Biological nitrogen cycle module

A taxon-neutral decomposition of the biological nitrogen cycle: the set of microbially driven redox transformations that interconvert dinitrogen, ammonia, hydroxylamine, nitrite, nitrate, nitric oxide, nitrous oxide, and hydrazine. The module is organized by transformation (fixation, nitrification, denitrification, DNRA, anammox, assimilatory reduction, and ammonification) rather than by organism, and uses variant sets where convergent enzyme chemistries (e.g. cd1 vs Cu nitrite reductase) implement the same step. Leaf steps are grounded to canonical reviewed Swiss-Prot exemplars where one exists; abstract function selectors are used where no reviewed exemplar is available (nitrite-oxidizer NXR). Companion to projects/NITROGEN_CYCLE.md and the GO:0071941 obsoletion project (projects/NITROGEN_CYCLE_OBSOLETION.md).

MODULE:nitrogen_cycleDRAFTMetabolic Pathwaymodules/nitrogen_cycle.yaml

nitrogen cycle metabolic processGO:0071941

GO:0071941

nitrogen cycle metabolic process

The module is grounded in the GO biological process grouping term for the nitrogen cycle.

GO:0009399

nitrogen fixation

Reductive fixation of N2 to ammonia by nitrogenase is the reductive entry point of the cycle.

GO:0019333

denitrification pathway

Stepwise reduction of nitrate to dinitrogen is represented as a four-reaction denitrification submodule.

26Nodes

19Parts

3Variant Sets

6Variants

19Annotons

11Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:nitrogen_cycle deep-research report alongside the module YAML.

Leaf nodes lacking representative members

1 leaf node(s) with no concrete protein grounding:

Nitrite oxidation ANY_WITH_FUNCTION

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (0/25 grounded genes reviewed)

0 complete review(s) · 0 with deep research · 25 missing review · 0 reviewed but lacking deep research

Gene	Review	Complete	Deep research
NifH (nitrogenase Fe protein) P00458	✗	—	—
NifD (MoFe protein alpha) P07328	✗	—	—
NifK (MoFe protein beta) P07329	✗	—	—
NirB P08201	✗	—	—
NarG P09152	✗	—	—
GltB P09831	✗	—	—
GlnA P0A9C5	✗	—	—
NrfA P0ABK9	✗	—	—
UreC P18314	✗	—	—
NirS P24474	✗	—	—
NirK P25006	✗	—	—
NarB P39458	✗	—	—
NirA P39661	✗	—	—
NorB P98008	✗	—	—
AmoA Q04507	✗	—	—
AmoB Q04508	✗	—	—
HDH Q1PW30	✗	—	—
HzsA Q1Q0T2	✗	—	—
HzsG Q1Q0T3	✗	—	—
HzsB Q1Q0T4	✗	—	—
HAO Q50925	✗	—	—
NorC Q51662	✗	—	—
NosZ Q51705	✗	—	—
NapA Q56350	✗	—	—
AmoC Q82W83	✗	—	—

Tree

Biological nitrogen cycleMetabolic Pathwaynitrogen_cycle

Parts
1. 1. reductive entry — dinitrogen fixation
2. Nitrogen fixationMetabolic Pathwaynitrogen_fixation
  
  Annotons
  - Nitrogenase (Fe protein + MoFe protein) Protein Complex: nitrogenase complex
3. 2. oxidative — nitrification (NH3 -> NO2- -> NO3-)
4. NitrificationMetabolic Pathwaynitrification
  
  Parts
  1. 1. ammonia to hydroxylamine
  2. Ammonia monooxygenationReactionammonia_oxidation
    
    Annotons
    
    Ammonia monooxygenase (AMO) Protein Complex: ammonia monooxygenase
  3. 2. hydroxylamine to nitrite
  4. Hydroxylamine oxidationReactionhydroxylamine_oxidation
    
    Annotons
    
    Hydroxylamine oxidoreductase (HAO) Gene Product: HAO
  5. 3. nitrite to nitrate (nitrite-oxidizing bacteria)
  6. Nitrite oxidationReactionnitrite_oxidation
    
