# This file is the result of combining several RDB files, specifically # T0305.t04.dssp-ebghstl.rdb (weight 1.53986) # T0305.t04.stride-ebghtl.rdb (weight 1.24869) # T0305.t04.str2.rdb (weight 1.54758) # T0305.t04.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 T0305.t04.dssp-ebghstl.rdb # ============================================ # TARGET T0305 # 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 T0305.t04-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 1132 # # ============================================ # Comments from T0305.t04.stride-ebghtl.rdb # ============================================ # TARGET T0305 # 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 T0305.t04-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 1132 # # ============================================ # Comments from T0305.t04.str2.rdb # ============================================ # TARGET T0305 # 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 T0305.t04-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 1132 # # ============================================ # Comments from T0305.t04.alpha.rdb # ============================================ # TARGET T0305 # 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 T0305.t04-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 1132 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 Y 0.0644 0.0901 0.8456 2 F 0.0891 0.1503 0.7606 3 Q 0.0937 0.2857 0.6206 4 S 0.1096 0.2864 0.6040 5 M 0.0124 0.8779 0.1097 6 K 0.0070 0.9335 0.0595 7 Q 0.0062 0.9402 0.0535 8 F 0.0056 0.9477 0.0467 9 V 0.0059 0.9508 0.0433 10 K 0.0057 0.9461 0.0482 11 H 0.0066 0.9342 0.0592 12 I 0.0096 0.9074 0.0830 13 G 0.0161 0.8396 0.1443 14 E 0.0246 0.8129 0.1625 15 L 0.0428 0.7495 0.2077 16 Y 0.0742 0.5863 0.3395 17 S 0.0367 0.4981 0.4652 18 N 0.0281 0.2832 0.6887 19 N 0.0491 0.1613 0.7896 20 Q 0.0311 0.2711 0.6978 21 H 0.0566 0.2857 0.6577 22 G 0.0975 0.2977 0.6048 23 F 0.1174 0.5651 0.3175 24 S 0.0461 0.7892 0.1646 25 E 0.0294 0.8699 0.1007 26 D 0.0262 0.8848 0.0890 27 F 0.0119 0.9212 0.0669 28 E 0.0083 0.9268 0.0649 29 E 0.0093 0.9041 0.0867 30 V 0.0129 0.8529 0.1342 31 Q 0.0186 0.8099 0.1715 32 R 0.0325 0.6543 0.3132 33 C 0.0729 0.4468 0.4804 34 T 0.1253 0.1459 0.7289 35 A 0.0818 0.1779 0.7403 36 D 0.0936 0.1191 0.7872 37 M 0.1210 0.1232 0.7557 38 N 0.1767 0.0819 0.7414 39 I 0.3548 0.0686 0.5766 40 T 0.3640 0.0712 0.5649 41 A 0.2329 0.2775 0.4897 42 E 0.1962 0.3322 0.4716 43 H 0.1461 0.3925 0.4613 44 S 0.1018 0.2623 0.6359 45 N 0.0735 0.1726 0.7539 46 H 0.0723 0.0436 0.8841 47 P 0.0218 0.3634 0.6148 48 E 0.0271 0.4203 0.5526 49 N 0.0528 0.4517 0.4955 50 K 0.0404 0.5148 0.4448 51 H 0.0495 0.4843 0.4662 52 K 0.0663 0.4507 0.4829 53 N 0.1190 0.2977 0.5833 54 R 0.1432 0.2272 0.6296 55 Y 0.2209 0.1578 0.6213 56 I 0.1792 0.1351 0.6857 57 N 0.2083 0.0688 0.7229 58 I 0.3968 0.0579 0.5453 59 L 0.3896 0.0499 0.5605 60 A 0.3310 0.0881 0.5809 61 Y 0.2096 0.1057 0.6846 62 D 0.1613 0.1403 0.6983 63 H 0.1205 0.1457 0.7338 64 S 0.2584 0.0724 0.6692 65 R 0.5203 0.0296 0.4501 66 V 0.8041 0.0087 0.1872 67 K 0.8085 0.0079 0.1835 