| 3966_3 |
| ID: | 1433411384 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 40 (40) | ||
| Sequences: | 737 (451) | ||
| Seq/Len: | 18.425 | ||
| Nf(neff/√len): | 71.3 |
HHblits Results: (2013_03)
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: 18.425).
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 |
| 28_C | 31_D | 3.748 | 1.00 |
| 13_C | 31_D | 3.125 | 1.00 |
| 18_W | 29_K | 3.032 | 1.00 |
| 13_C | 28_C | 2.609 | 1.00 |
| 25_E | 34_A | 2.550 | 1.00 |
| 19_Y | 37_L | 2.285 | 1.00 |
| 20_N | 23_K | 2.064 | 1.00 |
| 19_Y | 24_Q | 1.341 | 0.99 |
| 4_L | 14_N | 1.309 | 0.99 |
| 15_G | 30_L | 1.306 | 0.99 |
| 10_C | 28_C | 1.265 | 0.99 |
| 9_A | 14_N | 1.211 | 0.98 |
| 8_I | 16_K | 1.163 | 0.97 |
| 33_L | 38_R | 1.132 | 0.97 |
| 4_L | 7_I | 1.110 | 0.96 |
| 25_E | 36_P | 1.042 | 0.94 |
| 15_G | 29_K | 1.013 | 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
- 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 | |
| 2js4A | 1 | 1 | 99.3 | 0.057 | Contact Map |
| 2hf1A | 2 | 1 | 99.3 | 0.058 | Contact Map |
| 2jr6A | 1 | 1 | 99.3 | 0.059 | Contact Map |
| 2pk7A | 2 | 0.975 | 99.3 | 0.06 | Contact Map |
| 2jnyA | 1 | 1 | 99.3 | 0.061 | Contact Map |
| 2k5rA | 1 | 1 | 99.3 | 0.092 | Contact Map |
| 2kpiA | 1 | 0.95 | 99.1 | 0.15 | Contact Map |
| 1dl6A | 1 | 1 | 97.7 | 0.452 | Contact Map |
| 3q87A | 1 | 0.9 | 97.7 | 0.453 | Contact Map |
| 1pftA | 1 | 0.95 | 97.5 | 0.469 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)