| sigma |
| ID: | 1466172583 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 30 (30) | ||
| Sequences: | 211 (202.1) | ||
| Seq/Len: | 7.033 | ||
| Nf(neff/√len): | 36.9 |
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: 7.033).
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 |
| 3_A | 6_G | 2.190 | 1.00 |
| 17_K | 30_L | 1.864 | 1.00 |
| 3_A | 12_S | 1.612 | 1.00 |
| 4_G | 8_Q | 1.570 | 1.00 |
| 17_K | 26_I | 1.409 | 0.99 |
| 9_Y | 21_T | 1.370 | 0.99 |
| 1_F | 12_S | 1.352 | 0.98 |
| 7_K | 10_N | 1.304 | 0.98 |
| 1_F | 4_G | 1.291 | 0.98 |
| 18_Y | 30_L | 1.261 | 0.97 |
| 11_G | 21_T | 1.243 | 0.97 |
| 4_G | 17_K | 1.218 | 0.96 |
| 16_E | 30_L | 1.129 | 0.94 |
| 12_S | 16_E | 1.126 | 0.93 |
| 1_F | 30_L | 1.115 | 0.93 |
| 11_G | 29_T | 1.025 | 0.88 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3iylA | 20 | 0.7333 | 1.4 | 0.505 | Contact Map |
| 1jmuA | 3 | 0.4667 | 0.6 | 0.62 | Contact Map |
| 2wq4A | 3 | 0.0667 | 0.3 | 0.689 | Contact Map |
| 3m5qA | 1 | 0.6667 | 0.2 | 0.758 | Contact Map |
| 3vc3A | 6 | 0 | 0.2 | 0.766 | Contact Map |
| 4mwfC | 2 | 0.4333 | 0.2 | 0.766 | Contact Map |
| 3sbmA | 1 | 0.8667 | 0.2 | 0.77 | Contact Map |
| 2cuyA | 2 | 0.8667 | 0.2 | 0.777 | Contact Map |
| 4faiA | 2 | 0.1333 | 0.2 | 0.781 | Contact Map |
| 2qc3A | 1 | 0.8333 | 0.1 | 0.789 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)