nitrate reduction I (denitrification)

MetaCyc:DENITRIFICATION-PWY

Complete native nitrate-to-dinitrogen route with five listed objects: vectorial Nar nitrate reduction, nitrate/nitrite exchange, c551-dependent nitrite reduction, cytochrome-c-dependent NO reduction and N2O reduction. PAO1 experiments support the respiratory system; strict NarK2 antiport versus uniport remains unresolved, so native antiport is explicitly a database convention and has no assigned PAO1 catalyst. Whole carrier classes and side-specific proton coefficients are retained without choosing a quinone species or a unique NosZ donor. Functional gene-product edges do not imply isolated subunit catalysis. Other-species native complex IDs are not transferred; NirS/NosZ dimer and Nar/Nor assembly annotations retain source-specific evidence tiers. Current NorB proton-pump annotation conflicts with cNOR structural evidence and is excluded; RCSB 3O0R has source-PAO1 protein sequences differing from current entries. Inferred cofactors retain their evidence tiers; ligand-state IDs do not fix catalytic redox state. Native background nitrite-to-ammonium prose, Nap compensation, qNOR variants, assimilatory reduction, electron-carrier regeneration and ATP synthesis are outside this selected route.

Pathway type

anaerobic respiration

Organism scope

Pseudomonas aeruginosa PAO1 NCBITaxon:208964

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Pathway network

45 nodes · 75 asserted directed edges

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Components and activities

Declared biological components and source reaction directions
Node	Kind or role	Source direction
Pseudomonas aeruginosa PAO1 `NCBITaxon:208964`	taxon
nitrate `CHEBI:17632`	small molecule
nitrite `CHEBI:16301`	small molecule
nitric oxide `CHEBI:16480`	small molecule
dinitrogen oxide `CHEBI:17045`	small molecule
dinitrogen `CHEBI:17997`	small molecule
water `CHEBI:15377`	small molecule
hydron `CHEBI:15378`	small molecule
Mo(=O)-bis(molybdopterin guanine dinucleotide)(4-) `CHEBI:60539`	cofactor
tetra-mu3-sulfido-tetrairon `CHEBI:49883`	cofactor
tri-mu-sulfido-mu3-sulfido-triiron `CHEBI:21137`	cofactor
ferroheme c(2-) `CHEBI:61717`	cofactor
ferroheme d1(4-) `CHEBI:60549`	cofactor
ferroheme b(2-) `CHEBI:60344`	cofactor
iron cation `CHEBI:24875`	cofactor
binuclear copper ion `CHEBI:47357`	cofactor
mu4-sulfido-quadro-tetracopper `CHEBI:33730`	cofactor
calcium(2+) `CHEBI:29108`	cofactor
an electron-transfer quinol `MetaCyc:ETR-Quinols`	chemical entity
an electron-transfer quinone `MetaCyc:ETR-Quinones`	chemical entity
a reduced cytochrome c551 `MetaCyc:Reduced-cytochromes-c551`	protein
an oxidized cytochrome c551 `MetaCyc:Oxidized-cytochromes-c551`	protein
a reduced c-type cytochrome `MetaCyc:Cytochromes-C-Reduced`	protein
an oxidized c-type cytochrome `MetaCyc:Cytochromes-C-Oxidized`	protein
nitrate reductase (quinone) `UniProtKB:G3XCX1`	protein
nitrate reductase (quinone) `UniProtKB:G3XD87`	protein
nitrate reductase (quinone) `UniProtKB:G3XD18`	protein
Nitrite reductase `UniProtKB:P24474`	protein
Nitric oxide reductase subunit B `UniProtKB:Q59647`	protein
Nitric oxide reductase subunit C `UniProtKB:Q59646`	protein
Nitrous-oxide reductase `UniProtKB:Q9HYL2`	protein
Nitrate/nitrite transporter `UniProtKB:Q9HXD4`	protein
Nitrite extrusion protein 1 `UniProtKB:G3XD60`	protein
Cytochrome c-551 `UniProtKB:P00099`	protein
Transcriptional activator protein anr `UniProtKB:P23926`	protein
Transcriptional regulator Dnr `UniProtKB:G3XCW6`	protein
Two-component response regulator NarL `UniProtKB:Q9HXD3`	protein
periplasmic space `GO:0042597`	cellular component
plasma membrane `GO:0005886`	cellular component
membrane `GO:0016020`	cellular component
nitrate + an electron-transfer quinol[inner membrane] + 2 H+ nitrite + an electron-transfer quinone[inner membrane] + 2 H+[periplasm] + H2O `MetaCyc:RXN-11236`	reaction	left to right
nitrate[periplasm] + nitrite[cytosol] -> nitrate[cytosol] + nitrite[periplasm] `MetaCyc:TRANS-RXN0-239`	reaction	left to right
nitrite[periplasm] + a reduced cytochrome c551[periplasm] + 2 H+[periplasm] nitric oxide[periplasm] + an oxidized cytochrome c551[periplasm] + H2O[periplasm] `MetaCyc:RXN-15838`	reaction	left to right
2 a reduced c-type cytochrome[periplasm] + 2 nitric oxide[periplasm] + 2 H+[periplasm] -> nitrous oxide[periplasm] + 2 an oxidized c-type cytochrome[periplasm] + H2O[periplasm] `MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN`	reaction	left to right
2 a reduced c-type cytochrome[periplasm] + nitrous oxide[periplasm] + 2 H+[periplasm] -> 2 an oxidized c-type cytochrome[periplasm] + N2[periplasm] + H2O[periplasm] `MetaCyc:RXN-12130`	reaction	left to right

