| HAMP |
| ID: | 1428407156 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 64 (64) | ||
| Sequences: | 2009 (1543) | ||
| Seq/Len: | 31.391 | ||
| Nf(neff/√len): | 192.9 |
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: 31.391).
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 |
| 13_S | 18_H | 4.019 | 1.00 |
| 27_D | 32_S | 2.886 | 1.00 |
| 29_S | 32_S | 2.347 | 1.00 |
| 23_L | 35_V | 2.073 | 1.00 |
| 22_K | 46_R | 2.059 | 1.00 |
| 14_L | 41_L | 1.961 | 1.00 |
| 23_L | 39_N | 1.894 | 1.00 |
| 14_L | 42_S | 1.887 | 1.00 |
| 8_N | 37_N | 1.863 | 1.00 |
| 11_V | 37_N | 1.796 | 1.00 |
| 7_L | 38_V | 1.770 | 1.00 |
| 20_T | 46_R | 1.581 | 1.00 |
| 8_N | 33_E | 1.560 | 1.00 |
| 13_S | 21_D | 1.447 | 1.00 |
| 22_K | 42_S | 1.420 | 1.00 |
| 38_V | 41_L | 1.283 | 0.99 |
| 22_K | 43_E | 1.282 | 0.99 |
| 19_Y | 45_F | 1.263 | 0.99 |
| 5_K | 8_N | 1.245 | 0.98 |
| 10_K | 38_V | 1.217 | 0.98 |
| 22_K | 39_N | 1.193 | 0.98 |
| 59_L | 62_I | 1.182 | 0.98 |
| 12_R | 33_E | 1.172 | 0.98 |
| 11_V | 34_L | 1.147 | 0.97 |
| 18_H | 21_D | 1.090 | 0.96 |
| 41_L | 45_F | 1.081 | 0.95 |
| 6_Q | 24_K | 1.080 | 0.95 |
| 55_E | 58_R | 1.052 | 0.95 |
| 12_R | 37_N | 1.037 | 0.94 |
| 33_E | 36_N | 1.008 | 0.93 |
| 44_V | 48_T | 1.008 | 0.93 |
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 | |
| 2f95B | 1 | 0 | 98.5 | 0.202 | Contact Map |
| 4cq4A | 4 | 0.8906 | 98.4 | 0.235 | Contact Map |
| 4i5sA | 2 | 1 | 98.4 | 0.246 | Contact Map |
| 4i3mA | 1 | 1 | 98.3 | 0.254 | Contact Map |
| 2rm8A | 1 | 0.7969 | 98.2 | 0.28 | Contact Map |
| 4gycB | 1 | 0 | 98.1 | 0.291 | Contact Map |
| 3zx6A | 2 | 1 | 98 | 0.315 | Contact Map |
| 3zccA | 2 | 1 | 97.8 | 0.35 | Contact Map |
| 4bixA | 2 | 0.4375 | 97.3 | 0.407 | Contact Map |
| 4ctiA | 4 | 0.9375 | 96.3 | 0.478 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)