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Prediction CRP binding sites

Hi,

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

Thanks

genome bacteria
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updated by Ram Ram • written by Prasad Prasad

1 answer

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.

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written by natasha.sernova natasha.sernova

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