Mechanistic edges

Mechanistic edges and their cited evidence
Subject	Predicate and description	Object	Evidence
`MetaCyc:DENITRIFICATION-PWY`	has_part Complete native route member; source reaction direction is retained separately from the pathway L2R traversal.	nitrate + an electron-transfer quinol[inner membrane] + 2 H+ nitrite + an electron-transfer quinone[inner membrane] + 2 H+[periplasm] + H2O `MetaCyc:RXN-11236`	MetaCyc:DENITRIFICATION-PWY Source assertion: The pathway explicitly lists RXN-11236 and assigns L2R traversal. Source location `XPath /ptools-xml/Pathway/reaction-list/Reaction[@frameid="RXN-11236"]; /ptools-xml/Pathway/reaction-layout[Reaction/@frameid="RXN-11236"]/direction`
`MetaCyc:DENITRIFICATION-PWY`	has_part Native nitrate/nitrite antiport convention is retained as a complete source-defined step. PAO1 transport function is experimentally supported, but strict antiport versus uniport and its exact catalyst assignment remain unresolved.	nitrate[periplasm] + nitrite[cytosol] -> nitrate[cytosol] + nitrite[periplasm] `MetaCyc:TRANS-RXN0-239`	MetaCyc:DENITRIFICATION-PWY Source assertion: The pathway explicitly lists TRANS-RXN0-239 and assigns L2R traversal. Source location `XPath /ptools-xml/Pathway/reaction-list/Reaction[@frameid="TRANS-RXN0-239"]; /ptools-xml/Pathway/reaction-layout[Reaction/@frameid="TRANS-RXN0-239"]/direction` PMID:16391109 Source assertion: The authors explicitly state that antiport versus uniport remains to be conclusively experimentally proven. Source location `XPath //article/section[2]/section/section[4]/p[5]`
`MetaCyc:DENITRIFICATION-PWY`	has_part Complete native route member; source reaction direction is retained separately from the pathway L2R traversal.	nitrite[periplasm] + a reduced cytochrome c551[periplasm] + 2 H+[periplasm] nitric oxide[periplasm] + an oxidized cytochrome c551[periplasm] + H2O[periplasm] `MetaCyc:RXN-15838`	MetaCyc:DENITRIFICATION-PWY Source assertion: The pathway explicitly lists RXN-15838 and assigns L2R traversal. Source location `XPath /ptools-xml/Pathway/reaction-list/Reaction[@frameid="RXN-15838"]; /ptools-xml/Pathway/reaction-layout[Reaction/@frameid="RXN-15838"]/direction`
`MetaCyc:DENITRIFICATION-PWY`	has_part Complete native route member; source reaction direction is retained separately from the pathway L2R traversal.	2 a reduced c-type cytochrome[periplasm] + 2 nitric oxide[periplasm] + 2 H+[periplasm] -> nitrous oxide[periplasm] + 2 an oxidized c-type cytochrome[periplasm] + H2O[periplasm] `MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN`	MetaCyc:DENITRIFICATION-PWY Source assertion: The pathway explicitly lists NITRIC-OXIDE-REDUCTASE-RXN and assigns L2R traversal. Source location `XPath /ptools-xml/Pathway/reaction-list/Reaction[@frameid="NITRIC-OXIDE-REDUCTASE-RXN"]; /ptools-xml/Pathway/reaction-layout[Reaction/@frameid="NITRIC-OXIDE-REDUCTASE-RXN"]/direction`
`MetaCyc:DENITRIFICATION-PWY`	has_part Complete native route member; source reaction direction is retained separately from the pathway L2R traversal.	2 a reduced c-type cytochrome[periplasm] + nitrous oxide[periplasm] + 2 H+[periplasm] -> 2 an oxidized c-type cytochrome[periplasm] + N2[periplasm] + H2O[periplasm] `MetaCyc:RXN-12130`	MetaCyc:DENITRIFICATION-PWY Source assertion: The pathway explicitly lists RXN-12130 and assigns L2R traversal. Source location `XPath /ptools-xml/Pathway/reaction-list/Reaction[@frameid="RXN-12130"]; /ptools-xml/Pathway/reaction-layout[Reaction/@frameid="RXN-12130"]/direction`
an electron-transfer quinol `MetaCyc:ETR-Quinols`	consumes Coefficient 1; membrane electron-transfer class; side not specified. Native compartmental equation and class identity retained.	nitrate + an electron-transfer quinol[inner membrane] + 2 H+ nitrite + an electron-transfer quinone[inner membrane] + 2 H+[periplasm] + H2O `MetaCyc:RXN-11236`	MetaCyc:RXN-11236 Source assertion: The left side contains coefficient 1 of ETR-Quinols; no side compartment is specified. Source location `XPath /ptools-xml/Reaction/left[1]` MetaCyc:ETR-Quinols Source assertion: The issuing native object identifies this whole class as an electron-transfer quinol; no unique molecular formula or sequence is asserted. Source location `XPath /ptools-xml/Compound/common-name`
nitrate `CHEBI:17632`	consumes Coefficient 1; cytoplasmic side. Native compartmental equation and class identity retained.	nitrate + an electron-transfer quinol[inner membrane] + 2 H+ nitrite + an electron-transfer quinone[inner membrane] + 2 H+[periplasm] + H2O `MetaCyc:RXN-11236`	MetaCyc:RXN-11236 Source assertion: The left side contains coefficient 1 of NITRATE in CCO-IN. Source location `XPath /ptools-xml/Reaction/left[2]` MetaCyc:NITRATE Source assertion: The native NITRATE object has InChI InChI=1S/NO3/c2-1(3)4/q-1. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:17632 Source assertion: The selected ChEBI structure has the same InChI; formula NO3, charge -1. Source location `Semantic SQL statements: subject=CHEBI:17632; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
hydron `CHEBI:15378`	consumes Coefficient 2; cytoplasmic side. Native compartmental equation and class identity retained.	nitrate + an electron-transfer quinol[inner membrane] + 2 H+ nitrite + an electron-transfer quinone[inner membrane] + 2 H+[periplasm] + H2O `MetaCyc:RXN-11236`	MetaCyc:RXN-11236 Source assertion: The left side contains coefficient 2 of PROTON in CCO-IN. Source location `XPath /ptools-xml/Reaction/left[3]` MetaCyc:PROTON Source assertion: The native PROTON object has InChI InChI=1S/p+1. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:15378 Source assertion: The selected ChEBI structure has the same InChI; formula H, charge 1. Source location `Semantic SQL statements: subject=CHEBI:15378; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
nitrate + an electron-transfer quinol[inner membrane] + 2 H+ nitrite + an electron-transfer quinone[inner membrane] + 2 H+[periplasm] + H2O `MetaCyc:RXN-11236`	produces Coefficient 1; membrane electron-transfer class; side not specified. Native compartmental equation and class identity retained.	an electron-transfer quinone `MetaCyc:ETR-Quinones`	MetaCyc:RXN-11236 Source assertion: The right side contains coefficient 1 of ETR-Quinones; no side compartment is specified. Source location `XPath /ptools-xml/Reaction/right[1]` MetaCyc:ETR-Quinones Source assertion: The issuing native object identifies this whole class as an electron-transfer quinone; no unique molecular formula or sequence is asserted. Source location `XPath /ptools-xml/Compound/common-name`
nitrate + an electron-transfer quinol[inner membrane] + 2 H+ nitrite + an electron-transfer quinone[inner membrane] + 2 H+[periplasm] + H2O `MetaCyc:RXN-11236`	produces Coefficient 2; periplasmic side. Native compartmental equation and class identity retained.	hydron `CHEBI:15378`	MetaCyc:RXN-11236 Source assertion: The right side contains coefficient 2 of PROTON in CCO-OUT. Source location `XPath /ptools-xml/Reaction/right[2]` MetaCyc:PROTON Source assertion: The native PROTON object has InChI InChI=1S/p+1. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:15378 Source assertion: The selected ChEBI structure has the same InChI; formula H, charge 1. Source location `Semantic SQL statements: subject=CHEBI:15378; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
nitrate + an electron-transfer quinol[inner membrane] + 2 H+ nitrite + an electron-transfer quinone[inner membrane] + 2 H+[periplasm] + H2O `MetaCyc:RXN-11236`	produces Coefficient 1; cytoplasmic side. Native compartmental equation and class identity retained.	nitrite `CHEBI:16301`	MetaCyc:RXN-11236 Source assertion: The right side contains coefficient 1 of NITRITE in CCO-IN. Source location `XPath /ptools-xml/Reaction/right[3]` MetaCyc:NITRITE Source assertion: The native NITRITE object has InChI InChI=1S/HNO2/c2-1-3/h(H,2,3)/p-1. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:16301 Source assertion: The selected ChEBI structure has the same InChI; formula NO2, charge -1. Source location `Semantic SQL statements: subject=CHEBI:16301; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
nitrate + an electron-transfer quinol[inner membrane] + 2 H+ nitrite + an electron-transfer quinone[inner membrane] + 2 H+[periplasm] + H2O `MetaCyc:RXN-11236`	produces Coefficient 1; cytoplasmic side. Native compartmental equation and class identity retained.	water `CHEBI:15377`	MetaCyc:RXN-11236 Source assertion: The right side contains coefficient 1 of WATER in CCO-IN. Source location `XPath /ptools-xml/Reaction/right[4]` MetaCyc:WATER Source assertion: The native WATER object has InChI InChI=1S/H2O/h1H2. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:15377 Source assertion: The selected ChEBI structure has the same InChI; formula H2O, charge 0. Source location `Semantic SQL statements: subject=CHEBI:15377; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
nitrate[periplasm] + nitrite[cytosol] -> nitrate[cytosol] + nitrite[periplasm] `MetaCyc:TRANS-RXN0-239`	has_input Coefficient 1; periplasmic side. Native compartmental equation and class identity retained. Formal antiport convention; exact PAO1 mode/catalyst is unassigned, not experimentally established stoichiometry.	nitrate `CHEBI:17632`	MetaCyc:TRANS-RXN0-239 Source assertion: The left side contains coefficient 1 of NITRATE in CCO-OUT. Source location `XPath /ptools-xml/Reaction/left[1]` MetaCyc:NITRATE Source assertion: The native NITRATE object has InChI InChI=1S/NO3/c2-1(3)4/q-1. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:17632 Source assertion: The selected ChEBI structure has the same InChI; formula NO3, charge -1. Source location `Semantic SQL statements: subject=CHEBI:17632; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
