| 1127 |
| ID: | 1439912912 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 39 (39) | ||
| Sequences: | 1982 (1247.6) | ||
| Seq/Len: | 50.821 | ||
| Nf(neff/√len): | 199.8 |
HHblits Results: (2015_06)
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: 50.821).
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_E | 11_K | 2.888 | 1.00 |
| 31_H | 34_H | 2.638 | 1.00 |
| 3_C | 6_H | 2.305 | 1.00 |
| 22_C | 25_C | 2.001 | 1.00 |
| 17_D | 34_H | 1.901 | 1.00 |
| 16_D | 35_N | 1.816 | 1.00 |
| 5_E | 30_K | 1.541 | 1.00 |
| 15_K | 37_L | 1.397 | 0.99 |
| 3_C | 25_C | 1.349 | 0.99 |
| 23_V | 26_R | 1.343 | 0.99 |
| 3_C | 22_C | 1.315 | 0.99 |
| 6_H | 14_C | 1.280 | 0.99 |
| 14_C | 25_C | 1.221 | 0.98 |
| 27_D | 36_F | 1.203 | 0.98 |
| 6_H | 25_C | 1.190 | 0.98 |
| 15_K | 35_N | 1.183 | 0.98 |
| 14_C | 31_H | 1.152 | 0.97 |
| 9_R | 18_G | 1.078 | 0.95 |
| 14_C | 22_C | 1.072 | 0.95 |
| 3_C | 13_Y | 1.036 | 0.94 |
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 | |
| 4tn3A | 2 | 1 | 97.2 | -0.232 | Contact Map |
| 2egmA | 1 | 1 | 96.4 | -0.157 | Contact Map |
| 2didA | 1 | 1 | 96.2 | -0.136 | Contact Map |
| 2yrgA | 1 | 1 | 96.2 | -0.136 | Contact Map |
| 1freA | 1 | 1 | 96.2 | -0.136 | Contact Map |
| 4cfgA | 2 | 0 | 95.9 | -0.118 | Contact Map |
| 2djaA | 1 | 1 | 95.9 | -0.115 | Contact Map |
| 3ddtA | 3 | 1 | 95.9 | -0.113 | Contact Map |
| 2d8uA | 1 | 1 | 95.8 | -0.109 | Contact Map |
| 2csvA | 1 | 0.9744 | 95.6 | -0.099 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)