# This file is the result of combining several RDB files, specifically # T0246.t2k.dssp-ebghstl.rdb (weight 1.53986) # T0246.t2k.stride-ebghtl.rdb (weight 1.24869) # T0246.t2k.str2.rdb (weight 1.54758) # T0246.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 T0246.t2k.dssp-ebghstl.rdb # ============================================ # TARGET T0246 # 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 T0246.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 478 # # ============================================ # Comments from T0246.t2k.stride-ebghtl.rdb # ============================================ # TARGET T0246 # 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 T0246.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 478 # # ============================================ # Comments from T0246.t2k.str2.rdb # ============================================ # TARGET T0246 # 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 T0246.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 478 # # ============================================ # Comments from T0246.t2k.alpha.rdb # ============================================ # TARGET T0246 # 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 T0246.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 478 # # ============================================ Pos AA E H C 10N 1S 5N 5N 5N 1 M 0.3053 0.0079 0.6868 2 K 0.6468 0.0069 0.3463 3 I 0.8342 0.0047 0.1611 4 A 0.8699 0.0052 0.1249 5 V 0.8665 0.0054 0.1282 6 L 0.7106 0.0093 0.2800 7 P 0.3374 0.0293 0.6333 8 G 0.1020 0.0467 0.8513 9 D 0.0678 0.1306 0.8016 10 G 0.0750 0.1433 0.7817 11 I 0.1072 0.1864 0.7064 12 G 0.0519 0.2438 0.7043 13 P 0.0101 0.8704 0.1196 14 E 0.0089 0.8922 0.0989 15 V 0.0068 0.9234 0.0698 16 V 0.0053 0.9437 0.0509 17 R 0.0048 0.9553 0.0399 18 E 0.0047 0.9559 0.0394 19 A 0.0047 0.9570 0.0383 20 L 0.0047 0.9599 0.0354 21 K 0.0047 0.9588 0.0365 22 V 0.0047 0.9575 0.0379 23 L 0.0047 0.9573 0.0381 24 E 0.0047 0.9545 0.0408 25 V 0.0048 0.9493 0.0458 26 V 0.0049 0.9400 0.0551 27 E 0.0058 0.9127 0.0815 28 K 0.0094 0.8118 0.1789 29 K 0.0269 0.6014 0.3717 30 T 0.0499 0.2020 0.7481 31 G 0.0322 0.0467 0.9211 32 K 0.0913 0.0139 0.8949 33 T 0.2215 0.0122 0.7662 34 F 0.7224 0.0052 0.2724 35 E 0.8799 0.0042 0.1158 36 K 0.9072 0.0037 0.0890 37 V 0.8846 0.0078 0.1076 38 F 0.8710 0.0050 0.1240 39 G 0.6885 0.0115 0.3000 40 H 0.5743 0.0249 0.4008 41 I 0.3364 0.0874 0.5763 42 G 0.2010 0.1684 0.6306 43 G 0.0463 0.7191 0.2346 44 D 0.0374 0.8199 0.1426 45 A 0.0436 0.8376 0.1187 46 I 0.0558 0.8198 0.1244 47 D 0.0430 0.7692 0.1879 48 R 0.0220 0.6717 0.3063 49 F 0.0495 0.3102 0.6403 50 G 0.0283 0.0459 0.9259 51 E 0.0774 0.0278 0.8948 52 P 0.2470 0.0258 0.7272 