| sp_box |
| ID: | 1433330438 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 40 (40) | ||
| Sequences: | 54 (29.4) | ||
| Seq/Len: | 1.350 | ||
| Nf(neff/√len): | 4.6 |
Jackhmmer Results: (2015_01_07)
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: 1.350).
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 |
| 12_L | 16_V | 1.756 | 0.94 |
| 23_M | 30_M | 1.703 | 0.92 |
| 25_R | 34_Y | 1.629 | 0.90 |
| 25_R | 35_Q | 1.603 | 0.89 |
| 8_K | 34_Y | 1.585 | 0.88 |
| 27_L | 30_M | 1.582 | 0.88 |
| 14_A | 23_M | 1.531 | 0.86 |
| 12_L | 18_D | 1.528 | 0.85 |
| 32_V | 37_L | 1.438 | 0.80 |
| 26_Q | 34_Y | 1.404 | 0.78 |
| 7_S | 21_A | 1.400 | 0.78 |
| 25_R | 28_I | 1.397 | 0.78 |
| 8_K | 21_A | 1.384 | 0.77 |
| 3_L | 34_Y | 1.380 | 0.76 |
| 7_S | 24_E | 1.302 | 0.70 |
| 18_D | 38_K | 1.299 | 0.70 |
| 12_L | 38_K | 1.186 | 0.60 |
| 23_M | 27_L | 1.097 | 0.51 |
| 3_L | 33_K | 1.095 | 0.51 |
| 26_Q | 35_Q | 1.095 | 0.51 |
| 8_K | 35_Q | 1.093 | 0.51 |
| 6_N | 39_K | 1.039 | 0.45 |
| 5_P | 24_E | 1.013 | 0.43 |
| 25_R | 37_L | 1.008 | 0.42 |
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 | |
| 3qprA | 7 | 0 | 13.2 | 0.855 | Contact Map |
| 1g6uA | 2 | 0.975 | 12.5 | 0.856 | Contact Map |
| 2azeA | 1 | 0.75 | 10 | 0.863 | Contact Map |
| 3vkgA | 2 | 1 | 9.1 | 0.865 | Contact Map |
| 1slqA | 6 | 0.95 | 8.9 | 0.866 | Contact Map |
| 3iv1A | 8 | 0.8 | 8.2 | 0.868 | Contact Map |
| 4n78D | 1 | 1 | 8.1 | 0.868 | Contact Map |
| 4ddpA | 1 | 0.425 | 6.8 | 0.873 | Contact Map |
| 4rh7A | 1 | 1 | 6.6 | 0.874 | Contact Map |
| 3p8cD | 1 | 1 | 6.3 | 0.875 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)