text: user1857: 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?
  
  user982: Im not 100% on what you are looking for - you seem to jump from annotation to detection of genes in your question. 
  But if you have a database of genes you want to detect (presence/ absence) you could try srst2
  which basically takes your raw reads (fastq) and maps them to the database.  it will give you a report on any hits, and any snps/ indels in the hit. The only problem is making you own database is difficult as you must adhere to the fasta header format.
  
  user1859: 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.
  
original_text: 1857: <p>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.</p>
  
  <p>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). </p>
  
  <p>Or posed in a different way, how would you identify all genes with a specific function from prokaryotic whole genome sequence data?</p>
  
  <p>Are there any scripts that can do this?</p>
   982: <p>Im not 100% on what you are looking for - you seem to jump from annotation to detection of genes in your question. </p>
  
  <p>But if you have a database of genes you want to detect (presence/ absence) you could try <a href="https://github.com/katholt/srst2" rel="nofollow noreferrer">srst2</a>
  which basically takes your raw reads (fastq) and maps them to the database.  it will give you a report on any hits, and any snps/ indels in the hit. The only problem is making you own database is difficult as you must adhere to the <a href="https://github.com/katholt/srst2#generating-srst2-compatible-clustered-database-from-raw-sequences" rel="nofollow noreferrer">fasta header format</a>.</p>
   1859: <p>The PATRICBrc.org is a free resource you can annotate your genome and compare it with publicly available genomes.</p>
  
  <p>Refer this <a href="http://docs.patricbrc.org/tutorial/genome_annotation/annotation.html" rel="nofollow noreferrer" title="tutorial">tutorial</a> for more detail.</p>
  
  <p>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.</p>
  