Protein clustering is useful for refinement of protein annotation as well as cluster finding by its phylogenetic profile. We performed clustering of plastid encoded proteins from Rhodophyta as well as other plastid containing species related to Rhodophyta branch on species tree. Data base for cluster finding by its phylogenetic profile is available on http://lab6.iitp.ru/ppc/redline. By means of the database distinctive proteins for plastoms from small taxonomy groups of algae and protozoa were found. We performed finding and analysis of RNA polymerases encoded in Apicomplexa nuclei.