I have to compare a single protein in different organisms.For that i want to know the conserved domains in the protein in the selected organisms.I was trying this by using KEGG database but iam not able to find out conserved domains in all the selected organisms.pls suggest me what to do?
You should do evolution of this protein, use PSI-blast, then do ClusterW or Mafft , to compare diffirent species and see which domain is conservation. You can go to Pfam, SMART database
Go to SMART Domain database this will give type of domains exist in your choice of protein along with different organisms exist.
Then U can see also InterPro database to search for the domain wise.
You should do evolution of this protein, use PSI-blast, then do ClusterW or Mafft , to compare diffirent species and see which domain is conservation. You can go to Pfam, SMART database
I have attached a picture of the NCBI's conserved domains database, as you can see, you can submit your query from here to different databases. such as SMART, Pfam, etc, already mentioned by other researchers http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml Good luck!
Yes, you can use motif of protein, see http://expasy.org/tools/ you can find many tools.good luck
http://molbiol-tools.ca/Motifs.htm
have look on this link it will definitely help you
thanks
Use a sequence logo - see my web site. The logo displays sequence conservation in a very robust way in bits of information.
One place for protein domains: InterPro at http://www.ebi.ac.uk/interpro/. It integrates different motif and domain databases. You can see the distribution in different species of your domain of interest: I think this is very convenient in your case.
CDD is a protein annotation resource that consists of a collection of well-annotated multiple sequence alignment models for ancient domains and full-length proteins
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
I recommend an online tool "ConSurf" which runs a multiple sequence alignment across a huge data available and yields a colorful chart along with those amino acid residues which are exposed and conserved or buried and conserved.
You can use it for both a protein or nucleotide sequence.
Follow the link http://consurf.tau.ac.il/2016/
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology