| c-cdc37 helices |
| ID: | 1477321023 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 20 (20) | ||
| Sequences: | 20 (13.2) | ||
| Seq/Len: | 1.000 | ||
| Nf(neff/√len): | 3.0 |
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: 1.000).
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 |
| 14_K | 20_Q | 2.794 | 1.00 |
| 6_Y | 18_D | 2.736 | 1.00 |
| 11_D | 14_K | 1.555 | 0.80 |
| 1_D | 16_C | 1.422 | 0.71 |
| 15_K | 19_A | 1.282 | 0.59 |
| 2_P | 16_C | 1.269 | 0.58 |
| 11_D | 15_K | 1.180 | 0.50 |
| 12_E | 19_A | 1.144 | 0.47 |
| 6_Y | 19_A | 1.123 | 0.45 |
| 5_V | 9_L | 1.005 | 0.34 |
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 | |
| 1us7B | 1 | 0.8 | 97.7 | 0.116 | Contact Map |
| 2kwvA | 1 | 0.95 | 44.4 | 0.62 | Contact Map |
| 3ai4A | 1 | 0.95 | 40 | 0.63 | Contact Map |
| 2khuA | 1 | 0.95 | 37.9 | 0.634 | Contact Map |
| 2mbbA | 1 | 0.95 | 35.8 | 0.639 | Contact Map |
| 1vw4b | 1 | 0.95 | 21.8 | 0.676 | Contact Map |
| 4mdaA | 1 | 1 | 15.1 | 0.698 | Contact Map |
| 3f2kA | 2 | 1 | 14.9 | 0.699 | Contact Map |
| 4lzgA | 1 | 0.8 | 14.1 | 0.702 | Contact Map |
| 4oj8A | 3 | 1 | 13.8 | 0.703 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)