# This file is the result of combining several RDB files, specifically # T0142.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0142.t2k.stride-ebghtl.rdb (weight 1.24869) # T0142.t2k.str.rdb (weight 1.53983) # T0142.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 T0142.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0142 # 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 T0142.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 61 # # ============================================ # Comments from T0142.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0142 # 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 T0142.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 61 # # ============================================ # Comments from T0142.t2k.str.rdb # ============================================ # TARGET T0142 # Using neural net t2k-5651-IDaaHr-5-15-7-15-9-15-13-str-seeded.net # This is a 4-layer network, with # window units # 5 15 # 7 15 # 9 15 # 13 13 (1 str ) # The input amino acid frequencies were determined from # alignment T0142.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 61 # # ============================================ # Comments from T0142.t2k.alpha.rdb # ============================================ # TARGET T0142 # 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 T0142.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 61 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 G 0.1700 0.0342 0.7958 2 S 0.1687 0.0276 0.8037 3 P 0.1788 0.0258 0.7954 4 P 0.1450 0.1634 0.6916 5 A 0.1889 0.1756 0.6355 6 Q 0.4114 0.0959 0.4927 7 L 0.7403 0.0082 0.2515 8 S 0.8689 0.0060 0.1251 9 V 0.9258 0.0034 0.0708 10 H 0.9205 0.0038 0.0757 11 T 0.9149 0.0036 0.0815 12 V 0.8761 0.0061 0.1177 13 S 0.7829 0.0143 0.2028 14 W 0.6363 0.0376 0.3262 15 N 0.5042 0.0548 0.4410 16 S 0.2603 0.1026 0.6371 17 G 0.0993 0.0888 0.8118 18 H 0.0915 0.0690 0.8395 19 E 0.1623 0.0545 0.7832 20 R 0.1820 0.0422 0.7758 21 A 0.1041 0.0573 0.8386 22 P 0.0706 0.1980 0.7314 23 T 0.0428 0.3308 0.6264 24 N 0.0514 0.4091 0.5395 25 L 0.0546 0.5273 0.4181 26 E 0.0526 0.6171 0.3303 27 E 0.0390 0.6888 0.2722 28 L 0.0418 0.6769 0.2813 29 L 0.0554 0.5796 0.3650 30 G 0.0761 0.3717 0.5522 31 L 0.0613 0.2266 0.7121 32 N 0.0623 0.1806 0.7571 33 S 0.0543 0.2217 0.7240 34 G 0.0579 0.1610 0.7811 35 E 0.0964 0.0762 0.8274 36 T 0.1326 0.0568 0.8106 37 P 0.2186 0.0242 0.7571 38 D 0.3835 0.0307 0.5858 39 V 0.8564 0.0042 0.1393 40 I 0.9184 0.0036 0.0780 41 A 0.9246 0.0037 0.0717 42 V 0.8835 0.0143 0.1021 43 A 0.7902 0.0097 0.2000 44 V 0.6650 0.0471 0.2879 45 Q 0.6181 0.0736 0.3083 46 G 0.5903 0.0863 0.3234 47 F 0.4247 0.1054 0.4699 48 G 0.3471 0.1343 0.5186 49 F 0.2255 0.2335 0.5410 50 Q 0.1234 0.2933 0.5832 51 T 0.0862 0.3154 0.5984 52 D 0.0491 0.4092 0.5417 53 K 0.0556 0.4037 0.5407 54 P 0.0705 0.3612 0.5683 55 Q 0.0898 0.3154 0.5948 56 Q 0.0694 0.2991 0.6316 57 G 0.0549 0.3246 0.6205 58 P 0.0265 0.6637 0.3098 59 A 0.0246 0.7745 0.2009 60 C 