# This file is the result of combining several RDB files, specifically # T0200.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0200.t2k.stride-ebghtl.rdb (weight 1.24869) # T0200.t2k.str2.rdb (weight 1.54758) # T0200.t2k.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 T0200.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0200 # Using neural net t2k-5740-IDaaHr-5-15-7-15-9-15-13-ebghstl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0200.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 52 # # ============================================ # Comments from T0200.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0200 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-ebghtl-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0200.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 52 # # ============================================ # Comments from T0200.t2k.str2.rdb # ============================================ # TARGET T0200 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str2-from-empty.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str2 ) # The input amino acid frequencies were determined from # alignment T0200.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 52 # # ============================================ # Comments from T0200.t2k.alpha.rdb # ============================================ # TARGET T0200 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-alpha-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 11 (1 ABCDEFGHIST ) # The input amino acid frequencies were determined from # alignment T0200.t2k-thin90.a2m.gz # with weighted counts, using HenikoffWeight(-1 bits/column, 1) # Counts were regularized to probabilities using # /projects/compbio/lib/recode3.20comp # Total sequence weight for alignment was 52 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0935 0.0123 0.8942 2 R 0.4915 0.0124 0.4960 3 V 0.8673 0.0061 0.1266 4 L 0.8955 0.0102 0.0942 5 F 0.9027 0.0074 0.0899 6 I 0.7395 0.0421 0.2184 7 G 0.5396 0.0332 0.4272 8 D 0.3769 0.0875 0.5356 9 V 0.2373 0.1628 0.5999 10 F 0.1553 0.1360 0.7087 11 G 0.0669 0.0998 0.8333 12 Q 0.0451 0.4354 0.5196 13 P 0.0216 0.7684 0.2101 14 G 0.0169 0.8185 0.1646 15 R 0.0081 0.9279 0.0641 16 R 0.0051 0.9488 0.0461 17 V 0.0048 0.9517 0.0435 18 L 0.0051 0.9447 0.0503 19 Q 0.0050 0.9394 0.0557 20 N 0.0061 0.8925 0.1015 21 H 0.0118 0.7725 0.2157 22 L 0.0394 0.5047 0.4559 23 P 0.0077 0.6675 0.3248 24 T 0.0099 0.6753 0.3148 25 I 0.0262 0.7320 0.2418 26 R 0.0541 0.5399 0.4060 27 P 0.0885 0.4917 0.4198 28 Q 0.1097 0.3073 0.5829 29 F 0.1335 0.0547 0.8118 30 D 0.1412 0.0538 0.8050 31 F 0.8212 0.0095 0.1693 32 V 0.9179 0.0040 0.0781 33 I 0.9189 0.0045 0.0766 34 V 0.8722 0.0115 0.1164 35 N 0.6177 0.0257 0.3566 36 M 0.2523 0.1033 0.6444 37 E 0.3085 0.1662 0.5253 38 N 0.3179 0.1823 0.4998 39 S 0.1827 0.1732 0.6442 40 A 0.1382 0.1308 