# This file is the result of combining several RDB files, specifically # T0328.t06.dssp-ebghstl.rdb (weight 1.53986) # T0328.t06.stride-ebghtl.rdb (weight 1.24869) # T0328.t06.str2.rdb (weight 1.54758) # T0328.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 T0328.t06.dssp-ebghstl.rdb # ============================================ # TARGET T0328 # Using neural net t04-2621-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 T0328.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 142.03 # # ============================================ # Comments from T0328.t06.stride-ebghtl.rdb # ============================================ # TARGET T0328 # Using neural net t04-2621-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 T0328.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 142.03 # # ============================================ # Comments from T0328.t06.str2.rdb # ============================================ # TARGET T0328 # Using neural net dunbrack-30pc-1763-t2k-thin90-IDGaaH13-3-13-7-13-9-13-11-t1c2-str2-from-empty.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 T0328.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 142.03 # # ============================================ # Comments from T0328.t06.alpha.rdb # ============================================ # TARGET T0328 # Using neural net t04-2621-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 T0328.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 142.03 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.0834 0.0611 0.8555 2 D 0.1525 0.0566 0.7909 3 I 0.1496 0.1059 0.7445 4 Q 0.1123 0.1431 0.7447 5 N 0.0940 0.1243 0.7817 6 M 0.0769 0.0539 0.8692 7 P 0.0788 0.1442 0.7770 8 R 0.0438 0.4020 0.5542 9 E 0.0594 0.4042 0.5364 10 Q 0.0898 0.4051 0.5050 11 L 0.0591 0.4670 0.4739 12 G 0.1028 0.3796 0.5176 13 V 0.2201 0.3411 0.4388 14 C 0.2294 0.2857 0.4849 15 A 0.1321 0.2048 0.6631 16 E 0.0814 0.1932 0.7254 17 G 0.0691 0.1630 0.7679 18 N 0.0892 0.0853 0.8255 19 L 0.1549 0.1567 0.6884 20 H 0.3898 0.0843 0.5258 21 S 0.7598 0.0216 0.2185 22 V 0.8949 0.0078 0.0972 23 Y 0.9254 0.0047 0.0698 24 L 0.9247 0.0044 0.0709 25 M 0.9195 0.0048 0.0757 26 F 0.8813 0.0078 0.1109 27 N 0.7898 0.0064 0.2039 28 A 0.2943 0.0595 0.6462 29 N 0.0923 0.0759 0.8318 30 D 0.0385 0.1564 0.8051 31 N 0.0362 0.1634 0.8004 32 V 0.0245 0.4973 0.4782 33 E 0.0143 0.7829 0.2028 34 S 0.0072 0.8414 0.1515 35 Q 0.0059 0.8844 0.1097 36 L 0.0065 0.9197 0.0737 37 R 0.0047 