KEGG   PATHWAY: ajs00910Help
Entry
ajs00910                    Pathway                                

Name
Nitrogen metabolism - Acidovorax sp. JS42
Description
The biological process of the nitrogen cycle is a complex interplay among many microorganisms catalyzing different reactions, where nitrogen is found in various oxidation states ranging from +5 in nitrate to -3 in ammonia. 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 amino acids and other vital compounds. The ability of fixing atmospheric nitrogen by the nitrogenase enzyme complex is present in restricted prokaryotes (diazotrophs). The other reduction pathways are assimilatory nitrate reduction [MD:M00531] and dissimilatory nitrate reduction [MD:M00530] both for conversion to ammonia, and denitrification [MD:M00529]. Denitrification is a respiration in which nitrate or nitrite is reduced as a terminal electron acceptor under low oxygen or anoxic conditions, producing gaseous nitrogen compounds (N2, NO and N2O) to the atmosphere. The two oxidation pathways are nitrification [MD:M00528] and anaerobic ammonium oxidation (anammox). Nitrification is the oxidation of ammonia (NH3) with oxygen into nitrite followed by the oxidation of nitrite into nitrate. The first step is performed by ammonia-oxidizing microorganisms (e.g., Nitrosomonas and Nitrosococcus) and the second step by nitrite-oxidizing microorganisms (e.g., Nitrobacter). Anammox is a biochemical process of oxidizing ammonium (NH4+) into dinitrogen gas (N2) using nitrite as an electron acceptor. It occurs in the anammoxosome, a membrane bound compartment inside the cytoplasm, of anammox bacteria (e.g., Planctomycetes).
Class
Metabolism; Energy metabolism
BRITE hierarchy
Pathway map
ajs00910  Nitrogen metabolism
ajs00910

