TraB is a structural subunit of the outer-membrane core complex of the F-type type IV secretion system, encoded on the F plasmid and on the related IncFII plasmid ColB2 rather than on the chromosome. It is the VirB10 counterpart of that machine. In the cryo-EM structure of an F-family core complex, TraB forms the central cone as a seventeen-fold symmetrical ring of beta-barrels, seated inside an outer ring built from TraK and TraV; the cone is the passage through which the machine's substrate and its pilus reach the cell surface. TraB is required for assembly of the F pilus, the extracellular filament that establishes contact with a recipient cell, and so for conjugative transfer. Its role is architectural: it holds the core complex together across the symmetry mismatch between the outer ring and the cone, and it contributes no catalytic activity of its own.
The preferred accession for this review is P41067. These relationships are manually assessed.
Reviewed 2026-10-19 Β· Searched: UP000000625
Retain P41067 as the primary Swiss-Prot accession. No significant reference-proteome hit was returned. The reviewed entry explicitly cites F and ColB2 plasmids, making accessory-replicon differences relevant. The negative result applies to the searched reference proteome, not all E. coli strains or plasmids.
MMseqs2 searched 4,403 sequences across UP000000625 at E <= 1e-5 and sensitivity 7.5, returning 0 hits. The search table and candidate FASTA are empty; no alignments were generated. The heuristic search does not establish genomic absence or unique locus identity.
file:ECOLI/traB/traB-record-evidence.yaml
target_sequence_count: 4403
file:ECOLI/traB/traB-record-evidence.yaml
candidate_count: 0
The primary accession is outside every searched exact-taxon reference proteome.
file:ECOLI/traB/traB-record-evidence.yaml
primary_in_any_reference_proteome: false
Sampled UniSave observations: 16-SEP-2015, entry version 71.: no Proteomes cross-reference; 12-AUG-2020, entry version 85.: no Proteomes cross-reference; 27-NOV-2024, entry version 97.: no Proteomes cross-reference. These dated observations do not establish uninterrupted membership/absence, the exact change date, or UniProt's motivation.
file:ECOLI/traB/traB-record-evidence.yaml
entry_date: 16-SEP-2015, entry version 71. proteomes: []
file:ECOLI/traB/traB-record-evidence.yaml
entry_date: 12-AUG-2020, entry version 85. proteomes: []
file:ECOLI/traB/traB-record-evidence.yaml
entry_date: 27-NOV-2024, entry version 97. proteomes: []
The primary UniProt entry records plasmid origin. Reference-proteome membership at species or strain level does not ensure coverage of every accessory plasmid.
file:ECOLI/traB/traB-record-evidence.yaml
geneEncodingType: Plasmid
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0016887 ATP hydrolysis activity | IDA PMID:20172994 Biochemical dissection of the ATPase TraB, the VirB4 homolog... | REMOVE | Summary: This annotation is attributed to the wrong protein. The cited paper characterizes the VirB4 homologue of the pKM101 conjugation system, which its abstract states outright, and that protein has its own UniProt entry (Q46698, 866 aa, TrbE/VirB4 family). P41067 is the 475 aa TraB of plasmid F and ColB2, assigned by UniProt to the TraB family, and the F plasmid's own VirB4-family ATPase is a different gene product, TraC (P18004). The structural evidence for P41067 places it in the outer-membrane core complex as the central-cone beta-barrel subunit, a role with no ATPase activity. The collision is nomenclatural: on pKM101 the symbol TraB names the protein that on F is called TraC. Reason: Removal here is not second-guessing an assay whose full text is unavailable, which is the case that calls for UNDECIDED. The cached abstract explicitly names the plasmid and the protein family, which is the condition under which a reference-scope objection is warranted, and four independent facts separate the two proteins: plasmid of origin, protein family, length, and the fact that F already assigns the VirB4-family role to TraC. Retaining the annotation would give a structural subunit a catalytic activity that no experiment on it supports, and would leave the F-type core complex looking as though it contained two VirB4-family ATPases. An independent OpenScientist function-assignment run reached the same conclusion from sequence: P41067 is in the VirB10/TraB/TrbI family and lacks a Walker-A motif, so it cannot hydrolyse ATP. Supporting Evidence: PMID:20172994 Biochemical dissection of the ATPase TraB, the VirB4 homologue of the Escherichia coli pKM101 conjugation machinery. file:ECOLI/traB/traB-hypotheses/function-hypothesis-go-0016887/openscientist.md P41067 lacks a Walker-A / P-loop motif |
