Fine-tuning the prediction of sequences cleaved by signal peptidase II: a curated set of proven and predicted lipoproteins of Escherichia coli K-12.
A curated set of 81 proven and 44 predicted lipoproteins of Escherichia coli K-12 was defined with the combined use of a literature survey, a variety of predictive tools and human expertise. The well-documented Gram-negative proteome of E. coli K-12 was chosen to assess how the different approaches complement each other and to ensure a stable definition of a consistent set of lipoproteins. The results of detailed analysis of such proteins at the level of a single proteome are presented, corroborated and rationalized.
Gonnet
Pedro
P
Institute of Computational Science, Swiss Federal Institute of Technology, Zürich, Switzerland. gonnetp@inf.ethz.ch
Rudd
Kenneth E
KE
Lisacek
Frédérique
F
D020816:Amino Acid Motifs; D016282:Aspartic Acid Endopeptidases / Q000378:metabolism*; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism*; D019295:Computational Biology; D016208:Databases, Factual; D004926:Escherichia coli / Q000378:metabolism*; D008074:Lipoproteins / Q000737:chemistry* / Q000378:metabolism; D021382:Protein Sorting Signals; D020543:Proteome
D001426:Bacterial Proteins; D008074:Lipoproteins; D021382:Protein Sorting Signals; D020543:Proteome; D016282:Aspartic Acid Endopeptidases; C095652:signal peptidase II