0.7310 41 G 0.0900 0.0936 0.8164 42 G 0.1061 0.1177 0.7763 43 F 0.1264 0.1222 0.7513 44 G 0.1566 0.0965 0.7469 45 M 0.1931 0.0753 0.7316 46 H 0.0717 0.0735 0.8548 47 R 0.0051 0.9444 0.0505 48 D 0.0047 0.9557 0.0396 49 A 0.0049 0.9545 0.0406 50 A 0.0047 0.9571 0.0382 51 R 0.0048 0.9563 0.0389 52 G 0.0047 0.9531 0.0422 53 A 0.0051 0.9509 0.0441 54 L 0.0051 0.9381 0.0568 55 E 0.0060 0.8494 0.1447 56 A 0.0406 0.3612 0.5982 57 G 0.0460 0.0291 0.9249 58 A 0.1061 0.0119 0.8820 59 G 0.2899 0.0315 0.6787 60 C 0.9165 0.0069 0.0766 61 L 0.9231 0.0049 0.0720 62 T 0.9071 0.0069 0.0859 63 L 0.6786 0.0313 0.2901 64 G 0.1346 0.0631 0.8024 65 N 0.0638 0.2429 0.6933 66 H 0.0908 0.4224 0.4867 67 A 0.0625 0.5476 0.3899 68 W 0.0559 0.5258 0.4184 69 H 0.0628 0.4611 0.4761 70 H 0.0301 0.6895 0.2804 71 K 0.0093 0.8770 0.1137 72 D 0.0152 0.8746 0.1103 73 I 0.0106 0.9071 0.0823 74 Y 0.0095 0.9134 0.0771 75 P 0.0092 0.8886 0.1021 76 M 0.0100 0.8445 0.1455 77 L 0.0373 0.7464 0.2162 78 S 0.0243 0.6165 0.3591 79 E 0.0285 0.4071 0.5643 80 D 0.0618 0.2593 0.6789 81 T 0.0506 0.1806 0.7688 82 Y 0.1101 0.1412 0.7487 83 P 0.1721 0.0794 0.7484 84 I 0.3952 0.0589 0.5459 85 V 0.5478 0.0393 0.4130 86 R 0.4209 0.0260 0.5530 87 P 0.2884 0.0839 0.6276 88 L 0.2405 0.1113 0.6482 89 N 0.2585 0.0870 0.6546 90 Y 0.2120 0.0373 0.7508 91 A 0.1215 0.0647 0.8138 92 D 0.0571 0.1344 0.8085 93 P 0.0509 0.1176 0.8315 94 G 0.0660 0.0797 0.8543 95 T 0.1457 0.0296 0.8247 96 P 0.1917 0.0646 0.7437 97 G 0.2354 0.0534 0.7112 98 V 0.4117 0.0344 0.5539 99 G 0.6431 0.0181 0.3388 100 W 0.8378 0.0068 0.1554 101 R 0.9118 0.0042 0.0840 102 T 0.9264 0.0032 0.0704 103 F 0.9182 0.0045 0.0773 104 D 0.9067 0.0039 0.0894 105 V 0.7865 0.0135 0.1999 106 N 0.0667 0.0278 0.9055 107 G 0.0307 0.0540 0.9153 108 E 0.6745 0.0111 0.3144 109 K 0.8889 0.0036 0.1075 110 L 0.9152 0.0038 0.0810 111 T 0.9175 0.0062 0.0763 112 V 0.9269 0.0051 0.0680 113 V 0.8787 0.0237 0.0976 114 N 0.7860 0.0504 0.1635 115 L 0.5422 0.1320 0.3258 116 L 0.2801 0.1986 0.5213 117 G 0.1891 0.2419 0.5690 118 R 0.2286 0.2640 0.5074 119 V 0.2439 0.2702 0.4860 120 F 0.1652 0.2219 0.6129 121 M 0.1190 0.1338 0.7472 122 E 0.0871 0.1064 0.8065 123 A 0.0590 0.2222 0.7188 124 V 0.0634 0.1868 0.7497 125 D 0.0518 0.1245 0.8237 126 N 0.0995 0.0643 0.8362 127 P 0.0080 0.7038 0.2882 128 F 0.0062 0.8529 0.1409 129 R 0.0066 0.9131 0.0803 130 T 0.0092 0.9236 0.0672 131 M 0.0053 0.9444 0.0503 132 D 0.0047 0.9504 0.0449 133 A 0.0048 0.9518 0.0434 134 L 0.0048 0.9498 0.0454 135 L 0.0053 0.9299 0.0648 136 E 0.0057 0.8815 0.1128 137 R 0.0119 0.6833 0.3049 138 D 0.0620 0.2132 0.7248 139 D 0.0365 0.0696 0.8939 140 L 0.0753 0.0217 0.9031 141 G 0.0946 0.0474 0.8580 142 T 0.7831 0.0052 0.2118 143 V 0.9290 0.0033 0.0677 144 F 0.9320 0.0032 0.0649 145 V 0.9172 0.0048 0.0780 146 D 0.8031 0.0122 0.1847 147 F 0.3165 0.0651 0.6184 148 H 0.1966 0.1115 0.6918 149 A 0.1719 