| eff458_711_1_gaps50 |
| ID: | 1457972983 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 31 (31) | ||
| Sequences: | 80 (59.4) | ||
| Seq/Len: | 2.581 | ||
| Nf(neff/√len): | 10.7 |
HHblits Results: (2015_06)
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: 2.581).
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 |
| 15_G | 18_N | 2.353 | 1.00 |
| 10_F | 17_Q | 2.280 | 1.00 |
| 27_F | 31_T | 1.563 | 0.96 |
| 18_N | 31_T | 1.494 | 0.94 |
| 16_T | 31_T | 1.491 | 0.94 |
| 13_P | 26_Q | 1.374 | 0.90 |
| 12_A | 29_G | 1.359 | 0.89 |
| 25_N | 29_G | 1.319 | 0.87 |
| 25_N | 28_P | 1.302 | 0.86 |
| 1_F | 7_G | 1.257 | 0.84 |
| 3_N | 7_G | 1.250 | 0.83 |
| 2_N | 22_G | 1.236 | 0.82 |
| 8_D | 21_K | 1.185 | 0.78 |
| 1_F | 5_G | 1.184 | 0.78 |
| 1_F | 9_Q | 1.159 | 0.76 |
| 4_Y | 23_S | 1.133 | 0.74 |
| 1_F | 23_S | 1.083 | 0.69 |
| 10_F | 21_K | 1.074 | 0.68 |
| 9_Q | 14_H | 1.039 | 0.64 |
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 | |
| 3ptwA | 1 | 0.5806 | 1.4 | 0.806 | Contact Map |
| 3im8A | 1 | 0.5484 | 1.3 | 0.811 | Contact Map |
| 2pffB | 3 | 0.2903 | 1.1 | 0.82 | Contact Map |
| 2qc3A | 1 | 0.5806 | 1 | 0.826 | Contact Map |
| 3fewX | 1 | 0 | 1 | 0.827 | Contact Map |
| 3k89A | 1 | 0.6774 | 0.9 | 0.829 | Contact Map |
| 3qatA | 2 | 0.5806 | 0.9 | 0.832 | Contact Map |
| 3riqA | 1 | 1 | 0.8 | 0.835 | Contact Map |
| 3tqeA | 1 | 0.7419 | 0.8 | 0.836 | Contact Map |
| 1mlaA | 1 | 0.5484 | 0.8 | 0.838 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)