| PDHA1 |
| ID: | 1446558110 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 390 (323) | ||
| Sequences: | 2507 (1496.4) | ||
| Seq/Len: | 7.762 | ||
| Nf(neff/√len): | 83.3 |
HHblits Results: (2015_06)
Sequences per length for each position, BEFORE the coverage/gap filter was applied
Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 7.762).
Sequences per length for each position, AFTER the coverage/gap filter was applied
Residue pairs sorted by coevolution strength:
Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.
| i | j | Scaled score | Prob |
| 66_R | 341_E | 4.054 | 1.00 |
| 219_I | 273_C | 3.456 | 1.00 |
| 331_S | 334_E | 3.358 | 1.00 |
| 332_V | 336_K | 2.924 | 1.00 |
| 252_L | 268_F | 2.905 | 1.00 |
| 270_A | 274_R | 2.848 | 1.00 |
| 271_A | 275_S | 2.672 | 1.00 |
| 253_R | 285_Q | 2.624 | 1.00 |
| 132_R | 348_D | 2.551 | 1.00 |
| 321_K | 339_D | 2.511 | 1.00 |
| 258_D | 261_C | 2.505 | 1.00 |
| 175_A | 220_F | 2.451 | 1.00 |
| 194_Y | 222_C | 2.411 | 1.00 |
| 175_A | 207_A | 2.397 | 1.00 |
| 132_R | 352_F | 2.389 | 1.00 |
| 272_Y | 280_I | 2.328 | 1.00 |
| 197_G | 228_G | 2.315 | 1.00 |
| 86_I | 354_T | 2.306 | 1.00 |
| 351_Q | 355_A | 2.230 | 1.00 |
| 104_L | 266_T | 2.221 | 1.00 |
| 322_D | 326_N | 2.199 | 1.00 |
| 204_I | 208_Y | 2.197 | 1.00 |
| 171_V | 204_I | 2.178 | 1.00 |
| 70_T | 345_E | 2.107 | 1.00 |
| 254_V | 265_A | 2.078 | 1.00 |
| 71_V | 122_G | 2.061 | 1.00 |
| 254_V | 261_C | 1.993 | 1.00 |
| 363_E | 366_Y | 1.983 | 1.00 |
| 325_V | 332_V | 1.972 | 1.00 |
| 149_K | 367_H | 1.939 | 1.00 |
| 337_E | 341_E | 1.933 | 1.00 |
| 272_Y | 277_K | 1.929 | 1.00 |
| 58_R | 334_E | 1.871 | 1.00 |
| 273_C | 280_I | 1.869 | 1.00 |
| 57_T | 60_D | 1.786 | 1.00 |
| 104_L | 193_L | 1.775 | 1.00 |
| 205_F | 247_D | 1.742 | 1.00 |
| 111_T | 188_E | 1.740 | 1.00 |
| 330_A | 335_L | 1.730 | 1.00 |
| 224_N | 283_E | 1.724 | 1.00 |
| 147_K | 367_H | 1.703 | 1.00 |
| 222_C | 242_Y | 1.700 | 1.00 |
| 58_R | 62_L | 1.694 | 1.00 |
| 115_I | 177_I | 1.671 | 1.00 |
| 104_L | 191_L | 1.669 | 1.00 |
| 267_R | 271_A | 1.664 | 1.00 |
| 325_V | 335_L | 1.648 | 1.00 |
| 269_A | 280_I | 1.632 | 1.00 |
| 257_M | 289_Y | 1.626 | 1.00 |
| 61_G | 324_M | 1.624 | 1.00 |
| 64_Y | 106_A | 1.595 | 1.00 |
| 106_A | 263_R | 1.589 | 1.00 |
| 181_C | 190_C | 1.588 | 1.00 |
| 76_L | 95_D | 1.577 | 1.00 |
| 243_Y | 253_R | 1.569 | 1.00 |
| 143_G | 356_D | 1.564 | 1.00 |
| 189_V | 273_C | 1.558 | 1.00 |
| 63_K | 67_M | 1.558 | 1.00 |
| 349_A | 353_A | 1.557 | 1.00 |
| 181_C | 188_E | 1.552 | 1.00 |
| 252_L | 265_A | 1.495 | 0.99 |
| 250_P | 278_G | 1.476 | 0.99 |
| 221_I | 284_L | 1.466 | 0.99 |
| 189_V | 219_I | 1.459 | 0.99 |
| 90_F | 293_S | 1.455 | 0.99 |
| 215_K | 238_A | 1.451 | 0.99 |
| 323_R | 327_S | 1.442 | 0.99 |
| 189_V | 270_A | 1.442 | 0.99 |
| 221_I | 266_T | 1.410 | 0.99 |
| 62_L | 330_A | 1.399 | 0.99 |
| 65_Y | 339_D | 1.375 | 0.99 |
| 321_K | 325_V | 1.374 | 0.99 |
| 252_L | 280_I | 1.371 | 0.99 |
| 65_Y | 338_I | 1.370 | 0.99 |
| 194_Y | 199_A | 1.367 | 0.99 |
| 321_K | 335_L | 1.365 | 0.99 |
| 61_G | 320_L | 1.357 | 0.99 |
| 113_H | 181_C | 1.357 | 0.99 |
| 78_A | 138_L | 1.350 | 0.99 |
| 136_A | 143_G | 1.335 | 0.99 |
| 181_C | 186_K | 1.331 | 0.98 |
| 246_G | 249_I | 1.331 | 0.98 |
| 70_T | 131_V | 1.331 | 0.98 |
| 69_Q | 342_V | 1.330 | 0.98 |
