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Where Can I Find A Db Of Remotely Conserved Orthologous Proteins

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

orthologues protein annotation database
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updated by 2184687-1231-83- 2184687-1231-83- • written by Assa Yeroslaviz Assa Yeroslaviz

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?

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written by Lars Juhl Jensen Lars Juhl Jensen

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.

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written by Assa Yeroslaviz Assa Yeroslaviz

1 answer

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.

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written by 2184687-1231-83- 2184687-1231-83-

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

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written by Lars Juhl Jensen Lars Juhl Jensen

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