0.0122 0.8875 0.1004 61 V 0.0082 0.9235 0.0683 62 K 0.0071 0.9347 0.0582 63 N 0.0057 0.9405 0.0537 64 F 0.0063 0.9361 0.0576 65 Q 0.0057 0.9292 0.0651 66 S 0.0079 0.8964 0.0957 67 L 0.0123 0.8166 0.1711 68 L 0.0533 0.4598 0.4869 69 T 0.0513 0.2018 0.7469 70 S 0.0563 0.1476 0.7961 71 K 0.0662 0.1023 0.8314 72 G 0.1537 0.0765 0.7698 73 Y 0.6460 0.0230 0.3310 74 T 0.8184 0.0182 0.1634 75 K 0.8465 0.0274 0.1261 76 L 0.7924 0.0380 0.1696 77 K 0.7002 0.0476 0.2522 78 N 0.5925 0.1123 0.2952 79 T 0.5227 0.1694 0.3079 80 I 0.5009 0.2422 0.2569 81 T 0.5367 0.2523 0.2110 82 E 0.4937 0.3111 0.1951 83 T 0.6093 0.2631 0.1276 84 M 0.7058 0.2005 0.0937 85 G 0.7516 0.1608 0.0876 86 L 0.7918 0.1248 0.0833 87 T 0.8065 0.1021 0.0915 88 V 0.8198 0.0776 0.1026 89 Y 0.8151 0.0669 0.1180 90 C 0.7219 0.0662 0.2118 91 L 0.4889 0.0804 0.4307 92 E 0.0590 0.5698 0.3712 93 K 0.0352 0.5258 0.4390 94 H 0.0432 0.5355 0.4214 95 L 0.0870 0.3416 0.5714 96 D 0.0882 0.3120 0.5998 97 Q 0.1879 0.3089 0.5032 98 N 0.3096 0.2067 0.4837 99 T 0.2710 0.1847 0.5443 100 L 0.2975 0.1156 0.5869 101 K 0.2307 0.1274 0.6418 102 N 0.2127 0.1502 0.6371 103 E 0.3286 0.1480 0.5233 104 T 0.4108 0.1055 0.4836 105 I 0.4103 0.1249 0.4648 106 I 0.4561 0.1350 0.4089 107 V 0.4381 0.1134 0.4485 108 T 0.4242 0.1503 0.4256 109 V 0.3428 0.1885 0.4688 110 D 0.2191 0.2398 0.5411 111 D 0.1788 0.2756 0.5456 112 Q 0.1708 0.1538 0.6754 113 K 0.1380 0.0698 0.7922 114 K 0.1639 0.0468 0.7892 115 S 0.2736 0.0367 0.6896 116 G 0.4274 0.0229 0.5497 117 G 0.7059 0.0078 0.2863 118 I 0.8830 0.0047 0.1124 119 V 0.9238 0.0035 0.0727 120 T 0.9241 0.0035 0.0724 121 S 0.9272 0.0036 0.0693 122 F 0.9189 0.0038 0.0773 123 T 0.9149 0.0037 0.0815 124 I 0.8495 0.0123 0.1382 125 Y 0.4285 0.0333 0.5381 126 N 0.1158 0.0736 0.8106 127 K 0.4275 0.0271 0.5453 128 R 0.8037 0.0112 0.1851 129 F 0.8933 0.0064 0.1003 130 S 0.9049 0.0108 0.0843 131 F 0.9116 0.0123 0.0761 132 T 0.8587 0.0357 0.1057 133 T 0.7640 0.0615 0.1745 134 S 0.4968 0.1713 0.3319 135 R 0.3808 0.2156 0.4036 136 M 0.2605 0.3002 0.4394 137 S 0.1625 0.2844 0.5531 138 D 0.0749 0.2688 0.6564 139 E 0.0592 0.1506 0.7902 140 D 0.0729 0.3407 0.5864 141 V 0.0399 0.4202 0.5399 142 T 0.0469 0.4583 0.4947 143 S 0.0317 0.6672 0.3010 144 T 0.0266 0.7309 0.2425 145 N 0.0406 0.7339 0.2255 146 T 0.0314 0.7701 0.1985 147 K 0.0127 0.8647 0.1225 148 Y 0.0075 0.8843 0.1082 149 A 0.0081 0.8969 0.0950 150 Y 0.0045 0.9465 0.0490 151 D 0.0044 0.9542 0.0414 152 T 0.0045 0.9514 0.0442 153 R 0.0045 0.9479 0.0477 154 L 0.0048 0.9301 0.0651 155 D 0.0061 0.8425 0.1513 156 Y 0.0121 0.6508 0.3371 157 S 0.0643 0.4223 0.5134 158 K 0.0712 0.2900 0.6388 159 K 0.0768 0.2018 0.7214 160 D 0.0875 0.1527 0.7598 161 D 0.0723 0.1138 0.8139 162 P 0.0824 0.0999 0.8177 163 S 0.1960 0.0387 0.7654 164 D 0.3374 0.0383 0.6243 165 F 0.8409 0.0092 0.1498 166 L 0.9164 0.0050 0.0787 167 F 0.9193 0.0051 0.0756 168 W 0.8876 0.0060 0.1065 169 I 0.6387 0.0306 0.3306 170 G 0.4162 0.0541 0.5298 171 D 0.2414 0.1132 0.6453 172 L 