| rhim |
| ID: | 1444722735 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 26 (26) | ||
| Sequences: | 26 (21.7) | ||
| Seq/Len: | 1.000 | ||
| Nf(neff/√len): | 4.3 |
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: 1.000).
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 |
| 7_V | 15_V | 2.262 | 0.98 |
| 2_T | 11_N | 1.803 | 0.91 |
| 2_T | 13_S | 1.784 | 0.90 |
| 14_G | 22_Y | 1.729 | 0.89 |
| 10_Y | 24_T | 1.667 | 0.86 |
| 19_D | 24_T | 1.395 | 0.69 |
| 5_P | 11_N | 1.346 | 0.65 |
| 5_P | 19_D | 1.301 | 0.61 |
| 19_D | 22_Y | 1.248 | 0.56 |
| 5_P | 23_L | 1.227 | 0.54 |
| 20_N | 26_Q | 1.179 | 0.50 |
| 6_L | 17_V | 1.121 | 0.45 |
| 2_T | 8_N | 1.081 | 0.41 |
| 8_N | 24_T | 1.037 | 0.37 |
| 4_R | 17_V | 1.012 | 0.35 |
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 | |
| 3bh7B | 1 | 0.9231 | 9.2 | 0.777 | Contact Map |
| 2ygwA | 2 | 0.9231 | 8.3 | 0.781 | Contact Map |
| 4ksaA | 4 | 0.9231 | 7.4 | 0.786 | Contact Map |
| 4ksfA | 1 | 0.9231 | 7.4 | 0.786 | Contact Map |
| 4ks9A | 2 | 0.9231 | 7 | 0.788 | Contact Map |
| 2ozuA | 1 | 0.5385 | 5.3 | 0.8 | Contact Map |
| 2yuhA | 1 | 0.9231 | 5.2 | 0.801 | Contact Map |
| 5aj8A | 2 | 0.9231 | 3.4 | 0.819 | Contact Map |
| 3sz8A | 4 | 0.8077 | 3.1 | 0.822 | Contact Map |
| 3zpeA | 1 | 1 | 2.6 | 0.829 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)