Computational protocol: A Plastid Protein That Evolved from Ubiquitin and Is Required for Apicoplast Protein Import in Toxoplasma gondii

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Protocol publication

[…] A maximum likelihood phylogenetic tree was constructed using the software tools offered through Phylogeny.fr () and was visualized using figtree. T. gondii ubiquitin was arbitrarily chosen to root the tree. Ab initio protein folding and structure predictions were generated using the Quark algorithm (). The resulting three-dimensional (3D) protein model and the established human ubiquitin structure were visualized using UCSF Chimera (). Sequences were aligned using default T-Coffee settings and were viewed through Jalview (). Analysis of the conservation between sequences was performed using JABAWS (). […]

Pipeline specifications

Software tools Phylogeny.fr, FigTree, QUARK, UCSF Chimera, T-Coffee, Jalview, JABAWS
Applications Phylogenetics, Protein structure analysis
Organisms Toxoplasma gondii, Homo sapiens
Diseases Communicable Diseases, Malaria, Toxoplasmosis, Congenital
Chemicals Heme