MTBC Gene Atlas

virS Family assigned · medium auto-curated

H37Rv Rv3082c · MTBC0 mtbc0_003276 · 340 aa · 3468768–3469790 (-) · RefSeq NP_217598.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)HTH-type transcriptional regulator VirS
MTBC0 PGAP re-annotationAraC family transcriptional regulator
Revised (this work)AraC family transcriptional regulator. Pfam: Arabinose_bd (PF12625.13), HTH_18 (PF12833.14), HTH_AraC (PF00165.30).

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

Curated reference (UniProt)

UniProt P9WMJ3 SwissProt · reviewed · Evidence at protein level
UniProt nameHTH-type transcriptional regulator VirS
Curated functionRegulates the expression of the mymA operon (Rv3083-Rv3089).

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category K Transcription
Preferred namevirS
eggNOG descriptionTranscriptional regulatory protein (Probably AraC XylS-family)
Orthologous groupCOG2207
Gene Ontology (89) GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006081, GO:0006082, GO:0006089, GO:0006355, GO:0008150 +77 more

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 0.494 · purifying
Polymorphic sites (≥ 0.1% of strains) 5 synonymous, 7 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
Arabinose_bdPF12625.13 5.8e-4023–207 Arabinose-binding domain of AraC transcription regulator, N-term
HTH_18PF12833.14 6.9e-18256–333 Helix-turn-helix domain
HTH_AraCPF00165.30 6.9e-06300–332 Bacterial regulatory helix-turn-helix proteins, AraC family

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv1931c transcriptional regulator 888 883 coexpression:831
Rv1190 hyp hypothetical protein 858 858 coexpression:839
Rv1267c embR transcriptional regulator EmbR 857 857 coexpression:857
Rv3167c TetR family transcriptional regulator 883 848 coexpression:848
Rv1674c transcriptional regulator 853 845 coexpression:841
Rv3736 AraC/XylS family transcriptional regulator 839 839 coexpression:805
Rv1189 sigI ECF RNA polymerase sigma factor SigI 844 838 coexpression:804
Rv1675c cmr HTH-type transcriptional regulator Cmr 837 831 coexpression:831
Rv0887c hyp hypothetical protein 829 830 coexpression:796
Rv3840 transcriptional regulator 827 827 coexpression:827
Rv0603 hyp hypothetical protein 827 827 coexpression:827
Rv0602c tcrA two component DNA binding transcriptional regulator TcrA 832 826 coexpression:826
Rv0494 HTH-type transcriptional regulator 827 826 coexpression:826
Rv1151c cobB NAD-dependent protein deacylase 833 823 coexpression:817
Rv1167c transcriptional regulator 826 823 coexpression:797

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: HTH-type transcriptional regulator VirS
  • MTBC0 PGAP product: AraC family transcriptional regulator
  • Pfam (hmmscan --cut_ga): Arabinose_bd PF12625.13 (E=6e-40), HTH_18 PF12833.14 (E=7e-18), HTH_AraC PF00165.30 (E=7e-06)
  • (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_217598.1)
  • Domains: Pfam-A via hmmscan --cut_ga — Arabinose_bd (PF12625.13), HTH_18 (PF12833.14), HTH_AraC (PF00165.30)
  • 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 COG2207
  • Curated reference: UniProt P9WMJ3 (SwissProt, reviewed; 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)
  • Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 90 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_003276|Rv3082c|virS
MELGSLIRATNLWGYTDLMRELGADPLPFLRRFDIPPGIEHQEDAFMSLAGFVRMLEASAAELDCPDFGLRLARWQGLGILGPVAVIARNAATLFGGLEAIGRYLYVHSPALTLTVSSTTARSNVRFGYEVTEPGIPYPLQGYELSMANAARMIRLLGGPQARARVFSFRHAQLGTDAAYREALGCTVRFGRTWCGFEVDHRLAGRPIDHADPETKRIATKYLESQYLPSDATLSERVVGLARRLLPTGQCSAEAIADQLDMHPRTLQRRLAAEGLRCHDLIERERRAQAARYLAQPGLYLSQIAVLLGYSEQSALNRSCRRWFGMTPRQYRAYGGVSGR