| GLEBS_1 |
| ID: | 1473158503 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 40 (38) | ||
| Sequences: | 351 (206.1) | ||
| Seq/Len: | 9.237 | ||
| Nf(neff/√len): | 33.4 |
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: 9.237).
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_S | 6_P | 2.250 | 1.00 |
| 14_M | 20_L | 2.211 | 1.00 |
| 15_Y | 32_L | 1.704 | 1.00 |
| 16_C | 23_G | 1.665 | 1.00 |
| 26_E | 34_A | 1.533 | 1.00 |
| 32_L | 36_K | 1.439 | 1.00 |
| 15_Y | 33_R | 1.438 | 0.99 |
| 36_K | 39_Q | 1.426 | 0.99 |
| 12_Q | 35_Q | 1.291 | 0.99 |
| 10_A | 35_Q | 1.253 | 0.98 |
| 15_Y | 30_E | 1.189 | 0.97 |
| 10_A | 36_K | 1.188 | 0.97 |
| 16_C | 19_K | 1.185 | 0.97 |
| 20_L | 25_S | 1.175 | 0.97 |
| 22_R | 25_S | 1.135 | 0.96 |
| 30_E | 34_A | 1.096 | 0.95 |
| 18_E | 35_Q | 1.067 | 0.94 |
| 9_E | 17_K | 1.042 | 0.93 |
| 16_C | 29_F | 1.032 | 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
- 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 | |
| 4bl0B | 2 | 1 | 97.5 | 0.251 | Contact Map |
| 2i3sB | 3 | 0.8 | 96.6 | 0.342 | Contact Map |
| 2i3tB | 4 | 0.75 | 95.3 | 0.41 | Contact Map |
| 3mmyB | 4 | 0.975 | 9 | 0.758 | Contact Map |
| 1nktA | 2 | 1 | 3.9 | 0.796 | Contact Map |
| 1q35A | 1 | 1 | 3.8 | 0.796 | Contact Map |
| 3j61L | 1 | 0.95 | 2.6 | 0.812 | Contact Map |
| 4w20L | 1 | 0.95 | 2.6 | 0.814 | Contact Map |
| 4ujqN | 1 | 0.95 | 2.6 | 0.814 | Contact Map |
| 3j39L | 1 | 0.95 | 2.5 | 0.815 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)