nitrate[periplasm] + nitrite[cytosol] -> nitrate[cytosol] + nitrite[periplasm] `MetaCyc:TRANS-RXN0-239`	has_input Coefficient 1; cytoplasmic side. Native compartmental equation and class identity retained. Formal antiport convention; exact PAO1 mode/catalyst is unassigned, not experimentally established stoichiometry.	nitrite `CHEBI:16301`	MetaCyc:TRANS-RXN0-239 Source assertion: The left side contains coefficient 1 of NITRITE in CCO-IN. Source location `XPath /ptools-xml/Reaction/left[2]` MetaCyc:NITRITE Source assertion: The native NITRITE object has InChI InChI=1S/HNO2/c2-1-3/h(H,2,3)/p-1. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:16301 Source assertion: The selected ChEBI structure has the same InChI; formula NO2, charge -1. Source location `Semantic SQL statements: subject=CHEBI:16301; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
nitrate[periplasm] + nitrite[cytosol] -> nitrate[cytosol] + nitrite[periplasm] `MetaCyc:TRANS-RXN0-239`	has_output Coefficient 1; cytoplasmic side. Native compartmental equation and class identity retained. Formal antiport convention; exact PAO1 mode/catalyst is unassigned, not experimentally established stoichiometry.	nitrate `CHEBI:17632`	MetaCyc:TRANS-RXN0-239 Source assertion: The right side contains coefficient 1 of NITRATE in CCO-IN. Source location `XPath /ptools-xml/Reaction/right[1]` MetaCyc:NITRATE Source assertion: The native NITRATE object has InChI InChI=1S/NO3/c2-1(3)4/q-1. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:17632 Source assertion: The selected ChEBI structure has the same InChI; formula NO3, charge -1. Source location `Semantic SQL statements: subject=CHEBI:17632; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
nitrate[periplasm] + nitrite[cytosol] -> nitrate[cytosol] + nitrite[periplasm] `MetaCyc:TRANS-RXN0-239`	has_output Coefficient 1; periplasmic side. Native compartmental equation and class identity retained. Formal antiport convention; exact PAO1 mode/catalyst is unassigned, not experimentally established stoichiometry.	nitrite `CHEBI:16301`	MetaCyc:TRANS-RXN0-239 Source assertion: The right side contains coefficient 1 of NITRITE in CCO-OUT. Source location `XPath /ptools-xml/Reaction/right[2]` MetaCyc:NITRITE Source assertion: The native NITRITE object has InChI InChI=1S/HNO2/c2-1-3/h(H,2,3)/p-1. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:16301 Source assertion: The selected ChEBI structure has the same InChI; formula NO2, charge -1. Source location `Semantic SQL statements: subject=CHEBI:16301; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
nitrite `CHEBI:16301`	consumes Coefficient 1; periplasmic side. Native compartmental equation and class identity retained.	nitrite[periplasm] + a reduced cytochrome c551[periplasm] + 2 H+[periplasm] nitric oxide[periplasm] + an oxidized cytochrome c551[periplasm] + H2O[periplasm] `MetaCyc:RXN-15838`	MetaCyc:RXN-15838 Source assertion: The left side contains coefficient 1 of NITRITE in CCO-OUT. Source location `XPath /ptools-xml/Reaction/left[1]` MetaCyc:NITRITE Source assertion: The native NITRITE object has InChI InChI=1S/HNO2/c2-1-3/h(H,2,3)/p-1. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:16301 Source assertion: The selected ChEBI structure has the same InChI; formula NO2, charge -1. Source location `Semantic SQL statements: subject=CHEBI:16301; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
a reduced cytochrome c551 `MetaCyc:Reduced-cytochromes-c551`	consumes Coefficient 1; periplasmic side. Native compartmental equation and class identity retained.	nitrite[periplasm] + a reduced cytochrome c551[periplasm] + 2 H+[periplasm] nitric oxide[periplasm] + an oxidized cytochrome c551[periplasm] + H2O[periplasm] `MetaCyc:RXN-15838`	MetaCyc:RXN-15838 Source assertion: The left side contains coefficient 1 of Reduced-cytochromes-c551 in CCO-OUT. Source location `XPath /ptools-xml/Reaction/left[2]` MetaCyc:Reduced-cytochromes-c551 Source assertion: The issuing native object identifies this whole class as a reduced cytochrome c551; no unique molecular formula or sequence is asserted. Source location `XPath /ptools-xml/Protein/common-name`
hydron `CHEBI:15378`	consumes Coefficient 2; periplasmic side. Native compartmental equation and class identity retained.	nitrite[periplasm] + a reduced cytochrome c551[periplasm] + 2 H+[periplasm] nitric oxide[periplasm] + an oxidized cytochrome c551[periplasm] + H2O[periplasm] `MetaCyc:RXN-15838`	MetaCyc:RXN-15838 Source assertion: The left side contains coefficient 2 of PROTON in CCO-OUT. Source location `XPath /ptools-xml/Reaction/left[3]` MetaCyc:PROTON Source assertion: The native PROTON object has InChI InChI=1S/p+1. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:15378 Source assertion: The selected ChEBI structure has the same InChI; formula H, charge 1. Source location `Semantic SQL statements: subject=CHEBI:15378; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
nitrite[periplasm] + a reduced cytochrome c551[periplasm] + 2 H+[periplasm] nitric oxide[periplasm] + an oxidized cytochrome c551[periplasm] + H2O[periplasm] `MetaCyc:RXN-15838`	produces Coefficient 1; periplasmic side. Native compartmental equation and class identity retained.	water `CHEBI:15377`	MetaCyc:RXN-15838 Source assertion: The right side contains coefficient 1 of WATER in CCO-OUT. Source location `XPath /ptools-xml/Reaction/right[1]` MetaCyc:WATER Source assertion: The native WATER object has InChI InChI=1S/H2O/h1H2. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:15377 Source assertion: The selected ChEBI structure has the same InChI; formula H2O, charge 0. Source location `Semantic SQL statements: subject=CHEBI:15377; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
nitrite[periplasm] + a reduced cytochrome c551[periplasm] + 2 H+[periplasm] nitric oxide[periplasm] + an oxidized cytochrome c551[periplasm] + H2O[periplasm] `MetaCyc:RXN-15838`	produces Coefficient 1; periplasmic side. Native compartmental equation and class identity retained.	nitric oxide `CHEBI:16480`	MetaCyc:RXN-15838 Source assertion: The right side contains coefficient 1 of NITRIC-OXIDE in CCO-OUT. Source location `XPath /ptools-xml/Reaction/right[2]` MetaCyc:NITRIC-OXIDE Source assertion: The native NITRIC-OXIDE object has InChI InChI=1S/NO/c1-2. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:16480 Source assertion: The selected ChEBI structure has the same InChI; formula NO, charge 0. Source location `Semantic SQL statements: subject=CHEBI:16480; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
nitrite[periplasm] + a reduced cytochrome c551[periplasm] + 2 H+[periplasm] nitric oxide[periplasm] + an oxidized cytochrome c551[periplasm] + H2O[periplasm] `MetaCyc:RXN-15838`	produces Coefficient 1; periplasmic side. Native compartmental equation and class identity retained.	an oxidized cytochrome c551 `MetaCyc:Oxidized-cytochromes-c551`	MetaCyc:RXN-15838 Source assertion: The right side contains coefficient 1 of Oxidized-cytochromes-c551 in CCO-OUT. Source location `XPath /ptools-xml/Reaction/right[3]` MetaCyc:Oxidized-cytochromes-c551 Source assertion: The issuing native object identifies this whole class as an oxidized cytochrome c551; no unique molecular formula or sequence is asserted. Source location `XPath /ptools-xml/Protein/common-name`
a reduced c-type cytochrome `MetaCyc:Cytochromes-C-Reduced`	consumes Coefficient 2; periplasmic side. Native compartmental equation and class identity retained.	2 a reduced c-type cytochrome[periplasm] + 2 nitric oxide[periplasm] + 2 H+[periplasm] -> nitrous oxide[periplasm] + 2 an oxidized c-type cytochrome[periplasm] + H2O[periplasm] `MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN`	MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN Source assertion: The left side contains coefficient 2 of Cytochromes-C-Reduced in CCO-OUT. Source location `XPath /ptools-xml/Reaction/left[1]` MetaCyc:Cytochromes-C-Reduced Source assertion: The issuing native object identifies this whole class as a reduced c-type cytochrome; no unique molecular formula or sequence is asserted. Source location `XPath /ptools-xml/Protein/common-name`
nitric oxide `CHEBI:16480`	consumes Coefficient 2; periplasmic side. Native compartmental equation and class identity retained.	2 a reduced c-type cytochrome[periplasm] + 2 nitric oxide[periplasm] + 2 H+[periplasm] -> nitrous oxide[periplasm] + 2 an oxidized c-type cytochrome[periplasm] + H2O[periplasm] `MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN`	MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN Source assertion: The left side contains coefficient 2 of NITRIC-OXIDE in CCO-OUT. Source location `XPath /ptools-xml/Reaction/left[2]` MetaCyc:NITRIC-OXIDE Source assertion: The native NITRIC-OXIDE object has InChI InChI=1S/NO/c1-2. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:16480 Source assertion: The selected ChEBI structure has the same InChI; formula NO, charge 0. Source location `Semantic SQL statements: subject=CHEBI:16480; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
hydron `CHEBI:15378`	consumes Coefficient 2; periplasmic side. Native compartmental equation and class identity retained.	2 a reduced c-type cytochrome[periplasm] + 2 nitric oxide[periplasm] + 2 H+[periplasm] -> nitrous oxide[periplasm] + 2 an oxidized c-type cytochrome[periplasm] + H2O[periplasm] `MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN`	MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN Source assertion: The left side contains coefficient 2 of PROTON in CCO-OUT. Source location `XPath /ptools-xml/Reaction/left[3]` MetaCyc:PROTON Source assertion: The native PROTON object has InChI InChI=1S/p+1. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:15378 Source assertion: The selected ChEBI structure has the same InChI; formula H, charge 1. Source location `Semantic SQL statements: subject=CHEBI:15378; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
