| het-s related |
| ID: | 1423063718 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 21 (21) | ||
| Sequences: | 240 (201.6) | ||
| Seq/Len: | 11.429 | ||
| Nf(neff/√len): | 44.0 |
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: 11.429).
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 | 2.258 | 1.00 |
| 3_S | 16_V | 2.191 | 1.00 |
| 5_Y | 18_Y | 1.879 | 1.00 |
| 4_L | 7_K | 1.683 | 1.00 |
| 17_H | 21_A | 1.663 | 1.00 |
| 3_S | 20_D | 1.606 | 1.00 |
| 12_G | 20_D | 1.241 | 0.98 |
| 9_E | 17_H | 1.205 | 0.98 |
| 2_G | 11_S | 1.044 | 0.94 |
| 4_L | 15_T | 1.025 | 0.93 |
| 18_Y | 21_A | 1.021 | 0.93 |
| 8_N | 14_V | 1.008 | 0.93 |
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 | |
| 2kj3A | 3 | 1 | 57.3 | 0.133 | Contact Map |
| 1wchA | 1 | 1 | 2.1 | 0.58 | Contact Map |
| 1larA | 2 | 1 | 1.4 | 0.615 | Contact Map |
| 3ps5A | 1 | 1 | 1.4 | 0.615 | Contact Map |
| 2b3oA | 1 | 1 | 1.4 | 0.618 | Contact Map |
| 2shpA | 2 | 0.9524 | 1.3 | 0.624 | Contact Map |
| 1ygrA | 2 | 1 | 1.3 | 0.624 | Contact Map |
| 1p15A | 2 | 1 | 1.3 | 0.624 | Contact Map |
| 4grzA | 1 | 1 | 1.3 | 0.627 | Contact Map |
| 2jjdA | 6 | 1 | 1.3 | 0.627 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)