0.2407 0.5874 150 E 0.1555 0.3165 0.5280 151 A 0.1247 0.4114 0.4640 152 T 0.0972 0.4796 0.4232 153 S 0.0686 0.5406 0.3907 154 E 0.0670 0.7574 0.1756 155 K 0.0531 0.8172 0.1297 156 E 0.1206 0.7418 0.1376 157 A 0.1822 0.7005 0.1173 158 M 0.2117 0.6711 0.1172 159 G 0.2573 0.6132 0.1294 160 W 0.2578 0.5842 0.1580 161 H 0.2617 0.4951 0.2431 162 L 0.2727 0.2952 0.4321 163 A 0.0623 0.0672 0.8706 164 G 0.1236 0.0306 0.8457 165 R 0.6180 0.0273 0.3548 166 V 0.7972 0.0086 0.1942 167 A 0.8463 0.0219 0.1319 168 A 0.8898 0.0062 0.1040 169 V 0.8837 0.0052 0.1111 170 I 0.7759 0.0170 0.2071 171 G 0.5536 0.0270 0.4193 172 T 0.3149 0.0527 0.6324 173 H 0.1878 0.1231 0.6892 174 T 0.1713 0.1704 0.6583 175 H 0.1999 0.1632 0.6368 176 V 0.1590 0.1017 0.7393 177 P 0.1572 0.0987 0.7441 178 T 0.1166 0.1879 0.6954 179 A 0.0549 0.4512 0.4939 180 D 0.0483 0.5656 0.3860 181 T 0.0851 0.5532 0.3617 182 R 0.1508 0.4363 0.4129 183 I 0.2592 0.2304 0.5105 184 L 0.1209 0.0585 0.8206 185 K 0.0299 0.0997 0.8705 186 G 0.0341 0.0407 0.9252 187 G 0.2357 0.0342 0.7301 188 T 0.6844 0.0165 0.2991 189 A 0.8531 0.0289 0.1180 190 Y 0.8721 0.0158 0.1121 191 Q 0.8050 0.0232 0.1718 192 T 0.6342 0.0338 0.3320 193 D 0.3940 0.0566 0.5493 194 A 0.2066 0.1390 0.6544 195 G 0.1592 0.1653 0.6755 196 F 0.1777 0.1709 0.6513 197 T 0.1676 0.0997 0.7328 198 G 0.1153 0.0752 0.8095 199 P 0.0970 0.1128 0.7902 200 H 0.0731 0.2602 0.6667 201 D 0.1030 0.2653 0.6317 202 S 0.1876 0.2776 0.5348 203 I 0.3370 0.2543 0.4086 204 I 0.2180 0.2073 0.5747 205 G 0.1928 0.0986 0.7086 206 S 0.2011 0.0577 0.7411 207 A 0.1505 0.0602 0.7893 208 I 0.0215 0.6994 0.2792 209 E 0.0132 0.8048 0.1820 210 G 0.0106 0.8810 0.1084 211 P 0.0109 0.9174 0.0717 212 L 0.0123 0.9243 0.0634 213 Q 0.0123 0.9302 0.0575 214 R 0.0116 0.9243 0.0641 215 F 0.0144 0.9017 0.0838 216 L 0.0184 0.8455 0.1361 217 T 0.0426 0.5153 0.4421 218 E 0.0467 0.1782 0.7752 219 R 0.0845 0.0388 0.8767 220 P 0.1020 0.0504 0.8476 221 H 0.2006 0.0779 0.7215 222 R 0.3828 0.0496 0.5676 223 Y 0.5367 0.0198 0.4435 224 G 0.5973 0.0121 0.3906 225 V 0.5174 0.0228 0.4598 226 A 0.2983 0.0479 0.6538 227 E 0.1110 0.0471 0.8419 228 G 0.0794 0.0292 0.8914 229 R 0.2128 0.0570 0.7302 230 A 0.6382 0.0259 0.3358 231 E 0.8243 0.0148 0.1609 232 L 0.8569 0.0091 0.1340 233 N 0.8106 0.0258 0.1636 234 G 0.8781 0.0065 0.1154 235 V 0.9159 0.0039 0.0802 236 A 0.9264 0.0035 0.0701 237 L 0.9148 0.0052 0.0800 238 H 0.9107 0.0051 0.0842 239 F 0.8629 0.0059 0.1312 240 E 0.5962 0.0078 0.3960 241 G 0.0328 0.1317 0.8354 242 G 0.0222 0.1166 0.8613 243 K 0.0890 0.0485 0.8625 244 A 0.1252 0.0267 0.8480 245 T 0.5772 0.0145 0.4084 246 A 0.8904 0.0044 0.1052 247 A 0.8529 0.0168 0.1303 248 E 0.8980 0.0048 0.0972 249 R 0.8676 0.0055 0.1269 250 Y 0.8436 0.0106 0.1459 251 R 0.8496 0.0064 0.1439 252 F 0.8034 0.0143 0.1823 253 I 0.7895 0.0160 0.1945 254 E 0.5402 0.0176 0.4422 255 D 0.1072 0.0205 0.8723