2 a reduced c-type cytochrome[periplasm] + 2 nitric oxide[periplasm] + 2 H+[periplasm] -> nitrous oxide[periplasm] + 2 an oxidized c-type cytochrome[periplasm] + H2O[periplasm] `MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN`	produces Coefficient 1; periplasmic side. Native compartmental equation and class identity retained.	dinitrogen oxide `CHEBI:17045`	MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN Source assertion: The right side contains coefficient 1 of NITROUS-OXIDE in CCO-OUT. Source location `XPath /ptools-xml/Reaction/right[1]` MetaCyc:NITROUS-OXIDE Source assertion: The native NITROUS-OXIDE object has InChI InChI=1S/N2O/c1-2-3. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:17045 Source assertion: The selected ChEBI structure has the same InChI; formula N2O, charge 0. Source location `Semantic SQL statements: subject=CHEBI:17045; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
2 a reduced c-type cytochrome[periplasm] + 2 nitric oxide[periplasm] + 2 H+[periplasm] -> nitrous oxide[periplasm] + 2 an oxidized c-type cytochrome[periplasm] + H2O[periplasm] `MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN`	produces Coefficient 2; periplasmic side. Native compartmental equation and class identity retained.	an oxidized c-type cytochrome `MetaCyc:Cytochromes-C-Oxidized`	MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN Source assertion: The right side contains coefficient 2 of Cytochromes-C-Oxidized in CCO-OUT. Source location `XPath /ptools-xml/Reaction/right[2]` MetaCyc:Cytochromes-C-Oxidized Source assertion: The issuing native object identifies this whole class as an oxidized c-type cytochrome; no unique molecular formula or sequence is asserted. Source location `XPath /ptools-xml/Protein/common-name`
2 a reduced c-type cytochrome[periplasm] + 2 nitric oxide[periplasm] + 2 H+[periplasm] -> nitrous oxide[periplasm] + 2 an oxidized c-type cytochrome[periplasm] + H2O[periplasm] `MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN`	produces Coefficient 1; periplasmic side. Native compartmental equation and class identity retained.	water `CHEBI:15377`	MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN Source assertion: The right side contains coefficient 1 of WATER in CCO-OUT. Source location `XPath /ptools-xml/Reaction/right[3]` MetaCyc:WATER Source assertion: The native WATER object has InChI InChI=1S/H2O/h1H2. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:15377 Source assertion: The selected ChEBI structure has the same InChI; formula H2O, charge 0. Source location `Semantic SQL statements: subject=CHEBI:15377; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
a reduced c-type cytochrome `MetaCyc:Cytochromes-C-Reduced`	consumes Coefficient 2; periplasmic side. Native compartmental equation and class identity retained.	2 a reduced c-type cytochrome[periplasm] + nitrous oxide[periplasm] + 2 H+[periplasm] -> 2 an oxidized c-type cytochrome[periplasm] + N2[periplasm] + H2O[periplasm] `MetaCyc:RXN-12130`	MetaCyc:RXN-12130 Source assertion: The left side contains coefficient 2 of Cytochromes-C-Reduced in CCO-OUT. Source location `XPath /ptools-xml/Reaction/left[1]` MetaCyc:Cytochromes-C-Reduced Source assertion: The issuing native object identifies this whole class as a reduced c-type cytochrome; no unique molecular formula or sequence is asserted. Source location `XPath /ptools-xml/Protein/common-name`
dinitrogen oxide `CHEBI:17045`	consumes Coefficient 1; periplasmic side. Native compartmental equation and class identity retained.	2 a reduced c-type cytochrome[periplasm] + nitrous oxide[periplasm] + 2 H+[periplasm] -> 2 an oxidized c-type cytochrome[periplasm] + N2[periplasm] + H2O[periplasm] `MetaCyc:RXN-12130`	MetaCyc:RXN-12130 Source assertion: The left side contains coefficient 1 of NITROUS-OXIDE in CCO-OUT. Source location `XPath /ptools-xml/Reaction/left[2]` MetaCyc:NITROUS-OXIDE Source assertion: The native NITROUS-OXIDE object has InChI InChI=1S/N2O/c1-2-3. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:17045 Source assertion: The selected ChEBI structure has the same InChI; formula N2O, charge 0. Source location `Semantic SQL statements: subject=CHEBI:17045; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
hydron `CHEBI:15378`	consumes Coefficient 2; periplasmic side. Native compartmental equation and class identity retained.	2 a reduced c-type cytochrome[periplasm] + nitrous oxide[periplasm] + 2 H+[periplasm] -> 2 an oxidized c-type cytochrome[periplasm] + N2[periplasm] + H2O[periplasm] `MetaCyc:RXN-12130`	MetaCyc:RXN-12130 Source assertion: The left side contains coefficient 2 of PROTON in CCO-OUT. Source location `XPath /ptools-xml/Reaction/left[3]` MetaCyc:PROTON Source assertion: The native PROTON object has InChI InChI=1S/p+1. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:15378 Source assertion: The selected ChEBI structure has the same InChI; formula H, charge 1. Source location `Semantic SQL statements: subject=CHEBI:15378; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
2 a reduced c-type cytochrome[periplasm] + nitrous oxide[periplasm] + 2 H+[periplasm] -> 2 an oxidized c-type cytochrome[periplasm] + N2[periplasm] + H2O[periplasm] `MetaCyc:RXN-12130`	produces Coefficient 2; periplasmic side. Native compartmental equation and class identity retained.	an oxidized c-type cytochrome `MetaCyc:Cytochromes-C-Oxidized`	MetaCyc:RXN-12130 Source assertion: The right side contains coefficient 2 of Cytochromes-C-Oxidized in CCO-OUT. Source location `XPath /ptools-xml/Reaction/right[1]` MetaCyc:Cytochromes-C-Oxidized Source assertion: The issuing native object identifies this whole class as an oxidized c-type cytochrome; no unique molecular formula or sequence is asserted. Source location `XPath /ptools-xml/Protein/common-name`
2 a reduced c-type cytochrome[periplasm] + nitrous oxide[periplasm] + 2 H+[periplasm] -> 2 an oxidized c-type cytochrome[periplasm] + N2[periplasm] + H2O[periplasm] `MetaCyc:RXN-12130`	produces Coefficient 1; periplasmic side. Native compartmental equation and class identity retained.	water `CHEBI:15377`	MetaCyc:RXN-12130 Source assertion: The right side contains coefficient 1 of WATER in CCO-OUT. Source location `XPath /ptools-xml/Reaction/right[2]` MetaCyc:WATER Source assertion: The native WATER object has InChI InChI=1S/H2O/h1H2. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:15377 Source assertion: The selected ChEBI structure has the same InChI; formula H2O, charge 0. Source location `Semantic SQL statements: subject=CHEBI:15377; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
2 a reduced c-type cytochrome[periplasm] + nitrous oxide[periplasm] + 2 H+[periplasm] -> 2 an oxidized c-type cytochrome[periplasm] + N2[periplasm] + H2O[periplasm] `MetaCyc:RXN-12130`	produces Coefficient 1; periplasmic side. Native compartmental equation and class identity retained.	dinitrogen `CHEBI:17997`	MetaCyc:RXN-12130 Source assertion: The right side contains coefficient 1 of NITROGEN-MOLECULE in CCO-OUT. Source location `XPath /ptools-xml/Reaction/right[3]` MetaCyc:NITROGEN-MOLECULE Source assertion: The native NITROGEN-MOLECULE object has InChI InChI=1S/N2/c1-2. Source location `XPath /ptools-xml/Compound/inchi` CHEBI:17997 Source assertion: The selected ChEBI structure has the same InChI; formula N2, charge 0. Source location `Semantic SQL statements: subject=CHEBI:17997; chemrof:inchi_string, chemrof:generalized_empirical_formula, chemrof:charge`
nitrate + an electron-transfer quinol[inner membrane] + 2 H+ nitrite + an electron-transfer quinone[inner membrane] + 2 H+[periplasm] + H2O `MetaCyc:RXN-11236`	precedes Source-defined reaction ordering; transport is coupled to nitrate reduction and no exclusive temporal separation or in vivo flux is inferred.	nitrate[periplasm] + nitrite[cytosol] -> nitrate[cytosol] + nitrite[periplasm] `MetaCyc:TRANS-RXN0-239`	MetaCyc:DENITRIFICATION-PWY Source assertion: The reaction-ordering object identifies RXN-11236 as a predecessor of TRANS-RXN0-239. Source location `XPath /ptools-xml/Pathway/reaction-ordering[Reaction/@frameid="TRANS-RXN0-239"]`
nitrate[periplasm] + nitrite[cytosol] -> nitrate[cytosol] + nitrite[periplasm] `MetaCyc:TRANS-RXN0-239`	precedes Source-defined reaction ordering; transport is coupled to nitrate reduction and no exclusive temporal separation or in vivo flux is inferred.	nitrite[periplasm] + a reduced cytochrome c551[periplasm] + 2 H+[periplasm] nitric oxide[periplasm] + an oxidized cytochrome c551[periplasm] + H2O[periplasm] `MetaCyc:RXN-15838`	MetaCyc:DENITRIFICATION-PWY Source assertion: The reaction-ordering object identifies TRANS-RXN0-239 as a predecessor of RXN-15838. Source location `XPath /ptools-xml/Pathway/reaction-ordering[Reaction/@frameid="RXN-15838"]`
nitrite[periplasm] + a reduced cytochrome c551[periplasm] + 2 H+[periplasm] nitric oxide[periplasm] + an oxidized cytochrome c551[periplasm] + H2O[periplasm] `MetaCyc:RXN-15838`	precedes Source-defined reaction ordering; transport is coupled to nitrate reduction and no exclusive temporal separation or in vivo flux is inferred.	2 a reduced c-type cytochrome[periplasm] + 2 nitric oxide[periplasm] + 2 H+[periplasm] -> nitrous oxide[periplasm] + 2 an oxidized c-type cytochrome[periplasm] + H2O[periplasm] `MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN`	MetaCyc:DENITRIFICATION-PWY Source assertion: The reaction-ordering object identifies RXN-15838 as a predecessor of NITRIC-OXIDE-REDUCTASE-RXN. Source location `XPath /ptools-xml/Pathway/reaction-ordering[Reaction/@frameid="NITRIC-OXIDE-REDUCTASE-RXN"]`
