How Many Proteins With A Given Fold In A Genome?

Question

[Gareth Morgan]

Is there a way to find all of the proteins that are known or predicted to have a specific fold in an organism's genome? I'm sure there should be a way to filter the CATH or SCOP databases by organism but I can't see how.

The specific question that I'd like answered is: how many TIM barrel proteins (CATH 3.20.20) are there in E. coli K12?

But I'd like to know how to go about answering these more generally.

Thanks!

Answer 1

[Neilfws]

SUPERFAMILY is a good resource for this kind of question. From their front page:

SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes. The SUPERFAMILY annotation is based on a collection of hidden Markov models, which represent structural protein domains at the SCOP superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from over 2,414 completely sequenced genomes against the hidden Markov models.

I don't know precisely the best way to answer your questions using SUPERFAMILY; it does have web services and downloads in addition to many query methods. Worth a look to see how it works for you.

[Gareth Morgan]

That's great, thanks. I can't get my answer directly because "TIM barrel" is a fold, the level above superfamily, but I can add up the numbers of proteins in the 33 superfamilies that share the TIM barrel fold to give me a figure of 203 TIM barrels. Cheers :)