Computational protocol: Proteomic Profiling of the Outer Membrane Fraction of the Obligate Intracellular Bacterial Pathogen Ehrlichia ruminantium

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Protocol publication

[…] The publicly available proteome of the E. ruminantium strain Gardel, which was extracted from the Uniprot database [] in FASTA format, was used for bioinformatics studies. The subcellular localization of the 948 E. ruminantium protein-coding genes was predicted using three global programs: PSORTb 3.0 [], CELLO 2.5 [], and MetaLocGramN []. The predicted utilization locations of each protein were filtered from raw software output using in-house scripts written in the R programming language and exported to Excel. In some cases, CELLO 2.5 predicted multiple localization sites for the same protein. The proteins involved were grouped under the heading “unknown localization.”As a result of the varying predictions for a given protein, the consensus prediction was calculated using a majority vote procedure. If two of three algorithms agreed on localization, this localization was attributed to the protein. As for the remaining results, when outer or inner membrane localization was predicted by only one program, protein subcellular localization was refined manually, based on the experimental data in the literature, or the presence of signal peptides, transmembrane domains using dedicated algorithms (; ). […]

Pipeline specifications

Software tools PSORTb, MetaLocGramN
Application Protein sequence analysis
Organisms Ehrlichia ruminantium, Bacteria, Escherichia coli
Diseases Tetralogy of Fallot