    Annotons
    
    Nitrite oxidoreductase (NXR) Any With Function: nitrite oxidoreductase (NXR) activity
5. 3. reductive anaerobic respiration — denitrification (NO3- -> N2)
6. DenitrificationMetabolic Pathwaydenitrification
  
  Parts
  1. 1. nitrate to nitrite
  2. Dissimilatory nitrate reductionReactiondenit_nitrate_reduction
    
    Variants
    
    Respiratory nitrate reductase variants by enzyme localization / chemistry (Exactly One)
    
    Membrane-bound nitrate reductase (Nar)Reactionmembrane_nar_variant
    
    Annotons
    
    Respiratory nitrate reductase alpha (NarG) Gene Product: NarG
    
    Periplasmic nitrate reductase (Nap)Reactionperiplasmic_nap_variant
    
    Annotons
    
    Periplasmic nitrate reductase (NapA) Gene Product: NapA
  3. 2. nitrite to nitric oxide (committed denitrification step)
  4. Nitrite reduction to NOReactiondenit_nitrite_reduction
    
    Variants
    
    Respiratory nitrite reductase variants by enzyme chemistry (Exactly One)
    
    Cytochrome cd1 nitrite reductase (NirS)Reactioncd1_nirS_variant
    
    Annotons
    
    Cytochrome cd1 nitrite reductase (NirS) Gene Product: NirS
    
    Copper nitrite reductase (NirK)Reactioncu_nirK_variant
    
    Annotons
    
    Copper-containing nitrite reductase (NirK) Gene Product: NirK
  5. 3. nitric oxide to nitrous oxide
  6. Nitric oxide reductionReactiondenit_no_reduction
    
    Annotons
    
    Nitric oxide reductase (cNOR, NorBC) Protein Complex: nitric oxide reductase complex (cNOR)
  7. 4. nitrous oxide to dinitrogen (terminal step)
  8. Nitrous oxide reductionReactiondenit_n2o_reduction
    
    Annotons
    
    Nitrous-oxide reductase (NosZ) Gene Product: NosZ
7. 4. reductive — dissimilatory nitrate/nitrite reduction to ammonium (DNRA)
8. DNRA (nitrite to ammonium)Reactiondnra
  
  Annotons
  - Cytochrome c nitrite reductase (NrfA) Gene Product: NrfA
9. 5. redox-coupled — anaerobic ammonium oxidation (anammox)
10. AnammoxMetabolic Pathwayanammox
  
  Parts
  1. 1. ammonium + NO to hydrazine
  2. Hydrazine synthesisReactionhydrazine_synthesis
    
    Annotons
    
    Hydrazine synthase (HZS, alpha/beta/gamma) Protein Complex: hydrazine synthase complex
  3. 2. hydrazine to dinitrogen
  4. Hydrazine oxidationReactionhydrazine_oxidation
    
    Annotons
    
    Hydrazine dehydrogenase (HDH) Gene Product: HDH
11. 6. assimilatory reduction and ammonia incorporation
12. Assimilatory nitrate reduction and ammonia assimilationMetabolic Pathwaynitrogen_assimilation
  
  Parts
  1. 1. assimilatory nitrate to nitrite
  2. Assimilatory nitrate reductionReactionassim_nitrate_reduction
    
    Annotons
    
    Ferredoxin nitrate reductase (NarB) Gene Product: NarB
  3. 2. assimilatory nitrite to ammonia
  4. Assimilatory nitrite reductionReactionassim_nitrite_reduction
    
    Variants
    
    Assimilatory nitrite reductase variants by electron donor (Exactly One)
    
    Ferredoxin-nitrite reductase (NirA)Reactionferredoxin_nir_variant
    
    Annotons
    
    Ferredoxin-nitrite reductase (NirA) Gene Product: NirA
    
    NADH-nitrite reductase (NirB)Reactionnadh_nir_variant
    
    Annotons
    
    NADH nitrite reductase large subunit (NirB) Gene Product: NirB
  5. 3. ammonia incorporation into glutamine/glutamate (GS/GOGAT)
  6. Ammonia assimilation (GS/GOGAT cycle)Metabolic Pathwayammonia_assimilation
    
