# This file is the result of combining several RDB files, specifically # T0222.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0222.t2k.stride-ebghtl.rdb (weight 1.24869) # T0222.t2k.str2.rdb (weight 1.54758) # T0222.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 T0222.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0222 # 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 T0222.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 92 # # ============================================ # Comments from T0222.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0222 # 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 T0222.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 92 # # ============================================ # Comments from T0222.t2k.str2.rdb # ============================================ # TARGET T0222 # 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 T0222.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 92 # # ============================================ # Comments from T0222.t2k.alpha.rdb # ============================================ # TARGET T0222 # 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 T0222.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 92 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.1036 0.0121 0.8844 2 A 0.4827 0.0113 0.5060 3 A 0.7813 0.0065 0.2122 4 F 0.8654 0.0059 0.1288 5 Q 0.8619 0.0037 0.1344 6 I 0.7211 0.0155 0.2633 7 A 0.1647 0.0268 0.8085 8 N 0.0850 0.0442 0.8709 9 K 0.6238 0.0126 0.3636 10 T 0.7807 0.0069 0.2124 11 V 0.6005 0.0255 0.3740 12 G 0.1854 0.0315 0.7831 13 K 0.0335 0.0872 0.8794 14 D 0.0430 0.0520 0.9050 15 A 0.1164 0.0255 0.8581 16 P 0.1504 0.0174 0.8322 17 V 0.5970 0.0074 0.3956 18 F 0.8916 0.0070 0.1014 19 I 0.9290 0.0035 0.0675 20 I 0.9209 0.0055 0.0736 21 A 0.8930 0.0099 0.0971 22 E 0.8149 0.0181 0.1670 23 A 0.4627 0.0459 0.4914 24 G 0.2193 0.0609 0.7199 25 I 0.1387 0.2015 0.6598 26 N 0.1041 0.2055 0.6903 27 H 0.0763 0.1724 0.7514 28 D 0.0429 0.1368 0.8203 29 G 0.0454 0.0881 0.8665 30 K 0.0619 0.1407 0.7975 31 L 0.0051 0.9481 0.0468 32 D 0.0050 0.9565 0.0385 33 Q 0.0048 0.9571 0.0381 34 A 0.0047 0.9599 0.0354 35 F 0.0047 0.9591 0.0362 36 A 0.0047 0.9586 0.0367 37 L 0.0047 0.9586 0.0367 38 I 0.0047 0.9603 0.0350 39 D 0.0047 0.9599 0.0354 40 A 0.0047 0.9595 0.0358 41 A 0.0048 0.9576 0.0376 42 A 0.0049 0.9481 0.0470 43 E 0.0056 0.8857 0.1088 44 A 0.0373 0.3755 0.5872 45 G 0.0408 0.0316 0.9277 46 A 0.0777 0.0237 0.8986 47 D 0.1718 0.0796 0.7486 48 A 0.7753 0.0513 0.1734 49 V 0.8207 0.0492 0.1301 50 K 0.8243 0.0372 0.1385 51 F 0.6426 0.0689 0.2885 52 Q 0.3679 0.0732 0.5589 53 M 0.3084 0.0707 0.6208 54 F 0.3692 0.0500 0.5808 55 Q 0.2605 0.0380 0.7015 56 A 0.0650 0.6665 0.2685 57 D 0.0451 0.7062 0.2487 58 R 0.0775 0.7101 0.2124 59 M 0.1513 0.5523 0.2964 60 Y 0.2440 0.3385 0.4175 61 Q 0.2123 0.2356 