MTBC Gene Atlas

Rv3209 Family assigned · medium auto-curated

H37Rv Rv3209 · MTBC0 mtbc0_003415 · 186 aa · 3608415–3608975 (+) · RefSeq NP_217725.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationMmpS family transport accessory protein
Revised (this work)MmpS family transport accessory protein. Pfam: Mycobact_memb (PF05423.19).

Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.

Curated reference (UniProt)

UniProt O05857 TrEMBL · unreviewed · Inferred from homology
UniProt nameConserved hypothetical threonine and proline rich protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

Orthologous group2A3D5

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 1.587 · diversifying/relaxed
Polymorphic sites (≥ 0.1% of strains) 1 synonymous, 4 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
Mycobact_membPF05423.19 4.0e-0591–169 Mycobacterium membrane protein

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv3717 hyp hypothetical protein 804 804 coexpression:804
Rv2154c ftsW lipid II flippase FtsW 793 793 coexpression:793
Rv3096 hyp hypothetical protein 730 730 coexpression:730
Rv2894c xerC tyrosine recombinase XerC 729 729 coexpression:729
Rv0063 oxidoreductase 716 716 coexpression:716
Rv3208A TB9.4 hyp hypothetical protein 705 706 ctx neighborhood:704
Rv3267 lcp1 hyp hypothetical protein 422 423 coexpression:423

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

  • Legacy H37Rv annotation: hypothetical protein
  • MTBC0 PGAP product: MmpS family transport accessory protein
  • Pfam (hmmscan --cut_ga): Mycobact_memb PF05423.19 (E=4e-05)
  • (auto-curated by rules from PGAP + Pfam + Foldseek; not hand-reviewed)

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_217725.1)
  • Domains: Pfam-A via hmmscan --cut_ga — Mycobact_memb (PF05423.19)
  • 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 2A3D5
  • Curated reference: UniProt O05857 (TrEMBL, unreviewed; Inferred from homology)
  • Intra-MTBC selection: pN/pS and disruption from SPDI variants of 145 209 MTBC strains (this work, local collection vs H37Rv NC_000962.3)
  • Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 7 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_003415|Rv3209|
MALGAVATAVIINSGDSTSTKAIVGAPAPRTVISTSPRPTAPTSTSPHPSPSTLRPQLPPETVTTVAPPGTGPTTVPTRTPTAAPPQTAVPPPAPLNPRTVVYRVTGTKQLFDLVNVVYTDARGFPVTDFNVSLPWTKMVVLNPGVQTESVVATSLYSRLNCSIVNTGAQTVVASTNNAIIATCTR