4864 0.1785 0.3352 96 I 0.4167 0.2101 0.3732 97 F 0.3626 0.1982 0.4392 98 L 0.2570 0.2117 0.5314 99 S 0.1941 0.1793 0.6266 100 D 0.1199 0.2536 0.6265 101 S 0.1254 0.1904 0.6842 102 N 0.1530 0.1731 0.6739 103 P 0.0947 0.2920 0.6132 104 L 0.1126 0.3429 0.5445 105 E 0.1008 0.4082 0.4910 106 Q 0.1136 0.3724 0.5140 107 K 0.1230 0.3216 0.5555 108 D 0.1257 0.2297 0.6446 109 Y 0.0159 0.7444 0.2396 110 K 0.0091 0.8862 0.1047 111 D 0.0083 0.9222 0.0695 112 A 0.0083 0.9222 0.0695 113 F 0.0083 0.9235 0.0682 114 R 0.0083 0.9245 0.0673 115 E 0.0083 0.9244 0.0673 116 A 0.0084 0.9191 0.0726 117 K 0.0086 0.8959 0.0954 118 K 0.0129 0.8086 0.1785 119 Q 0.0581 0.3639 0.5780 120 G 0.0574 0.0720 0.8706 121 A 0.2124 0.0492 0.7384 122 F 0.5329 0.0284 0.4387 123 M 0.7595 0.0173 0.2233 124 F 0.7691 0.0230 0.2079 125 W 0.7139 0.0442 0.2419 126 N 0.5708 0.0592 0.3700 127 H 0.2916 0.0357 0.6727 128 P 0.1334 0.2320 0.6345 129 G 0.1143 0.2004 0.6852 130 W 0.1610 0.2831 0.5559 131 D 0.1569 0.2807 0.5624 132 S 0.1486 0.2507 0.6007 133 Q 0.1701 0.1361 0.6937 134 Q 0.1849 0.0704 0.7447 135 P 0.0902 0.3447 0.5651 136 D 0.0861 0.3874 0.5265 137 T 0.1100 0.3907 0.4993 138 T 0.1139 0.3833 0.5029 139 K 0.1081 0.4443 0.4476 140 W 0.1225 0.3937 0.4838 141 W 0.1380 0.3001 0.5619 142 P 0.0468 0.6710 0.2822 143 E 0.0186 0.8416 0.1398 144 H 0.0149 0.8812 0.1039 145 T 0.0193 0.8781 0.1026 146 A 0.0186 0.8756 0.1058 147 L 0.0310 0.7967 0.1723 148 Y 0.0630 0.5217 0.4152 149 Q 0.0901 0.2622 0.6477 150 E 0.1170 0.1713 0.7117 151 G 0.1622 0.1359 0.7018 152 C 0.4396 0.0975 0.4629 153 M 0.6062 0.0709 0.3229 154 H 0.6678 0.0597 0.2725 155 G 0.6066 0.0748 0.3187 156 I 0.5154 0.0886 0.3960 157 E 0.3836 0.1073 0.5091 158 V 0.2570 0.1581 0.5849 159 A 0.1443 0.2619 0.5937 160 N 0.1169 0.1997 0.6834 161 G 0.0958 0.2094 0.6948 162 H 0.1087 0.3322 0.5591 163 L 0.1090 0.3638 0.5272 164 Y 0.1132 0.3340 0.5528 165 M 0.0996 0.3585 0.5419 166 P 0.0116 0.8088 0.1796 167 E 0.0092 0.8837 0.1071 168 A 0.0083 0.9210 0.0707 169 I 0.0083 0.9233 0.0684 170 Q 0.0083 0.9246 0.0671 171 W 0.0083 0.9227 0.0690 172 C 0.0086 0.9132 0.0782 173 L 0.0093 0.8671 0.1236 174 D 0.0158 0.7848 0.1994 175 K 0.0567 0.2142 0.7291 176 N 0.0573 0.0703 0.8724 177 L 0.2640 0.0231 0.7129 178 T 0.5927 0.0231 0.3842 179 M 0.7557 0.0139 0.2304 180 I 0.7359 0.0219 0.2422 181 G 0.6445 0.0331 0.3224 182 T 0.4542 0.0628 0.4830 183 S 0.2543 0.1370 0.6087 184 D 0.1717 0.2425 0.5858 185 I 0.1499 0.2957 0.5544 186 H 0.1638 0.1966 0.6396 187 Q 0.1760 0.1360 0.6880 188 P 0.1277 0.2966 0.5756 189 I 0.1486 0.2666 0.5848 190 Q 0.1955 0.2185 0.5860 191 T 0.1853 0.2617 0.5530 192 D 0.1876 0.2713 0.5411 193 Y 0.1993 0.3377 0.4630 194 D 0.1934 0.3203 0.4862 195 F 0.1702 0.3766 0.4532 196 E 0.1785 0.2964 0.5252 197 K 0.1953 0.1936 0.6110 198 G 0.2224 0.1413 0.6363 199 E 0.3064 0.1568 0.5368 200 H 0.3420 0.1387 0.5193 201 R 0.3140 0.1983 0.4877 202 T 0.2405 0.2674 0.4921 203 M 0.2007 0.2496 0.5498 204 T 0.2264 0.2211 0.5525 205 F 0.2704 0.2431 0.4865 206 V 0.3141 0.2688 0.4171 207 F 0.2369 0.4019 0.3613 208 A 0.0769 0.7308 0.1923 209 K 0.0324 0.8433 0.1243 210 E 0.0277 0.8624 0.1099 211 R 0.0264 0.8560 0.1175 212 S 0.0239 0.8326 0.1435 213 L 0.0261 0.7409 0.2330 214 Q 0.0511 0.4519 0.4970 215 G 0.0494 0.3447 0.6060 216 I 0.0792 0.5674 0.3534 217 R 0.0259 0.8171 0.1570 218 E 0.0111 0.8863 0.1025 219 A 0.0108 0.9011 0.0880 220 L 0.0137 0.8835 0.1028 221 D 0.0176 0.8139 0.1685 222 N 0.0298 0.6602 0.3100 223 R 0.0577 0.5089 0.4334 224 R 0.0824 0.4857 0.4319 225 T 0.1192 0.5215 0.3593 226 A 0.1266 0.6212 0.2522 227 A 0.1793 0.5563 0.2643 228 Y 0.2921 0.3644 0.3435 229 F 0.3274 0.2009 0.4717 230 H 0.2333 0.1386 0.6281