    Annotons
    
    Glutamine synthetase (GS) Gene Product: GlnA
    
    Glutamate synthase (GOGAT) large chain Gene Product: GltB
13. 7. mineralization — organic nitrogen to ammonia (ammonification)
14. Ammonification (urea hydrolysis)Reactionammonification
  
  Annotons
  - Urease alpha subunit (UreC) Gene Product: UreC

Details

Biological nitrogen cycleMetabolic Pathwaynitrogen_cycle

nitrogen cycle metabolic processGO:0071941

Taxon-neutral sketch. A species-specific realization selects one variant per variant set (e.g. NirS vs NirK), grounds the NXR leaf to a concrete exemplar, and may add accessory/maturation and regulatory subunits (nifEN, nosDFYL, ntrBC/narXL) that are intentionally omitted from this marker-enzyme seed. Subunit-grounding convention: a step modeled as a PROTEIN_COMPLEX grounds the experimentally characterized catalytic-and-structural subunits as active_units (nitrogenase NifHDK, AMO AmoABC, NOR NorBC, HZS HzsABG); single-subunit enzymes ground one exemplar. Mono-subunit alternates (e.g. assimilatory NasA) and electron-partner proteins (e.g. HAO-linked cytochrome c-554 / CycA) are deferred to species realizations rather than added to this seed.

Connections

nitrogen_fixation -> ammonia_assimilation Provides Input For

Fixed ammonia feeds the GS/GOGAT assimilation cycle.

ammonia_oxidation -> hydroxylamine_oxidation Provides Input For

Hydroxylamine from AMO is the substrate for HAO.

hydroxylamine_oxidation -> nitrite_oxidation Provides Input For

Nitrite from ammonia-oxidizers is oxidized to nitrate by NOB.

denit_nitrate_reduction -> denit_nitrite_reduction Precedes

denit_nitrite_reduction -> denit_no_reduction Precedes

denit_no_reduction -> denit_n2o_reduction Precedes

denit_nitrate_reduction -> dnra Provides Input For

Nitrate reduction supplies the shared nitrite pool. DNRA (NO2- -> NH4+) and denitrification (NO2- -> NO, the denit_nitrite_reduction step) are competing parallel fates of that nitrite, not sequential steps.

hydrazine_synthesis -> hydrazine_oxidation Provides Input For

Hydrazine made by HZS is oxidized to N2 by HDH.

assim_nitrate_reduction -> assim_nitrite_reduction Precedes

assim_nitrite_reduction -> ammonia_assimilation Provides Input For

ammonification -> ammonia_oxidation Provides Input For

Mineralized ammonia re-enters the cycle via nitrification (or assimilation).

Part 1: reductive entry — dinitrogen fixation

Nitrogen fixationMetabolic Pathwaynitrogen_fixation

nitrogen fixationGO:0009399

Annotons

Nitrogenase (Fe protein + MoFe protein)

nitrogenase_complex

Participant: Protein Complex: nitrogenase complex

Protein Complex:

nitrogenase complex Two-component metalloenzyme: the homodimeric Fe protein (NifH, ATP-dependent electron donor) and the alpha2beta2 MoFe protein (NifDK, site of N2 reduction at the FeMo cofactor).

Active units:

Nitrogenase iron protein (NifH)

Participant: Gene Product: NifH (nitrogenase Fe protein)

Gene Product:

NifH (nitrogenase Fe protein)UniProtKB:P00458

Role: ATP-dependent electron donor to the MoFe protein

Nitrogenase MoFe protein alpha chain (NifD)

Participant: Gene Product: NifD (MoFe protein alpha)

Gene Product:

NifD (MoFe protein alpha)UniProtKB:P07328

Role: harbors the FeMo cofactor (N2 reduction site)

Nitrogenase MoFe protein beta chain (NifK)

Participant: Gene Product: NifK (MoFe protein beta)

Gene Product:

NifK (MoFe protein beta)UniProtKB:P07329

Role: MoFe protein beta subunit; P-cluster ligation

Function

nitrogenase activityGO:0016163

Substrates: dinitrogen ATP

Products: ammonia ADP

Reduces N2 to 2 NH3 with obligate ATP hydrolysis and an H2-evolution side reaction. Strongly O2-sensitive; many implementations add protection or temporal/spatial separation.