68 L 0.6947 0.0099 0.2954 69 R 0.5311 0.0121 0.4569 70 P 0.4200 0.0157 0.5643 71 L 0.2137 0.0218 0.7646 72 P 0.0819 0.0578 0.8603 73 G 0.0464 0.0504 0.9032 74 K 0.0977 0.0551 0.8473 75 D 0.1209 0.0517 0.8275 76 S 0.0849 0.0618 0.8533 77 K 0.0699 0.0894 0.8407 78 H 0.1022 0.1008 0.7970 79 S 0.1478 0.0730 0.7792 80 D 0.2338 0.0658 0.7004 81 Y 0.6704 0.0288 0.3008 82 I 0.7646 0.0203 0.2151 83 N 0.7022 0.0184 0.2794 84 A 0.5373 0.0727 0.3900 85 N 0.4656 0.1171 0.4172 86 Y 0.4860 0.1071 0.4068 87 V 0.4743 0.0400 0.4857 88 D 0.3140 0.0603 0.6257 89 G 0.1523 0.0955 0.7522 90 Y 0.1071 0.1371 0.7557 91 N 0.0783 0.1254 0.7963 92 K 0.1104 0.1248 0.7647 93 A 0.1355 0.1091 0.7554 94 K 0.2524 0.0663 0.6813 95 A 0.7059 0.0189 0.2752 96 Y 0.9100 0.0063 0.0837 97 I 0.9150 0.0078 0.0772 98 A 0.8811 0.0124 0.1065 99 T 0.7087 0.0227 0.2685 100 Q 0.3692 0.0365 0.5942 101 G 0.1179 0.0375 0.8446 102 P 0.0928 0.0542 0.8530 103 L 0.0661 0.1258 0.8081 104 K 0.0240 0.5581 0.4179 105 S 0.0327 0.5119 0.4554 106 T 0.0524 0.6158 0.3318 107 F 0.0071 0.9111 0.0818 108 E 0.0047 0.9309 0.0644 109 D 0.0058 0.9291 0.0652 110 F 0.0072 0.9376 0.0553 111 W 0.0096 0.9327 0.0576 112 R 0.0171 0.9258 0.0571 113 M 0.0177 0.9271 0.0552 114 I 0.0173 0.9204 0.0622 115 W 0.0259 0.8849 0.0892 116 E 0.0244 0.8441 0.1315 117 Q 0.0303 0.5232 0.4465 118 N 0.0352 0.1187 0.8461 119 T 0.1365 0.0267 0.8368 120 G 0.2684 0.0284 0.7032 121 I 0.9068 0.0040 0.0892 122 I 0.9301 0.0035 0.0664 123 V 0.9313 0.0037 0.0650 124 M 0.9009 0.0063 0.0928 125 I 0.6715 0.0205 0.3080 126 T 0.3356 0.0580 0.6064 127 N 0.2269 0.0743 0.6988 128 L 0.3022 0.2504 0.4474 129 V 0.2747 0.3648 0.3606 130 E 0.1976 0.3782 0.4242 131 K 0.0541 0.1513 0.7946 132 G 0.0376 0.0519 0.9105 133 R 0.1679 0.0559 0.7762 134 R 0.4540 0.0537 0.4923 135 K 0.4902 0.0505 0.4593 136 C 0.4700 0.0684 0.4617 137 D 0.4114 0.1304 0.4582 138 Q 0.5035 0.1215 0.3751 139 Y 0.4373 0.1124 0.4503 140 W 0.2996 0.0369 0.6636 141 P 0.1425 0.0475 0.8100 142 T 0.0965 0.0582 0.8453 143 E 0.0799 0.1043 0.8158 144 N 0.1337 0.0797 0.7866 145 S 0.3550 0.1086 0.5364 146 E 0.5153 0.1497 0.3350 147 E 0.6221 0.1144 0.2635 148 Y 0.4884 0.0757 0.4359 149 G 0.2794 0.0244 0.6962 150 N 0.4201 0.0154 0.5645 151 I 0.8050 0.0043 0.1908 152 I 0.9114 0.0036 0.0850 153 V 0.9196 0.0032 0.0772 154 T 0.8919 0.0044 0.1037 155 L 0.8512 0.0048 0.1441 156 K 0.6880 0.0286 0.2834 157 S 0.6541 0.0187 0.3272 158 T 0.6785 0.0376 0.2839 159 K 0.7446 0.0292 0.2262 160 I 0.7042 0.0381 0.2577 161 H 0.5516 0.0420 0.4064 162 A 0.3998 0.0891 0.5112 163 C 0.4113 0.0517 0.5370 164 Y 0.7012 0.0142 0.2846 165 T 0.8560 0.0072 0.1369 166 V 0.8884 0.0051 0.1064 167 R 0.8662 0.0134 0.1204 168 R 0.9082 0.0048 0.0871 169 F 0.9136 0.0040 0.0823 170 S 0.9183 0.0040 0.0777 171 I 0.9081 0.0054 0.0865 172 R 0.7795 0.0278 0.1927 173 N 0.6449 0.0167 0.3383 174 T 0.6669 0.0258 0.3073 175 K 0.7702 0.0256 0.2041 176 V 0.7895 0.0299 0.1805 177 K 0.7756 0.0409 0.1835 178 K 0.6252 0.0741 0.3006 179 G 0.4280 0.0843 0.4877 180 Q 0.3158 0.1265 0.5577 181 K 0.1820 0.0966 0.7214 182 G 0.1113 0.0702 0.8185 183 N 0.1222 