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I cannot for the life of me figure this out. In the following figure, you can find ajuA and AjuA for example.

I do understand that the lower-case ones are the genes. The arrows indicate the direction of transcription. However, what is the difference to the upper-case AjuA? The text speaks of subunits. How are the two related? When do I speak of ajuA and when would I be talking about AjuA?

I would also be happy if you could point me in the direction of some literature about the basics of this kind of notation.

PS: I do understand the mechanisms of the biosynthetic route and am familiar with the different domains in the modules as well as PKS and NRPS modules.

enter image description here

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It's just the nomenclature:

Bacteria: Gene symbols are typically composed of three lower-case, italicized letters that serve as an abbreviation of the process or pathway in which the gene product is involved (e.g., rpo genes encode RNA polymerase). To distinguish among different [but related genes], the abbreviation is followed by an upper-case letter (e.g., the rpoB gene encodes the β subunit of RNA polymerase). Protein symbols are not italicized, and the first letter is upper-case (e.g., RpoB).

[source]

You can check out the Wikipedia article on Gene Nomenclature for more information.

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  • $\begingroup$ But what is the relationship between gene and protein symbols? Can they be used interchangeably? The paper talks about AjuK containing a module, while "genes ajuK and ajuL encode the first two biosynthetic proteins". Does that mean, the gene ajuK for example encodes the protein AjuK, which in turn does biosynthetic stuff? $\endgroup$ – basseur May 24 '18 at 18:12
  • $\begingroup$ @basseur "Does that mean, the gene ajuK for example encodes the protein AjuK, which in turn does biosynthetic stuff?" Without reading the paper, yes that's what it sounds like. $\endgroup$ – canadianer May 24 '18 at 18:41

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