0.1916 0.2027 0.6057 173 N 0.3167 0.1711 0.5121 174 V 0.4347 0.1105 0.4548 175 R 0.5121 0.0759 0.4120 176 V 0.4026 0.0627 0.5347 177 E 0.2015 0.0588 0.7397 178 T 0.0828 0.1218 0.7954 179 N 0.0731 0.1532 0.7737 180 A 0.0237 0.6509 0.3254 181 T 0.0134 0.8329 0.1537 182 H 0.0145 0.8834 0.1021 183 A 0.0106 0.9065 0.0828 184 K 0.0104 0.9216 0.0680 185 S 0.0107 0.9232 0.0661 186 L 0.0122 0.9092 0.0786 187 V 0.0154 0.8727 0.1118 188 D 0.0166 0.7882 0.1952 189 Q 0.0236 0.6134 0.3631 190 N 0.0335 0.3504 0.6161 191 N 0.0606 0.2803 0.6591 192 I 0.0127 0.8116 0.1757 193 D 0.0083 0.8583 0.1334 194 G 0.0078 0.8604 0.1318 195 L 0.0111 0.8269 0.1620 196 M 0.0178 0.8120 0.1703 197 A 0.0089 0.8404 0.1507 198 F 0.0089 0.8303 0.1608 199 D 0.0132 0.7988 0.1880 200 Q 0.0155 0.8553 0.1291 201 L 0.0138 0.8829 0.1032 202 K 0.0129 0.8930 0.0942 203 K 0.0251 0.8403 0.1346 204 A 0.0253 0.8037 0.1711 205 K 0.0297 0.7080 0.2623 206 E 0.0439 0.4055 0.5506 207 Q 0.0336 0.1822 0.7842 208 K 0.0924 0.1450 0.7626 209 L 0.1798 0.1862 0.6340 210 F 0.1846 0.1612 0.6542 211 D 0.1172 0.2165 0.6663 212 G 0.1520 0.1710 0.6770 213 W 0.2736 0.1418 0.5846 214 T 0.3928 0.0939 0.5133 215 E 0.4016 0.0728 0.5256 216 P 0.3110 0.0447 0.6443 217 Q 0.3140 0.0320 0.6540 218 V 0.2974 0.0204 0.6822 219 T 0.2681 0.0242 0.7077 220 F 0.2549 0.0177 0.7273 221 K 0.1296 0.0229 0.8475 222 P 0.1327 0.0262 0.8411 223 T 0.3120 0.0321 0.6560 224 Y 0.4701 0.0210 0.5089 225 K 0.4874 0.0263 0.4863 226 F 0.4550 0.0232 0.5218 227 K 0.2779 0.0273 0.6948 228 P 0.0630 0.1094 0.8275 229 N 0.0465 0.0697 0.8838 230 T 0.1057 0.0676 0.8267 231 D 0.1183 0.1018 0.7798 232 E 0.1107 0.1245 0.7648 233 Y 0.1555 0.0938 0.7507 234 D 0.1562 0.0802 0.7636 235 L 0.1258 0.0782 0.7960 236 S 0.1594 0.0674 0.7733 237 A 0.3180 0.0547 0.6273 238 T 0.2890 0.0299 0.6811 239 P 0.2742 0.0589 0.6669 240 S 0.3240 0.1039 0.5721 241 W 0.4041 0.1266 0.4693 242 T 0.4386 0.0986 0.4628 243 D 0.4539 0.1287 0.4174 244 R 0.6607 0.1183 0.2210 245 A 0.7250 0.1127 0.1623 246 L 0.7421 0.0984 0.1595 247 Y 0.7199 0.0611 0.2190 248 K 0.4546 0.0547 0.4907 249 S 0.1658 0.0768 0.7574 250 G 0.0862 0.0743 0.8395 251 T 0.1042 0.0777 0.8182 252 G 0.1384 0.1221 0.7394 253 K 0.2346 0.1479 0.6175 254 T 0.3706 0.1181 0.5114 255 I 0.5226 0.1162 0.3612 256 Q 0.5963 0.0960 0.3076 257 P 0.6227 0.1032 0.2741 258 L 0.5647 0.1294 0.3059 259 S 0.5154 0.1321 0.3525 260 Y 0.4187 0.1533 0.4280 261 N 0.3240 0.1617 0.5142 262 S 0.2422 0.1487 0.6091 263 L 0.2032 0.1400 0.6568 264 T 0.1460 0.1554 0.6986 265 N 0.2707 0.1141 0.6152 266 Y 0.4112 0.0556 0.5332 267 K 0.5317 0.0505 0.4178 268 Q 0.3627 0.1010 0.5363 269 T 0.1760 0.1176 0.7064 270 E 0.0995 0.1404 0.7601 271 H 0.1568 0.0810 0.7622 272 R 0.2222 0.0293 0.7485 273 P 0.4179 0.0202 0.5618 274 V 0.7159 0.0244 0.2597 275 L 0.8609 0.0099 0.1292 276 A 0.8981 0.0064 0.0956 277 K 0.9122 0.0043 0.0835 278 F 0.9041 0.0048 0.0911 279 R 0.8816 0.0054 0.1130 280 V 0.7986 0.0064 0.1950 281 T 0.6297 0.0078 0.3626 282 L 0.0982 0.0124 0.8894