0.0423 0.8355 184 P 0.1164 0.1249 0.7588 185 K 0.0911 0.1275 0.7814 186 G 0.0759 0.1134 0.8107 187 R 0.1061 0.1042 0.7897 188 Q 0.1506 0.0828 0.7666 189 N 0.2952 0.0502 0.6546 190 E 0.5958 0.0216 0.3826 191 R 0.8024 0.0074 0.1902 192 V 0.8937 0.0044 0.1020 193 V 0.8998 0.0043 0.0958 194 I 0.8966 0.0068 0.0966 195 Q 0.9120 0.0050 0.0830 196 Y 0.9030 0.0076 0.0894 197 H 0.8696 0.0095 0.1209 198 Y 0.7258 0.0185 0.2557 199 T 0.4590 0.0543 0.4867 200 Q 0.2734 0.0481 0.6785 201 W 0.1583 0.0426 0.7991 202 P 0.0973 0.0929 0.8097 203 D 0.0809 0.1348 0.7843 204 M 0.0676 0.1123 0.8201 205 G 0.0545 0.0492 0.8962 206 V 0.1057 0.0193 0.8750 207 P 0.1082 0.0337 0.8582 208 E 0.0496 0.3085 0.6419 209 Y 0.0468 0.2984 0.6548 210 A 0.0230 0.6004 0.3766 211 L 0.0125 0.8394 0.1480 212 P 0.0079 0.9202 0.0718 213 V 0.0048 0.9550 0.0403 214 L 0.0047 0.9597 0.0356 215 T 0.0047 0.9599 0.0354 216 F 0.0047 0.9590 0.0363 217 V 0.0047 0.9591 0.0362 218 R 0.0047 0.9568 0.0385 219 R 0.0049 0.9467 0.0484 220 S 0.0060 0.9142 0.0798 221 S 0.0121 0.8293 0.1586 222 A 0.0137 0.7592 0.2271 223 A 0.0369 0.5918 0.3713 224 R 0.0656 0.2942 0.6402 225 M 0.0851 0.0410 0.8739 226 P 0.0499 0.0827 0.8674 227 E 0.0382 0.1065 0.8552 228 T 0.0694 0.0531 0.8775 229 G 0.1077 0.0156 0.8767 230 P 0.3501 0.0075 0.6425 231 V 0.8855 0.0042 0.1104 232 L 0.9249 0.0034 0.0717 233 V 0.9229 0.0037 0.0734 234 H 0.8475 0.0069 0.1456 235 C 0.4641 0.0212 0.5147 236 S 0.1501 0.0612 0.7887 237 A 0.0834 0.1042 0.8124 238 G 0.0783 0.1310 0.7907 239 V 0.1220 0.1956 0.6823 240 G 0.1113 0.2634 0.6253 241 R 0.0673 0.5647 0.3679 242 T 0.0348 0.8215 0.1437 243 G 0.0147 0.9156 0.0697 244 T 0.0076 0.9527 0.0397 245 Y 0.0049 0.9598 0.0353 246 I 0.0047 0.9609 0.0345 247 V 0.0047 0.9610 0.0343 248 I 0.0047 0.9610 0.0343 249 D 0.0046 0.9615 0.0338 250 S 0.0046 0.9603 0.0351 251 M 0.0047 0.9581 0.0372 252 L 0.0047 0.9582 0.0371 253 Q 0.0047 0.9522 0.0431 254 Q 0.0049 0.9412 0.0539 255 I 0.0061 0.9168 0.0771 256 K 0.0067 0.8611 0.1321 257 D 0.0131 0.6724 0.3145 258 K 0.0453 0.2426 0.7120 259 S 0.0343 0.0788 0.8869 260 T 0.1521 0.0518 0.7962 261 V 0.4120 0.0228 0.5652 262 N 0.2247 0.0262 0.7491 263 V 0.0074 0.9375 0.0552 264 L 0.0052 0.9520 0.0428 265 G 0.0047 0.9568 0.0385 266 F 0.0047 0.9581 0.0372 267 L 0.0047 0.9605 0.0349 268 K 0.0046 0.9602 0.0351 269 H 0.0047 0.9576 0.0377 270 I 0.0047 0.9534 0.0419 271 R 0.0050 0.9394 0.0556 272 T 0.0067 0.8764 0.1169 273 Q 0.0190 0.7703 0.2107 274 R 0.0507 0.4885 0.4608 275 N 0.0209 0.4286 0.5506 276 Y 0.0322 0.2764 0.6914 277 L 0.1466 0.1889 0.6646 278 V 0.2526 0.0724 0.6750 279 Q 0.1712 0.0407 0.7881 280 T 0.0673 0.0477 0.8849 281 E 0.0048 0.9440 0.0512 282 E 0.0047 0.9564 0.0389 283 Q 0.0047 0.9588 0.0365 284 Y 0.0047 0.9608 0.0346 285 I 0.0046 0.9612 0.0342 286 F 0.0046 0.9613 0.0340 287 I 0.0046 0.9613 0.0341 288 H 0.0046 0.9612 0.0341 289 D 0.0046 0.9617 0.0336 290 A 0.0046 0.9614 0.0340 291 L 0.0047 0.9605 0.0348 292 L 0.0047 0.9596 0.0357 293 E 0.0048 0.9529 0.0424 294 A 0.0053 0.9271 0.0676 295 I 0.0081 0.8619 0.1300 296 L 0.0188 0.6134 0.3679 297 G 0.0306 0.0812 0.8883