I want to do a project but I need to use NCBI to find which bacteria has similar sequences and structure to human Dihydrolipoyl transacetylase. The method starts using Blast but I dont know further than that
Thanks Marisol, I am not sure which methos I can use. Dihydrolipoyl transacetylase is an enzym Pyruvate dehydrogenase complex. It is the E2 enzyme. This is attacked by Anti-mitochondrial antibody in Primary biliary cirrhosis patients, so this is an autoimmune disease that is thought to be caused by molecular mimicry that is bacteria which has same epitope as the PDC-E2 that first starts the disease before the immune system breks the tolerance and launches an attack to the self protein. So what I need find which bacteria has the epitope that AMA recognises and starts the diseases. So which bioinformatic I can use?
Hi Abdi,
I think that on line software HHPred (http://toolkit.tuebingen.mpg.de/hhpred) can help you. My suggestion is that in HHPRED you use as input the aminoacid sequence of human dihydrolipoyl transacetylase in hope to find any homologue in bacteria. HHPred is able to identidy homologues crystal structures of your query. If you want, in the field proteome, you can select a specific proteome of any bacteria.
I think that you can use the software PFAM (http://pfam.xfam.org) to avaliate the domains of this protein and search these domains in bacteria sequences.
Hello Abdi!
Seeing your question and the colleagues answers, you have some tools to work. If you find pertinent, take a look at Gene Ontology or STRING, make a search for orthologous genes. This could save you a little time.
http://string-db.org
http://geneontology.org/
Hope will help you.
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