2 a reduced c-type cytochrome[periplasm] + 2 nitric oxide[periplasm] + 2 H+[periplasm] -> nitrous oxide[periplasm] + 2 an oxidized c-type cytochrome[periplasm] + H2O[periplasm] `MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN`	precedes Source-defined reaction ordering; transport is coupled to nitrate reduction and no exclusive temporal separation or in vivo flux is inferred.	2 a reduced c-type cytochrome[periplasm] + nitrous oxide[periplasm] + 2 H+[periplasm] -> 2 an oxidized c-type cytochrome[periplasm] + N2[periplasm] + H2O[periplasm] `MetaCyc:RXN-12130`	MetaCyc:DENITRIFICATION-PWY Source assertion: The reaction-ordering object identifies NITRIC-OXIDE-REDUCTASE-RXN as a predecessor of RXN-12130. Source location `XPath /ptools-xml/Pathway/reaction-ordering[Reaction/@frameid="RXN-12130"]`
nitrate reductase (quinone) `UniProtKB:G3XCX1`	enables Gene-product component of the Nar respiratory ensemble, not isolated-subunit catalysis. Current activity is ARBA inference; the source vectorial proton convention is not derived from that chemical-class annotation.	nitrate + an electron-transfer quinol[inner membrane] + 2 H+ nitrite + an electron-transfer quinone[inner membrane] + 2 H+[periplasm] + H2O `MetaCyc:RXN-11236`	UniProtKB:G3XCX1 Source assertion: This current UniProtKB unreviewed (TrEMBL) entry assigns G3XCX1 to taxon 208964, narG / PA3875, with a 1261-residue sequence. It does not establish sequence identity to every historical preparation. Source location `JSON pointer /primaryAccession; /organism/taxonId; /genes; /sequence` UniProtKB:G3XCX1 Source assertion: The unreviewed catalytic annotation cites Rhea 56144 with ECO:0000256 ARBA evidence; it supports the nitrate/quinol reaction class. Source location `JSON pointer /comments/0` PMID:16391109 Source assertion: PAO1 narG mutant showed no nitrate uptake, connecting intracellular nitrite generation with uptake; this is physiological coupling, not a purified subunit assay. Source location `XPath //article/section[2]/section/section[4]/p[3]`
nitrate reductase (quinone) `UniProtKB:G3XD87`	enables Gene-product component of the Nar respiratory ensemble, not isolated-subunit catalysis. Current activity is ARBA inference; the source vectorial proton convention is not derived from that chemical-class annotation.	nitrate + an electron-transfer quinol[inner membrane] + 2 H+ nitrite + an electron-transfer quinone[inner membrane] + 2 H+[periplasm] + H2O `MetaCyc:RXN-11236`	UniProtKB:G3XD87 Source assertion: This current UniProtKB unreviewed (TrEMBL) entry assigns G3XD87 to taxon 208964, narH / PA3874, with a 513-residue sequence. It does not establish sequence identity to every historical preparation. Source location `JSON pointer /primaryAccession; /organism/taxonId; /genes; /sequence` UniProtKB:G3XD87 Source assertion: The unreviewed catalytic annotation cites Rhea 56144 with ECO:0000256 ARBA evidence; it supports the nitrate/quinol reaction class. Source location `JSON pointer /comments/0` PMID:16391109 Source assertion: PAO1 narG mutant showed no nitrate uptake, connecting intracellular nitrite generation with uptake; this is physiological coupling, not a purified subunit assay. Source location `XPath //article/section[2]/section/section[4]/p[3]`
nitrate reductase (quinone) `UniProtKB:G3XD18`	enables Gene-product component of the Nar respiratory ensemble, not isolated-subunit catalysis. Current activity is ARBA inference; the source vectorial proton convention is not derived from that chemical-class annotation.	nitrate + an electron-transfer quinol[inner membrane] + 2 H+ nitrite + an electron-transfer quinone[inner membrane] + 2 H+[periplasm] + H2O `MetaCyc:RXN-11236`	UniProtKB:G3XD18 Source assertion: This current UniProtKB unreviewed (TrEMBL) entry assigns G3XD18 to taxon 208964, narI / PA3872, with a 227-residue sequence. It does not establish sequence identity to every historical preparation. Source location `JSON pointer /primaryAccession; /organism/taxonId; /genes; /sequence` UniProtKB:G3XD18 Source assertion: The unreviewed catalytic annotation cites Rhea 56144 with ECO:0000256 ARBA evidence; it supports the nitrate/quinol reaction class. Source location `JSON pointer /comments/0` PMID:16391109 Source assertion: PAO1 narG mutant showed no nitrate uptake, connecting intracellular nitrite generation with uptake; this is physiological coupling, not a purified subunit assay. Source location `XPath //article/section[2]/section/section[4]/p[3]`
Nitrite reductase `UniProtKB:P24474`	enables Current NirS nitrite-reductase activity with source c551 donor convention; the protein is reported as a homodimer, but no other-species MetaCyc complex ID is transferred.	nitrite[periplasm] + a reduced cytochrome c551[periplasm] + 2 H+[periplasm] nitric oxide[periplasm] + an oxidized cytochrome c551[periplasm] + H2O[periplasm] `MetaCyc:RXN-15838`	UniProtKB:P24474 Source assertion: This current UniProtKB reviewed (Swiss-Prot) entry assigns P24474 to taxon 208964, nirS / PA0519, with a 568-residue sequence. It does not establish sequence identity to every historical preparation. Source location `JSON pointer /primaryAccession; /organism/taxonId; /genes; /sequence` UniProtKB:P24474 Source assertion: The reviewed entry records nitrite-reductase catalytic activity (Rhea 15233) and homodimeric subunit organization. The Rhea class uses generic cytochrome c, broader than native c551. Source location `JSON pointer /comments/0; /comments/4` PMID:25386171 Source assertion: The study distinguishes PAO0001 reporter PAO1 from Holloway PAO1 wild-type and its nirS-N and nosZ deletion mutants; these are physiological strain preparations, not sequence-exact recombinant NirS assays. Source location `XPath /article/body/sec[2]/sec[1]/p[1]`
Nitric oxide reductase subunit B `UniProtKB:Q59647`	enables Subunit function in the NorBC ensemble, not isolated-subunit catalysis. Current NorB proton-pump prose is excluded. RCSB 3O0R PAO1 preparations differ from current sequences (NorB lacks current R301; NorC K100 versus N100), so no exact construct equivalence is asserted.	2 a reduced c-type cytochrome[periplasm] + 2 nitric oxide[periplasm] + 2 H+[periplasm] -> nitrous oxide[periplasm] + 2 an oxidized c-type cytochrome[periplasm] + H2O[periplasm] `MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN`	UniProtKB:Q59647 Source assertion: This current UniProtKB reviewed (Swiss-Prot) entry assigns Q59647 to taxon 208964, norB / PA0524, with a 466-residue sequence. It does not establish sequence identity to every historical preparation. Source location `JSON pointer /primaryAccession; /organism/taxonId; /genes; /sequence` UniProtKB:Q59647 Source assertion: The reviewed entry describes a heterodimer consisting of a large cytochrome b subunit and a small cytochrome c subunit. Source location `JSON pointer /comments/3` UniProtKB:Q59647 Source assertion: The catalytic annotation is Rhea 30211, a cytochrome-c NO/N2O reaction class; reduction proceeds in its reverse direction. Source location `JSON pointer /comments/1` PMID:21109633 Source assertion: The primary abstract reports a P. aeruginosa NOR structure, an FeB center with three His and one Glu ligands, and no D- or K-proton pathway; extracellular proton delivery is proposed. Source location `XPath //result[id="21109633"]/abstractText` DOI:10.2210/pdb3o0r/pdb Source assertion: The mmCIF assigns entity 3, NorB, a 465-residue sequence and natural PAO1 source. Source location `CIF category _entity_poly.; _entity_src_nat.` UniProtKB:Q59647 Source assertion: The inferred FUNCTION annotation (ECO:0000250) states proton-pump activity. This source statement is retained as a conflict and is not adopted as a transport or energy-coupling assertion. Source location `JSON pointer /comments/0` DOI:10.1126/science.1195591 Source assertion: The structural discussion states that no obvious D/K proton-pumping channel or hydrogen-bond network connects cytoplasm and periplasm, consistent with cNOR lacking proton-pumping ability. Source location `Original author-uploaded main article, Science 330 pp.1666–1670 (2010), final structural discussion paragraph beginning “Considering the regions of cNOR”; Figure 4 context; web-inspected text, no local full-text body`
Nitric oxide reductase subunit C `UniProtKB:Q59646`	enables Subunit function in the NorBC ensemble, not isolated-subunit catalysis. Current NorB proton-pump prose is excluded. RCSB 3O0R PAO1 preparations differ from current sequences (NorB lacks current R301; NorC K100 versus N100), so no exact construct equivalence is asserted.	2 a reduced c-type cytochrome[periplasm] + 2 nitric oxide[periplasm] + 2 H+[periplasm] -> nitrous oxide[periplasm] + 2 an oxidized c-type cytochrome[periplasm] + H2O[periplasm] `MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN`	UniProtKB:Q59646 Source assertion: This current UniProtKB reviewed (Swiss-Prot) entry assigns Q59646 to taxon 208964, norC / PA0523, with a 146-residue sequence. It does not establish sequence identity to every historical preparation. Source location `JSON pointer /primaryAccession; /organism/taxonId; /genes; /sequence` UniProtKB:Q59646 Source assertion: The reviewed entry describes a heterodimer consisting of a large cytochrome b subunit and a small cytochrome c subunit. Source location `JSON pointer /comments/1` PMID:21109633 Source assertion: The primary abstract reports a P. aeruginosa NOR structure, an FeB center with three His and one Glu ligands, and no D- or K-proton pathway; extracellular proton delivery is proposed. Source location `XPath //result[id="21109633"]/abstractText` DOI:10.2210/pdb3o0r/pdb Source assertion: The mmCIF assigns entity 4, NorC, a 146-residue sequence including K100 and natural PAO1 source. Source location `CIF category _entity_poly.; _entity_src_nat.`
