| CDI |
| ID: | 1450195868 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 33 (24) | ||
| Sequences: | 137 (68.2) | ||
| Seq/Len: | 5.708 | ||
| Nf(neff/√len): | 13.9 |
Jackhmmer Results: (2015_08)
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: 5.708).
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 |
| 6_S | 19_L | 3.305 | 1.00 |
| 11_T | 16_A | 2.064 | 1.00 |
| 18_I | 24_Q | 1.853 | 1.00 |
| 5_P | 19_L | 1.801 | 1.00 |
| 6_S | 11_T | 1.710 | 1.00 |
| 10_H | 15_L | 1.599 | 0.99 |
| 18_I | 21_I | 1.413 | 0.98 |
| 20_D | 24_Q | 1.371 | 0.98 |
| 17_D | 25_P | 1.368 | 0.98 |
| 21_I | 27_R | 1.307 | 0.97 |
| 20_D | 23_N | 1.278 | 0.96 |
| 18_I | 25_P | 1.171 | 0.93 |
| 15_L | 26_L | 1.030 | 0.85 |
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 | |
| 4hatC | 1 | 0.6061 | 17 | 0.811 | Contact Map |
| 4v0qA | 1 | 1 | 13 | 0.82 | Contact Map |
| 4k6mA | 2 | 1 | 10 | 0.829 | Contact Map |
| 3tutA | 1 | 1 | 7.9 | 0.837 | Contact Map |
| 3gjxA | 2 | 0.5758 | 6.5 | 0.843 | Contact Map |
| 3zdlB | 1 | 0.4848 | 6.3 | 0.845 | Contact Map |
| 4o89A | 2 | 1 | 6.2 | 0.845 | Contact Map |
| 4hhjA | 1 | 1 | 5.9 | 0.847 | Contact Map |
| 4yfkD | 2 | 0.3636 | 5.9 | 0.847 | Contact Map |
| 4hdhA | 2 | 1 | 5.6 | 0.848 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)