Curation Notes for ssuC5 (VPARA_09240, A0A0H2M6G6) in Variovorax paradoxus TBEA6

1. Gene & Protein Overview

• UniProtKB Accession: A0A0H2M6G6 (A0A0H2M6G6_VARPD, unreviewed, 284 aa, 29,638 Da)
• Gene Symbol / Locus Tag: ssuC5 / VPARA_09240 (EMBL:KLN57913.1 on genomic contig JZWI01000005, RefSeq:WP_021006428.1)
• Organism: Variovorax paradoxus strain TBEA6 (NCBITaxon:34073)
• Genomic Context: Encoded on contig JZWI01000005 immediately downstream of ssuB2 (VPARA_09230, KLN57912.1) and immediately upstream of ssuD (VPARA_09250, KLN57914.1), with ssuA2 (VPARA_09270, KLN57916.1) and ssuE (VPARA_09290, KLN57918.1) in the same cluster.
• Domain Architecture & Topology:
• Five Phobius-predicted transmembrane alpha-helices at residues 34..56, 91..114, 126..144, 150..169, and 245..264 (FT TRANSMEM).
• ABC transporter transmembrane type-1 domain (PROSITE:PS50928, Pfam:PF00528, InterPro:IPR000515, residues 80..264).
• Family classification: NCBIfam:NF008470 (SsuC, aliphatic sulfonates ABC transporter permease SsuC), PANTHER:PTHR30151:SF38 (ALIPHATIC SULFONATES TRANSPORT PERMEASE PROTEIN SSUC-RELATED).

2. Literature & Comparative Evidence

• PMID:10781534(https://pubmed.ncbi.nlm.nih.gov/10781534/) (Eichhorn, van der Ploeg & Leisinger 2000, J Bacteriol 182:2687-2695): Established that ssuABC encodes the aliphatic sulfonate ABC importer in E. coli, whose components are not functionally exchangeable with tauABC.
• PMID:10781557(https://pubmed.ncbi.nlm.nih.gov/10781557/) (Kahnert et al. 2000, J Bacteriol 182:2869-2878): Characterized the ssuEADCBF operon in P. putida S-313, identifying ssuC as the integral membrane permease component of the ABC-type sulfonate importer.

3. Review of Existing GOA Annotations (5 IEA rows)

1. GO:0005886 (plasma membrane, located_in, IEA GO_REF:0000120 from UniProtKB-SubCell:SL-0037, PANTHER:PTN001319101, UniRule:UR000083623) -> ACCEPT:
2. Core subcellular localization of the 5-TM integral inner-membrane permease (PROSITE:PS50928, PROSITE-ProRule:PRU00441).
3. GO:0016020 (membrane, located_in, IEA GO_REF:0000120 from PROSITE-ProRule:PRU00441, InterPro:IPR000515, UniProtKB-SubCell:SL-0162) -> TOO_GENERAL:
4. True but uninformative parent cellular component already entailed by the accepted specific annotation GO:0005886 (plasma membrane).
5. GO:0022857 (transmembrane transporter activity, enables, IEA GO_REF:0000104 from UniRule:UR000083623) -> MARK_AS_OVER_ANNOTATED:
6. Following the PSEPK/ssuC comparator convention, SsuC5 is the transmembrane channel subunit of a multi-subunit binding-protein-dependent ABC importer (GO:0055052) and cannot catalyze ATP-driven alkanesulfonate import independently of the periplasmic binding subunit SsuA2 and the ATPase subunit SsuB2. Its contribution to complex-level GO:0042959 (ABC-type alkanesulfonate transporter transporter activity) is recorded via contributes_to_molecular_function in core_functions.
7. GO:0055085 (transmembrane transport, involved_in, IEA GO_REF:0000120 from PROSITE-ProRule:PRU00441, PANTHER:PTN001319101) -> MODIFY to GO:0042918 (alkanesulfonate transmembrane transport):
8. GO:0055085 is true but general; membership in NCBIfam:NF008470 (SsuC) and PANTHER:PTHR30151:SF38 (ALIPHATIC SULFONATES TRANSPORT PERMEASE PROTEIN SSUC-RELATED) and syntenic placement between ssuB2 (VPARA_09230, KLN57912.1) and ssuD (VPARA_09250, KLN57914.1) on contig JZWI01000005 support refinement to GO:0042918 (alkanesulfonate transmembrane transport).
9. GO:0058024 (sulfonate transmembrane transporter activity, enables, IEA GO_REF:0000118 from PANTHER:PTN001319101) -> MARK_AS_OVER_ANNOTATED:
10. As with GO:0022857, an isolated SsuC5 permease subunit does not have standalone transporter activity outside the intact SsuABC complex; its contribution is captured via contributes_to_molecular_function (GO:0042959) on the GO:0055052 complex.

4. Proposed New Annotations

• GO:0055052 (ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing, part_of, IC from file:VARPD/ssuC5/ssuC5-uniprot.txt) -> NEW:
• SsuC5 (VPARA_09240, KLN57913.1) forms the transmembrane translocation pathway of the substrate-binding-subunit-containing SsuABC importer complex (GO:0055052) with ssuB2 (VPARA_09230, KLN57912.1) and ssuA2 (VPARA_09270, KLN57916.1).