Nitrous-oxide reductase `UniProtKB:Q9HYL2`	enables NosZ activity is annotated by HAMAP; PAO1 deletion physiology independently supports terminal N2O reduction. Generic c-type electron donor is a source reaction convention, not a uniquely identified physiological partner.	2 a reduced c-type cytochrome[periplasm] + nitrous oxide[periplasm] + 2 H+[periplasm] -> 2 an oxidized c-type cytochrome[periplasm] + N2[periplasm] + H2O[periplasm] `MetaCyc:RXN-12130`	UniProtKB:Q9HYL2 Source assertion: This current UniProtKB reviewed (Swiss-Prot) entry assigns Q9HYL2 to taxon 208964, nosZ / PA3392, with a 636-residue sequence. It does not establish sequence identity to every historical preparation. Source location `JSON pointer /primaryAccession; /organism/taxonId; /genes; /sequence` UniProtKB:Q9HYL2 Source assertion: The entry assigns nitrous-oxide reductase activity (Rhea 43108) using ECO:0000255 HAMAP-Rule MF_00716. Source location `JSON pointer /comments/1` PMID:30093706 Source assertion: The PAO1 nosZ deletion strain accumulates N2O during denitrification; NosZ loss is the engineered physiological block. Source location `XPath /article/body/sec[2]/sec[1]/p[2]` PMID:25386171 Source assertion: The nosZ mutant accumulates N2O under anoxia, whereas wild-type PAO1 produces less than 10 micromolar N2O under the experimental nitrate concentrations. Source location `XPath /article/body/sec[3]/sec[4]/p`
Nitrate/nitrite transporter `UniProtKB:Q9HXD4`	enables Nitrate/nitrite transport contribution to the complete pathway; this edge does not assign strict 1:1 antiport or isolated exact transport stoichiometry. NarK2 has the dominant phenotype and NarK1 a smaller contribution in the tested PAO1 conditions.	`MetaCyc:DENITRIFICATION-PWY`	UniProtKB:Q9HXD4 Source assertion: This current UniProtKB unreviewed (TrEMBL) entry assigns Q9HXD4 to taxon 208964, narK2 / PA3876, with a 468-residue sequence. It does not establish sequence identity to every historical preparation. Source location `JSON pointer /primaryAccession; /organism/taxonId; /genes; /sequence` PMID:16391109 Source assertion: PAO1 narK1 deletion only slightly affected anaerobic growth, while narK2 and double deletion were severely compromised; all mutants retained nitrate-reductase activity. Source location `XPath //article/section[2]/section/section[4]/p[2]` PMID:16391109 Source assertion: The authors explicitly leave antiport versus uniport experimentally unresolved. Source location `XPath //article/section[2]/section/section[4]/p[5]`
Nitrite extrusion protein 1 `UniProtKB:G3XD60`	enables Nitrate/nitrite transport contribution to the complete pathway; this edge does not assign strict 1:1 antiport or isolated exact transport stoichiometry. NarK2 has the dominant phenotype and NarK1 a smaller contribution in the tested PAO1 conditions.	`MetaCyc:DENITRIFICATION-PWY`	UniProtKB:G3XD60 Source assertion: This current UniProtKB unreviewed (TrEMBL) entry assigns G3XD60 to taxon 208964, narK1 / PA3877, with a 431-residue sequence. It does not establish sequence identity to every historical preparation. Source location `JSON pointer /primaryAccession; /organism/taxonId; /genes; /sequence` PMID:16391109 Source assertion: PAO1 narK1 deletion only slightly affected anaerobic growth, while narK2 and double deletion were severely compromised; all mutants retained nitrate-reductase activity. Source location `XPath //article/section[2]/section/section[4]/p[2]` PMID:16391109 Source assertion: The authors explicitly leave antiport versus uniport experimentally unresolved. Source location `XPath //article/section[2]/section/section[4]/p[5]`
Cytochrome c-551 `UniProtKB:P00099`	enables NirM electron-donor contribution to nitrite reduction, not catalytic nitrite-reductase assignment. The whole c551 redox classes remain distinct from the sequence entry.	nitrite[periplasm] + a reduced cytochrome c551[periplasm] + 2 H+[periplasm] nitric oxide[periplasm] + an oxidized cytochrome c551[periplasm] + H2O[periplasm] `MetaCyc:RXN-15838`	UniProtKB:P00099 Source assertion: This current UniProtKB reviewed (Swiss-Prot) entry assigns P00099 to taxon 208964, nirM / PA0518, with a 104-residue sequence. It does not establish sequence identity to every historical preparation. Source location `JSON pointer /primaryAccession; /organism/taxonId; /genes; /sequence` UniProtKB:P00099 Source assertion: The reviewed entry identifies cytochrome c-551 as an electron donor for cytochrome cd1 in nitrite and nitrate respiration. Source location `JSON pointer /comments/0`
nitrate reductase (quinone) `UniProtKB:G3XCX1`	has_cofactor Current entry annotation of Mo-bisMGD; ECO:0000256 ARBA. Issuing cofactor-state identifier is retained without asserting a fixed redox state throughout catalysis or direct measurement in every PAO1 preparation.	Mo(=O)-bis(molybdopterin guanine dinucleotide)(4-) `CHEBI:60539`	UniProtKB:G3XCX1 Source assertion: The exact annotation records Mo-bisMGD with ECO:0000256 ARBA; the selected ChEBI cofactor identifier is the entry-assigned ligand identity. Source location `JSON pointer /comments/1`
nitrate reductase (quinone) `UniProtKB:G3XCX1`	has_cofactor Current entry annotation of [4Fe-4S]; ECO:0000256 ARBA. Issuing cofactor-state identifier is retained without asserting a fixed redox state throughout catalysis or direct measurement in every PAO1 preparation.	tetra-mu3-sulfido-tetrairon `CHEBI:49883`	UniProtKB:G3XCX1 Source assertion: The exact annotation records [4Fe-4S] with ECO:0000256 ARBA; the selected ChEBI cofactor identifier is the entry-assigned ligand identity. Source location `JSON pointer /comments/2`
nitrate reductase (quinone) `UniProtKB:G3XD87`	has_cofactor Current entry annotation of [3Fe-4S]; ECO:0000256 ARBA. Issuing cofactor-state identifier is retained without asserting a fixed redox state throughout catalysis or direct measurement in every PAO1 preparation.	tri-mu-sulfido-mu3-sulfido-triiron `CHEBI:21137`	UniProtKB:G3XD87 Source assertion: The exact annotation records [3Fe-4S] with ECO:0000256 ARBA; the selected ChEBI cofactor identifier is the entry-assigned ligand identity. Source location `JSON pointer /comments/1`
nitrate reductase (quinone) `UniProtKB:G3XD87`	has_cofactor Current entry annotation of [4Fe-4S]; ECO:0000256 ARBA. Issuing cofactor-state identifier is retained without asserting a fixed redox state throughout catalysis or direct measurement in every PAO1 preparation.	tetra-mu3-sulfido-tetrairon `CHEBI:49883`	UniProtKB:G3XD87 Source assertion: The exact annotation records [4Fe-4S] with ECO:0000256 ARBA; the selected ChEBI cofactor identifier is the entry-assigned ligand identity. Source location `JSON pointer /comments/2`
nitrate reductase (quinone) `UniProtKB:G3XD18`	has_cofactor Current entry annotation of heme b; ECO:0000256 PIRSR. Issuing cofactor-state identifier is retained without asserting a fixed redox state throughout catalysis or direct measurement in every PAO1 preparation.	ferroheme b(2-) `CHEBI:60344`	UniProtKB:G3XD18 Source assertion: The exact annotation records heme b with ECO:0000256 PIRSR; the selected ChEBI cofactor identifier is the entry-assigned ligand identity. Source location `JSON pointer /features/6`
Nitrite reductase `UniProtKB:P24474`	has_cofactor Current entry annotation of heme c; ECO:0000269 PMID9331415. Issuing cofactor-state identifier is retained without asserting a fixed redox state throughout catalysis or direct measurement in every PAO1 preparation.	ferroheme c(2-) `CHEBI:61717`	UniProtKB:P24474 Source assertion: The exact annotation records heme c with ECO:0000269 PMID9331415; the selected ChEBI cofactor identifier is the entry-assigned ligand identity. Source location `JSON pointer /comments/2`
Nitrite reductase `UniProtKB:P24474`	has_cofactor Current entry annotation of heme d1; ECO:0000269 PMID9331415 and PDB mapping. Issuing cofactor-state identifier is retained without asserting a fixed redox state throughout catalysis or direct measurement in every PAO1 preparation.	ferroheme d1(4-) `CHEBI:60549`	UniProtKB:P24474 Source assertion: The exact annotation records heme d1 with ECO:0000269 PMID9331415 and PDB mapping; the selected ChEBI cofactor identifier is the entry-assigned ligand identity. Source location `JSON pointer /features/11`
Nitric oxide reductase subunit B `UniProtKB:Q59647`	has_cofactor Current entry annotation of heme b; ECO:0000305 curator inference. Issuing cofactor-state identifier is retained without asserting a fixed redox state throughout catalysis or direct measurement in every PAO1 preparation.	ferroheme b(2-) `CHEBI:60344`	UniProtKB:Q59647 Source assertion: The exact annotation records heme b with ECO:0000305 curator inference; the selected ChEBI cofactor identifier is the entry-assigned ligand identity. Source location `JSON pointer /features/13`
Nitric oxide reductase subunit B `UniProtKB:Q59647`	has_cofactor Current entry annotation of non-heme Fe cation; ECO:0000305 curator inference. Issuing cofactor-state identifier is retained without asserting a fixed redox state throughout catalysis or direct measurement in every PAO1 preparation.	iron cation `CHEBI:24875`	UniProtKB:Q59647 Source assertion: The exact annotation records non-heme Fe cation with ECO:0000305 curator inference; the selected ChEBI cofactor identifier is the entry-assigned ligand identity. Source location `JSON pointer /features/14`
