| ALLCTERM |
| ID: | 1469694599 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 29 (29) | ||
| Sequences: | 169 (81.2) | ||
| Seq/Len: | 5.828 | ||
| Nf(neff/√len): | 15.1 |
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: 5.828).
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 |
| 4_G | 7_G | 2.299 | 1.00 |
| 1_E | 5_G | 1.664 | 1.00 |
| 21_M | 29_C | 1.603 | 0.99 |
| 23_I | 28_R | 1.497 | 0.99 |
| 8_K | 19_T | 1.466 | 0.99 |
| 6_V | 10_M | 1.385 | 0.98 |
| 9_T | 22_A | 1.296 | 0.97 |
| 10_M | 16_T | 1.293 | 0.96 |
| 24_G | 28_R | 1.286 | 0.96 |
| 5_G | 22_A | 1.283 | 0.96 |
| 16_T | 21_M | 1.191 | 0.94 |
| 18_G | 22_A | 1.174 | 0.93 |
| 2_L | 15_G | 1.140 | 0.92 |
| 12_Q | 27_I | 1.130 | 0.91 |
| 10_M | 23_I | 1.096 | 0.89 |
| 9_T | 13_S | 1.083 | 0.89 |
| 3_M | 20_F | 1.026 | 0.85 |
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 | |
| 4cbfA | 3 | 1 | 8.6 | 0.763 | Contact Map |
| 3j27A | 3 | 1 | 8.2 | 0.765 | Contact Map |
| 4cctA | 3 | 1 | 8 | 0.766 | Contact Map |
| 1yewB | 3 | 1 | 2.6 | 0.815 | Contact Map |
| 4phzB | 3 | 1 | 2.6 | 0.815 | Contact Map |
| 2qtsA | 6 | 1 | 2.4 | 0.819 | Contact Map |
| 2lorA | 1 | 1 | 2.1 | 0.824 | Contact Map |
| 3duzA | 1 | 0 | 2 | 0.828 | Contact Map |
| 3cr3A | 2 | 1 | 1.7 | 0.831 | Contact Map |
| 4xjnA | 13 | 0.9655 | 1.4 | 0.841 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)