| 352_F | 356_D | 1.327 | 0.98 |
| 344_K | 348_D | 1.322 | 0.98 |
| 226_R | 285_Q | 1.320 | 0.98 |
| 215_K | 277_K | 1.318 | 0.98 |
| 182_K | 215_K | 1.315 | 0.98 |
| 340_V | 344_K | 1.302 | 0.98 |
| 191_L | 221_I | 1.298 | 0.98 |
| 202_G | 206_E | 1.292 | 0.98 |
| 200_N | 245_R | 1.281 | 0.98 |
| 334_E | 337_E | 1.273 | 0.98 |
| 130_S | 133_E | 1.271 | 0.98 |
| 255_D | 261_C | 1.265 | 0.98 |
| 215_K | 278_G | 1.261 | 0.98 |
| 108_I | 270_A | 1.247 | 0.97 |
| 341_E | 345_E | 1.238 | 0.97 |
| 67_M | 102_V | 1.234 | 0.97 |
| 100_C | 284_L | 1.232 | 0.97 |
| 65_Y | 335_L | 1.227 | 0.97 |
| 222_C | 281_L | 1.223 | 0.97 |
| 179_L | 183_Y | 1.220 | 0.97 |
| 333_E | 337_E | 1.217 | 0.97 |
| 191_L | 219_I | 1.213 | 0.97 |
| 266_T | 282_M | 1.212 | 0.97 |
| 108_I | 191_L | 1.208 | 0.97 |
| 100_C | 221_I | 1.200 | 0.97 |
| 62_L | 334_E | 1.196 | 0.96 |
| 161_Y | 177_I | 1.192 | 0.96 |
| 90_F | 294_M | 1.192 | 0.96 |
| 208_Y | 281_L | 1.179 | 0.96 |
| 219_I | 280_I | 1.179 | 0.96 |
| 65_Y | 69_Q | 1.167 | 0.96 |
| 62_L | 66_R | 1.161 | 0.96 |
| 269_A | 273_C | 1.146 | 0.95 |
| 320_L | 324_M | 1.139 | 0.95 |
| 318_M | 322_D | 1.134 | 0.95 |
| 124_T | 160_F | 1.132 | 0.95 |
| 133_E | 145_C | 1.131 | 0.95 |
| 265_A | 282_M | 1.131 | 0.95 |
| 265_A | 269_A | 1.123 | 0.94 |
| 103_G | 262_V | 1.122 | 0.94 |
| 64_Y | 259_I | 1.119 | 0.94 |
| 113_H | 161_Y | 1.114 | 0.94 |
| 227_Y | 306_E | 1.112 | 0.94 |
| 207_A | 220_F | 1.100 | 0.94 |
| 177_I | 190_C | 1.098 | 0.94 |
| 141_R | 358_E | 1.092 | 0.93 |
| 302_R | 306_E | 1.087 | 0.93 |
| 73_R | 343_R | 1.080 | 0.93 |
| 69_Q | 73_R | 1.080 | 0.93 |
| 178_A | 218_C | 1.079 | 0.93 |
| 70_T | 342_V | 1.072 | 0.92 |
| 309_E | 313_K | 1.071 | 0.92 |
| 347_E | 351_Q | 1.069 | 0.92 |
| 337_E | 340_V | 1.065 | 0.92 |
| 69_Q | 339_D | 1.064 | 0.92 |
| 319_L | 323_R | 1.062 | 0.92 |
| 348_D | 352_F | 1.062 | 0.92 |
| 74_M | 135_L | 1.061 | 0.92 |
| 254_V | 282_M | 1.059 | 0.92 |
| 77_K | 350_A | 1.050 | 0.91 |
| 204_I | 281_L | 1.050 | 0.91 |
| 246_G | 251_G | 1.046 | 0.91 |
| 142_K | 357_P | 1.040 | 0.91 |
| 210_M | 214_W | 1.040 | 0.91 |
| 164_N | 169_A | 1.034 | 0.91 |
| 107_G | 263_R | 1.033 | 0.91 |
| 132_R | 349_A | 1.029 | 0.90 |
| 345_E | 349_A | 1.024 | 0.90 |
| 143_G | 357_P | 1.013 | 0.89 |
| 246_G | 281_L | 1.009 | 0.89 |
| 250_P | 272_Y | 1.003 | 0.89 |
| 257_M | 286_T | 1.000 | 0.89 |
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
- Text file of contact predictions (all 3L/2 predictions)
- Generate restraints for ROSETTA Structure Modeling
- Import to GREMLIN BETA - features includes ability to upload PDB and latest P(contact) calculation based on eLife 2015 fitting to PDB data.
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
| PDB | M | Cov | P(%) | HHΔ | |
| 2ozlA | 2 | 0.9282 | 100 | 0.348 | Contact Map |
| 2bfdA | 1 | 0.8897 | 100 | 0.361 | Contact Map |
| 1umdA | 2 | 0.9103 | 100 | 0.365 | Contact Map |
| 1qs0A | 1 | 0.9462 | 100 | 0.365 | Contact Map |
| 1w85A | 4 | 0.9256 | 100 | 0.406 | Contact Map |
| 2xt6A | 2 | 0.9128 | 100 | 0.478 | Contact Map |
| 2yicA | 4 | 0.8949 | 100 | 0.484 | Contact Map |
| 2jgdA | 1 | 0.8872 | 100 | 0.5 | Contact Map |
| 5c4iC | 2 | 0 | 100 | 0.706 | Contact Map |
| 1itzA | 3 | 0.7872 | 100 | 0.728 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)