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LAMP


NAR Molecular Biology Database Collection entry number 1580
Achchuthan Shanmugasundram1,2,*, Faviel F Gonzalez-Galarza1, Jonathan Wastling2, Olga Vasieva1 and Andrew R Jones1
1Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK

2Institute of Infection and Global Health, University of Liverpool, Liverpool Science Park Innovation Centre 2, 146 Brownlow Hill, Liverpool L3 5RF, UK

Database Description

The Library of Apicomplexan Metabolic Pathways (LAMP, http://www.llamp.net) is a web database that provides near complete mapping from genes to the central metabolic functions for some of the prominent intracellular parasites of the phylum Apicomplexa. We have systematically assigned genes to functions within pathways/networks for Toxoplasma gondii, Neospora caninum, Cryptosporidium and Theileria species, and Babesia bovis. Several functions missing from pathways have been identified, where the corresponding gene for an essential process appears to be absent from the current genome annotation. There had been extensive manual curation carried out for these species (especially T. gondii) with the use of available experimental data from publications and the genome database EuPathDB (3). For each species, LAMP contains interactive diagrams of each pathway, hyperlinked to external resources and annotated with detailed information, including the sources of evidence used. We have also developed a section to highlight the overall metabolic capabilities of each species, such as the ability to synthesise or the dependence upon the host for a particular metabolite. We are also expecting to include the annotations and metabolic pathways for other apicomplexans, when the genomes become available. As a recent development, the annotations of LAMP have been linked out from the respective gene pages from the beta release of ToxoDB version 8.0, and are expected to be part of the full release (4). We expect that LAMP will be a valuable resource for fundamental and applied research on the Apicomplexa.

Acknowledgements

LAMP is indirectly funded through several grants from Biotechnology and Biological Sciences Research Council. ARJ and JMW would like to acknowledge funding from BBSRC for proteomics analysis of the Apicomplexa [BB/G010781/1 grant to ARJ and JMW]. AS is funded by a BBSRC DTG studentship awarded to the University of Liverpool. FG is funded by BBSRC [BB/I00095X/1, grant to ARJ].

References

1. Ginsburg, H. (2006) Progress in in silico functional genomics: the malaria Metabolic Pathways database. Trends Parasitol, 22, 238-240.

2. Ginsburg, H. (2009) Caveat emptor: limitations of the automated reconstruction of metabolic pathways in Plasmodium. Trends Parasitol, 25, 37-43.

3. Aurrecoechea, C., Brestelli, J., Brunk, B.P., Fischer, S., Gajria, B., Gao, X., Gingle, A., Grant, G., Harb, O.S., Heiges, M. et al. (2010) EuPathDB: a portal to eukaryotic pathogen databases. Nucleic Acids Res, 38, D415-D419.

4. Gajria, B., Bahl, A., Brestelli, J., Dommer, J., Fischer, S., Gao, X., Heiges, M., Iodice, J., Kissinger, J.C., Mackey, A.J. et al. (2008) ToxoDB: an integrated Toxoplasma gondii database resource. Nucleic Acids Res, 36, D553-D556.


Subcategory: Metabolic pathways

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