Gene function annotation - bacterial genome I'm trying to annotate a genome to find all genes with a specific function. I have a FASTA and the read FASTQs - I'd like to assign the functional group of the identified proteins (e.g. Kegg orthology) automatically.

For more context, I have whole genome sequences of bacteria - I'm trying to find all genes involved in membrane transport. I'd either like a tool to retrieve gene ontologies from a list of gene names (input: genA output: Membrane Transport), or a tool that outputs the function as part of the annotation pipeline (e.g. genbank output with GO function defined). 

Or posed in a different way, how would you identify all genes with a specific function from prokaryotic whole genome sequence data?

Are there any scripts that can do this?
The PATRICBrc.org is a free resource you can annotate your genome and compare it with publicly available genomes.

Refer this tutorial for more detail.

Once you have annotated your genome in PATRIC, you will have PATRIC Local families (k-mer based protein family), which will help you identify all genes with a specific function.