nirK2 encodes a second predicted copper-containing nitrite reductase in Rhodopseudomonas palustris CGA009. The UniProt/GOA profile supports NO-forming nitrite reductase activity; organism-level evidence supports nitrite reduction and NOx metabolism in CGA009, even though a dissimilatory nitrate reductase was not evident in the cited genome survey.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005507 copper ion binding | IEA GO_REF:0000002 | ACCEPT | Summary: ACCEPT. Copper binding is expected for a copper-containing nitrite reductase. Reason: nirK2 has the same conserved copper nitrite reductase architecture as bacterial NirK enzymes, including NO2-reductase_Cu/cupredoxin signatures and type 1 copper-site features. Falcon recovered RPA4145/nirK2 in comparative NirK literature but no purified nirK2 metal biochemistry. Supporting Evidence: file:RHOPA/nirK2/nirK2-uniprot.txt InterPro; IPR001287; NO2-reductase_Cu. file:RHOPA/nirK2/nirK2-deep-research-falcon.md Comparative NirK analyses include R. palustris CGA009 nirK2/RPA4145 with conserved copper-nitrite-reductase motifs. |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000118 | KEEP AS NON CORE | Summary: KEEP_AS_NON_CORE. The annotation is correct but less informative than the specific nitrite reductase activity. Reason: Oxidoreductase activity is a true parent for the nitrite reductase reaction, but GO:0050421 captures the specific molecular function and should be treated as the core activity. Supporting Evidence: file:RHOPA/nirK2/nirK2-uniprot.txt RecName: Full=Copper-containing nitrite reductase; EC=1.7.2.1. |
| GO:0042597 periplasmic space | IEA GO_REF:0000044 | ACCEPT | Summary: ACCEPT. NirK-family nitrite reductases are periplasmic enzymes. Reason: UniProt predicts periplasmic localization and a signal peptide, consistent with exported bacterial copper nitrite reductase biology. Supporting Evidence: file:RHOPA/nirK2/nirK2-uniprot.txt SUBCELLULAR LOCATION: Periplasm. file:RHOPA/nirK2/nirK2-uniprot.txt SIGNAL 1..26 |
| GO:0050421 nitrite reductase (NO-forming) activity | IEA GO_REF:0000120 | ACCEPT | Summary: ACCEPT. This specific molecular function is consistent with the copper-containing nitrite reductase assignment. Reason: This is the precise EC-supported activity for the predicted enzyme. UniProt assigns EC 1.7.2.1 and both NCBIfam and PANTHER place the sequence in conserved multicopper/copper nitrite reductase families. The broad PTHR11709 family is functionally diverse, so the specific activity is justified by EC 1.7.2.1 plus TIGR02376/NO2-reductase_Cu rather than by multicopper oxidase membership alone. Falcon adds organism-level support: CGA009 cells grown with nitrite show detectable nitrite reductase activity and taxis toward nitrite, although those data are not a purified nirK2 assay. Supporting Evidence: file:RHOPA/nirK2/nirK2-uniprot.txt RecName: Full=Copper-containing nitrite reductase; EC=1.7.2.1. file:RHOPA/nirK2/nirK2-uniprot.txt NCBIfam; TIGR02376; Cu_nitrite_red; 1. file:interpro/panther/PTHR11709/PTHR11709-deep-research-falcon.md PTHR11709 family research found multicopper oxidases are functionally diverse, so substrate-specific nitrite reductase activity requires specific EC/clade evidence. file:RHOPA/nirK2/nirK2-deep-research-falcon.md R. palustris CGA009 encodes nitrite reductase and NO-reductase genes, and nitrite-grown cells show detectable nitrite reductase activity, supporting physiological NO-forming nitrite reduction capacity. |
| GO:0019333 denitrification pathway | IEA GO_REF:0000041 | ACCEPT | Summary: ACCEPT. UniPathway adds appropriate denitrification-pathway context for a NO-forming nitrite reductase. Reason: NO-forming nitrite reductase activity is the denitrification nitrite-to-NO step. The evidence is conserved EC/family inference plus UniProt pathway mapping. Falcon adds an important boundary: CGA009 encodes nitrite reductase and NO-reductase genes but lacked an obvious dissimilatory nitrate reductase in the cited genome survey, so this should be read as step-level denitrification/NOx pathway context rather than proof of a full nitrate-to-N2 route from nitrate. Supporting Evidence: file:RHOPA/nirK2/nirK2-uniprot.txt PATHWAY: Nitrogen metabolism; nitrate reduction (denitrification); dinitrogen from nitrate: step 2/4. file:RHOPA/nirK2/nirK2-deep-research-falcon.md CGA009 genome information indicates nitrite reductase and nitric oxide reductase capacity but no obvious dissimilatory nitrate reductase, supporting a nitrite/NOx segment rather than overclaiming complete nitrate respiration. |
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