Part 2: oxidative — nitrification (NH3 -> NO2- -> NO3-)

NitrificationMetabolic Pathwaynitrification

Aerobic oxidation of ammonia to nitrate, classically split between ammonia-oxidizers (AOB/AOA: NH3 -> NO2-) and nitrite-oxidizers (NOB: NO2- -> NO3-); comammox organisms run the whole chain.

ammonia oxidationGO:0019329

Part 1: ammonia to hydroxylamine

Ammonia monooxygenationReactionammonia_oxidation

Annotons

Ammonia monooxygenase (AMO)

amo_complex

Participant: Protein Complex: ammonia monooxygenase

Protein Complex:

ammonia monooxygenase Membrane-bound heterotrimeric copper enzyme (AmoCAB); evolutionarily related to particulate methane monooxygenase.

Active units:

AMO alpha subunit (AmoA)

Participant: Gene Product: AmoA

Gene Product:

AmoAUniProtKB:Q04507

Role: catalytic subunit (ammonia hydroxylation)

AMO beta subunit (AmoB)

Participant: Gene Product: AmoB

Gene Product:

AmoBUniProtKB:Q04508

Role: substrate/copper-coordinating subunit

AMO gamma subunit (AmoC)

Participant: Gene Product: AmoC

Gene Product:

AmoCUniProtKB:Q82W83

Role: membrane gamma subunit

Function

ammonia monooxygenase activityGO:0018597

Substrates: ammonia dioxygen

Products: hydroxylamine

Part 2: hydroxylamine to nitrite

Hydroxylamine oxidationReactionhydroxylamine_oxidation

Annotons

Hydroxylamine oxidoreductase (HAO)

hao_activity

Participant: Gene Product: HAO

Gene Product:

HAOUniProtKB:Q50925

Function

hydroxylamine oxidoreductase activityGO:0033740

Substrates: hydroxylamine

Products: nitrite

Part 3: nitrite to nitrate (nitrite-oxidizing bacteria)

Nitrite oxidationReactionnitrite_oxidation

Annotons

Nitrite oxidoreductase (NXR)

nxr_activity

Participant: Any With Function: nitrite oxidoreductase (NXR) activity

Required Function:

nitrite oxidoreductase (NXR) activityGO:0160182 NOB nitrite oxidoreductase (Nitrobacter/Nitrospira) runs the nitrate reductase reaction in the oxidative direction. No reviewed Swiss-Prot exemplar exists; the molecular function is the membrane (quinone) nitrate reductase reaction read in reverse.

Function

nitrite oxidation to nitrateGO:0160182

Substrates: nitrite

Products: nitrate

Abstract leaf: needs a concrete UniProt/PTN exemplar once a reviewed NXR entry is available.

Part 3: reductive anaerobic respiration — denitrification (NO3- -> N2)

DenitrificationMetabolic Pathwaydenitrification

denitrification pathwayGO:0019333

Part 1: nitrate to nitrite

Dissimilatory nitrate reductionReactiondenit_nitrate_reduction

Variant set: Respiratory nitrate reductase variants by enzyme localization / chemistry (Exactly One)

Membrane-bound nitrate reductase (Nar)Reactionmembrane_nar_variant

Annotons

Respiratory nitrate reductase alpha (NarG)

narG_activity

Participant: Gene Product: NarG

Gene Product:

NarGUniProtKB:P09152

Function

nitrate reductase (quinone) activityGO:0160182

Substrates: nitrate

Products: nitrite

Periplasmic nitrate reductase (Nap)Reactionperiplasmic_nap_variant

Annotons

Periplasmic nitrate reductase (NapA)

napA_activity

Participant: Gene Product: NapA

Gene Product:

NapAUniProtKB:Q56350

Function

nitrate reductase (cytochrome) activityGO:0050140

Substrates: nitrate

Products: nitrite

Part 2: nitrite to nitric oxide (committed denitrification step)

Nitrite reduction to NOReactiondenit_nitrite_reduction

NirS and NirK are convergent, mutually exclusive solutions to the same NO2- -> NO step; their distribution partitions denitrifiers.

