# This file is the result of combining several RDB files, specifically # T0295.t06.dssp-ebghstl.rdb (weight 1.53986) # T0295.t06.stride-ebghtl.rdb (weight 1.24869) # T0295.t06.str2.rdb (weight 1.54758) # T0295.t06.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 T0295.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0295 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghstl-dssp-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 7 (1 EBGHSTL ) # The input amino acid frequencies were determined from # alignment T0295.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 2966 # # ============================================ # Comments from T0295.t06.stride-ebghtl.rdb # ============================================ # TARGET T0295 # Using neural net t06-IDGaaH13-3-13-7-13-9-13-11-ebghtl-stride-seeded.net # This is a 4-layer network, with # window units # 3 13 # 7 13 # 9 13 # 11 6 (1 EBGHTL ) # The input amino acid frequencies were determined from # alignment T0295.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 2966 # # ============================================ # Comments from T0295.t06.str2.rdb # ============================================ # TARGET T0295 # Using neural net 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 T0295.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 2966 # # ============================================ # Comments from T0295.t06.alpha.rdb # ============================================ # TARGET T0295 # Using neural net 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 T0295.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 2966 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 H 0.0782 0.1203 0.8015 2 L 0.1627 0.2003 0.6370 3 L 0.1846 0.1436 0.6718 4 K 0.1467 0.1099 0.7434 5 N 0.0814 0.0368 0.8818 6 P 0.0073 0.7764 0.2163 7 G 0.0076 0.8290 0.1634 8 I 0.0061 0.9205 0.0734 9 L 0.0048 0.9497 0.0455 10 D 0.0047 0.9567 0.0386 11 K 0.0047 0.9585 0.0368 12 I 0.0048 0.9570 0.0383 13 I 0.0054 0.9509 0.0437 14 Y 0.0068 0.9233 0.0699 15 A 0.0092 0.8199 0.1709 16 A 0.0539 0.5368 0.4093 17 K 0.0675 0.1510 0.7815 18 I 0.0988 0.0531 0.8481 19 K 0.0840 0.0479 0.8681 20 S 0.0361 0.1220 0.8418 21 S 0.0442 0.0571 0.8987 22 D 0.1855 0.0287 0.7858 23 I 0.8221 0.0050 0.1729 24 V 0.9225 0.0035 0.0741 25 L 0.9252 0.0034 0.0714 26 E 0.9021 0.0034 0.0945 27 I 0.6624 0.0324 0.3052 28 G 0.2538 0.0215 0.7247 29 C 0.0910 0.0705 0.8386 30 G 0.0795 0.0871 0.8334 31 T 0.0661 0.3733 0.5606 32 G 0.0300 0.7228 0.2471 33 N 0.0223 0.8797 0.0980 34 L 0.0145 0.9105 0.0750 35 T 0.0118 0.9284 0.0598 36 V 0.0095 0.9316 0.0589 37 K 0.0087 0.9025 0.0888 38 L 0.0099 0.8531 0.1370 39 L 0.0147 0.8299 0.1554 40 P 0.0116 0.7405 0.2478 41 L 0.0190 0.5827 0.3983 42 A 0.1118 0.1614 0.7268 43 K 0.1279 0.1438 0.7283 44 K 0.5572 0.0473 0.3956 45 V 0.8896 0.0048 0.1056 46 I 0.9188 0.0057 0.0755 47 T 0.9240 0.0041 0.0719 48 I 0.9029 0.0058 0.0913 49 D 0.7305 0.0060 0.2635 50 I 0.1856 0.0293 0.7851 51 D 0.0843 0.0124 0.9033 52 S 