title: A Database of Plastid Protein Families from Red Algae and Apicomplexa and Expression Regulation of the moeB Gene.
abstract: We report the database of plastid protein families from red algae, secondary and tertiary rhodophyte-derived plastids, and Apicomplexa constructed with the novel method to infer orthology. The families contain proteins with maximal sequence similarity and minimal paralogous content. The database contains 6509 protein entries, 513 families and 278 nonsingletons (from which 230 are paralog-free, and among the remaining 48, 46 contain at maximum two proteins per species, and 2 contain at maximum three proteins per species). The method is compared with other approaches. Expression regulation of the moeB gene is studied using this database and the model of RNA polymerase competition. An analogous database obtained for green algae and their symbiotic descendants, and applications based on it are published earlier.
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny Pereulok 19, Moscow 127994, Russia.
authors.forename: Oleg A
authors.identifier: 0000-0002-8546-364X
authors.initials: OA
authors.lastname: Zverkov
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny Pereulok 19, Moscow 127994, Russia.
authors.forename: Alexandr V
authors.identifier: 0000-0003-4746-6396
authors.initials: AV
authors.lastname: Seliverstov
authors.affiliation: Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny Pereulok 19, Moscow 127994, Russia.
authors.forename: Vassily A
authors.identifier: 0000-0002-3739-9161
authors.initials: VA
authors.lastname: Lyubetsky
mesh_terms: D016782:Apicomplexa / Q000235:genetics; D001426:Bacterial Proteins / Q000096:biosynthesis / Q000235:genetics; D005075:Biological Evolution; D060365:Chloroplast Proteins / Q000096:biosynthesis / Q000235:genetics*; D030562:Databases, Protein; D005786:Gene Expression Regulation; D010802:Phylogeny; D018087:Plastids / Q000235:genetics; D000461:Rhodophyta / Q000235:genetics*; D013559:Symbiosis / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D060365:Chloroplast Proteins; C403342:moeB protein, Bacteria