title: Experimentally constrained topology models for 51,208 bacterial inner membrane proteins.
abstract: We have used 502 Escherichia coli inner membrane proteins with experimentally determined C-terminal locations (cytoplasmic or periplasmic) from a recently published data set, together with an additional 106 bacterial membrane proteins with known topology, as queries in BLAST searches against a data base of 658,210 bacterial open reading frames from GenBank. We find 51,208 homologs to the query sequences for which we can assign the location of the C terminus or an internal residue to the same side of the membrane as the query's C terminus. These assignments are then used as constraints for topology prediction. The 51,208 much improved topology models derived in this way cover approximately 30% of all predicted bacterial inner membrane proteins in 225 fully sequenced bacterial genomes.
authors.affiliation: Stockholm Bioinformatics Center, AlbaNova, SE-106 91 Stockholm, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Granseth
authors.forename: Daniel O
authors.initials: DO
authors.lastname: Daley
authors.forename: Mikaela
authors.initials: M
authors.lastname: Rapp
authors.forename: Karin
authors.initials: K
authors.lastname: Melén
authors.forename: Gunnar
authors.initials: G
authors.lastname: von Heijne
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000737:chemistry / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics; D030541:Databases, Genetic; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics; D008565:Membrane Proteins / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D016366:Open Reading Frames; D017433:Protein Structure, Secondary
chemical_list: D001426:Bacterial Proteins; D029968:Escherichia coli Proteins; D008565:Membrane Proteins; C043426:inner membrane protein, E coli