| aa |
| ID: | 1461960586 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 45 (45) | ||
| Sequences: | 128 (79.9) | ||
| Seq/Len: | 2.844 | ||
| Nf(neff/√len): | 11.9 |
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: 2.844).
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 |
| 40_K | 44_D | 2.775 | 1.00 |
| 24_T | 36_I | 2.661 | 1.00 |
| 35_I | 42_L | 1.997 | 1.00 |
| 33_T | 37_Y | 1.670 | 0.98 |
| 23_G | 37_Y | 1.550 | 0.96 |
| 9_D | 12_Q | 1.526 | 0.96 |
| 26_F | 40_K | 1.517 | 0.96 |
| 8_S | 12_Q | 1.479 | 0.95 |
| 20_T | 37_Y | 1.388 | 0.92 |
| 14_P | 21_P | 1.372 | 0.91 |
| 9_D | 27_S | 1.309 | 0.89 |
| 16_D | 19_T | 1.297 | 0.88 |
| 19_T | 43_L | 1.284 | 0.87 |
| 36_I | 40_K | 1.229 | 0.84 |
| 20_T | 23_G | 1.228 | 0.84 |
| 7_I | 11_A | 1.198 | 0.82 |
| 20_T | 34_R | 1.174 | 0.80 |
| 25_L | 28_T | 1.106 | 0.74 |
| 14_P | 17_Y | 1.083 | 0.72 |
| 11_A | 25_L | 1.028 | 0.66 |
| 14_P | 20_T | 1.024 | 0.66 |
| 3_R | 44_D | 1.023 | 0.66 |
| 1_P | 24_T | 1.014 | 0.65 |
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 | |
| 2mx4A | 1 | 0.9556 | 99.9 | 0.033 | Contact Map |
| 5bxvB | 2 | 0 | 98.9 | 0.487 | Contact Map |
| 4ue8B | 1 | 0.3556 | 98 | 0.605 | Contact Map |
| 4uedB | 1 | 0.3111 | 98 | 0.605 | Contact Map |
| 3hxiC | 1 | 0.2889 | 97.6 | 0.644 | Contact Map |
| 3gfuC | 2 | 0.4222 | 15.8 | 0.875 | Contact Map |
| 1klfA | 8 | 0.4222 | 8.9 | 0.887 | Contact Map |
| 2xg5A | 1 | 0.4222 | 7.2 | 0.892 | Contact Map |
| 1l4iA | 2 | 0.4222 | 6.6 | 0.894 | Contact Map |
| 3c25A | 2 | 0.4222 | 5.7 | 0.897 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)