0.0052 0.8598 0.1350 53 R 0.0057 0.8903 0.1040 54 M 0.0055 0.9293 0.0652 55 I 0.0047 0.9560 0.0392 56 S 0.0047 0.9600 0.0353 57 E 0.0047 0.9591 0.0362 58 V 0.0048 0.9575 0.0377 59 K 0.0047 0.9577 0.0376 60 K 0.0048 0.9520 0.0432 61 R 0.0050 0.9416 0.0535 62 C 0.0058 0.9239 0.0703 63 L 0.0070 0.8747 0.1183 64 Y 0.0084 0.7818 0.2099 65 E 0.0429 0.4041 0.5530 66 G 0.0359 0.0693 0.8948 67 Y 0.1060 0.0508 0.8432 68 N 0.0857 0.0891 0.8252 69 N 0.2144 0.0480 0.7376 70 L 0.7035 0.0081 0.2884 71 E 0.8957 0.0064 0.0979 72 V 0.9184 0.0041 0.0775 73 Y 0.8829 0.0103 0.1068 74 E 0.7438 0.0272 0.2290 75 G 0.4342 0.0436 0.5223 76 D 0.3327 0.0912 0.5762 77 A 0.1279 0.4494 0.4227 78 I 0.1324 0.4257 0.4419 79 K 0.1573 0.3918 0.4509 80 T 0.1720 0.1090 0.7189 81 V 0.1526 0.0589 0.7885 82 F 0.0980 0.0478 0.8542 83 P 0.0586 0.1062 0.8352 84 K 0.0787 0.1236 0.7976 85 F 0.1986 0.0219 0.7795 86 D 0.1713 0.0473 0.7814 87 V 0.8991 0.0044 0.0965 88 C 0.9288 0.0035 0.0677 89 T 0.9255 0.0038 0.0708 90 A 0.8416 0.0116 0.1468 91 N 0.2912 0.0297 0.6791 92 I 0.1177 0.0492 0.8331 93 P 0.0905 0.2137 0.6958 94 Y 0.1043 0.4254 0.4702 95 K 0.1223 0.4497 0.4279 96 I 0.0979 0.3836 0.5184 97 S 0.0756 0.3404 0.5840 98 S 0.0360 0.6085 0.3554 99 P 0.0085 0.9043 0.0872 100 L 0.0062 0.9382 0.0556 101 I 0.0061 0.9464 0.0475 102 F 0.0067 0.9453 0.0480 103 K 0.0070 0.9369 0.0561 104 L 0.0069 0.9162 0.0769 105 I 0.0111 0.8672 0.1217 106 S 0.0119 0.7474 0.2406 107 H 0.0189 0.6519 0.3292 108 R 0.0323 0.4758 0.4919 109 P 0.0153 0.6472 0.3375 110 L 0.0325 0.6666 0.3008 111 F 0.1230 0.5387 0.3383 112 K 0.1632 0.4532 0.3836 113 C 0.1601 0.4608 0.3791 114 A 0.1980 0.4054 0.3966 115 V 0.3947 0.3621 0.2432 116 L 0.5672 0.2881 0.1446 117 M 0.5601 0.2954 0.1445 118 F 0.5288 0.2692 0.2021 119 Q 0.3337 0.2946 0.3717 120 K 0.0823 0.7312 0.1865 121 E 0.0676 0.7638 0.1686 122 F 0.0710 0.8027 0.1264 123 A 0.1068 0.7519 0.1413 124 E 0.2060 0.6719 0.1221 125 R 0.2311 0.6593 0.1096 126 M 0.2381 0.6184 0.1435 127 L 0.3324 0.3924 0.2752 128 A 0.3121 0.2041 0.4839 129 N 0.2016 0.0793 0.7191 130 V 0.0779 0.1492 0.7729 131 G 0.0491 0.0732 0.8778 132 D 0.0741 0.0809 0.8451 133 S 0.0281 0.3352 0.6367 134 N 0.0455 0.3514 0.6031 135 Y 0.0846 0.4060 0.5094 136 S 0.1010 0.3834 0.5156 137 R 0.1741 0.4809 0.3450 138 L 0.2885 0.4167 0.2948 139 T 0.3866 0.3991 0.2143 140 I 0.4404 0.4130 0.1466 141 N 0.4380 0.4113 0.1506 142 V 0.4546 0.3694 0.1760 143 K 0.4018 0.3950 0.2032 144 L 0.3940 0.3689 0.2372 145 F 0.3967 0.2727 0.3306 146 C 0.4504 0.1954 0.3541 147 K 0.4998 0.1304 0.3699 148 V 0.4951 0.1290 0.3759 149 T 0.5377 0.1316 0.3307 150 K 0.6376 0.1158 0.2466 151 V 0.6376 0.1056 0.2568 152 C 0.6875 0.0629 0.2496 153 N 0.6292 0.0403 0.3305 154 V 0.4138 0.0301 0.5562 155 N 0.2389 0.0276 0.7336 156 R 0.0394 0.4137 0.5470 157 S 0.0503 0.4415 0.5081 158 S 0.0960 0.4130 0.4910 159 F 0.1939 0.0896 0.7165 160 N 0.1374 0.0269 0.8357 161 P 0.0903 0.0156 0.8941 162 P 0.0717 0.0204 0.9079 163 P 0.0758 0.0545 0.8697 164 K 0.1625 0.0517 0.7858 