0.9537 0.0416 38 P 0.0047 0.9514 0.0439 39 C 0.0047 0.9550 0.0403 40 I 0.0047 0.9576 0.0377 41 A 0.0047 0.9509 0.0444 42 N 0.0047 0.9279 0.0673 43 V 0.0049 0.9476 0.0475 44 A 0.0047 0.9537 0.0416 45 Q 0.0047 0.9530 0.0422 46 Y 0.0048 0.9537 0.0415 47 I 0.0048 0.9509 0.0443 48 Y 0.0048 0.9481 0.0472 49 E 0.0050 0.9324 0.0625 50 L 0.0078 0.8931 0.0991 51 T 0.0155 0.7888 0.1957 52 D 0.0191 0.5396 0.4413 53 Q 0.0299 0.3572 0.6129 54 Y 0.0652 0.1402 0.7946 55 S 0.0701 0.1640 0.7659 56 D 0.0324 0.3949 0.5727 57 S 0.0617 0.3423 0.5960 58 A 0.1301 0.1821 0.6879 59 F 0.4529 0.0263 0.5208 60 N 0.6323 0.0287 0.3390 61 G 0.8968 0.0068 0.0964 62 F 0.9213 0.0062 0.0726 63 V 0.9097 0.0110 0.0793 64 A 0.8254 0.0136 0.1610 65 I 0.4378 0.0346 0.5276 66 G 0.1540 0.0410 0.8050 67 A 0.0180 0.5846 0.3974 68 N 0.0118 0.7025 0.2857 69 Y 0.0109 0.8398 0.1493 70 W 0.0107 0.8523 0.1370 71 D 0.0072 0.8032 0.1897 72 S 0.0114 0.6765 0.3120 73 L 0.0344 0.4651 0.5005 74 Y 0.0622 0.1684 0.7695 75 P 0.0247 0.2654 0.7099 76 E 0.0246 0.2878 0.6877 77 S 0.0556 0.2539 0.6905 78 R 0.0994 0.1315 0.7690 79 P 0.0335 0.6040 0.3625 80 E 0.0141 0.7398 0.2461 81 M 0.0210 0.6515 0.3275 82 L 0.0936 0.3315 0.5749 83 K 0.0623 0.1616 0.7761 84 P 0.0803 0.1083 0.8114 85 F 0.0916 0.0958 0.8126 86 P 0.0758 0.2390 0.6852 87 A 0.1117 0.2833 0.6050 88 M 0.1115 0.1858 0.7027 89 Q 0.0760 0.1490 0.7751 90 E 0.0483 0.1973 0.7544 91 G 0.0378 0.1268 0.8355 92 N 0.0974 0.1097 0.7928 93 R 0.1849 0.0765 0.7386 94 E 0.1986 0.0596 0.7418 95 A 0.1056 0.0506 0.8438 96 P 0.0982 0.1000 0.8017 97 A 0.1375 0.1001 0.7624 98 I 0.1643 0.0750 0.7607 99 E 0.1271 0.1438 0.7292 100 Y 0.2079 0.0640 0.7282 101 D 0.3328 0.0249 0.6423 102 L 0.8678 0.0048 0.1273 103 F 0.9268 0.0033 0.0700 104 V 0.9320 0.0033 0.0647 105 H 0.9222 0.0035 0.0743 106 L 0.8514 0.0074 0.1413 107 R 0.6113 0.0127 0.3760 108 C 0.2560 0.0442 0.6998 109 D 0.0541 0.1086 0.8373 110 R 0.0394 0.4776 0.4830 111 Y 0.0138 0.8106 0.1756 112 D 0.0100 0.8797 0.1103 113 I 0.0066 0.9479 0.0455 114 L 0.0049 0.9586 0.0365 115 H 0.0048 0.9598 0.0354 116 L 0.0047 0.9599 0.0354 117 V 0.0048 0.9570 0.0382 118 A 0.0047 0.9597 0.0356 119 N 0.0047 0.9589 0.0364 120 E 0.0048 0.9543 0.0410 121 I 0.0050 0.9488 0.0463 122 S 0.0053 0.9412 0.0535 123 Q 0.0055 0.8833 0.1112 124 M 0.0100 0.7633 0.2268 125 F 0.0217 0.5908 0.3874 126 E 0.0107 0.6087 0.3806 127 D 0.0172 0.5077 0.4751 128 L 0.0996 0.5302 0.3702 129 V 0.2722 0.3390 0.3888 130 E 0.5232 