| 806 |
| ID: | 1433418072 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 35 (33) | ||
| Sequences: | 2582 (1929.9) | ||
| Seq/Len: | 78.242 | ||
| Nf(neff/√len): | 336.0 |
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: 78.242).
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_F | 17_Y | 3.388 | 1.00 |
| 5_N | 8_T | 2.109 | 1.00 |
| 16_N | 20_Q | 1.956 | 1.00 |
| 7_L | 11_Q | 1.912 | 1.00 |
| 29_R | 32_D | 1.892 | 1.00 |
| 30_F | 33_S | 1.759 | 1.00 |
| 29_R | 33_S | 1.736 | 1.00 |
| 31_A | 34_L | 1.426 | 1.00 |
| 12_D | 15_G | 1.414 | 1.00 |
| 17_Y | 20_Q | 1.323 | 0.99 |
| 12_D | 16_N | 1.320 | 0.99 |
| 9_L | 15_G | 1.273 | 0.99 |
| 18_V | 22_V | 1.154 | 0.97 |
| 13_P | 22_V | 1.098 | 0.96 |
| 10_V | 16_N | 1.083 | 0.96 |
| 29_R | 34_L | 1.064 | 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 | |
| 4wzrA | 2 | 1 | 97.2 | 0.142 | Contact Map |
| 3k49A | 3 | 1 | 97.1 | 0.153 | Contact Map |
| 3gvoA | 1 | 1 | 97 | 0.164 | Contact Map |
| 3v71A | 1 | 1 | 96.8 | 0.192 | Contact Map |
| 3k62A | 1 | 1 | 96.7 | 0.201 | Contact Map |
| 3bwtA | 1 | 1 | 96.6 | 0.21 | Contact Map |
| 2vpqA | 2 | 1 | 6.3 | 0.729 | Contact Map |
| 4aklA | 2 | 1 | 4.8 | 0.744 | Contact Map |
| 4u9bA | 1 | 1 | 4.2 | 0.751 | Contact Map |
| 3sj5A | 2 | 1 | 3.9 | 0.756 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)