| gremlin001 |
| ID: | 1480918580 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 40 (40) | ||
| Sequences: | 830 (830) | ||
| Seq/Len: | 20.750 | ||
| Nf(neff/√len): | 131.2 |
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: 20.750).
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 |
| 6_A | 21_T | 1.901 | 1.00 |
| 18_A | 24_A | 1.533 | 1.00 |
| 2_G | 30_G | 1.509 | 1.00 |
| 27_A | 30_G | 1.441 | 1.00 |
| 18_A | 39_G | 1.418 | 1.00 |
| 19_C | 31_A | 1.378 | 0.99 |
| 7_T | 13_G | 1.325 | 0.99 |
| 19_C | 22_A | 1.311 | 0.99 |
| 24_A | 31_A | 1.308 | 0.99 |
| 13_G | 28_G | 1.294 | 0.99 |
| 27_A | 40_T | 1.250 | 0.99 |
| 4_A | 16_A | 1.226 | 0.98 |
| 8_T | 11_C | 1.214 | 0.98 |
| 6_A | 9_C | 1.198 | 0.98 |
| 29_C | 36_C | 1.193 | 0.98 |
| 7_T | 40_T | 1.150 | 0.97 |
| 16_A | 36_C | 1.144 | 0.97 |
| 15_C | 31_A | 1.107 | 0.96 |
| 23_T | 29_C | 1.091 | 0.96 |
| 4_A | 14_T | 1.088 | 0.96 |
| 11_C | 20_C | 1.070 | 0.95 |
| 21_T | 29_C | 1.065 | 0.95 |
| 14_T | 25_A | 1.041 | 0.94 |
| 28_G | 37_C | 1.024 | 0.93 |
| 1_A | 7_T | 1.015 | 0.93 |
| 2_G | 10_A | 1.014 | 0.93 |
| 10_A | 29_C | 1.005 | 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 | |
| 4kblA | 2 | 0 | 0.5 | 0.487 | Contact Map |
| 2pk2A | 4 | 0 | 0.5 | 0.493 | Contact Map |
| 1cn3F | 1 | 0.275 | 0.2 | 0.63 | Contact Map |
| 1s58A | 1 | 0.125 | 0.2 | 0.653 | Contact Map |
| 2aanA | 1 | 0 | 0.2 | 0.658 | Contact Map |
| 2wolA | 1 | 0.25 | 0.1 | 0.702 | Contact Map |
| 4aenA | 1 | 0 | 0.1 | 0.724 | Contact Map |
| 3n44F | 1 | 0 | 0.1 | 0.785 | Contact Map |
| 1airA | 1 | 0.6 | 0.1 | 0.785 | Contact Map |
| 4ladB | 1 | 0.075 | 0.1 | 0.801 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)