0.2564 0.2204 131 L 0.6268 0.2244 0.1488 132 V 0.6103 0.2232 0.1665 133 E 0.6085 0.1618 0.2296 134 E 0.5011 0.2193 0.2796 135 E 0.3482 0.2628 0.3891 136 R 0.2189 0.1684 0.6128 137 G 0.1531 0.0754 0.7715 138 F 0.2391 0.0506 0.7103 139 R 0.3532 0.0481 0.5987 140 F 0.2287 0.0557 0.7157 141 M 0.1456 0.0672 0.7872 142 D 0.0979 0.0468 0.8553 143 S 0.0330 0.5181 0.4489 144 R 0.0544 0.5367 0.4089 145 D 0.1024 0.5497 0.3479 146 L 0.1371 0.4540 0.4089 147 T 0.1469 0.2564 0.5967 148 G 0.1398 0.1395 0.7207 149 F 0.2337 0.1037 0.6626 150 V 0.3414 0.0763 0.5823 151 D 0.2016 0.0682 0.7302 152 G 0.1325 0.1052 0.7623 153 T 0.1729 0.1255 0.7016 154 E 0.1801 0.1085 0.7114 155 N 0.0969 0.0455 0.8575 156 P 0.0536 0.1204 0.8260 157 K 0.0484 0.1295 0.8221 158 G 0.0464 0.1670 0.7866 159 R 0.0630 0.2309 0.7061 160 H 0.1240 0.2255 0.6505 161 R 0.1743 0.2145 0.6112 162 Q 0.2421 0.1126 0.6453 163 E 0.3779 0.0748 0.5473 164 V 0.7616 0.0319 0.2065 165 A 0.8485 0.0182 0.1333 166 L 0.8865 0.0100 0.1035 167 V 0.7058 0.0261 0.2681 168 G 0.3408 0.0295 0.6296 169 S 0.1205 0.0568 0.8227 170 E 0.0702 0.0617 0.8682 171 D 0.0798 0.0405 0.8797 172 P 0.0171 0.3890 0.5939 173 E 0.0289 0.3969 0.5742 174 F 0.0711 0.3719 0.5570 175 K 0.0448 0.2628 0.6924 176 G 0.0326 0.1872 0.7802 177 G 0.0513 0.3950 0.5537 178 S 0.0684 0.6676 0.2640 179 Y 0.0395 0.8931 0.0674 180 I 0.0437 0.9063 0.0500 181 H 0.0288 0.9308 0.0404 182 V 0.0279 0.9297 0.0424 183 Q 0.0127 0.9452 0.0421 184 K 0.0138 0.9378 0.0484 185 Y 0.0106 0.9238 0.0656 186 A 0.0083 0.9007 0.0910 187 H 0.0206 0.7218 0.2576 188 N 0.0403 0.4061 0.5536 189 L 0.0138 0.7234 0.2628 190 S 0.0075 0.8183 0.1741 191 K 0.0094 0.8007 0.1900 192 W 0.0179 0.7776 0.2044 193 H 0.0197 0.5153 0.4650 194 R 0.0340 0.3209 0.6451 195 L 0.0738 0.0774 0.8488 196 P 0.0619 0.0515 0.8866 197 L 0.0067 0.8723 0.1210 198 K 0.0075 0.8992 0.0934 199 K 0.0108 0.8860 0.1032 200 Q 0.0207 0.8757 0.1037 201 E 0.0288 0.8376 0.1336 202 D 0.0549 0.7283 0.2168 203 I 0.1561 0.5516 0.2924 204 I 0.2117 0.3921 0.3962 205 G 0.1647 0.1833 0.6520 206 R 0.1934 0.0889 0.7177 207 T 0.2414 0.0779 0.6807 208 K 0.1464 0.1305 0.7232 209 Q 0.1012 0.1608 0.7379 210 D 0.0596 0.0956 0.8449 211 N 0.0484 0.0643 0.8873 212 I 0.1731 0.0332 0.7938 213 E 0.3962 0.0385 0.5653 214 Y 0.3297 0.0838 0.5865 215 E 0.1816 0.0921 0.7263 216 S 0.0818 0.1349 0.7833 217 E 0.0624 0.1121 0.8256 218 D 0.0619 0.0894 0.8487 219 K 0.0895 0.0354 0.8751 220 P 0.0855 0.0454 0.8691 221 L 