PMID:16120447

Citation	Granseth, E, Daley, DO, Rapp, M, Melén, K and von Heijne, G (2005) Experimentally constrained topology models for 51,208 bacterial inner membrane proteins. J. Mol. Biol. 352:489-94
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.
Links	PubMed Online version:10.1016/j.jmb.2005.07.053
Keywords	Algorithms; Bacteria/chemistry; Bacteria/genetics; Bacterial Proteins/chemistry; Bacterial Proteins/genetics; Databases, Genetic; Escherichia coli/chemistry; Escherichia coli/genetics; Escherichia coli Proteins/chemistry; Escherichia coli Proteins/genetics; Membrane Proteins/chemistry; Membrane Proteins/genetics; Models, Molecular; Open Reading Frames; Protein Structure, Secondary
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