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Nitrogen metabolism - Puniceispirillum marinum (strain IMCC1322)


Model information
Identifier: BMID000000055738
Format: SBML L3 V1 (Layout)
Project: path2models
Categories: metabolic
Submission: 18 May 2012 04:03:27 UTC
Last modified: 09 Dec 2012 16:13:08 UTC
Published: 20 May 2012 00:49:21 UTC
isDescribedBy nitrogen compound metabolic process Gene Ontology
occursIn Puniceispirillum marinum (strain IMCC1322) Taxonomy
isDerivedFrom Nitrogen metabolism KEGG Pathway
Model of “Nitrogen metabolism” in “Candidatus Puniceispirillum marinum IMCC1322”
The biological process of the nitrogen cycle is a complex interplay among many microorganisms catalyzing different reactions. In biological world, nitrogen is found in varying oxidation states from nitrate (the most oxidized form) to ammonia (the most reduced form). Gaseous nitrogen cannot be absorbed and used as a nutrient by plants and animals. It must first be converted to ammonia by microorganisms, so that it can enter the ecological chain as part of the nitrogen cycle. The core nitrogen cycle involves four reduction pathways and two oxidation pathways. Nitrogen fixation [MD:M00175] is the process of reducing atmospheric molecular nitrogen to ammonia, a biologically useful reduced form incorporated into the amino acids and other vital compounds. The ability of fixing atmospheric nitrogen by the nitrogenase enzyme complex is present in restricted prokaryotes (diazotroph). Assimilatory nitrate reduction [MD:M00531] is the biological conversion of nitrite or nitrate to ammonia. Dissimilatory nitrate reduction includes two different processes: denitrification [MD:M00529] and dissimilatory nitrate reduction to ammonium [MD:M00530]. Denitrification is a respiration in which nitrate or nitrite is reduced as a terminal electron acceptor under low oxygen or anoxic conditions. As a consequence, gaseous nitrogen compounds (N2, NO and N2O) are produced to the atmosphere. Denitrifying organisms are found among bacteria, archaea and eukaryotes, but mainly in heterotrophic microorganism. The two oxidation pathways are anammox and nitrification [MD:M00528]. Anammox (anaerobic ammonium oxidation) is a recently discovered biochemical process of oxidizing ammonium into dinitrogen gas using nitrite as an electron acceptor. It is catabolized in the anammoxosome that is a membrane bound compartment inside the cytoplasm. Planctomycetes (e.g., K. stuttgartiensis), known chemolithoautotroph, performs this anammox process. Nitrification is the biological conversion of ammonia to nitrite or nitrate. Ammonia-oxidizing microorganisms (e.g., Nitrosomonas and Nitrosococcus) oxidize ammonia with oxygen into nitrite and, following this metabolic process, nitrite-oxidizing microorganisms (e.g., Nitrobacter) oxidize nitrite into nitrate under an aerobic condition. These chemolithoautotrophic microorganisms use ammonia or nitrite as a respiratory substance and use electrons from the oxidation of compounds to produce energy.

Graphical representation of 'Nitrogen metabolism (Candidatus Puniceispirillum marinum IMCC1322)'
(PNG image hosted by the Kyoto Encyclopedia of Genes and Genomes, KEGG).
This model has been automatically generated by KEGGtranslator V2.2.0 (KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats. Wrzodek C, Dräger A, Zell A. Bioinformatics . 2011, 27 :2314-2315) using information coming from the KEGG PATHWAY Database ( original pathway ).
The missing kinetic equations were added by SBMLsqueezer .
This model has been produced by the path2models project, it is currently hosted on BioModels Database and identified by: BMID000000055738 .
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