53 L 0.1353 0.0174 0.8473 54 P 0.0624 0.0326 0.9050 55 E 0.0054 0.9070 0.0876 56 E 0.0048 0.9320 0.0632 57 T 0.0050 0.9451 0.0498 58 K 0.0047 0.9554 0.0398 59 K 0.0047 0.9517 0.0436 60 I 0.0049 0.9419 0.0532 61 C 0.0060 0.9246 0.0695 62 L 0.0059 0.8761 0.1180 63 E 0.0094 0.6542 0.3364 64 A 0.0610 0.2575 0.6815 65 D 0.0678 0.0469 0.8853 66 A 0.6657 0.0208 0.3135 67 I 0.8919 0.0101 0.0981 68 F 0.9033 0.0074 0.0893 69 L 0.8167 0.0211 0.1621 70 G 0.4627 0.0186 0.5188 71 S 0.2905 0.0421 0.6674 72 V 0.2574 0.0650 0.6776 73 G 0.2156 0.0473 0.7372 74 G 0.1333 0.0373 0.8294 75 P 0.1481 0.0954 0.7565 76 K 0.1027 0.1464 0.7509 77 W 0.0946 0.1670 0.7384 78 D 0.0754 0.1545 0.7700 79 D 0.0877 0.1435 0.7688 80 L 0.1119 0.0861 0.8020 81 P 0.0939 0.0865 0.8196 82 P 0.0670 0.2485 0.6845 83 E 0.0491 0.2437 0.7072 84 K 0.0798 0.1897 0.7304 85 R 0.1414 0.1252 0.7333 86 P 0.1436 0.1125 0.7439 87 E 0.1069 0.3036 0.5895 88 I 0.0675 0.4423 0.4902 89 G 0.0677 0.4980 0.4343 90 G 0.0419 0.7036 0.2545 91 L 0.0300 0.7911 0.1789 92 L 0.0253 0.8747 0.1000 93 A 0.0160 0.9196 0.0644 94 L 0.0114 0.9298 0.0588 95 R 0.0103 0.9274 0.0622 96 K 0.0104 0.9033 0.0863 97 M 0.0136 0.8518 0.1346 98 L 0.0598 0.5667 0.3736 99 N 0.0559 0.1848 0.7593 100 L 0.1949 0.1741 0.6311 101 Y 0.4323 0.1273 0.4404 102 A 0.5784 0.0795 0.3421 103 N 0.5877 0.0487 0.3636 104 I 0.5693 0.0432 0.3874 105 R 0.5698 0.0313 0.3989 106 P 0.5474 0.0429 0.4097 107 I 0.5000 0.0768 0.4232 108 K 0.5746 0.0957 0.3297 109 V 0.4612 0.0885 0.4503 110 Y 0.2422 0.0567 0.7011 111 R 0.0633 0.1436 0.7931 112 S 0.0473 0.1154 0.8373 113 L 0.1240 0.1178 0.7581 114 V 0.1115 0.1678 0.7207 115 H 0.1297 0.1903 0.6801 116 V 0.1300 0.1893 0.6807 117 S 0.1093 0.1070 0.7837 118 P 0.0902 0.1627 0.7471 119 L 0.1046 0.1461 0.7493 120 K 0.1254 0.1549 0.7197 121 E 0.1404 0.1445 0.7151 122 K 0.1676 0.1593 0.6731 123 V 0.2345 0.1604 0.6051 124 I 0.2525 0.1805 0.5670 125 G 0.1746 0.1302 0.6952 126 S 0.0420 0.1181 0.8399 127 G 0.0522 0.0470 0.9009 128 V 0.2852 0.0089 0.7058 129 D 0.4516 0.0316 0.5168 130 L 0.9214 0.0039 0.0747 131 V 0.9330 0.0032 0.0638 132 T 0.9284 0.0033 0.0684 133 V 0.8973 0.0065 0.0961 134 R 0.7117 0.0146 0.2737 135 E 0.4429 0.0427 0.5143 136 L 0.2925 0.0811 0.6264 137 S 0.1979 0.1202 0.6819 138 Y 0.1084 0.1767 0.7149 139 G 0.1429 0.2234 0.6337 140 V 0.2351 0.2849 0.4800 141 Y 0.3220 0.2212 0.4568 142 Y 0.2702 0.1597 0.5701 143 G 0.2068 0.0873 0.7059 144 Q 0.2260 0.0725 0.7015 145 P 0.2149 0.0918 0.6933 146 R 0.1743 0.0848 0.7409 147 G 0.1879 0.0660 0.7462 148 L 0.1801 0.0598 0.7601 149 D 0.1531 0.0654 0.7816 150 E 0.1101 0.1137 0.7763 151 E 0.2054 0.1027 0.6919 152 K 0.6080 0.0644 0.3276 153 G 0.7892 0.0386 0.1722 154 F 0.8197 0.0437 