| 806_7 |
| ID: | 1433406863 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 35 (35) | ||
| Sequences: | 162 (108.7) | ||
| Seq/Len: | 4.629 | ||
| Nf(neff/√len): | 18.4 |
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: 4.629).
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 |
| 14_Y | 18_V | 2.100 | 1.00 |
| 6_I | 15_G | 1.929 | 1.00 |
| 9_L | 16_C | 1.834 | 1.00 |
| 2_L | 19_I | 1.768 | 1.00 |
| 2_L | 25_V | 1.635 | 0.99 |
| 11_L | 24_E | 1.566 | 0.99 |
| 9_L | 14_Y | 1.391 | 0.97 |
| 20_Q | 24_E | 1.365 | 0.96 |
| 7_L | 21_K | 1.342 | 0.96 |
| 6_I | 31_K | 1.314 | 0.95 |
| 5_Q | 15_G | 1.267 | 0.94 |
| 1_R | 25_V | 1.255 | 0.93 |
| 2_L | 27_D | 1.248 | 0.93 |
| 6_I | 26_I | 1.222 | 0.92 |
| 7_L | 15_G | 1.131 | 0.88 |
| 10_S | 19_I | 1.126 | 0.87 |
| 3_L | 33_Q | 1.062 | 0.83 |
| 28_L | 32_A | 1.054 | 0.82 |
| 7_L | 11_L | 1.048 | 0.82 |
| 9_L | 18_V | 1.016 | 0.79 |
| 10_S | 17_R | 1.005 | 0.78 |
| 16_C | 22_A | 1.003 | 0.77 |
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 | |
| 3k49A | 3 | 1 | 98 | 0.402 | Contact Map |
| 3v71A | 1 | 1 | 98 | 0.404 | Contact Map |
| 3gvoA | 1 | 1 | 97.9 | 0.419 | Contact Map |
| 3k62A | 1 | 1 | 97.8 | 0.433 | Contact Map |
| 4wzrA | 2 | 1 | 97.4 | 0.47 | Contact Map |
| 3bwtA | 1 | 1 | 95.3 | 0.578 | Contact Map |
| 2o3aA | 2 | 0.9143 | 8.1 | 0.831 | Contact Map |
| 1kwgA | 1 | 0.5143 | 6 | 0.84 | Contact Map |
| 3qr0A | 1 | 0.8571 | 4 | 0.854 | Contact Map |
| 4i86A | 2 | 0.8571 | 3.7 | 0.856 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)