0.5521 62 K 0.0977 0.2993 0.6030 63 D 0.0994 0.2290 0.6716 64 P 0.0880 0.2381 0.6739 65 G 0.1136 0.2142 0.6722 66 L 0.1934 0.1930 0.6135 67 Y 0.2351 0.1679 0.5970 68 K 0.2107 0.1513 0.6380 69 T 0.1620 0.1288 0.7092 70 A 0.1419 0.1306 0.7275 71 A 0.1029 0.1710 0.7261 72 G 0.0883 0.1731 0.7386 73 K 0.0693 0.1765 0.7542 74 D 0.1035 0.1237 0.7728 75 V 0.2346 0.1167 0.6488 76 S 0.3003 0.1482 0.5514 77 I 0.0984 0.6259 0.2756 78 F 0.0560 0.7442 0.1998 79 S 0.0544 0.7709 0.1746 80 L 0.0321 0.8429 0.1249 81 V 0.0335 0.8402 0.1263 82 Q 0.0359 0.8009 0.1632 83 S 0.0331 0.6957 0.2711 84 M 0.0765 0.3467 0.5768 85 E 0.0801 0.1334 0.7865 86 M 0.0710 0.0280 0.9010 87 P 0.0581 0.0244 0.9175 88 A 0.0073 0.8745 0.1181 89 E 0.0052 0.9082 0.0867 90 W 0.0057 0.9145 0.0798 91 I 0.0049 0.9470 0.0481 92 L 0.0051 0.9541 0.0408 93 P 0.0049 0.9570 0.0381 94 L 0.0049 0.9562 0.0390 95 L 0.0048 0.9591 0.0361 96 D 0.0048 0.9593 0.0360 97 Y 0.0048 0.9591 0.0361 98 C 0.0048 0.9585 0.0367 99 R 0.0050 0.9485 0.0465 100 E 0.0052 0.9176 0.0772 101 K 0.0434 0.3367 0.6199 102 Q 0.0384 0.0190 0.9425 103 V 0.0956 0.0111 0.8932 104 I 0.5677 0.0124 0.4199 105 F 0.8857 0.0079 0.1065 106 L 0.8793 0.0111 0.1096 107 S 0.7802 0.0152 0.2046 108 T 0.4763 0.0155 0.5082 109 V 0.1505 0.0950 0.7544 110 C 0.0679 0.0803 0.8519 111 D 0.0796 0.0677 0.8527 112 E 0.0066 0.8542 0.1393 113 G 0.0060 0.8951 0.0989 114 S 0.0066 0.9248 0.0686 115 A 0.0059 0.9402 0.0539 116 D 0.0058 0.9441 0.0501 117 L 0.0056 0.9447 0.0498 118 L 0.0067 0.9397 0.0535 119 Q 0.0056 0.9199 0.0745 120 S 0.0067 0.8250 0.1683 121 T 0.0509 0.4341 0.5150 122 S 0.0560 0.0775 0.8664 123 P 0.0793 0.0317 0.8891 124 S 0.1615 0.0578 0.7807 125 A 0.5908 0.1663 0.2429 126 F 0.7081 0.1413 0.1506 127 K 0.7140 0.1490 0.1370 128 I 0.5956 0.1484 0.2560 129 A 0.3659 0.1380 0.4962 130 S 0.1747 0.1900 0.6354 131 Y 0.1144 0.3272 0.5585 132 E 0.1294 0.3879 0.4827 133 I 0.1139 0.3785 0.5075 134 N 0.0682 0.2171 0.7148 135 H 0.0557 0.1596 0.7847 136 L 0.0268 0.5564 0.4168 137 P 0.0100 0.8928 0.0972 138 L 0.0061 0.9406 0.0533 139 L 0.0053 0.9504 0.0442 140 K 0.0053 0.9516 0.0430 141 Y 0.0049 0.9551 0.0400 142 V 0.0051 0.9512 0.0437 143 A 0.0054 0.9414 0.0532 144 R 0.0074 0.8869 0.1056 145 L 0.0496 0.5235 0.4269 146 N 0.0361 0.0414 0.9225 147 R 0.0581 0.0094 0.9325 148 P 0.3152 0.0083 0.6765 149 M 0.8029 0.0113 0.1859 150 I 0.8738 0.0084 0.1179 151 F 0.8493 0.0180 0.1327 152 S 0.6340 0.0362 0.3298 153 T 0.2701 0.0508 0.6791 154 A 0.1377 0.0579 0.8045 155 G 0.1766 0.0892 0.7342 156 A 0.1914 0.0573 0.7513 157 E 0.0913 0.0362 0.8725 158 I 0.0050 0.9331 0.0619 159 S 0.0048 0.9486 0.0466 160 D 0.0048 0.9537 0.0415 161 V 0.0047 0.9591 0.0362 162 H 0.0047 0.9601 0.0352 163 E 0.0046 0.9600 0.0354 164 A 0.0047 0.9606 0.0348 165 W 0.0047 0.9605 0.0349 166 R 0.0047 0.9607 0.0346 167 T 0.0047 0.9589 0.0364 168 I 0.0047 0.9568 0.0385 169 