Nitric oxide reductase subunit C `UniProtKB:Q59646`	has_cofactor Current entry annotation of heme c; ECO:0000255 PROSITE. Issuing cofactor-state identifier is retained without asserting a fixed redox state throughout catalysis or direct measurement in every PAO1 preparation.	ferroheme c(2-) `CHEBI:61717`	UniProtKB:Q59646 Source assertion: The exact annotation records heme c with ECO:0000255 PROSITE; the selected ChEBI cofactor identifier is the entry-assigned ligand identity. Source location `JSON pointer /features/3`
Nitrous-oxide reductase `UniProtKB:Q9HYL2`	has_cofactor Current entry annotation of CuA binuclear copper center; ECO:0000255 HAMAP. Issuing cofactor-state identifier is retained without asserting a fixed redox state throughout catalysis or direct measurement in every PAO1 preparation.	binuclear copper ion `CHEBI:47357`	UniProtKB:Q9HYL2 Source assertion: The exact annotation records CuA binuclear copper center with ECO:0000255 HAMAP; the selected ChEBI cofactor identifier is the entry-assigned ligand identity. Source location `JSON pointer /comments/2`
Nitrous-oxide reductase `UniProtKB:Q9HYL2`	has_cofactor Current entry annotation of CuZ [4Cu-S] cluster; ECO:0000255 HAMAP. Issuing cofactor-state identifier is retained without asserting a fixed redox state throughout catalysis or direct measurement in every PAO1 preparation.	mu4-sulfido-quadro-tetracopper `CHEBI:33730`	UniProtKB:Q9HYL2 Source assertion: The exact annotation records CuZ [4Cu-S] cluster with ECO:0000255 HAMAP; the selected ChEBI cofactor identifier is the entry-assigned ligand identity. Source location `JSON pointer /comments/3`
Nitrous-oxide reductase `UniProtKB:Q9HYL2`	has_cofactor Current entry annotation of Ca2+; ECO:0000255 HAMAP. Issuing cofactor-state identifier is retained without asserting a fixed redox state throughout catalysis or direct measurement in every PAO1 preparation.	calcium(2+) `CHEBI:29108`	UniProtKB:Q9HYL2 Source assertion: The exact annotation records Ca2+ with ECO:0000255 HAMAP; the selected ChEBI cofactor identifier is the entry-assigned ligand identity. Source location `JSON pointer /comments/4`
Cytochrome c-551 `UniProtKB:P00099`	has_cofactor Covalently attached heme c; the whole redox carrier is retained separately. Current heme annotation does not assert a permanently reduced in vivo state.	ferroheme c(2-) `CHEBI:61717`	UniProtKB:P00099 Source assertion: The entry states that one heme c group is covalently bound per subunit. Source location `JSON pointer /comments/3` UniProtKB:P00099 Source assertion: The current cytochrome c-551 heme-binding feature assigns CHEBI:61717. Source location `JSON pointer /features/2`
Transcriptional activator protein anr `UniProtKB:P23926`	regulates Expression-level regulatory support under tested PAO1 nitrate/anaerobic conditions; no direct catalytic activation/inhibition or IHF CHA-A2 strain transfer is inferred.	`MetaCyc:DENITRIFICATION-PWY`	UniProtKB:P23926 Source assertion: This current UniProtKB reviewed (Swiss-Prot) entry assigns P23926 to taxon 208964, anr / PA1544, with a 244-residue sequence. It does not establish sequence identity to every historical preparation. Source location `JSON pointer /primaryAccession; /organism/taxonId; /genes; /sequence` PMID:17400734 Source assertion: Anr is essential for anaerobic narK1 promoter activity; promoter motif mutation and complementation support the expression effect. Source location `XPath //article/section[2]/section/section[4]/p[position() >= 1 and position() <= 2]`
Transcriptional regulator Dnr `UniProtKB:G3XCW6`	regulates Expression-level regulatory support under tested PAO1 nitrate/anaerobic conditions; no direct catalytic activation/inhibition or IHF CHA-A2 strain transfer is inferred.	`MetaCyc:DENITRIFICATION-PWY`	UniProtKB:G3XCW6 Source assertion: This current UniProtKB unreviewed (TrEMBL) entry assigns G3XCW6 to taxon 208964, dnr / PA0527, with a 227-residue sequence. It does not establish sequence identity to every historical preparation. Source location `JSON pointer /primaryAccession; /organism/taxonId; /genes; /sequence` PMID:17400734 Source assertion: Dnr deletion decreases anaerobic narK1 promoter activity and complementation supports an enhancing expression role. Source location `XPath //article/section[2]/section/section[4]/p[1]`
Two-component response regulator NarL `UniProtKB:Q9HXD3`	regulates Expression-level regulatory support under tested PAO1 nitrate/anaerobic conditions; no direct catalytic activation/inhibition or IHF CHA-A2 strain transfer is inferred.	`MetaCyc:DENITRIFICATION-PWY`	UniProtKB:Q9HXD3 Source assertion: This current UniProtKB unreviewed (TrEMBL) entry assigns Q9HXD3 to taxon 208964, narL / PA3879, with a 219-residue sequence. It does not establish sequence identity to every historical preparation. Source location `JSON pointer /primaryAccession; /organism/taxonId; /genes; /sequence` PMID:17400734 Source assertion: NarL deletion lowers narK1 promoter activity, complementation nearly restores it, and selected promoter-site mutations abolish reporter activity. Source location `XPath //article/section[2]/section/section[4]/p[2]`
Nitrite reductase `UniProtKB:P24474`	located_in Current entry localization; inferred/rule-based scope remains as in the cited source. Membrane role does not itself demonstrate proton pumping.	periplasmic space `GO:0042597`	UniProtKB:P24474 Source assertion: The subcellular-location annotation places the protein in the periplasm. Source location `JSON pointer /comments/5`
Nitric oxide reductase subunit B `UniProtKB:Q59647`	located_in Current entry localization; inferred/rule-based scope remains as in the cited source. Membrane role does not itself demonstrate proton pumping.	plasma membrane `GO:0005886`	UniProtKB:Q59647 Source assertion: The subcellular-location annotation places the protein in the cell/inner membrane. Source location `JSON pointer /comments/4`
Nitric oxide reductase subunit C `UniProtKB:Q59646`	located_in Current entry localization; inferred/rule-based scope remains as in the cited source. Membrane role does not itself demonstrate proton pumping.	plasma membrane `GO:0005886`	UniProtKB:Q59646 Source assertion: The subcellular-location annotation places the protein in the cell/inner membrane. Source location `JSON pointer /comments/2`
Nitrous-oxide reductase `UniProtKB:Q9HYL2`	located_in Current entry localization; inferred/rule-based scope remains as in the cited source. Membrane role does not itself demonstrate proton pumping.	periplasmic space `GO:0042597`	UniProtKB:Q9HYL2 Source assertion: The subcellular-location annotation places the protein in the periplasm. Source location `JSON pointer /comments/7`
nitrate reductase (quinone) `UniProtKB:G3XCX1`	located_in Current entry localization; inferred/rule-based scope remains as in the cited source. Membrane role does not itself demonstrate proton pumping.	plasma membrane `GO:0005886`	UniProtKB:G3XCX1 Source assertion: The subcellular-location annotation places the protein in the cell/inner membrane. Source location `JSON pointer /comments/3`
nitrate reductase (quinone) `UniProtKB:G3XD87`	located_in Current entry localization; inferred/rule-based scope remains as in the cited source. Membrane role does not itself demonstrate proton pumping.	plasma membrane `GO:0005886`	UniProtKB:G3XD87 Source assertion: The subcellular-location annotation places the protein in the cell/inner membrane. Source location `JSON pointer /comments/4`
nitrate reductase (quinone) `UniProtKB:G3XD18`	located_in Current entry localization; inferred/rule-based scope remains as in the cited source. Membrane role does not itself demonstrate proton pumping.	plasma membrane `GO:0005886`	UniProtKB:G3XD18 Source assertion: The subcellular-location annotation places the protein in the cell/inner membrane. Source location `JSON pointer /comments/3`
Nitrate/nitrite transporter `UniProtKB:Q9HXD4`	located_in Current entry localization; inferred/rule-based scope remains as in the cited source. Membrane role does not itself demonstrate proton pumping.	plasma membrane `GO:0005886`	UniProtKB:Q9HXD4 Source assertion: The subcellular-location annotation places the protein in the cell/inner membrane. Source location `JSON pointer /comments/0`
Nitrite extrusion protein 1 `UniProtKB:G3XD60`	located_in Generic membrane localization and multipass topology are inferred by ARBA (ECO:0000256). The current entry does not specify the inner/plasma membrane; no direct localization assay or proton-pumping role is inferred.	membrane `GO:0016020`	UniProtKB:G3XD60 Source assertion: The entry annotates Membrane and Multi-pass membrane protein with ECO:0000256 ARBA00004141. Its GO cross-reference is GO:0016020 membrane, with IEA:UniProtKB-SubCell; this does not specify the inner/plasma membrane. Source location `JSON pointer /comments/0; /uniProtKBCrossReferences/18` GO:0016020 Source assertion: The issuing active GO cellular-component term is membrane, defined as a lipid bilayer with embedded or attached proteins and complexes. This generic term does not assert plasma-membrane specificity. Source location `Semantic SQL statements: subject=GO:0016020; rdfs:label, IAO:0000115, oio:hasOBONamespace`
Cytochrome c-551 `UniProtKB:P00099`	located_in Current entry localization; inferred/rule-based scope remains as in the cited source. Membrane role does not itself demonstrate proton pumping.	periplasmic space `GO:0042597`	UniProtKB:P00099 Source assertion: The subcellular-location annotation places the protein in the periplasm. Source location `JSON pointer /comments/2`

