| 3E7R |
| ID: | 1427311666 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 40 (37) | ||
| Sequences: | 72 (48.4) | ||
| Seq/Len: | 1.946 | ||
| Nf(neff/√len): | 8.0 |
HHblits Results: (2013_03)
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: 1.946).
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 |
| 27_G | 40_Y | 2.480 | 1.00 |
| 12_D | 34_G | 1.833 | 0.98 |
| 3_G | 13_M | 1.637 | 0.95 |
| 25_Y | 36_V | 1.478 | 0.90 |
| 9_D | 33_G | 1.470 | 0.90 |
| 1_G | 29_Y | 1.418 | 0.87 |
| 11_D | 26_K | 1.398 | 0.86 |
| 10_E | 32_K | 1.391 | 0.86 |
| 8_W | 16_H | 1.370 | 0.85 |
| 1_G | 20_K | 1.345 | 0.83 |
| 21_S | 24_G | 1.342 | 0.83 |
| 12_D | 16_H | 1.308 | 0.81 |
| 32_K | 36_V | 1.302 | 0.80 |
| 11_D | 32_K | 1.296 | 0.80 |
| 2_F | 9_D | 1.264 | 0.77 |
| 33_G | 36_V | 1.174 | 0.70 |
| 26_K | 34_G | 1.164 | 0.69 |
| 14_Q | 38_K | 1.073 | 0.59 |
| 14_Q | 27_G | 1.071 | 0.59 |
| 31_A | 38_K | 1.043 | 0.56 |
| 1_G | 13_M | 1.017 | 0.53 |
| 11_D | 29_Y | 1.015 | 0.53 |
| 25_Y | 32_K | 1.002 | 0.52 |
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 | |
| 1zfuA | 1 | 1 | 99.3 | 0.1 | Contact Map |
| 2b68A | 1 | 0.875 | 99.1 | 0.211 | Contact Map |
| 2lr5A | 1 | 0.875 | 99 | 0.221 | Contact Map |
| 1fjnA | 1 | 0.875 | 98.9 | 0.263 | Contact Map |
| 2lt8A | 1 | 0.9 | 98.8 | 0.284 | Contact Map |
| 2rtyA | 1 | 0.75 | 98.5 | 0.352 | Contact Map |
| 2ru0A | 1 | 0.875 | 98.4 | 0.367 | Contact Map |
| 1icaA | 1 | 0.925 | 98.3 | 0.388 | Contact Map |
| 2e3gA | 1 | 0.925 | 98.2 | 0.412 | Contact Map |
| 2ln4A | 1 | 0.825 | 98 | 0.431 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)