Curation Notes: tonB (A0A0H2M2E3 / VPARA_25820) in Variovorax paradoxus TBEA6

1. Gene & Protein Identity

• UniProt Accession: A0A0H2M2E3 (A0A0H2M2E3_VARPD, unreviewed TrEMBL, 232 aa)
• Gene Symbol / Locus Tag: tonB / VPARA_25820
• Organism: Variovorax paradoxus strain TBEA6 (NCBITaxon:34073)
• Genomic Neighborhood: Encoded on contig JZWI01000012 (KLN56276.1) immediately upstream of the outer-membrane TonB-dependent ferric-siderophore receptor bfrD1 (VPARA_25830, KLN56277.1, A0A0H2M677) [UniProtKB:A0A0H2M2E3, "DE SubName: Full=Gram-negative bacterial tonB protein {ECO:0000313|EMBL:KLN56276.1};"].
• Domain Architecture:
• Residues 18–35: N-terminal inner-membrane transmembrane helix (SAM:Phobius)
• Residues 58–143: Proline-rich periplasmic linker (COMPBIAS Pro residues at 59–87 and 95–135)
• Residues 140–232: C-terminal globular TonB domain (PROSITE:PS52015, Pfam:PF03544, InterPro:IPR037682, TIGR01352).

2. Pathway Context & Module Linkage

• Pathway Module: modules/bacterial_tonb_siderophore_import.yaml (MODULE:bacterial_tonb_siderophore_import).
• Role in Module: Step 1 inner-membrane proton-motive-force energy transducer (tonB) within the TonB–ExbB–ExbD complex (GO:0098797), extending across the periplasm (GO:0030288) to engage the TonB box of outer-membrane TonB-dependent ferric-siderophore receptors such as bfrD1 (VPARA_25830) [PMID:20420522, "The C-terminal domain of TonB (residues ~150-239 in E. coli) crosses the periplasm to bind the TonB box of ligand-loaded TBDTs, mechanically pulling or partially unfolding the plug domain to open a translocation channel for the ferric-siderophore across the outer membrane."].

3. Review of Existing GOA Annotations

• GO:0031992 (energy transducer activity, IEA) -> ACCEPT: Core molecular function.
• GO:0005886 (plasma membrane, IEA) -> ACCEPT: Anchored in the bacterial inner membrane via residues 18–35.
• GO:0030288 (outer membrane-bounded periplasmic space, IEA) -> ACCEPT: Spans the periplasm via its proline-rich linker (58–143) and C-terminal domain (140–232).
• GO:0098797 (plasma membrane protein complex, IEA) -> ACCEPT: Part of the inner-membrane TonB–ExbB–ExbD complex.
• GO:0055085 (transmembrane transport, IEA) -> MODIFY to GO:0015891 (siderophore transport) + NEW (IC): Refined to reflect the specific role of the VPARA_25820–VPARA_25830 (tonB–bfrD1) locus in energizing outer-membrane ferric-siderophore import.
• GO:0015031 (protein transport, IEA via UniRule:UR001806740) -> REMOVE: Automated UniRule over-mapping resulting from colicin/phage parasitism of enteric TonB; physiologically TonB energizes small-molecule nutrient/siderophore import rather than protein translocation.