0.1366 155 D 0.8018 0.0445 0.1537 156 T 0.7274 0.0522 0.2204 157 M 0.6788 0.0524 0.2688 158 I 0.6801 0.0588 0.2611 159 Y 0.4612 0.0773 0.4615 160 D 0.1918 0.0704 0.7377 161 R 0.0094 0.8269 0.1637 162 K 0.0052 0.9129 0.0818 163 T 0.0048 0.9285 0.0667 164 V 0.0047 0.9508 0.0445 165 E 0.0047 0.9571 0.0382 166 R 0.0047 0.9597 0.0357 167 I 0.0047 0.9606 0.0347 168 A 0.0047 0.9605 0.0348 169 R 0.0047 0.9607 0.0347 170 T 0.0047 0.9606 0.0347 171 A 0.0047 0.9588 0.0365 172 F 0.0047 0.9573 0.0380 173 E 0.0047 0.9514 0.0438 174 I 0.0051 0.9298 0.0650 175 A 0.0067 0.8943 0.0990 176 K 0.0141 0.8130 0.1728 177 N 0.0396 0.5665 0.3939 178 R 0.0539 0.1159 0.8302 179 R 0.0495 0.0499 0.9006 180 K 0.1059 0.0266 0.8675 181 K 0.4564 0.0173 0.5262 182 V 0.7709 0.0091 0.2201 183 T 0.8639 0.0105 0.1256 184 S 0.8590 0.0090 0.1320 185 V 0.7473 0.0226 0.2301 186 D 0.4277 0.0320 0.5404 187 K 0.1252 0.2240 0.6507 188 A 0.0921 0.3097 0.5982 189 N 0.0812 0.3729 0.5460 190 V 0.1409 0.3604 0.4987 191 L 0.1627 0.3832 0.4542 192 Y 0.1349 0.3502 0.5149 193 S 0.0771 0.2740 0.6489 194 S 0.0331 0.4628 0.5041 195 M 0.0089 0.8599 0.1312 196 L 0.0072 0.9117 0.0810 197 W 0.0051 0.9430 0.0519 198 R 0.0050 0.9530 0.0420 199 K 0.0048 0.9543 0.0409 200 V 0.0049 0.9570 0.0381 201 V 0.0050 0.9530 0.0419 202 N 0.0048 0.9534 0.0418 203 E 0.0049 0.9503 0.0447 204 V 0.0053 0.9395 0.0552 205 A 0.0065 0.9110 0.0825 206 R 0.0073 0.8244 0.1683 207 E 0.0135 0.6924 0.2941 208 Y 0.0754 0.1372 0.7874 209 P 0.0206 0.0991 0.8804 210 D 0.0440 0.0635 0.8925 211 V 0.4598 0.0425 0.4977 212 E 0.7614 0.0199 0.2187 213 L 0.7760 0.0484 0.1757 214 T 0.6296 0.1272 0.2432 215 H 0.4093 0.2888 0.3019 216 I 0.2752 0.4217 0.3031 217 Y 0.2908 0.4808 0.2285 218 V 0.0799 0.8000 0.1201 219 D 0.0167 0.9169 0.0664 220 N 0.0066 0.9481 0.0454 221 A 0.0055 0.9554 0.0391 222 A 0.0048 0.9539 0.0414 223 M 0.0051 0.9470 0.0479 224 Q 0.0050 0.9376 0.0574 225 L 0.0087 0.9154 0.0760 226 I 0.0146 0.8379 0.1475 227 L 0.0247 0.6159 0.3594 228 K 0.0786 0.1024 0.8190 229 P 0.0150 0.3871 0.5978 230 S 0.0139 0.3974 0.5887 231 Q 0.0625 0.4221 0.5154 232 F 0.2153 0.0357 0.7490 233 D 0.3437 0.0475 0.6088 234 V 0.9070 0.0050 0.0880 235 I 0.9238 0.0040 0.0722 236 L 0.8982 0.0059 0.0959 237 T 0.6683 0.0110 0.3207 238 T 0.2389 0.0626 0.6985 239 N 0.0881 0.1255 0.7864 240 M 0.0827 0.2690 0.6483 241 F 0.0724 0.3674 0.5603 242 G 0.0509 0.5768 0.3723 243 D 0.0464 0.7454 0.2082 244 I 0.0580 0.8122 0.1297 245 L 0.0433 0.8456 0.1111 246 S 0.0240 0.8680 0.1080 247 D 0.0103 0.9033 0.0865 248 E 0.0078 0.9292 0.0630 249 S 0.0069 0.9321 0.0610 250 A 0.0089 0.9110 0.0801 251 A 0.0131 0.8760 0.1109 252 L 0.0328 0.7637 0.2035 253 P 0.0534 0.5535 0.3931 254 G 0.0685 0.2517 0.6797 