Re: back of the napkin metabolic engineering

Here ya go:
http://metacyc.org/SCO/NEW-IMAGE?type=PATHWAY&object=PWY1A0-6120

I found it by googling pathway prodigiosin metacyc, the first link was
in the "red biosynthesis" pathway... searching metacyc.org with google
for "Red Biosynthesis" doesn't find the pathway page, so it seems
something is broken or lacking with their service

It might be possible to mirror metacyc using a custom install of
pathway tools, then add some custom searching (that actually works)...
maybe include structure searches too, so you can plug in an
intermediate structure and find all involved pathways:
http://bioinformatics.ai.sri.com/ptools/

On Wed, Jan 18, 2012 at 9:28 PM, Mackenzie Cowell <mac@diybio.org> wrote:
> Hey folks,
>
> Just read an interesting article on Quora, "What are some of the most
> interesting bacteria?" that was shared w/ the list a while back.  My
> favorite answer (besides the one about Mixotricha), is Maria Suyay's post
> about Proteus mirabilis.  She notes that the bacteria synthesize an
> interesting red pigment, prodigiosin.  I'm always on the lookout for cool
> bacterially-produced pigments, and this is a new one for me.
>
> So this seems like a good opportunity to learn a little bit about basic
> metabolic engineering / syn bio: What databases might one check to figure
> out what genes P. mirabilis uses to synthesize prodigiosin?  How could one
> subsequently determine what subset of this pathway would be needed in E.
> coli for the synthesis?
>
> Cheers
> Mac
>
> --
> +1.231.313.9062 / mac@diybio.org / @100ideas
>
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--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

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