Identifying transcriptional regulators in bacterial genome

Question

[otterad]

Hi all,

I've recently got a genome of a new bacterium and looking to identify all the transcriptional regulators from the sequence. I've annotated it using Prokka but was hoping there'd be a program I can use to extract all predicted transcriptional regulators and then sort them into their family of regulators?

Or would it be easier to just BLAST my set of transcriptional regulators (ones i'm particularly interested in, 52 in total, extracted from my ref seq) against this new genome to identify any matches?

Any help would be greatly appreciated!

[natasha.sernova]

There are a lot of these factors, and you need to look at a particular bacterial branch from the phylogenetic tree, I would say.

Just one example (see tables in this articles - there are a lot of classes of bacterial TFs in Staphylococcus aureus):

Global analysis of transcriptional regulators in Staphylococcus aureus

http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-126

Many of Staphylococcus aureus TFs should have orthologs in other bacteria, you can explore this fact.

See abother article talking abot different approach:

Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis

http://jb.asm.org/content/195/11/2463.full