Comprehensive list of public protein databases

Question

[jm7618]

Hello,

Apologies for what will probably seem like an extremely trivial question. I'm a PhD student and have found some proteins with interesting bioactivities. To expand on these hits I want to order in proteins that are similar to them and have evolved in nature - hence I thought I would BLAST against the large protein databases that now exist based on genomic or metagenomic data. Currently I'm BLASTing against the following databases:

• EBI-MGnify
• UniProt (Swissprot and TrEMBL)
• NCBI non-redundant

I thought that these were fairly comprehensive but just wanted to make sure there aren't any large databases missing, looking online I also see JGI has its own database (IMG/M) that seems to include the NCBI?

Finding a trustworthy source on these databases has proven impossible and they all seem very fractured right now so any help on making sense of all the different databases available would be very much appreciated.

Best,
James

Answer 1

[Mensur Dlakic]

I suggest you try hidden Markov model databases, specifically InterPro and Conserved Domains. They will be faster to interrogate and already have proteins grouped by domains. Rather than finding individual matches to your protein, you find out what domains are in it and for each of them you get a list of proteins that share the same domain. You will also get a nice explanation for domain functions.

• https://www.ebi.ac.uk/interpro/
• https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi