fdnI

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005886 plasma membrane	IBA GO_REF:0000033	ACCEPT	Summary: IBA plasma membrane from E. coli FdnI/FdoI/HybB seeds. Reason: FdnI has four transmembrane helices and is the membrane anchor of the FDH complex, purified from a membrane particle fraction. Supporting Evidence: file:PSEAE/fdnI/fdnI-uniprot.txt TRANSMEM 21..41 PMID:3038081 The separation of the FDH enzyme from nitrate reductase (NiR), which are found together in a particle fraction and constitute the short respiratory chain of this bacterium
GO:0005886 plasma membrane	IEA GO_REF:0000120	ACCEPT	Summary: Plasma membrane from combined automated annotation. Reason: Same claim as the IBA row; four predicted transmembrane helices. Supporting Evidence: file:PSEAE/fdnI/fdnI-uniprot.txt TRANSMEM 21..41
GO:0008863 formate dehydrogenase (NAD+) activity	IEA GO_REF:0000002	REMOVE	Summary: InterPro2GO NAD+-dependent formate dehydrogenase activity from the gamma-subunit signature. Reason: FdnI is the membrane cytochrome b subunit of a quinone-linked respiratory FDH; it neither binds NAD+ nor belongs to an NAD+-dependent formate dehydrogenase. The IPR006471 (formate dehydrogenase gamma subunit) mapping to the NAD+ term is wrong for this family. Supporting Evidence: file:PSEAE/fdnI/fdnI-uniprot.txt NCBIfam; TIGR01583; formate-DH-gamm; 1. PMID:3038081 The separation of the FDH enzyme from nitrate reductase (NiR), which are found together in a particle fraction and constitute the short respiratory chain of this bacterium
GO:0009055 electron transfer activity	IEA GO_REF:0000002	ACCEPT	Summary: Electron transfer activity from the cytochrome b561 domain signature. Reason: The cytochrome b subunit passes electrons from FdnH through its haems to quinone; this is its subunit-level function. E. coli FdnI carries the term by IDA. Supporting Evidence: file:PSEAE/fdnI/fdnI-uniprot.txt Pfam; PF01292; Ni_hydr_CYTB; 1. PMID:3038081 In its purest state FDH contains one molecule of cytochrome co-ordinated by two histidine ligands in the oxidized state.
GO:0009061 anaerobic respiration	IBA GO_REF:0000033	ACCEPT	Summary: IBA anaerobic respiration. Reason: FdnI is the quinone-reducing subunit of the formate-to-nitrate respiratory chain made during anaerobic growth on nitrate. Supporting Evidence: PMID:3038081 The purification of formate dehydrogenase (FDH) from Pseudomonas aeruginosa after anaerobic growth on nitrate-containing medium was carried out.
GO:0009326 formate dehydrogenase complex	IBA GO_REF:0000033	ACCEPT	Summary: IBA formate dehydrogenase complex. Reason: FdnI is the gamma subunit of FdnGHI; the purified P. aeruginosa FDH retains one bis-histidine cytochrome, the haem of this subunit type. Supporting Evidence: PMID:3038081 In its purest state FDH contains one molecule of cytochrome co-ordinated by two histidine ligands in the oxidized state.
GO:0009326 formate dehydrogenase complex	IEA GO_REF:0000002	ACCEPT	Summary: InterPro2GO formate dehydrogenase complex. Reason: Same claim as the IBA row. Supporting Evidence: file:PSEAE/fdnI/fdnI-uniprot.txt NCBIfam; TIGR01583; formate-DH-gamm; 1.
GO:0015944 formate oxidation	IBA GO_REF:0000033	ACCEPT	Summary: IBA formate oxidation. Reason: FdnI provides the terminal electron acceptor step (quinone reduction) of respiratory formate oxidation by the complex. Supporting Evidence: PMID:3038081 The separation of the FDH enzyme from nitrate reductase (NiR), which are found together in a particle fraction and constitute the short respiratory chain of this bacterium
GO:0016020 membrane	IEA GO_REF:0000002	MODIFY	Summary: Generic membrane location. Reason: Correct but general; the specific location is the cytoplasmic (plasma) membrane, which the gene already carries (GO:0005886). Proposed replacements: plasma membrane Supporting Evidence: file:PSEAE/fdnI/fdnI-uniprot.txt TRANSMEM 21..41
GO:0022904 respiratory electron transport chain	IEA GO_REF:0000002	ACCEPT	Summary: Respiratory electron transport chain from the di-haem cytochrome TM signature. Reason: FdnI transfers electrons into the quinone pool of the formate-to-nitrate respiratory chain. Supporting Evidence: PMID:3038081 The separation of the FDH enzyme from nitrate reductase (NiR), which are found together in a particle fraction and constitute the short respiratory chain of this bacterium
GO:0036397 formate dehydrogenase (quinone) activity	IBA GO_REF:0000033	ACCEPT	Summary: IBA from PTN001247840 (FdnI/FdoI clade, 2 seeds, 14 leaf IBAs). Seeds are E. coli FdnI (P0AEK7, IDA PMID:1099093) and this gene (PseudoCAP IDA, PMID:3038081). Reason: The complex-level activity is annotated to the gamma subunits on the same convention as for E. coli FdnI, and the IBD stands on the E. coli seed alone. FdnI contributes the quinone-reduction step; core_functions records this with contributes_to_molecular_function. Supporting Evidence: PMID:3038081 The separation of the FDH enzyme from nitrate reductase (NiR), which are found together in a particle fraction and constitute the short respiratory chain of this bacterium
GO:0036397 formate dehydrogenase (quinone) activity	IDA PMID:3038081 Purification and properties of formate dehydrogenase from Ps...	ACCEPT	Summary: PseudoCAP IDA, the seed row for PTN001247840 (GO:0036397) and PTN001247839 (GO:0016491). Activity of the purified FDH complex, which retained one bis-histidine cytochrome b. Reason: Seed verdict SOUND as a complex-level activity: a biochemical assay of purified FDH, not an operon mutant phenotype, annotated to each subunit as EcoCyc does for E. coli FdnGHI. The paper predates gene assignments and I read only the abstract; attribution rests on fdnGHI being the only FDH-N-type cluster in PAO1 and on the cytochrome b signature. Supporting Evidence: PMID:3038081 In its purest state FDH contains one molecule of cytochrome co-ordinated by two histidine ligands in the oxidized state.
GO:0045333 cellular respiration	IEA GO_REF:0000002	TOO GENERAL	Summary: Cellular respiration from the gamma-subunit signature. Reason: True but uninformative; GO:0009061 anaerobic respiration, accepted in this review, is an is_a descendant of GO:0045333.
GO:0020037 heme binding	ISS file:PSEAE/fdnI/fdnI-uniprot.txt	NEW	Summary: Proposed cofactor binding. FdnI is a di-haem cytochrome b of the Ni_hydr_CYTB family, the purified FDH contains a bis-histidine b-type haem, and E. coli FdnI binds haem (IDA). Reason: Haem binding is the structural basis of the subunit's electron-transfer function and is not otherwise annotated. Supporting Evidence: file:PSEAE/fdnI/fdnI-uniprot.txt InterPro; IPR016174; Di-haem_cyt_TM. PMID:3038081 In its purest state FDH contains one molecule of cytochrome co-ordinated by two histidine ligands in the oxidized state.