Relaxosome protein TraY (traY) is a 131-residue protein from Escherichia coli (strain K12). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P06627.
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The mean pLDDT of this model is 83.1 (confident overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 63% |
| 70 to 90 | Confident: backbone generally right | 11% |
| 50 to 70 | Low: treat with caution | 18% |
| Below 50 | Very low: often disordered regions | 8% |
What pLDDT means and how to read it
Conjugative DNA transfer (CDT) is the unidirectional transfer of ssDNA plasmid from a donor to a recipient cell. It is the central mechanism by which antibiotic resistance and virulence factors are propagated in bacterial populations. Part of the relaxosome, which facilitates a site- and strand-specific cut in the origin of transfer by TraI, at the nic site. Relaxosome formation requires binding of IHF and TraY to the oriT region, which then facilitates binding of TraI (PubMed:7499339, PubMed:7499340). Upon binding to the oriT region TraY bends DNA 50 to 55 degrees. Also positively regulates tra gene expression
Part of the relaxosome, a complex composed of plasmid encoded TraI, TraM, TraY and host-encoded IHF bound to the F plasmid origin of transfer (oriT) (PubMed:7499339). Interacts with TraM, probably through its C-terminus (PubMed:17238924)
Cytoplasm
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9F10 | EM | 2.94 Å | E/F/G=1-131 |
| 9F0Z | EM | 3.42 Å | E/F/G=1-131 |
| 9F12 | EM | 3.42 Å | E/F/G=1-131 |
| 9F0Y | EM | 3.45 Å | E/F/G=1-131 |
| 9F11 | EM | 3.68 Å | E/F/G=1-131 |
| 9F0X | EM | 3.78 Å | E/F/G=1-131 |
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