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I am interested in finding a consensus sequence of a protein found in e.coli, in Pseudomonas aeruginosa. I am using pseudomonas.com to BLAST p the amino acid sequence of the protein that i have found with help of PDB. However i have seen that people do the BLAST N first and then BLAST P if they are interested to check whether they can find similarity of the protein sequence. Also in PDB the aa sequences are strange since they are not that specific.

Any advise on this issue or reliable links to databases when i can search and align sequences for similarities?

thanks

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