Prediction CRP binding sites

Question

[Prasad]

Hi,

Please suggest some tools/approaches for the prediction of CRP binding site in the genome (prokaryotic genome).

Thanks

[WouterDeCoster]

CRP = human C reactive protein? (https://en.wikipedia.org/wiki/C-reactive_protein)

[Prasad]

No, these are cAMP receptor protein binding site.

[GenoMax]

A google search brings this up: http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-10-23

Answer 1

[natasha.sernova]

CRP-sites are differently organized in different bacteria.

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0044194

We seached for them using 4-part PWM in case of CRP-conjunction with CytR.

There are a couple of new papers:

1) Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks.

http://www.ncbi.nlm.nih.gov/pubmed/23315382

Matsui M, Tomita M, Kanai A. Genome Biol Evol. 2013;5(2):267-82. doi: 10.1093/gbe/evt004.

2) Comparing binding site information to binding affinity reveals that Crp/DNA complexes have several distinct binding conformers.

http://www.ncbi.nlm.nih.gov/pubmed/21586590

Holmquist PC, Holmquist GP, Summers ML. Nucleic Acids Res. 2011 Aug;39(15):6813-24. doi: 10.1093/nar/gkr369. Epub 2011 May 17.