I have a sequence of a susceptibility gene and would like to blast it in KEGG or any other pathway database. How would one do that?
Well, there's certainly several possible answers, since this totally depends on what you actually are looking for.
If "susceptibility gene" means a gene related to antibiotic susceptibility, you can try the Antibiotic Resistance Genes database (ardb.cbcb.umd.edu). In most cases it's useful to look for specialized database suited for your kind of question.
For a more general approach, you should check out Blast2GO (www.blast2go.com). This offers connection to several databases and lets you first blast your gene (against NCBI database per default) and then annotate functional content like gene ontology (GO). If you're after pathways, the program will also let you download and display KEGG pathways and show your gene in this context.
Hope, that's useful.
http://ardb.cbcb.umd.edu/
https://www.blast2go.com
If you want to search KEGG, go to their website (link below). After searching by BLAST, the results will be pretty obvious. Click on the top results and that should take you to the gene page saying what that gene does, which pathways it participates in, things like that.
http://www.genome.jp/tools/blast/
a very convenient way to do this is to use Blast2GO (just google it).
Thank you all so much Andreas, Joao and Christoph. Do I need to have my sequence in FASTA format? Shall I get rid of repeats?
Either FASTA format or raw sequence should work fine, I believe. Don't worry about repeats, BLAST usually filters those (although the KEGG page is not explicit about it).
Your best bet is to either use protein as the query (and run BLASTP), or translated DNA query (and run BLASTX). Only if you know there is a very close relative of your organism in KEGG should you use BLASTN -- DNA sequence conservation over evolutionary time is much lower than that of protein.
Thank you soooo much Joao. In fact I am more interesting in knowing the secondary metabolites that might come out of an eventual pathway related to the identified genes. I think I should first try to figure out which enzymes could be produced through the identified sequence and then check for the related metabolites, unless you think there is a better way of approaching this.
It's best you blat the sequence in UCSC Genome Browser and find what it is. If you do know already, KEGG is a great way to find pathways. If you have commercial software e.g. MetaCore or Ingenuity, both are useful ways to find signalling pathways. Check Interactome as well.
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