Variant set: Respiratory nitrite reductase variants by enzyme chemistry (Exactly One)

Cytochrome cd1 nitrite reductase (NirS)Reactioncd1_nirS_variant

Annotons

Cytochrome cd1 nitrite reductase (NirS)

nirS_activity

Participant: Gene Product: NirS

Gene Product:

NirSUniProtKB:P24474

Function

nitrite reductase (NO-forming) activityGO:0050421

Substrates: nitrite

Products: nitric oxide

Copper nitrite reductase (NirK)Reactioncu_nirK_variant

Annotons

Copper-containing nitrite reductase (NirK)

nirK_activity

Participant: Gene Product: NirK

Gene Product:

NirKUniProtKB:P25006

Function

nitrite reductase (NO-forming) activityGO:0050421

Substrates: nitrite

Products: nitric oxide

Part 3: nitric oxide to nitrous oxide

Nitric oxide reductionReactiondenit_no_reduction

Annotons

Nitric oxide reductase (cNOR, NorBC)

nor_activity

Participant: Protein Complex: nitric oxide reductase complex (cNOR)

Protein Complex:

nitric oxide reductase complex (cNOR) Membrane cytochrome bc-type NO reductase; NorB is the catalytic large subunit and NorC the cytochrome c small subunit. Subunit exemplars are from different denitrifiers.

Active units:

NOR large (catalytic) subunit (NorB)

Participant: Gene Product: NorB

Gene Product:

NorBUniProtKB:P98008

Role: catalytic large subunit (NO reduction)

NOR cytochrome c small subunit (NorC)

Participant: Gene Product: NorC

Gene Product:

NorCUniProtKB:Q51662

Role: cytochrome c electron-entry subunit

Function

nitric oxide reductase activityGO:0016966

Substrates: nitric oxide

Products: nitrous oxide

Part 4: nitrous oxide to dinitrogen (terminal step)

Nitrous oxide reductionReactiondenit_n2o_reduction

Annotons

Nitrous-oxide reductase (NosZ)

nosZ_activity

Participant: Gene Product: NosZ

Gene Product:

NosZUniProtKB:Q51705

Function

nitrous-oxide reductase activityGO:0050304

Substrates: nitrous oxide

Products: dinitrogen

The only known biological N2O sink; loss or truncation of nosZ makes a denitrifier a net N2O emitter.

Part 4: reductive — dissimilatory nitrate/nitrite reduction to ammonium (DNRA)

DNRA (nitrite to ammonium)Reactiondnra

Fermentative/respiratory branch that retains nitrogen as ammonium instead of releasing N gases; competes with denitrification for nitrite.

Annotons

Cytochrome c nitrite reductase (NrfA)

nrfA_activity

Participant: Gene Product: NrfA

Gene Product:

NrfAUniProtKB:P0ABK9

Function

nitrite reductase (cytochrome, ammonia-forming) activityGO:0042279

Substrates: nitrite

Products: ammonia

Part 5: redox-coupled — anaerobic ammonium oxidation (anammox)

AnammoxMetabolic Pathwayanammox

Comproportionation of ammonium and nitrite to N2 via the hydrazine intermediate, within the anammoxosome organelle of Planctomycetes.

anaerobic ammonium oxidationGO:0019331

Part 1: ammonium + NO to hydrazine

Hydrazine synthesisReactionhydrazine_synthesis

Annotons

Hydrazine synthase (HZS, alpha/beta/gamma)

hzs_activity

Participant: Protein Complex: hydrazine synthase complex

Protein Complex:

hydrazine synthase complex Multiheme (alpha3-beta3-gamma3) hydrazine synthase that condenses ammonium and NO to hydrazine in the anammoxosome.

