Computational protocol: A new family of phosphoinositide phosphatases in microorganisms: identification and biochemical analysis

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Protocol publication

[…] Two approaches were taken to identify MptpB related sequences, a) Blast searches [] of SwissProt and TrEMBL using the full length sequence of MptpB and b) ScanProsite search of SwissProt and TrEMBL http://www.expasy.ch/tools/scanprosite using the signature motif "HCXXGKDR". In the Blast searches the sequences selected had E-values between 10-11 and 10-131(> 30% sequence identity). Multiple sequence alignments of MptpB-related phosphatases were performed using ClustalX [] and manually edited using the programs BioEdit (Hall T: Bioedit http://www.mbio.ncsu.edu/BioEdit/bioedit.html) and Cinema []. Phylogenetic trees were calculated using a maximum likelihood program, RAxML [], with a 100 bootstrap replicates. Trees were produced using the program Treeview []. Analysis of the domain architecture was preformed using InterProScan [] and SMART databases []. […]

Pipeline specifications

Software tools ScanProsite, Clustal W, BioEdit, RAxML, TreeViewX, InterProScan
Databases ExPASy
Applications Phylogenetics, Protein sequence analysis
Organisms Homo sapiens, Listeria monocytogenes, Leishmania major
Diseases Communicable Diseases, Tuberculosis