MTBC Gene Atlas

Rv0679c Family assigned · low

H37Rv Rv0679c · MTBC0 mtbc0_000718 · 165 aa · 783629–784126 (-) · RefSeq NP_215193.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationDUF3060 domain-containing protein
Revised (this work)Membrane protein (16.6 kDa) of the cell envelope implicated in host-cell invasion; a dimorphic antigen carrying a Beijing-genotype-specific Asn142Lys polymorphism with distinct antibody responses. Rv0679c-derived peptides bind A549/U937 cells and TLR2/TLR4 and inhibit bacillary entry, suggesting a role in invasion (Zhao 2017). Molecular function unfixed.

Curated reference (UniProt)

UniProt I6WZ30 TrEMBL · unreviewed · Evidence at protein level
UniProt nameConserved threonine rich protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category S Function unknown
eggNOG descriptionProtein of unknown function (DUF3060)
Orthologous group295VX

Orthology-based transfer (eggNOG 5.0.2, diamond). EC/KO/GO/CAZy are computed annotations, not manual curation; cross-check against the primary literature before treating a specific reaction as established.

Conservation & selection (intra-MTBC, 145 209 strains)

pN/pS 0.56 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 2 synonymous, 3 missense, 0 nonsense, 0 frameshift

pN/pS from segregating SNPs (singletons removed) normalised by possible sites. Low pN/pS = purifying selection (a strong signal that a "hypothetical" is a real, constrained gene). A high pN/pS is ambiguous: relaxed constraint or positive selection (drug resistance, antigenic variation) inflate it; e.g. rpoB/katG/pncA score high here for resistance, not loss of function. A clonal disruption (one allele over a clade) suggests lineage pseudogenisation; a convergent one (many independent alleles) is typical of resistance loss-of-function.

Domains (Pfam, hmmscan --cut_ga)

PfamAccessioni-EvalueResiduesDescription
DUF3060PF11259.14 9.1e-22101–159 Protein of unknown function (DUF3060)

Functional interaction network (STRING v12, guilt-by-association)

Closest characterised functional partner: Rv0680c (transmembrane protein), high confidence from genomic context alone (score 970 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.

PartnerProductScoreNo text-miningChannels (≥400)
Rv0680c transmembrane protein 970 970 ctx neighborhood:882 coexpression:759
Rv0681 transcriptional regulator 688 688 ctx neighborhood:679

STRING combines evidence channels (neighborhood, fusion, cooccurrence, coexpression, experimental, database, text-mining) into a 0–1000 score. The ctx badge marks edges carried by the genomic-context channels (conserved neighborhood, fusion, phylogenetic co-occurrence), which are independent of orthology and structure and the strongest signal for an unknown gene. The no text-mining column recomputes the score from data alone, so a link that does not depend on the literature is visible. Association is a function hypothesis, not proof: corroborate with the operon context and the primary literature before assigning a function.

Evidence

  • Membrane protein; invasion-inhibiting binding peptides; dimorphic Beijing N142K antigen (Zhao 2017, PMID 28506215)
  • Curated from the literature crible (project 'Still unknown gene function', 2026-06-09)

Sources

  • Ancestral sequence & coordinates: Harrison LB et al. (2024), An imputed ancestral reference genome for the MTBC, doi:10.1101/2023.09.07.556366
  • Product annotation: NCBI PGAP on MTBC0; legacy from H37Rv NC_000962.3 (RefSeq NP_215193.1)
  • Domains: Pfam-A via hmmscan --cut_ga — DUF3060 (PF11259.14)
  • Sequence-level signal: ESM Atlas (EvolutionaryScale × BioHub) — exploratory
  • Controlled vocabulary: eggNOG-mapper 2.1.12 (Cantalapiedra et al. 2021, doi:10.1093/molbev/msab293), eggNOG 5.0 DB (Huerta-Cepas et al. 2019) — OG 295VX
  • Curated reference: UniProt I6WZ30 (TrEMBL, unreviewed; Evidence at protein level)
  • Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
  • Model confidence: ESMFold per-residue pLDDT (mean 88.3, confident)
  • Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 2 functional partner(s); context anchor Rv0680c
  • Primary literature: Zhao J, Matsuba T, Zhang X, Leano S, Nakajima C, Chagan-Yasutan H, Telan EF, Suzuki Y, Hattori T (2017). Comparison of antibody responses against Mycobacterium tuberculosis antigen Rv0679c in tuberculosis patients from the endemic and non-endemic regions of the Beijing genotype: a case control study BMC Infect Dis 17(1):344. doi:10.1186/s12879-017-2442-5 PMID:28506215

Ancestral MTBC0 protein sequence

>mtbc0_000718|Rv0679c|
MVEKPLRADRATHSRLATFALALAAAALPLAGCSSTANPPAATTTPATATTTTATSGPTAAPTVTTGESTTASIQIGDMLTYGSIGTTATLDCADGKSLNVAGSDNTLTVNGTCETVTVGGANNKIAFDRIDERLVVVGLDNTVTYKNGDPTIDNLGAGNRINKE