255 S 0.1040 0.2842 0.6119 256 L 0.0985 0.2679 0.6336 257 G 0.1698 0.2035 0.6267 258 L 0.3257 0.1535 0.5208 259 L 0.2881 0.0844 0.6275 260 P 0.2686 0.0970 0.6344 261 S 0.2978 0.0945 0.6076 262 A 0.3604 0.0839 0.5558 263 S 0.3782 0.0552 0.5666 264 F 0.2010 0.0590 0.7400 265 G 0.0901 0.0542 0.8557 266 D 0.0634 0.0723 0.8643 267 K 0.1284 0.0764 0.7952 268 N 0.3156 0.0627 0.6217 269 L 0.4965 0.0754 0.4281 270 Y 0.5756 0.0653 0.3591 271 E 0.5422 0.0504 0.4074 272 P 0.4305 0.0679 0.5017 273 A 0.3022 0.0913 0.6065 274 G 0.1822 0.0886 0.7292 275 G 0.0960 0.0908 0.8132 276 S 0.1317 0.1213 0.7470 277 A 0.1064 0.2451 0.6484 278 P 0.0733 0.3627 0.5640 279 D 0.0728 0.4558 0.4714 280 I 0.0517 0.4883 0.4600 281 A 0.0490 0.3458 0.6052 282 G 0.0456 0.2227 0.7316 283 K 0.0878 0.1769 0.7352 284 N 0.0826 0.1748 0.7425 285 I 0.1212 0.2035 0.6753 286 A 0.1706 0.2156 0.6138 287 N 0.0634 0.2758 0.6608 288 P 0.0050 0.8916 0.1034 289 I 0.0047 0.9513 0.0440 290 A 0.0047 0.9563 0.0390 291 Q 0.0047 0.9595 0.0359 292 I 0.0047 0.9601 0.0353 293 L 0.0047 0.9595 0.0358 294 S 0.0047 0.9585 0.0369 295 L 0.0047 0.9596 0.0357 296 A 0.0047 0.9591 0.0362 297 M 0.0048 0.9554 0.0398 298 M 0.0048 0.9529 0.0422 299 L 0.0048 0.9502 0.0451 300 E 0.0050 0.9269 0.0681 301 H 0.0058 0.8390 0.1551 302 S 0.0130 0.6749 0.3122 303 F 0.0464 0.3764 0.5773 304 G 0.0490 0.1237 0.8272 305 M 0.0502 0.3344 0.6154 306 V 0.0130 0.7955 0.1914 307 E 0.0098 0.8656 0.1246 308 E 0.0059 0.9161 0.0781 309 A 0.0064 0.9471 0.0465 310 R 0.0057 0.9523 0.0420 311 K 0.0054 0.9537 0.0409 312 I 0.0047 0.9583 0.0369 313 E 0.0047 0.9599 0.0354 314 R 0.0047 0.9599 0.0354 315 A 0.0047 0.9599 0.0354 316 V 0.0047 0.9597 0.0356 317 E 0.0047 0.9600 0.0353 318 L 0.0047 0.9588 0.0365 319 V 0.0048 0.9565 0.0387 320 I 0.0050 0.9444 0.0506 321 E 0.0062 0.9089 0.0850 322 E 0.0407 0.4611 0.4982 323 G 0.0365 0.0562 0.9072 324 Y 0.0839 0.0348 0.8813 325 R 0.2594 0.0280 0.7127 326 T 0.1851 0.0711 0.7438 327 R 0.1194 0.3460 0.5346 328 D 0.1746 0.3548 0.4706 329 I 0.1014 0.4479 0.4507 330 A 0.0977 0.4025 0.4999 331 E 0.0974 0.3859 0.5167 332 D 0.0673 0.3287 0.6040 333 P 0.0532 0.1948 0.7520 334 E 0.0519 0.1096 0.8385 335 K 0.0770 0.1213 0.8017 336 A 0.1657 0.1422 0.6921 337 V 0.2558 0.1345 0.6096 338 S 0.1731 0.1682 0.6587 339 T 0.0473 0.6403 0.3124 340 S 0.0085 0.9155 0.0759 341 Q 0.0073 0.9350 0.0577 342 M 0.0052 0.9440 0.0508 343 G 0.0047 0.9553 0.0399 344 D 0.0047 0.9593 0.0360 345 L 0.0047 0.9598 0.0355 346 I 0.0047 0.9590 0.0363 347 C 0.0047 0.9570 0.0383 348 K 0.0048 0.9515 0.0438 349 K 0.0055 0.9264 0.0681 350 L 0.0067 0.9178 0.0755 351 E 0.0058 0.8990 0.0952 352 E 0.0078 0.7372 0.2550 353 I 0.0198 0.5211 0.4591 354 W 0.0212 0.1314 0.8474