Active units:

HZS alpha subunit (HzsA)

Participant: Gene Product: HzsA

Gene Product:

HzsAUniProtKB:Q1Q0T2

Role: catalytic alpha subunit

HZS beta subunit (HzsB)

Participant: Gene Product: HzsB

Gene Product:

HzsBUniProtKB:Q1Q0T4

Role: beta subunit

HZS gamma subunit (HzsG)

Participant: Gene Product: HzsG

Gene Product:

HzsGUniProtKB:Q1Q0T3

Role: gamma subunit

Function

hydrazine synthase activityGO:0140304

Substrates: ammonium nitric oxide

Products: hydrazine

Locations

anammoxosomeGO:0044222

Part 2: hydrazine to dinitrogen

Hydrazine oxidationReactionhydrazine_oxidation

Annotons

Hydrazine dehydrogenase (HDH)

hdh_activity

Participant: Gene Product: HDH

Gene Product:

HDHUniProtKB:Q1PW30

Function

hydrazine dehydrogenase activityGO:0140287

Substrates: hydrazine

Products: dinitrogen

Part 6: assimilatory reduction and ammonia incorporation

Assimilatory nitrate reduction and ammonia assimilationMetabolic Pathwaynitrogen_assimilation

nitrate assimilationGO:0042128

Part 1: assimilatory nitrate to nitrite

Assimilatory nitrate reductionReactionassim_nitrate_reduction

Annotons

Ferredoxin nitrate reductase (NarB)

narB_activity

Participant: Gene Product: NarB

Gene Product:

NarBUniProtKB:P39458

Function

ferredoxin-nitrate reductase activityGO:0047889

Substrates: nitrate reduced ferredoxin

Products: nitrite oxidized ferredoxin

Part 2: assimilatory nitrite to ammonia

Assimilatory nitrite reductionReactionassim_nitrite_reduction

Variant set: Assimilatory nitrite reductase variants by electron donor (Exactly One)

Ferredoxin-nitrite reductase (NirA)Reactionferredoxin_nir_variant

Annotons

Ferredoxin-nitrite reductase (NirA)

nirA_activity

Participant: Gene Product: NirA

Gene Product:

NirAUniProtKB:P39661

Function

ferredoxin-nitrite reductase activityGO:0048307

Substrates: nitrite

Products: ammonia

NADH-nitrite reductase (NirB)Reactionnadh_nir_variant

Annotons

NADH nitrite reductase large subunit (NirB)

nirB_activity

Participant: Gene Product: NirB

Gene Product:

NirBUniProtKB:P08201

Function

nitrite reductase (NADH) activityGO:0106316

Substrates: nitrite

Products: ammonia

Part 3: ammonia incorporation into glutamine/glutamate (GS/GOGAT)

Ammonia assimilation (GS/GOGAT cycle)Metabolic Pathwayammonia_assimilation

ammonia assimilation cycleGO:0019676

Annotons

Glutamine synthetase (GS)

glnA_activity

Participant: Gene Product: GlnA

Gene Product:

GlnAUniProtKB:P0A9C5

Function

glutamine synthetase activityGO:0004356

Substrates: glutamate ammonia ATP

Products: glutamine

Glutamate synthase (GOGAT) large chain

gltB_activity

Participant: Gene Product: GltB

Gene Product:

GltBUniProtKB:P09831

Function

glutamate synthase (NADPH) activityGO:0004355

Substrates: glutamine 2-oxoglutarate

Products: glutamate

Part 7: mineralization — organic nitrogen to ammonia (ammonification)

Ammonification (urea hydrolysis)Reactionammonification

Representative organic-N mineralization step returning fixed nitrogen to ammonia; ureolysis is the canonical example.

Annotons

Urease alpha subunit (UreC)

ureC_activity

Participant: Gene Product: UreC

Gene Product:

UreCUniProtKB:P18314

Function

urease activityGO:0009039

Substrates: urea

Products: ammonia carbon dioxide