Unicycler
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Spurious entry in dnaA.fasta
I noticed that dnaA.fasta includes S0G097, which is indeed annotated as DnaA in UniProt. But S0G097 is actually a dehydrogenase, as can be seen in its InterPro results
https://www.ebi.ac.uk/interpro/protein/unreviewed/S0G097/
For comparison, here is what the InterPro results for actual DnaA (from E. coli) looks like
https://www.ebi.ac.uk/interpro/protein/UniProt/P03004/