R 0.0049 0.9455 0.0496 170 A 0.0059 0.8932 0.1009 171 E 0.0393 0.3107 0.6500 172 G 0.0463 0.0289 0.9248 173 N 0.0857 0.0223 0.8921 174 N 0.1018 0.0429 0.8553 175 Q 0.4040 0.0394 0.5567 176 I 0.8904 0.0052 0.1044 177 A 0.9248 0.0039 0.0713 178 I 0.9281 0.0034 0.0685 179 M 0.8714 0.0071 0.1215 180 H 0.6216 0.0116 0.3668 181 C 0.4586 0.0365 0.5048 182 V 0.3263 0.0696 0.6041 183 A 0.2213 0.0999 0.6788 184 K 0.1411 0.0942 0.7646 185 Y 0.1194 0.0414 0.8391 186 P 0.1057 0.0419 0.8524 187 A 0.1199 0.0235 0.8565 188 P 0.0683 0.0285 0.9032 189 P 0.0201 0.6246 0.3553 190 E 0.0127 0.6957 0.2916 191 Y 0.0285 0.7549 0.2166 192 S 0.0784 0.5693 0.3523 193 N 0.0825 0.5122 0.4053 194 L 0.0136 0.8450 0.1414 195 S 0.0135 0.8860 0.1005 196 V 0.0117 0.9035 0.0848 197 I 0.0079 0.9391 0.0530 198 P 0.0054 0.9422 0.0524 199 M 0.0048 0.9490 0.0462 200 L 0.0048 0.9434 0.0518 201 A 0.0050 0.9292 0.0658 202 A 0.0066 0.8659 0.1275 203 A 0.0126 0.7453 0.2421 204 F 0.0795 0.3381 0.5824 205 P 0.0335 0.1235 0.8430 206 E 0.0492 0.0961 0.8547 207 A 0.1301 0.0304 0.8395 208 V 0.3283 0.0200 0.6516 209 I 0.6040 0.0263 0.3697 210 G 0.5633 0.0224 0.4143 211 F 0.4734 0.0351 0.4915 212 S 0.2647 0.0753 0.6600 213 D 0.1632 0.1117 0.7252 214 H 0.0870 0.1195 0.7936 215 S 0.0742 0.1530 0.7728 216 E 0.0611 0.1636 0.7753 217 H 0.0492 0.1103 0.8405 218 P 0.0536 0.3444 0.6020 219 T 0.0600 0.5914 0.3486 220 E 0.0295 0.8381 0.1324 221 A 0.0160 0.9133 0.0707 222 P 0.0127 0.9373 0.0500 223 C 0.0136 0.9419 0.0445 224 A 0.0230 0.9359 0.0411 225 A 0.0145 0.9418 0.0437 226 V 0.0167 0.9266 0.0567 227 R 0.0181 0.8765 0.1054 228 L 0.0477 0.4653 0.4870 229 G 0.0582 0.0289 0.9129 230 A 0.1021 0.0087 0.8891 231 K 0.3049 0.0382 0.6569 232 L 0.8924 0.0064 0.1012 233 I 0.9082 0.0081 0.0836 234 E 0.9169 0.0038 0.0793 235 K 0.8201 0.0129 0.1671 236 H 0.5347 0.0148 0.4506 237 F 0.3718 0.0223 0.6059 238 T 0.3637 0.0237 0.6126 239 I 0.2255 0.0411 0.7334 240 D 0.1099 0.0389 0.8513 241 K 0.0198 0.2332 0.7471 242 N 0.0324 0.1887 0.7789 243 L 0.0699 0.1379 0.7922 244 P 0.0841 0.1054 0.8106 245 G 0.0998 0.0701 0.8300 246 A 0.0956 0.1161 0.7883 247 D 0.0924 0.1319 0.7757 248 H 0.0766 0.2727 0.6506 249 S 0.0845 0.4057 0.5098 250 F 0.1143 0.3699 0.5157 251 A 0.1791 0.2477 0.5732 252 L 0.1692 0.1275 0.7033 253 N 0.0835 0.0457 0.8708 254 P 0.0060 0.9059 0.0881 255 D 0.0050 0.9360 0.0590 256 E 0.0052 0.9403 0.0545 257 L 0.0047 0.9563 0.0389 258 K 0.0047 0.9584 0.0369 259 E 0.0047 0.9576 0.0377 260 M 0.0047 0.9573 0.0380 261 V 0.0047 0.9582 0.0371 262 D 0.0047 0.9557 0.0396 263 G 0.0048 0.9518 0.0434 264 I 0.0047 0.9575 0.0378 265 R 0.0047 0.9593 0.0360 266 K 0.0047 0.9581 0.0372 267 T 0.0047 0.9571 0.0382 268 E 0.0048 0.9533 0.0418 269 A 0.0055 0.9339 0.0606 270 E 0.0093 0.8598 0.1309 271 L 0.0301 0.6492 0.3207 272 K 0.0372 0.2302 0.7326 273 Q 0.0535 0.1252 0.8213 274 G 0.0345 0.0650 0.9006