Abstract
Background The Apicomplexa is a large phylum of intracellular parasites that show great diversity and adaptability in the various ecological niches they occupy. They are the causative agents of human and animal infections including malaria, toxoplasmosis and theileriosis, which have a huge economic and social impact. A number of apicomplexan genomes have been sequenced and are publicly available. However, the prediction of gene models and annotation of gene functions remains challenging. Methods We have utilised an approach called ‘metabolic reconstruction’, in which genes are systematically assigned to functions within pathways/networks [1-4]. Functional annotation and metabolic reconstruction was carried out using a semi-automatic approach, integrating genomic information with biochemical evidence from the literature. The functions were automatically assigned using a sequence similarity-based approach and protein motif information. Experimental evidence was also
Highlights
The Apicomplexa is a large phylum of intracellular parasites that show great diversity and adaptability in the various ecological niches they occupy
B. bovis a Unique Enzymes represent total unique enzyme activities annotated to be present in the pathways for an organism. b Missing enzymes represent the enzymes need to be present to complete the metabolic pathways. They may either be missing in the gene model predictions or may be absent in the organism. c Total number of biochemical reactions annotated to metabolic pathways from KEGG REACTION database. d Total number of metabolites annotated to metabolic pathways from KEGG COMPOUND and KEGG GLYCAN databases. e Number of precursor metabolites in the metabolic pathways that are annotated to be obtained from host. This number does not include any other metabolites that are obtained from host and not part of any of the annotated pathways in LAMP. f Number of end metabolites in the metabolic pathways that does not end up in a downstream pathway
Each metabolic pathway page contains an interactive metabolic pathway map, gene annotations hyperlinked to external resources and detailed information about the metabolic capabilities
Summary
The Apicomplexa is a large phylum of intracellular parasites that show great diversity and adaptability in the various ecological niches they occupy. They are the causative agents of human and animal infections including malaria, toxoplasmosis and theileriosis, which have a huge economic and social impact. A number of apicomplexan genomes have been sequenced and are publicly available. The prediction of gene models and annotation of gene functions remains challenging
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