| test7 |
| ID: | 1496195360 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 55 (52) | ||
| Sequences: | 3769 (1873.2) | ||
| Seq/Len: | 72.481 | ||
| Nf(neff/√len): | 259.8 |
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: 72.481).
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 |
| 22_R | 37_D | 4.298 | 1.00 |
| 15_L | 21_A | 3.143 | 1.00 |
| 8_C | 11_C | 2.635 | 1.00 |
| 23_F | 30_G | 2.290 | 1.00 |
| 38_M | 42_S | 1.865 | 1.00 |
| 33_A | 37_D | 1.678 | 1.00 |
| 46_C | 49_C | 1.557 | 1.00 |
| 44_S | 52_T | 1.470 | 1.00 |
| 12_L | 31_F | 1.346 | 0.99 |
| 22_R | 33_A | 1.307 | 0.99 |
| 20_E | 33_A | 1.281 | 0.99 |
| 10_V | 48_L | 1.268 | 0.99 |
| 26_R | 51_L | 1.145 | 0.97 |
| 26_R | 52_T | 1.123 | 0.97 |
| 38_M | 41_G | 1.105 | 0.96 |
| 33_A | 36_V | 1.094 | 0.96 |
| 9_A | 48_L | 1.089 | 0.96 |
| 13_A | 21_A | 1.078 | 0.95 |
| 45_T | 50_R | 1.072 | 0.95 |
| 34_E | 38_M | 1.053 | 0.95 |
| 15_L | 42_S | 1.053 | 0.95 |
| 22_R | 36_V | 1.045 | 0.94 |
| 23_F | 28_G | 1.035 | 0.94 |
| 13_A | 42_S | 1.031 | 0.94 |
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 | |
| 3k1lB | 2 | 1 | 99.4 | 0.14 | Contact Map |
| 1iymA | 1 | 1 | 99.1 | 0.236 | Contact Map |
| 4ccgX | 2 | 0.9818 | 99.1 | 0.237 | Contact Map |
| 2l0bA | 1 | 0.9818 | 99.1 | 0.24 | Contact Map |
| 3nw0A | 1 | 0.9455 | 99.1 | 0.243 | Contact Map |
| 4a0kB | 1 | 0.0909 | 99.1 | 0.25 | Contact Map |
| 3dplR | 1 | 0.9455 | 99.1 | 0.258 | Contact Map |
| 2m6mA | 1 | 0.9636 | 99 | 0.263 | Contact Map |
| 2d8sA | 1 | 0.9636 | 99 | 0.268 | Contact Map |
| 4v3lC | 1 | 0.9818 | 99 | 0.268 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)