| 3966_1 |
| ID: | 1433411227 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 38 (38) | ||
| Sequences: | 698 (419.3) | ||
| Seq/Len: | 18.368 | ||
| Nf(neff/√len): | 68.0 |
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: 18.368).
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 |
| 26_N | 29_L | 3.929 | 1.00 |
| 18_E | 27_P | 3.490 | 1.00 |
| 13_D | 29_L | 3.315 | 1.00 |
| 23_Y | 32_A | 2.898 | 1.00 |
| 13_D | 26_N | 2.478 | 1.00 |
| 15_Q | 28_R | 1.375 | 0.99 |
| 4_L | 14_R | 1.274 | 0.99 |
| 9_V | 14_R | 1.272 | 0.99 |
| 18_E | 30_N | 1.219 | 0.98 |
| 8_L | 16_P | 1.187 | 0.98 |
| 10_C | 26_N | 1.140 | 0.97 |
| 12_I | 33_Y | 1.130 | 0.97 |
| 23_Y | 34_P | 1.126 | 0.97 |
| 31_K | 36_Q | 1.063 | 0.95 |
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 | |
| 2jr6A | 1 | 1 | 99.1 | 0.101 | Contact Map |
| 2hf1A | 2 | 1 | 99.1 | 0.102 | Contact Map |
| 2pk7A | 2 | 0.9737 | 99.1 | 0.103 | Contact Map |
| 2jnyA | 1 | 1 | 99.1 | 0.106 | Contact Map |
| 2js4A | 1 | 1 | 99.1 | 0.109 | Contact Map |
| 2k5rA | 1 | 1 | 99.1 | 0.113 | Contact Map |
| 2kpiA | 1 | 1 | 99.1 | 0.121 | Contact Map |
| 1dl6A | 1 | 1 | 96.8 | 0.501 | Contact Map |
| 3q87A | 1 | 0.8947 | 96.2 | 0.53 | Contact Map |
| 1pftA | 1 | 0.9474 | 96.1 | 0.535 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)