| other repeats |
| ID: | 1423238742 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 21 (21) | ||
| Sequences: | 168 (142.3) | ||
| Seq/Len: | 8.000 | ||
| Nf(neff/√len): | 31.1 |
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: 8.000).
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 |
| 8_N | 18_Y | 2.429 | 1.00 |
| 5_Y | 18_Y | 2.341 | 1.00 |
| 9_E | 13_D | 1.904 | 1.00 |
| 9_E | 17_H | 1.594 | 1.00 |
| 3_S | 16_V | 1.519 | 1.00 |
| 4_L | 7_K | 1.400 | 0.99 |
| 6_E | 9_E | 1.110 | 0.94 |
| 3_S | 20_D | 1.069 | 0.93 |
| 1_P | 20_D | 1.038 | 0.91 |
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 | |
| 2kj3A | 3 | 1 | 13.2 | 0.413 | Contact Map |
| 2ts1A | 1 | 0.9048 | 1.3 | 0.644 | Contact Map |
| 2qedA | 1 | 1 | 1.3 | 0.647 | Contact Map |
| 1e9rA | 6 | 1 | 0.9 | 0.68 | Contact Map |
| 2vpaA | 1 | 1 | 0.9 | 0.683 | Contact Map |
| 1wchA | 1 | 1 | 0.9 | 0.683 | Contact Map |
| 2od5A | 1 | 1 | 0.9 | 0.685 | Contact Map |
| 1wxrA | 1 | 1 | 0.8 | 0.688 | Contact Map |
| 1gq2A | 16 | 1 | 0.8 | 0.688 | Contact Map |
| 3izxD | 2 | 0 | 0.8 | 0.688 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)