| flharc-hh-4-8-25-50 |
| ID: | 1485077584 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 396 (165) | ||
| Sequences: | 7170 (5772.3) | ||
| Seq/Len: | 43.455 | ||
| Nf(neff/√len): | 449.4 |
HHblits Results: (2016_02)
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: 43.455).
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 |
| 301_F | 328_T | 3.234 | 1.00 |
| 225_E | 268_K | 2.925 | 1.00 |
| 290_L | 304_R | 2.701 | 1.00 |
| 268_K | 272_L | 2.586 | 1.00 |
| 224_L | 228_L | 2.554 | 1.00 |
| 208_G | 247_N | 2.400 | 1.00 |
| 302_L | 325_V | 2.391 | 1.00 |
| 217_P | 271_F | 2.362 | 1.00 |
| 292_Q | 330_Q | 2.330 | 1.00 |
| 296_E | 304_R | 2.215 | 1.00 |
| 345_L | 349_I | 2.070 | 1.00 |
| 297_P | 300_Q | 2.048 | 1.00 |
| 344_T | 347_Q | 2.037 | 1.00 |
| 235_E | 238_W | 1.950 | 1.00 |
| 228_L | 238_W | 1.894 | 1.00 |
| 336_F | 339_H | 1.786 | 1.00 |
| 322_I | 348_L | 1.777 | 1.00 |
| 228_L | 233_G | 1.753 | 1.00 |
| 217_P | 221_L | 1.750 | 1.00 |
| 290_L | 296_E | 1.714 | 1.00 |
| 221_L | 272_L | 1.677 | 1.00 |
| 304_R | 307_D | 1.648 | 1.00 |
| 239_L | 267_F | 1.646 | 1.00 |
| 221_L | 268_K | 1.645 | 1.00 |
| 269_K | 273_Q | 1.624 | 1.00 |
| 217_P | 272_L | 1.619 | 1.00 |
| 302_L | 349_I | 1.534 | 1.00 |
| 301_F | 305_K | 1.518 | 1.00 |
| 325_V | 352_G | 1.475 | 1.00 |
| 283_A | 286_R | 1.442 | 1.00 |
| 242_I | 267_F | 1.438 | 1.00 |
| 305_K | 325_V | 1.405 | 0.99 |
| 288_L | 323_Q | 1.402 | 0.99 |
| 288_L | 324_Y | 1.381 | 0.99 |
| 224_L | 242_I | 1.375 | 0.99 |
| 210_D | 247_N | 1.367 | 0.99 |
| 347_Q | 350_Q | 1.364 | 0.99 |
| 290_L | 305_K | 1.352 | 0.99 |
| 285_Q | 327_G | 1.352 | 0.99 |
| 325_V | 328_T | 1.318 | 0.99 |
| 287_E | 324_Y | 1.291 | 0.99 |
| 264_W | 268_K | 1.277 | 0.99 |
| 235_E | 265_V | 1.274 | 0.99 |
| 265_V | 269_K | 1.268 | 0.99 |
| 247_N | 250_A | 1.267 | 0.99 |
| 299_D | 353_M | 1.261 | 0.99 |
| 326_V | 334_K | 1.258 | 0.99 |
| 288_L | 327_G | 1.247 | 0.99 |
| 283_A | 311_T | 1.231 | 0.98 |
| 217_P | 220_F | 1.211 | 0.98 |
| 356_Q | 360_E | 1.207 | 0.98 |
| 309_Y | 321_I | 1.206 | 0.98 |
| 346_E | 350_Q | 1.202 | 0.98 |
| 298_L | 352_G | 1.200 | 0.98 |
| 263_N | 266_E | 1.196 | 0.98 |
| 286_R | 308_L | 1.191 | 0.98 |
| 227_Y | 241_Q | 1.179 | 0.98 |
| 243_Q | 254_W | 1.173 | 0.98 |
| 238_W | 264_W | 1.163 | 0.97 |
| 282_E | 286_R | 1.150 | 0.97 |
| 242_I | 271_F | 1.146 | 0.97 |
| 246_M | 250_A | 1.128 | 0.97 |
| 222_S | 255_E | 1.125 | 0.97 |
| 270_E | 273_Q | 1.115 | 0.96 |
| 254_W | 267_F | 1.113 | 0.96 |
| 325_V | 348_L | 1.110 | 0.96 |
| 229_R | 240_S | 1.106 | 0.96 |
| 285_Q | 289_D | 1.102 | 0.96 |
| 322_I | 326_V | 1.100 | 0.96 |
| 355_V | 359_L | 1.096 | 0.96 |
| 290_L | 308_L | 1.082 | 0.96 |
| 206_S | 245_H | 1.076 | 0.95 |
| 305_K | 309_Y | 1.074 | 0.95 |
| 251_K | 255_E | 1.073 | 0.95 |
| 276_E | 279_L | 1.070 | 0.95 |
| 325_V | 329_L | 1.069 | 0.95 |
| 318_E | 321_I | 1.066 | 0.95 |
| 317_D | 320_E | 1.059 | 0.95 |
| 220_F | 245_H | 1.050 | 0.94 |
| 267_F | 271_F | 1.030 | 0.94 |
| 284_I | 323_Q | 1.029 | 0.94 |
| 242_I | 264_W | 1.029 | 0.94 |
| 226_E | 251_K | 1.024 | 0.93 |
| 227_Y | 231_V | 1.006 | 0.93 |
| 234_S | 237_Y | 1.000 | 0.92 |
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 | |
| 4x3iA | 1 | 0 | 98.2 | 0.914 | Contact Map |
| 4x3xA | 1 | 0 | 97.6 | 0.924 | Contact Map |
| 4bhxA | 2 | 0.2146 | 95.1 | 0.943 | Contact Map |
| 4e6sA | 1 | 0.197 | 93 | 0.948 | Contact Map |
| 3lhrA | 2 | 0.2172 | 91.5 | 0.95 | Contact Map |
| 1y7qA | 2 | 0.2298 | 90.3 | 0.952 | Contact Map |
| 2fi2A | 2 | 0.2197 | 90.1 | 0.952 | Contact Map |
| 3g1gA | 2 | 0.1843 | 69.6 | 0.961 | Contact Map |
| 3g21A | 1 | 0.1843 | 69.1 | 0.962 | Contact Map |
| 3ds4A | 2 | 0.1869 | 62.1 | 0.963 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)