Computational protocol: In Silico Identification of Specialized Secretory Organelle Proteins in Apicomplexan Parasites and In Vivo Validation in Toxoplasma gondii

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Protocol publication

[…] To identify Pfam domains present in microneme proteins, we first compiled a list of all known microneme antigens from representative apicomplexan parasites, based on an exhaustive search of biological sequence and literature databases for proteins annotated with the keywords “microneme” or “micronemal”. In all cases, the primary literature citation was consulted for further verification. Two P. falciparum proteins (Genbank CAB37326, ABW16954) were excluded from the ‘known microneme protein’ dataset due to conflicting localization data –, although this had no effect on final list of microneme domains, as rhomboid and peptidase_S8 domains are represented by other microneme proteins (e.g. AAK94670, AAT29065). This dataset was then searched for Pfam motifs (v21.0) using hmmpfam (http://hmmer.janelia.org/) with ‘gathering cutoff’ scores , to generate a comprehensive list of all domains and domain patterns represented. Remarkably, no Pfam domains were identified other than adhesin and protease domains, with the former dominant, as shown in .In order to identify parasite proteins containing the above domains, predicted proteins from all completely sequenced apicomplexan parasites (http://ApiDB.org) were first searched against Pfam as above. The results were then filtered based on the presence of any of the domains defined in . Results from this analysis are provided in .Prediction of secretory signal peptides and signal anchor sequences were performed using SignalP (http://www.cbs.dtu.dk/services/SignalP/) , and transmembrane domain identification was conducted using TMHMM (http://www.cbs.dtu.dk/services/TMHMM/) applying default parameters. […]

Pipeline specifications

Software tools HMMER, SignalP, TMHMM
Databases Pfam
Application Membrane protein analysis
Organisms Homo sapiens, Toxoplasma gondii, Plasmodium falciparum
Diseases Infection