Where Can I Find A Db Of Remotely Conserved Orthologous Proteins

Question

[Assa Yeroslaviz]

Hi everybody,

we are looking for information about protein orthology.

Can anyone tell me where I can find lists, data bases, or other information about weak orthologous proteins?

Thanks

Assa

[Lars Juhl Jensen]

Two proteins are either orthologous or they are not orthologous; there is no such thing as "weak" orthologues proteins. What is it you are looking for?

[Assa Yeroslaviz]

I am sorry, weak might be an internal term. What I mean is that we are looking fora database of remotely conserved proteins.

Sorry I wasn't that clear.

Answer 1

[2184687-1231-83-]

One can rephrase "weak orthologous proteins" as "orthology predictions including small amount of evidence or hits with low sequence similarity". To me this would mean going for high coverage above all. My preferred DBs in terms of coverage are COGs/KOGs and EggNOG. They do a great job at finding hits even for very distant homology relationships:

http://www.ncbi.nlm.nih.gov/COG/ (COGs)
http://www.ncbi.nlm.nih.gov/COG/grace/shokog.cgi (KOGs)
http://eggnog.embl.de (EggNOG)

If you want to find hits yourself for your own list of proteomes, jackhmmer in the HMMER package is worth trying.

[Lars Juhl Jensen]

Thank you - I happen to be one of the developers of eggNOG :-)

[Tancata]

OMA browser - has good coverage of available genomes, too...