Hello,
I need some help. So I want to look for putative homologous structures of some organisms (for example a receptor of a protein) in the complete genome sequence of another organism (a fungus for example). Then I have to build the 3D structure of the resulting and selected proteins (by homology modeling). A few tips would help me. Thank you very much!
So you mean you are looking for orthologs of a specific protein. You can blast the DNA or protein sequence in ncbi's BLAST tool and see the hits or you can look up your gene on ncbi and in the hits page you can find orthologs of it.
When you use BLAST as suggested by Al-Temaimi you can specify also the species you want to compare.
you can search through the OrthoDB database which links to UniProt so should help with your 3D modelling
kindly check https://www.ncbi.nlm.nih.gov/guide/howto/find-homolog-gene/
Thank you for the answers! But let's say i found some sequence similarities.
I select a sequence (relatively short, 20 nucleotides) and I want to annotate to see what possible role this gene plays in other organisms. Are there tools that can do this annotation automatically?
If your goal is to identify a conserved motif or domain that may be this short then CDD is the database to search (https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml) If you use CD-search feature it would translate the DNA with different reading frames to search for protein hits. Alternatively, BLAST also has short DNA sequence feature and you can select the species as Tomas Koltai suggested.
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