0.1416 0.1802 0.6782 222 T 0.2079 0.1773 0.6148 223 S 0.1972 0.3688 0.4340 224 H 0.2723 0.3307 0.3970 225 I 0.3306 0.3805 0.2889 226 K 0.4047 0.3568 0.2384 227 R 0.4483 0.2312 0.3205 228 V 0.3972 0.0911 0.5117 229 N 0.3221 0.0353 0.6426 230 L 0.2461 0.1540 0.5999 231 K 0.2807 0.1722 0.5472 232 D 0.0989 0.0976 0.8035 233 E 0.0158 0.1492 0.8350 234 N 0.0468 0.0292 0.9240 235 G 0.0431 0.0478 0.9092 236 K 0.1422 0.0930 0.7648 237 S 0.4440 0.2045 0.3514 238 I 0.4375 0.3421 0.2203 239 E 0.4127 0.4349 0.1525 240 I 0.4398 0.4531 0.1072 241 L 0.3849 0.4886 0.1266 242 R 0.3445 0.4463 0.2092 243 Q 0.2549 0.3173 0.4279 244 S 0.1399 0.1210 0.7391 245 M 0.1000 0.0258 0.8742 246 P 0.0931 0.0523 0.8545 247 Y 0.0880 0.0838 0.8282 248 G 0.0890 0.0804 0.8306 249 S 0.1261 0.1006 0.7733 250 L 0.0603 0.4142 0.5256 251 K 0.0584 0.4267 0.5149 252 E 0.0729 0.4305 0.4966 253 Q 0.1136 0.2111 0.6753 254 G 0.3413 0.0871 0.5716 255 L 0.6765 0.0332 0.2903 256 M 0.8945 0.0174 0.0881 257 F 0.9147 0.0166 0.0688 258 I 0.8956 0.0331 0.0714 259 S 0.8501 0.0453 0.1047 260 T 0.7032 0.0555 0.2412 261 C 0.4216 0.0514 0.5271 262 R 0.1360 0.0581 0.8059 263 T 0.0916 0.0254 0.8830 264 P 0.0078 0.8250 0.1672 265 D 0.0070 0.8819 0.1111 266 H 0.0069 0.9333 0.0598 267 F 0.0048 0.9566 0.0387 268 E 0.0047 0.9606 0.0347 269 K 0.0046 0.9618 0.0336 270 M 0.0049 0.9605 0.0346 271 L 0.0049 0.9593 0.0358 272 H 0.0055 0.9561 0.0384 273 S 0.0067 0.9479 0.0454 274 M 0.0121 0.9198 0.0681 275 V 0.0296 0.8187 0.1517 276 F 0.0559 0.5762 0.3679 277 G 0.0681 0.2972 0.6348 278 D 0.0717 0.0660 0.8623 279 G 0.0364 0.1032 0.8605 280 A 0.0452 0.0887 0.8661 281 G 0.0506 0.0830 0.8664 282 N 0.0888 0.1312 0.7800 283 H 0.1494 0.2037 0.6469 284 D 0.0866 0.2858 0.6276 285 H 0.0705 0.4132 0.5163 286 L 0.1109 0.4819 0.4073 287 M 0.1196 0.4560 0.4244 288 H 0.1511 0.3835 0.4654 289 F 0.2968 0.2638 0.4394 290 T 0.4006 0.1776 0.4218 291 S 0.4175 0.1105 0.4719 292 A 0.3076 0.1682 0.5242 293 L 0.2936 0.1298 0.5767 294 T 0.2147 0.1123 0.6730 295 G 0.1293 0.3126 0.5581 296 S 0.2198 0.3942 0.3860 297 S 0.4313 0.3354 0.2333 298 F 0.4947 0.2522 0.2531 299 F 0.4733 0.1962 0.3305 300 A 0.2907 0.2370 0.4722 301 P 0.1377 0.2427 0.6196 302 S 0.0623 0.4349 0.5028 303 L 0.0083 0.8841 0.1076 304 D 0.0057 0.9049 0.0895 305 F 0.0052 0.9086 0.0862 306 L 0.0056 0.8932 0.1012 307 M 0.0063 0.8354 0.1583 308 Q 0.0103 0.6985 0.2912 309 F 0.0250 0.4337 0.5413 310 D 0.0312 0.2423 0.7265 311 N 0.0271 0.1819 0.7911