How to identify the secretion system in a newly sequenced bacterial genome?

[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.

[Torst]

A good start would be to collect all the proteins from the standard bacterial secretion pathways, as described here: http://www.genome.jp/kegg/pathway/ko/ko03070.html

Then find orthologs (homologs) of those proteins in your annotated genome.

[ontheway]

I have done this work.I collected the COGs data of most of the proteins from the bacterial secretion pathways.And then ran a blast to the annotation result.But there exist an inconsistency between two results.That is what trouble me now.
for example:
protein A:the annotation of RAST is "IncI1 plasmid conjugative transfer ATPase PilQ",but with my way,the annotation is "virB11".

[Torst]

I guess that means PilQ is similar to VirB11 at a BLAST level.

You should try and use PFAM domains rather than arbirtray BLAST /product descriptions to connect your proteins as homologs perhaps.

[milo0615]

I have done this work.I collected the COGs data of most of the proteins from the bacterial secretion pathways.And then ran a blast to the annotation result.But there exist an inconsistency between two results.That is what trouble me now.
for example:
protein A:the annotation of RAST is "IncI1 plasmid conjugative transfer ATPase PilQ",but with my way,the annotation is "virB11".

Hi Ontheway,

When you said that you collected the COGs data and Blast it against the bacteria genome, did you used the standalone version of blast? Did you batch blast it? or how did you do the blasting part? I currently have multiple assemblies of a genome and I downloaded a whole bunch of COGS which I want to blast against my assemblies to select the best one. Please let me know.

Thank you,