Quantify leucine-rich repeats (LRR)

Question

[Bruna Avelino]

How do I determine the amount of LRR of a specific Glyma (example Glyma.18G280300), using NCBI's Conserved Domain Database (CDD) tool "https://www.ncbi.nlm.nih.gov/cdd", it has 4 LRR, 6 LRR. How do I analyze this? Are there any better tools than CDD for this purpose?

Thanks.

[Bruna Avelino]

Yes, thank you very much. In a job I saw that only using the NCBI's CDD was able to identify that it had X LRR domains, so I thought I was using it wrongly. Thank you for the tips.

[Ram]

Bruna Avelino

Why did you delete this post?

Answer 1

[Mensur Dlakic]

A simple Google search identifies many resources:

• https://journals.sagepub.com/doi/full/10.1177/1753425912465661
• https://www.mdpi.com/2073-4425/11/3/286
• https://lrrpredictor.biochim.ro/
• http://www.lrrfinder.com/

It is difficulty to nail down the exact number of repeats, especially if some of them are degenerate. You may want to try Pfam as well.

[Mensur Dlakic]

According to one of these predictors, the whole C-terminal part of your protein (starting at residue 834) may be comprised of LRRs.

https://lrrpredictor.biochim.ro/jobs/prot72901/prot72901.php