| AntF_4 |
| ID: | 1515687455 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 56 (55) | ||
| Sequences: | 98 (57.5) | ||
| Seq/Len: | 1.782 | ||
| Nf(neff/√len): | 7.8 |
HHblits Results: (2016_02)
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: 1.782).
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 |
| 5_S | 8_T | 1.974 | 0.98 |
| 21_Y | 25_L | 1.952 | 0.98 |
| 45_E | 52_T | 1.854 | 0.97 |
| 17_R | 25_L | 1.686 | 0.95 |
| 14_A | 17_R | 1.541 | 0.91 |
| 40_K | 50_A | 1.504 | 0.89 |
| 30_F | 40_K | 1.435 | 0.86 |
| 4_V | 12_Y | 1.408 | 0.85 |
| 13_A | 51_F | 1.258 | 0.75 |
| 14_A | 21_Y | 1.248 | 0.74 |
| 43_T | 55_R | 1.236 | 0.73 |
| 8_T | 22_A | 1.223 | 0.72 |
| 10_K | 21_Y | 1.211 | 0.70 |
| 33_T | 53_Q | 1.205 | 0.70 |
| 6_L | 22_A | 1.174 | 0.67 |
| 38_E | 43_T | 1.174 | 0.67 |
| 3_N | 21_Y | 1.145 | 0.64 |
| 4_V | 28_E | 1.127 | 0.62 |
| 11_A | 19_S | 1.124 | 0.62 |
| 2_G | 7_E | 1.103 | 0.60 |
| 43_T | 53_Q | 1.094 | 0.59 |
| 5_S | 13_A | 1.094 | 0.59 |
| 34_F | 48_L | 1.081 | 0.58 |
| 17_R | 23_A | 1.068 | 0.56 |
| 48_L | 52_T | 1.058 | 0.55 |
| 47_V | 51_F | 1.057 | 0.55 |
| 49_K | 53_Q | 1.022 | 0.51 |
| 2_G | 55_R | 1.020 | 0.51 |
| 19_S | 23_A | 1.012 | 0.50 |
| 9_K | 12_Y | 1.010 | 0.50 |
| 43_T | 46_E | 1.006 | 0.50 |
| 12_Y | 16_T | 1.004 | 0.49 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3shgB | 1 | 0.9286 | 15.2 | 0.862 | Contact Map |
| 3cucA | 2 | 1 | 10.7 | 0.871 | Contact Map |
| 3zs9C | 2 | 0.5714 | 6.2 | 0.884 | Contact Map |
| 1o1zA | 1 | 0.5714 | 5.6 | 0.886 | Contact Map |
| 2avuE | 2 | 0.9643 | 5.5 | 0.887 | Contact Map |
| 3hc1A | 1 | 0.375 | 4.7 | 0.891 | Contact Map |
| 2m09A | 1 | 0.9821 | 4.5 | 0.892 | Contact Map |
| 2hepA | 1 | 0.3929 | 4.4 | 0.893 | Contact Map |
| 1zdaA | 1 | 0.3393 | 4.3 | 0.893 | Contact Map |
| 1w4tA | 1 | 0.7321 | 4.2 | 0.893 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)