References

MetaCyc:DENITRIFICATION-PWY nitrate reduction I (denitrification) (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:RXN-11236 RXN-11236 (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:TRANS-RXN0-239 nitrate:nitrite antiport (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:RXN-15838 RXN-15838 (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:NITRIC-OXIDE-REDUCTASE-RXN NITRIC-OXIDE-REDUCTASE-RXN (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:RXN-12130 RXN-12130 (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:ETR-Quinols an electron-transfer quinol (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:ETR-Quinones an electron-transfer quinone (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:Reduced-cytochromes-c551 a reduced cytochrome c551 (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:Oxidized-cytochromes-c551 an oxidized cytochrome c551 (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:Cytochromes-C-Reduced a reduced c-type cytochrome (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:Cytochromes-C-Oxidized an oxidized c-type cytochrome (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:NITRATE nitrate (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:NITRITE nitrite (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:NITRIC-OXIDE nitric oxide (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:NITROUS-OXIDE nitrous oxide (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:NITROGEN-MOLECULE N2 (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:WATER H2O (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:PROTON H+ (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
CHEBI:17632 nitrate (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:16301 nitrite (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:16480 nitric oxide (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:17045 dinitrogen oxide (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:17997 dinitrogen (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:15377 water (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:15378 hydron (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:60539 Mo(=O)-bis(molybdopterin guanine dinucleotide)(4-) (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:49883 tetra-mu3-sulfido-tetrairon (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:21137 tri-mu-sulfido-mu3-sulfido-triiron (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:61717 ferroheme c(2-) (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:60549 ferroheme d1(4-) (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:60344 ferroheme b(2-) (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:24875 iron cation (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:47357 binuclear copper ion (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:33730 mu4-sulfido-quadro-tetracopper (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
CHEBI:29108 calcium(2+) (source version: ChEBI 255; SHA256 covers original complete uncompressed Semantic SQL database)
UniProtKB:G3XCX1 nitrate reductase (quinone) (source version: Original UniProt JSON retrieved 2026-10-11; UniProtKB unreviewed (TrEMBL); entryAudit {"entryVersion": 84, "firstPublicDate": "2011-11-16", "lastAnnotationUpdateDate": "2026-09-02", "lastSequenceUpdateDate": "2011-11-16", "sequenceVersion": 1})
UniProtKB:G3XD87 nitrate reductase (quinone) (source version: Original UniProt JSON retrieved 2026-10-11; UniProtKB unreviewed (TrEMBL); entryAudit {"entryVersion": 67, "firstPublicDate": "2011-11-16", "lastAnnotationUpdateDate": "2026-09-02", "lastSequenceUpdateDate": "2011-11-16", "sequenceVersion": 1})
UniProtKB:G3XD18 nitrate reductase (quinone) (source version: Original UniProt JSON retrieved 2026-10-11; UniProtKB unreviewed (TrEMBL); entryAudit {"entryVersion": 66, "firstPublicDate": "2011-11-16", "lastAnnotationUpdateDate": "2026-09-02", "lastSequenceUpdateDate": "2011-11-16", "sequenceVersion": 1})
UniProtKB:P24474 Nitrite reductase (source version: Original UniProt JSON retrieved 2026-10-11; UniProtKB reviewed (Swiss-Prot); entryAudit {"entryVersion": 177, "firstPublicDate": "1992-03-01", "lastAnnotationUpdateDate": "2026-09-02", "lastSequenceUpdateDate": "1992-03-01", "sequenceVersion": 1})
UniProtKB:Q59647 Nitric oxide reductase subunit B (source version: Original UniProt JSON retrieved 2026-10-11; UniProtKB reviewed (Swiss-Prot); entryAudit {"entryVersion": 155, "firstPublicDate": "1997-11-01", "lastAnnotationUpdateDate": "2026-09-02", "lastSequenceUpdateDate": "1996-11-01", "sequenceVersion": 1})
UniProtKB:Q59646 Nitric oxide reductase subunit C (source version: Original UniProt JSON retrieved 2026-10-11; UniProtKB reviewed (Swiss-Prot); entryAudit {"entryVersion": 160, "firstPublicDate": "1998-12-15", "lastAnnotationUpdateDate": "2026-09-02", "lastSequenceUpdateDate": "2007-01-23", "sequenceVersion": 3})
UniProtKB:Q9HYL2 Nitrous-oxide reductase (source version: Original UniProt JSON retrieved 2026-10-11; UniProtKB reviewed (Swiss-Prot); entryAudit {"entryVersion": 150, "firstPublicDate": "2001-01-11", "lastAnnotationUpdateDate": "2026-06-10", "lastSequenceUpdateDate": "2001-01-11", "sequenceVersion": 1})
UniProtKB:Q9HXD4 Nitrate/nitrite transporter (source version: Original UniProt JSON retrieved 2026-10-11; UniProtKB unreviewed (TrEMBL); entryAudit {"entryVersion": 117, "firstPublicDate": "2001-03-01", "lastAnnotationUpdateDate": "2026-09-02", "lastSequenceUpdateDate": "2001-03-01", "sequenceVersion": 1})
UniProtKB:G3XD60 Nitrite extrusion protein 1 (source version: Original UniProt JSON retrieved 2026-10-11; UniProtKB unreviewed (TrEMBL); entryAudit {"entryVersion": 66, "firstPublicDate": "2011-11-16", "lastAnnotationUpdateDate": "2026-09-02", "lastSequenceUpdateDate": "2011-11-16", "sequenceVersion": 1})
UniProtKB:P00099 Cytochrome c-551 (source version: Original UniProt JSON retrieved 2026-10-11; UniProtKB reviewed (Swiss-Prot); entryAudit {"entryVersion": 175, "firstPublicDate": "1986-07-21", "lastAnnotationUpdateDate": "2026-09-02", "lastSequenceUpdateDate": "1990-04-01", "sequenceVersion": 2})
UniProtKB:P23926 Transcriptional activator protein anr (source version: Original UniProt JSON retrieved 2026-10-11; UniProtKB reviewed (Swiss-Prot); entryAudit {"entryVersion": 152, "firstPublicDate": "1992-03-01", "lastAnnotationUpdateDate": "2026-09-02", "lastSequenceUpdateDate": "1992-03-01", "sequenceVersion": 1})
UniProtKB:G3XCW6 Transcriptional regulator Dnr (source version: Original UniProt JSON retrieved 2026-10-11; UniProtKB unreviewed (TrEMBL); entryAudit {"entryVersion": 85, "firstPublicDate": "2011-11-16", "lastAnnotationUpdateDate": "2026-09-02", "lastSequenceUpdateDate": "2011-11-16", "sequenceVersion": 1})
UniProtKB:Q9HXD3 Two-component response regulator NarL (source version: Original UniProt JSON retrieved 2026-10-11; UniProtKB unreviewed (TrEMBL); entryAudit {"entryVersion": 152, "firstPublicDate": "2001-03-01", "lastAnnotationUpdateDate": "2026-09-02", "lastSequenceUpdateDate": "2001-03-01", "sequenceVersion": 1})
PMID:16391109 Involvement of NarK1 and NarK2 Proteins in Transport of Nitrate and Nitrite in the Denitrifying Bacterium Pseudomonas aeruginosa PAO1 (source version: Original PMC primary HTML; full article inspected; retrieved 2026-10-11)
PMID:17400734 The Anaerobic Regulatory Network Required for Pseudomonas aeruginosa Nitrate Respiration (source version: Original PMC primary HTML; full article inspected; retrieved 2026-10-11)
PMID:19935885 Compensatory periplasmic nitrate reductase activity supports anaerobic growth of Pseudomonas aeruginosa PAO1 in the absence of membrane nitrate reductase (source version: Original PMC primary HTML; full article inspected; retrieved 2026-10-11)
PMID:7768875 Anaerobic activation of the entire denitrification pathway in Pseudomonas aeruginosa requires Anr, an analog of Fnr (source version: Original PMC primary HTML; abstract/scanned article page, no full scanned text extraction; retrieved 2026-10-11)
PMID:3937493 Inability of Pseudomonas stutzeri denitrification mutants with the phenotype of Pseudomonas aeruginosa to grow in nitrous oxide (source version: Original PMC primary HTML; abstract/scanned article page, no full scanned text extraction; retrieved 2026-10-11)
PMID:30093706 Significant enhancement of nitrous oxide energy yields from wastewater achieved by bioaugmentation with a recombinant strain of Pseudomonas aeruginosa (source version: Original full primary JATS from Europe PMC; retrieved 2026-10-11)
PMID:25386171 Physiological levels of nitrate support anoxic growth by denitrification of Pseudomonas aeruginosa at growth rates reported in cystic fibrosis lungs and sputum (source version: Original full primary JATS from Europe PMC; retrieved 2026-10-11)
PMID:9331415 N-terminal arm exchange is observed in the 2.15 A crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa. (source version: Original Europe PMC indexed primary abstract/metadata; not full article)
PMID:21109633 Structural basis of biological N2O generation by bacterial nitric oxide reductase. (source version: Original Europe PMC indexed primary abstract/metadata; not full article)
PMID:7711073 The structural genes for nitric oxide reductase from Pseudomonas aeruginosa. (source version: Original Europe PMC indexed primary abstract/metadata; not full article)
PMID:15504726 NO reduction by nitric-oxide reductase from denitrifying bacterium Pseudomonas aeruginosa: characterization of reaction intermediates that appear in the single turnover cycle. (source version: Original Europe PMC indexed primary abstract/metadata; not full article)
PMID:9308169 In vivo studies disprove an obligatory role of azurin in denitrification in Pseudomonas aeruginosa and show that azu expression is under control of rpoS and ANR. (source version: Original Europe PMC indexed primary abstract/metadata; not full article)
DOI:10.1126/science.1195591 Structural Basis of Biological N2O Generation by Bacterial Nitric Oxide Reductase (source version: Original author-uploaded main article inspected through web on 2026-10-11; publisher PDF/SI returned 403 and author download failed; no local full-text digest claimed)
MetaCyc:CPLX-7502 respiratory nitrate reductase (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:CPLX-1701 CPLX-1701 (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:CPLX-1741 nitric oxide reductase (cytochrome c) (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:CPLX-1742 nitrous oxide reductase (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:CPLX-8362 nitric oxide reductase (cytochrome c) (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:CPLX-8528 nitric oxide reductase (cytochrome c) (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:CPLX-8529 nitric oxide reductase (cytochrome c) (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:CPLX-9429 nitrous-oxide reductase (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
MetaCyc:CPLX-1964 hydroxylamine oxidoreductase (source version: Original MetaCyc 27.0 XML; Pathway Tools 27.0; retrieved 2026-10-11; direct object scope)
DOI:10.2210/pdb3o0r/pdb Crystal structure of nitric oxide reductase from Pseudomonas aeruginosa in complex with antibody fragment (source version: Original complete PDB mmCIF; revision 2.0, 2026-08-12; source natural PAO1, sequence differences retained)
GO:0016020 membrane (source version: GO 2026-07-26; SHA256 covers original complete uncompressed Semantic SQL database)

Curation history

2026-10-11T18:47:09Z claude-code
- CREATE — Add the complete native nitrate reduction I denitrification pathway
  Add MetaCyc:DENITRIFICATION-PWY with all five native objects, qualified nitrate/nitrite exchange, PAO1 context,39 participants,75 edges,156 evidence blocks and73 references. Preserve carrier specificity, compartments, transport-mode uncertainty, historical preparations and sequence differences, inferred cofactor/assembly tiers and source conflicts. The full original external scientific review and independent correction review support exact target7c5b3ca9. Anr source locator and NarK1 membrane-scope corrections are adopted. Current corpus gates, integration replay and canonical scientific review follow. Dossier: research/pathway_additions/2026-10-11-next-219.
Read this curation session
2026-10-11T18:56:50Z codex
- EDIT — Correct actor attribution for denitrification curation history
  Correct only the actor attribution in these three immutable history records: history/records/nitrate-reduction-i-denitrification/2026-10-11T184709Z-claude-code-b1b993.yaml; history/infrastructure/denitrification-authorities-and-review-evidence/2026-10-11T184711Z-claude-code-7226e8.yaml; history/infrastructure/denitrification-authorities-and-review-evidence/2026-10-11T184713Z-claude-code-7cc0a1.yaml. Their actor.name claude-code came from the scaffolder default because the structured invocation omitted --actor-name, despite correctly recording agent_tool codex. Codex performed all three changes. Preserve the original history bytes and their factual contents; this successor supplies the correct actor. Target7c5b3ca9, active helper70387ce2, original evidence and all scientific conclusions remain unchanged. Full initial render, validation, tests, lint and KGX gates completed successfully before this correction; rerender and full validation follow for the added history, with unchanged input hashes binding reuse of tests, lint and KGX.
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