| sel3 |
| ID: | 1466023687 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 36 (36) | ||
| Sequences: | 83 (47.8) | ||
| Seq/Len: | 2.306 | ||
| Nf(neff/√len): | 8.0 |
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: 2.306).
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 |
| 8_M | 16_L | 2.460 | 1.00 |
| 14_Y | 19_D | 1.836 | 0.98 |
| 30_A | 34_A | 1.767 | 0.98 |
| 28_T | 32_E | 1.587 | 0.95 |
| 4_R | 7_E | 1.436 | 0.91 |
| 31_A | 34_A | 1.416 | 0.90 |
| 2_L | 33_A | 1.365 | 0.88 |
| 1_M | 5_E | 1.352 | 0.87 |
| 6_A | 26_L | 1.315 | 0.85 |
| 9_L | 23_S | 1.296 | 0.84 |
| 19_D | 24_G | 1.281 | 0.83 |
| 4_R | 29_Q | 1.236 | 0.80 |
| 19_D | 26_L | 1.193 | 0.76 |
| 26_L | 30_A | 1.163 | 0.74 |
| 26_L | 34_A | 1.163 | 0.74 |
| 28_T | 36_E | 1.121 | 0.70 |
| 27_Y | 31_A | 1.121 | 0.70 |
| 11_T | 21_Q | 1.072 | 0.65 |
| 6_A | 20_P | 1.001 | 0.57 |
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 | |
| 4bwrA | 1 | 0.9722 | 52.3 | 0.748 | Contact Map |
| 1ouvA | 1 | 0.9722 | 43 | 0.761 | Contact Map |
| 1klxA | 1 | 0.9722 | 32.1 | 0.777 | Contact Map |
| 3e4bA | 4 | 0.9722 | 28.2 | 0.783 | Contact Map |
| 3rjvA | 1 | 1 | 10.3 | 0.823 | Contact Map |
| 3h7lA | 3 | 0.8611 | 3.4 | 0.859 | Contact Map |
| 2zanA | 1 | 0 | 3.3 | 0.859 | Contact Map |
| 3u64A | 1 | 1 | 3.2 | 0.86 | Contact Map |
| 1e2wA | 2 | 0.6111 | 3.2 | 0.861 | Contact Map |
| 4udxX | 1 | 0 | 3.1 | 0.862 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)