| sigma |
| ID: | 1458905513 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 31 (31) | ||
| Sequences: | 90 (67.9) | ||
| Seq/Len: | 2.903 | ||
| Nf(neff/√len): | 12.2 |
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: 2.903).
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 |
| 10_F | 17_Q | 1.821 | 0.99 |
| 18_N | 31_T | 1.766 | 0.99 |
| 15_G | 18_N | 1.725 | 0.98 |
| 16_T | 31_T | 1.610 | 0.97 |
| 25_N | 29_G | 1.511 | 0.96 |
| 13_P | 26_Q | 1.415 | 0.93 |
| 5_G | 17_Q | 1.305 | 0.89 |
| 10_F | 14_H | 1.303 | 0.89 |
| 27_F | 31_T | 1.300 | 0.88 |
| 25_N | 28_P | 1.254 | 0.86 |
| 24_G | 27_F | 1.234 | 0.85 |
| 5_G | 14_H | 1.213 | 0.83 |
| 7_G | 10_F | 1.201 | 0.83 |
| 1_F | 9_Q | 1.183 | 0.81 |
| 25_N | 30_A | 1.127 | 0.77 |
| 4_Y | 23_S | 1.055 | 0.70 |
| 21_K | 30_A | 1.025 | 0.66 |
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 | |
| 3ptwA | 1 | 0.5806 | 1.3 | 0.805 | Contact Map |
| 3fewX | 1 | 0 | 1.1 | 0.81 | Contact Map |
| 3im8A | 1 | 0.5484 | 1.1 | 0.813 | Contact Map |
| 2pffB | 3 | 0.2903 | 0.9 | 0.824 | Contact Map |
| 2qc3A | 1 | 0.5806 | 0.9 | 0.824 | Contact Map |
| 3k89A | 1 | 0.6774 | 0.8 | 0.83 | Contact Map |
| 3iylA | 20 | 0.7097 | 0.7 | 0.835 | Contact Map |
| 3tqeA | 1 | 0.7419 | 0.7 | 0.838 | Contact Map |
| 1mlaA | 1 | 0.5484 | 0.6 | 0.839 | Contact Map |
| 4rr5A | 1 | 0 | 0.6 | 0.842 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)