Question: Getting all ferredoxin genes/proteins from one organism
0
gravatar for kilikun
5 months ago by
kilikun0
kilikun0 wrote:

Hello together,

I'm interested in ferredoxins from hyperthermophiles. Currently I'm working on a ferredoxin from Pyrococcus furiosus, that was proposed to act a electron donor for a particular reaction in that organism. But based on my analysis, it seems rather questionable that this ferredoxin is catalyzing this reaction.

Therefore I'm looking for alternative ferredoxin proteins that P. furiosus does express, but at that point, I have more or less lost track for how many ferredoxins there are in that organism.

So, I would like to know what I could use to organize my search.

That I did so far:

A gene search in NCBI using "(Pyrococcus furiosus[Organism]) AND Ferredoxin[Gene/Protein Name]" But didn't find all ferredoxins, that I was finding through my literature search, probably the annotated genome of P. furiosus is still incomplete.

Thank you, :)

protein sequence gene • 180 views
ADD COMMENTlink modified 3 months ago by Elisabeth Gasteiger1.6k • written 5 months ago by kilikun0

You are assuming that the annotation for the genes is good for this to work.

You may want to take the sequence of gene you are working with and then blastp (or preferably Delta blast) against P. furiosus genome (use limit blast to genome feature of web blast). The result of that blast would tell you what is likely present.

ADD REPLYlink modified 5 months ago • written 5 months ago by genomax70k
0
gravatar for microfuge
5 months ago by
microfuge1.2k
microfuge1.2k wrote:

On approach would be to do NCBI protein blast with a known ferredoxin protein sequence but limit the blast results to specific taxonomy hierarchy. Putting Pyrococcus furiosus in NCBI taxonomy database and going one level up is Pyrococcus (Tax id 2260) which can be entered as a filter during blast (or Tax id 2261 https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=2261 ) which will restrict the blast results to that lineage. This also helps when there are sequences from multiple strains of an organism.

ADD COMMENTlink written 5 months ago by microfuge1.2k
0
gravatar for Elisabeth Gasteiger
3 months ago by
Geneva
Elisabeth Gasteiger1.6k wrote:

Here is the query in UniProtKB, using InterPro IPR001080 3Fe4S_ferredoxin

https://www.uniprot.org/uniprot/?query=database%3A%28type%3Ainterpro+IPR001080%29+pyrococcus&sort=score

There actually seems to be only 1 entry for P.furiosus:

database:(type:interpro ipr001080) AND organism:"Pyrococcus furiosus" https://www.uniprot.org/uniprot/?query=database%3A%28type%3Ainterpro+ipr001080%29+AND+organism%3A%22Pyrococcus+furiosus%22&sort=score

Your query at NCBI seems to return many ferredoxin oxidoreductases and other entries that are not ferredoxins themselves.

ADD COMMENTlink written 3 months ago by Elisabeth Gasteiger1.6k
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