Can GO term be obtained from Prokka Annotation?

Question

[Space_Life]

My annotation file from Prokka looks like this: Does prokka annotation has any information that can be used to get GO terms using any tool? I see some of the genes have "Similar to AA Sequence: UniProtKB". Can I use this to get GO terms from Uniprot? Does the gene ID used in the first column follow any format that can be used anywhere to get GO terms? Uniprot does not recognize it. What about Prodigal number? Is it linked to the gene annotation and GO term information? Thank you.

Answer 1

[oschwengers]

My short answer is also: NO.

As suggested before, you could try to fetch GO terms via UniProtKB.

However, a much more straightforward way would be to use an annotation tool that provides FAIR annotations, i.e. annotations with exact links to unique proteins sequences and db-cross references, like GO, COG, EC, etc ...

As I'm the author it's of course a bit biased, but you could give Bakta a try. It works almost as a drop-in replacement with a similar usage providing the requested information. #shameless-plug

Answer 2

[Mensur Dlakic]

A single-word answer to all your questions: NO.

prokka annotates based on similarity to other annotated proteins, followed by HMM-based annotation. Some of individual proteins, or indeed some individual HMMs, may have information in their headers that is relevant for GO, but that's not a general case. Prodigal numbers are meaningless - they are derived from genome/contig headers, followed by a chronological ORF number for that piece of DNA.

[Space_Life]

Thank you for the reply. Probably, the only option I have is to pick UniprotKB ID from "Similar to AA Sequence: UniprotKB" and then get GO terms from Uniprot. I also have the sequence of each gene (and amino acid sequence) in a FASTA format. It has a couple of hundred genes. Can the FASTA file be used to get GO Terms?