165 V 0.3181 0.0354 0.6465 166 D 0.4255 0.0326 0.5418 167 S 0.7668 0.0124 0.2208 168 V 0.8789 0.0080 0.1131 169 I 0.9019 0.0067 0.0914 170 V 0.8861 0.0107 0.1032 171 K 0.8682 0.0094 0.1224 172 L 0.8485 0.0108 0.1407 173 I 0.7163 0.0126 0.2711 174 P 0.5693 0.0171 0.4136 175 K 0.2135 0.0411 0.7454 176 E 0.1257 0.0709 0.8034 177 S 0.0840 0.1120 0.8041 178 S 0.1014 0.1285 0.7701 179 F 0.1945 0.0981 0.7075 180 L 0.2509 0.0682 0.6808 181 T 0.2299 0.0555 0.7146 182 N 0.1539 0.0239 0.8221 183 F 0.0071 0.8873 0.1055 184 D 0.0054 0.9221 0.0725 185 E 0.0054 0.9312 0.0635 186 W 0.0053 0.9393 0.0553 187 D 0.0048 0.9431 0.0521 188 N 0.0050 0.9397 0.0553 189 L 0.0048 0.9464 0.0487 190 L 0.0053 0.9481 0.0465 191 R 0.0051 0.9501 0.0449 192 I 0.0052 0.9449 0.0499 193 C 0.0064 0.9297 0.0639 194 F 0.0075 0.9077 0.0848 195 S 0.0098 0.8991 0.0911 196 R 0.0105 0.8962 0.0933 197 K 0.0102 0.8873 0.1025 198 R 0.0161 0.8912 0.0927 199 K 0.0092 0.9221 0.0687 200 T 0.0091 0.9346 0.0563 201 L 0.0050 0.9514 0.0435 202 H 0.0050 0.9543 0.0407 203 A 0.0048 0.9499 0.0453 204 I 0.0052 0.9406 0.0542 205 F 0.0061 0.9231 0.0708 206 K 0.0076 0.8860 0.1064 207 R 0.0106 0.8214 0.1679 208 N 0.0270 0.7136 0.2594 209 A 0.0503 0.5133 0.4364 210 V 0.0541 0.4392 0.5067 211 L 0.0112 0.8564 0.1324 212 N 0.0084 0.8859 0.1057 213 M 0.0077 0.9096 0.0828 214 L 0.0088 0.9146 0.0766 215 E 0.0081 0.9206 0.0713 216 H 0.0075 0.9097 0.0827 217 N 0.0076 0.9007 0.0917 218 Y 0.0105 0.8955 0.0940 219 K 0.0093 0.8642 0.1265 220 N 0.0122 0.8140 0.1738 221 W 0.0433 0.6136 0.3431 222 C 0.0679 0.2400 0.6921 223 T 0.1149 0.1613 0.7237 224 L 0.1147 0.1175 0.7678 225 N 0.0532 0.3191 0.6277 226 K 0.0541 0.2718 0.6740 227 Q 0.1115 0.2665 0.6220 228 V 0.1852 0.0559 0.7589 229 P 0.1880 0.0854 0.7266 230 V 0.2175 0.1241 0.6584 231 N 0.2356 0.0811 0.6833 232 F 0.1570 0.0123 0.8307 233 P 0.0972 0.0115 0.8913 234 F 0.0059 0.9350 0.0592 235 K 0.0048 0.9564 0.0388 236 K 0.0049 0.9550 0.0401 237 Y 0.0048 0.9584 0.0368 238 C 0.0047 0.9578 0.0375 239 L 0.0047 0.9568 0.0385 240 D 0.0048 0.9526 0.0426 241 V 0.0048 0.9506 0.0446 242 L 0.0050 0.9420 0.0530 243 E 0.0061 0.9054 0.0886 244 H 0.0076 0.8633 0.1291 245 L 0.0110 0.8216 0.1674 246 D 0.0126 0.7624 0.2250 247 M 0.0148 0.8034 0.1818 248 C 0.0418 0.6990 0.2591 249 E 0.0509 0.6234 0.3257 250 K 0.0628 0.5587 0.3786 251 R 0.0828 0.4036 0.5136 252 S 0.0852 0.3646 0.5502 253 I 0.1079 0.2936 0.5985 254 N 0.1785 0.2507 0.5708 255 L 0.1338 0.2416 0.6247 256 D 0.1208 0.2721 0.6071 257 E 0.0329 0.5750 0.3921 258 N 0.0240 0.5571 0.4189 259 D 0.0423 0.7735 0.1842 260 F 0.0397 0.8723 0.0880 261 L 0.0320 0.9000 0.0680 262 K 0.0514 0.8725 0.0761 263 L 0.0375 0.8754 0.0870 264 L 0.0322 0.8546 0.1132 265 L 0.0381 0.7903 0.1716 266 E 0.0265 0.7514 0.2221 267 F 0.0294 0.6741 0.2965 268 N 0.0563 0.3322 0.6115 269 K 0.0280 0.3392 0.6328 270 K 0.0591 0.1892 0.7517 271 G 0.0727 0.0880 0.8392 272 I 0.1515 0.0414 0.8072 273 H 0.3067 0.0372 0.6561 274 F 0.3278 0.0398 0.6324 275 F 0.1228 0.0304 0.8468