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!
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written
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Gareth Morgan
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.
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 :)
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