Sequence features, such as signal peptide, pI and molecular mass were evaluated using protein analysis tools (http://expasy.org/tools).org/tools
A protein sequence analysis tool from the ExPASy Proteomics website (http://expasy.org/) was used to predict molecular weight.
Nucleotide sequences were translated into protein sequences using the Translate tool on the ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (http://us.expasy.org/tools/dna.html).html
Common bioinformatics analyses were performed using tools provided by the ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics (SIB) with default settings (http://swissmodel.expasy.org).org
Theoretical isoelectric point (pI) and molecular weight were also identified by tools in an internet server, ExPASy (Expert Protein Analysis System, http://www.expasy.org/tools).org/tools
There are a number of web-based tools to visualize biochemical and metabolic pathways; for example, Biocarta (http://www.biocarta.com/), ExPaSy (Expert Protein Analysis System, http://www.expasy.org/), and KEGG (Kyoto Encyclopedia of Genes and Genomes) can be named; however, most are static pages with only a few resources allowing authorized users to edit the pathways.
For those of you working on avant-garde proteomics projects, don't miss the incredible resources at the ExPASy (Expert Protein Analysis System) proteomics server of the Swiss Institute of Bioinformatics.
The MIANS-labelling site of MsbA was identified by comparing the actual mass of the individual peptides from MALDI TOF analysis with the predicted mass of the corresponding peptides obtained from the ExPASy peptide mass analysis tool (http://ca.expasy.org/tools/peptide-mass.html).html
Other protein sequence analysis tools used in this study, including MW, pI, and topology prediction tools, were obtained from the ExPASy Proteomics website (http://expasy.org/).org/
Amino acid sequences were deducted by ExPASy Proteomics and Sequence Analysis tool [ 34, 35].
Peptide identifications were assigned on the basis of exact mass of all possible tryptic peptides (no missed cleavages) produced by the Expert Protein Analysis System (ExPASy) PeptideMass proteomics tool (Swiss Institute of Bioinformatics, Lausanne, Switzerland) using the SWISS-PROT database entry number for each intact protein (P00330, P02769, P00924, and P00489, respectively).
