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 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 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