| large align |
| ID: | 1490085955 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 40 (40) | ||
| Sequences: | 84 (73.5) | ||
| Seq/Len: | 2.100 | ||
| Nf(neff/√len): | 11.6 |
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: 2.100).
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 |
| 18_V | 27_Q | 1.882 | 0.98 |
| 11_V | 18_V | 1.861 | 0.98 |
| 33_F | 39_F | 1.818 | 0.98 |
| 5_N | 28_L | 1.630 | 0.95 |
| 21_S | 27_Q | 1.605 | 0.95 |
| 17_T | 31_A | 1.555 | 0.93 |
| 9_D | 22_K | 1.496 | 0.92 |
| 20_T | 27_Q | 1.325 | 0.83 |
| 1_S | 6_Y | 1.318 | 0.83 |
| 30_G | 35_G | 1.315 | 0.83 |
| 23_G | 33_F | 1.291 | 0.81 |
| 6_Y | 29_P | 1.238 | 0.77 |
| 6_Y | 24_S | 1.227 | 0.76 |
| 14_P | 31_A | 1.218 | 0.76 |
| 26_N | 30_G | 1.152 | 0.70 |
| 28_L | 34_L | 1.147 | 0.69 |
| 5_N | 37_V | 1.127 | 0.67 |
| 3_F | 13_A | 1.118 | 0.66 |
| 33_F | 37_V | 1.106 | 0.65 |
| 10_Q | 25_G | 1.080 | 0.63 |
| 6_Y | 14_P | 1.077 | 0.62 |
| 3_F | 10_Q | 1.076 | 0.62 |
| 32_T | 38_H | 1.048 | 0.59 |
| 34_L | 38_H | 1.020 | 0.56 |
| 21_S | 31_A | 1.012 | 0.55 |
| 4_Y | 26_N | 1.008 | 0.55 |
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 | |
| 4mzdA | 1 | 1 | 1.1 | 0.877 | Contact Map |
| 4h6xA | 2 | 1 | 0.8 | 0.885 | Contact Map |
| 2mcdA | 1 | 0.4 | 0.7 | 0.893 | Contact Map |
| 2iy9A | 1 | 1 | 0.6 | 0.897 | Contact Map |
| 4h6wA | 2 | 1 | 0.6 | 0.898 | Contact Map |
| 4tr2A | 2 | 1 | 0.6 | 0.9 | Contact Map |
| 3wiuA | 3 | 0.975 | 0.5 | 0.901 | Contact Map |
| 3t41A | 2 | 1 | 0.5 | 0.902 | Contact Map |
| 1xf1A | 2 | 1 | 0.5 | 0.903 | Contact Map |
| 1wmdA | 1 | 1 | 0.5 | 0.904 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)