| cwet |
| ID: | 1513357830 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 69 (69) | ||
| Sequences: | 405 (224.4) | ||
| Seq/Len: | 5.870 | ||
| Nf(neff/√len): | 27.0 |
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: 5.870).
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 |
| 30_A | 37_I | 2.723 | 1.00 |
| 11_C | 23_R | 1.756 | 1.00 |
| 43_T | 57_Q | 1.747 | 1.00 |
| 40_Q | 44_W | 1.698 | 1.00 |
| 65_F | 68_K | 1.672 | 1.00 |
| 47_V | 62_L | 1.644 | 1.00 |
| 34_L | 44_W | 1.460 | 0.99 |
| 59_I | 62_L | 1.414 | 0.98 |
| 29_I | 61_L | 1.405 | 0.98 |
| 34_L | 40_Q | 1.384 | 0.98 |
| 34_L | 37_I | 1.383 | 0.98 |
| 16_E | 19_L | 1.344 | 0.97 |
| 1_S | 5_E | 1.332 | 0.97 |
| 45_L | 50_S | 1.310 | 0.97 |
| 7_Y | 10_I | 1.292 | 0.97 |
| 33_V | 54_P | 1.286 | 0.96 |
| 28_D | 31_R | 1.224 | 0.95 |
| 46_G | 51_P | 1.216 | 0.95 |
| 31_R | 35_E | 1.205 | 0.94 |
| 27_F | 44_W | 1.201 | 0.94 |
| 8_V | 32_N | 1.189 | 0.94 |
| 60_K | 64_V | 1.187 | 0.94 |
| 9_A | 12_R | 1.177 | 0.93 |
| 46_G | 66_Y | 1.166 | 0.93 |
| 56_V | 64_V | 1.133 | 0.91 |
| 27_F | 40_Q | 1.128 | 0.91 |
| 15_S | 18_K | 1.125 | 0.91 |
| 16_E | 24_K | 1.113 | 0.91 |
| 37_I | 44_W | 1.104 | 0.90 |
| 8_V | 50_S | 1.079 | 0.89 |
| 47_V | 61_L | 1.075 | 0.88 |
| 15_S | 19_L | 1.066 | 0.88 |
| 49_F | 60_K | 1.023 | 0.85 |
| 1_S | 6_V | 1.022 | 0.85 |
| 25_P | 30_A | 1.020 | 0.85 |
| 63_L | 67_V | 1.019 | 0.84 |
| 14_I | 18_K | 1.016 | 0.84 |
| 33_V | 52_L | 1.006 | 0.83 |
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 | |
| 2wscI | 1 | 0.3768 | 2 | 0.913 | Contact Map |
| 4xk8I | 2 | 0 | 1.5 | 0.919 | Contact Map |
| 2yevA | 2 | 0.9855 | 1.4 | 0.919 | Contact Map |
| 4fzhA | 4 | 0 | 1.3 | 0.922 | Contact Map |
| 4bkfC | 2 | 0 | 1.1 | 0.926 | Contact Map |
| 2gsmA | 2 | 0.9855 | 1.1 | 0.926 | Contact Map |
| 1rzhH | 1 | 0.3333 | 1 | 0.927 | Contact Map |
| 4u4hA | 1 | 0.4493 | 1 | 0.928 | Contact Map |
| 3wu2I | 2 | 0.4058 | 0.9 | 0.929 | Contact Map |
| 1p4qA | 1 | 0.4783 | 0.9 | 0.929 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)