| GO:0005198 structural molecule activity | ISS PMID:35046412 Structure of a type IV secretion system core complex encoded... | NEW | Summary: The cryo-EM structure of an F-family outer-membrane core complex resolves TraB as a seventeen-fold ring of beta-barrels forming the central cone, with no catalytic role. A structural molecular function is the accurate description of what this protein does. Reason: Proposed rather than asserted from a direct assay on this polypeptide. The structure was solved for pED208, an F-family plasmid, so the evidence code is ISS rather than IDA. The protein currently has no correct molecular function annotation at all, its one GOA row being an ATPase activity attributed from a different plasmid's protein, so this fills a real gap rather than adding a redundant term. |
| GO:0043684 type IV secretion system complex | ISS PMID:35046412 Structure of a type IV secretion system core complex encoded... | NEW | Summary: TraB is one of the three proteins that build the F-type outer-membrane core complex, contributing the central cone within the TraK and TraV outer ring. Reason: Complex membership is read directly off the solved architecture of the F-family core complex. ISS rather than IDA because the structure is of a homolog from a related F-family plasmid, not of this polypeptide. |
| GO:0009279 cell outer membrane | ISS PMID:35046412 Structure of a type IV secretion system core complex encoded... | NEW | Summary: The structure places TraB's beta-barrels in the outer-membrane core complex. No subcellular location is currently annotated for this protein from any source. Reason: Proposed conservatively and as the only location asserted. VirB10-family proteins are generally also anchored in the inner membrane, but no F-specific experiment establishes that for this protein, so a second location is left for the suggested experiments rather than annotated here. |
| GO:0044097 secretion by the type IV secretion system | ISS PMID:35046412 Structure of a type IV secretion system core complex encoded... | NEW | Summary: TraB's domains are functionally important to the F-type secretion system, and it contributes the cone through which the machine reaches the surface. Reason: The cargo-agnostic parent term is used deliberately in preference to GO:0009291 unidirectional conjugation. The structural evidence supports TraB's participation in the secretion machinery; attributing the conjugation outcome to it would need F-specific mutant data, which is raised as a question instead. |
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Download this section (compressed HTML)Q: Should GO:0009297 pilus assembly be annotated to F TraB? UniProt states that the protein is involved in F pilus assembly, but GOA carries no biological process annotation for it at all, so the statement has never been captured.
Q: Does F TraB span both membranes? The core-complex structure places its beta-barrels in the outer membrane, while VirB10-family proteins are generally anchored in the inner membrane and reach the outer one. No subcellular location is annotated for P41067 from an F-specific experiment.
Q: How many other GOA rows on conjugative plasmid gene products have been attributed across plasmids because Tra symbols are reused? This annotation was found by checking one protein; the same collision pattern could affect others, TraC and TraB on F and pKM101 being the clearest pair.
Experiment: Test directly whether purified F TraB (P41067) hydrolyses ATP, under both the membrane-derived and soluble preparations that gave different answers for the pKM101 VirB4 homologue. A negative result on the F protein would close the question this review had to settle by sequence and family argument alone.
Experiment: Determine the subcellular topology of F TraB by protease accessibility or fractionation in an F-plasmid-bearing K-12 strain, to establish whether it is anchored in the inner membrane as VirB10-family proteins are while contributing beta-barrels to the outer-membrane cone.
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