Ortholog table
Module
ajs_M00438  Nitrate/nitrite transport system [PATH:ajs00910]
ajs_M00529  Denitrification, nitrate => nitrogen [PATH:ajs00910]
ajs_M00530  Dissimilatory nitrate reduction, nitrate => ammonia [PATH:ajs00910]
Other DBs
BSID: 44940
GO: 0006807
Organism
Acidovorax sp. JS42 [GN:ajs]
Gene
Ajs_0434  major facilitator superfamily MFS_1 [KO:K02575]
Ajs_0435  nitrite transporter [KO:K02575]
Ajs_2831  twin-arginine translocation pathway signal [KO:K15576]
Ajs_2832  nitrate ABC transporter, inner membrane subunit [KO:K15577]
Ajs_2833  nitrate ABC transporter, ATPase subunits C and D [KO:K15578] [EC:3.6.3.-]
Ajs_0436  respiratory nitrate reductase alpha subunit apoprotein [KO:K00370] [EC:1.7.99.- 1.7.5.1]
Ajs_0437  respiratory nitrate reductase beta subunit [KO:K00371] [EC:1.7.99.- 1.7.5.1]
Ajs_0439  respiratory nitrate reductase gamma subunit [KO:K00374] [EC:1.7.99.- 1.7.5.1]
Ajs_2841  assimilatory nitrate reductase (NADH) alpha subunit apoprotein [KO:K00372] [EC:1.7.99.-]
Ajs_2839  assimilatory nitrite reductase (NAD(P)H) large subunit precursor [KO:K00362] [EC:1.7.1.15]
Ajs_2840  assimilatory nitrite reductase (NAD(P)H) small subunit [KO:K00363] [EC:1.7.1.15]
Ajs_1912  dissimilatory nitrite reductase (NO-forming), cytochrome cd1 type apoprotein [KO:K15864] [EC:1.7.99.1 1.7.2.1]
Ajs_3435  nitric oxide reductase, NorB subunit apoprotein [KO:K04561] [EC:1.7.2.5]
Ajs_0092  nitric oxide reductase, NorZ apoprotein [KO:K04561] [EC:1.7.2.5]
Ajs_3436  nitric oxide reductase, NorC subunit apoprotein [KO:K02305]
Ajs_1139  nitrous oxide reductase apoprotein [KO:K00376] [EC:1.7.2.4]
Ajs_3732  2-nitropropane dioxygenase precursor [KO:K00459] [EC:1.13.12.16]
Ajs_0188  2-nitropropane dioxygenase, NPD [KO:K00459] [EC:1.13.12.16]
Ajs_2807  2-nitropropane dioxygenase, NPD [KO:K00459] [EC:1.13.12.16]
Ajs_3841  2-nitropropane dioxygenase, NPD [KO:K00459] [EC:1.13.12.16]
Ajs_0135  Glu/Leu/Phe/Val dehydrogenase, C terminal [KO:K00261] [EC:1.4.1.3]
Ajs_0977  glutamate dehydrogenase (NADP) [KO:K00262] [EC:1.4.1.4]
Ajs_1189  L-glutamine synthetase [KO:K01915] [EC:6.3.1.2]
Ajs_0741  glutamate synthase (NADH) large subunit [KO:K00265] [EC:1.4.1.14 1.4.1.13]
Ajs_0742  glutamate synthase (NADH) small subunit [KO:K00266] [EC:1.4.1.14 1.4.1.13]
Ajs_0441  Carbonate dehydratase [KO:K01673] [EC:4.2.1.1]
Ajs_3778  Carbonate dehydratase [KO:K01673] [EC:4.2.1.1]
Compound
C00011  CO2
C00014  Ammonia
C00025  L-Glutamate
C00058  Formate
C00064  L-Glutamine
C00088  Nitrite
C00169  Carbamoyl phosphate
C00192  Hydroxylamine
C00244  Nitrate
C00288  HCO3-
C00488  Formamide
C00533  Nitric oxide
C00697  Nitrogen
C00726  Nitrile
C00887  Nitrous oxide
C01417  Cyanate
C01563  Carbamate
C05361  Hydrazine
C06058  Nitroalkane
Reference
  Authors
Scott JD, Ludwig RA
  Title
Azorhizobium caulinodans electron-transferring flavoprotein N electrochemically couples pyruvate dehydrogenase complex activity to N2 fixation.
  Journal
Microbiology 150:117-26 (2004)
DOI:10.1099/mic.0.26603-0
Reference
  Authors
Kneip C, Lockhart P, Voss C, Maier UG
  Title
Nitrogen fixation in eukaryotes--new models for symbiosis.
  Journal
BMC Evol Biol 7:55 (2007)
DOI:10.1186/1471-2148-7-55
Reference
  Authors
Whittaker M, Bergmann D, Arciero D, Hooper AB
  Title
Electron transfer during the oxidation of ammonia by the chemolithotrophic bacterium Nitrosomonas europaea.
  Journal
Biochim Biophys Acta 1459:346-55 (2000)
DOI:10.1016/S0005-2728(00)00171-7
Reference
  Authors
Cabello P, Roldan MD, Moreno-Vivian C
  Title
Nitrate reduction and the nitrogen cycle in archaea.
  Journal
Microbiology 150:3527-46 (2004)
DOI:10.1099/mic.0.27303-0
Reference
  Authors
Stolz JF, Basu P
  Title
Evolution of nitrate reductase: molecular and structural variations on a common function.
  Journal
Reference
  Authors
Morozkina EV, Zvyagilskaya RA
  Title
Nitrate reductases: structure, functions, and effect of stress factors.
  Journal
Biochemistry (Mosc) 72:1151-60 (2007)
DOI:10.1134/S0006297907100124
Reference
  Authors
Jetten MS, Niftrik L, Strous M, Kartal B, Keltjens JT, Op den Camp HJ
  Title
Biochemistry and molecular biology of anammox bacteria.
  Journal
Crit Rev Biochem Mol Biol 44:65-84 (2009)
DOI:10.1080/10409230902722783
Reference
  Authors
Luesken FA, Wu ML, Op den Camp HJ, Keltjens JT, Stunnenberg H, Francoijs KJ, Strous M, Jetten MS
  Title
Effect of oxygen on the anaerobic methanotroph 'Candidatus Methylomirabilis oxyfera': kinetic and transcriptional analysis.
  Journal
Environ Microbiol 14:1024-34 (2012)
DOI:10.1111/j.1462-2920.2011.02682.x
Reference
  Authors
Daims H, Lebedeva EV, Pjevac P, Han P, Herbold C, Albertsen M, Jehmlich N, Palatinszky M, Vierheilig J, Bulaev A, Kirkegaard RH, von Bergen M, Rattei T, Bendinger B, Nielsen PH, Wagner M
  Title
Complete nitrification by Nitrospira bacteria.
  Journal
Nature 528:504-9 (2015)
DOI:10.1038/nature16461
Reference
  Authors
van Kessel MA, Speth DR, Albertsen M, Nielsen PH, Op den Camp HJ, Kartal B, Jetten MS, Lucker S
  Title
Complete nitrification by a single microorganism.
  Journal
Nature 528:555-9 (2015)
DOI:10.1038/nature16459
KO pathway
ko00910   

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