How To Identify The Secretion System In A Newly Sequenced Bacterial Genome?

Question

[Ontheway]

I hava a newly sequenced genome containing several hundred of scaffolds.Now I want to know how many secretion systems there are in this strain.I have annotated the draft genome using RAST.But the annotation information can not tell whether a protein is involved in a scretion system.So how to find out what I want from the annotation results, or is there another way to get what I want? Thank you.

[Neilfws]

Just bear in mind that no computational method can "tell whether a protein is involved in a secretion system." Only experimental validation can do that. However, bioinformatics can make useful predictions.

Answer 1

[Zev.Kronenberg]

One approach...

Use IPR scan to get GO terms for your proteins. GO annotations should contain information regarding biological function.

Basically you want GO terms. There are a couple ways to get there.