MTBC Gene Atlas

oxyS Family assigned · medium auto-curated

H37Rv Rv0117 · MTBC0 mtbc0_000128 · 314 aa · 141366–142310 (+) · RefSeq NP_214631.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)oxidative stress response regulatory protein OxyS
MTBC0 PGAP re-annotationLysR family transcriptional regulator OxyS
Revised (this work)LysR family transcriptional regulator OxyS. Pfam: HTH_1 (PF00126.34), LysR_substrate (PF03466.26).

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

Curated reference (UniProt)

UniProt L7N677 TrEMBL · unreviewed · Evidence at protein level
UniProt nameProbable hydrogen peroxide-inducible genes activator
Curated functionRequired for the induction the katG gene for catalase. Involved in the response to hydrogen peroxide.

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category K Transcription
Preferred nameoxyS
eggNOG descriptionBacterial regulatory helix-turn-helix protein, lysR family
Orthologous groupCOG0583

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 0.841 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 3 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
HTH_1PF00126.34 1.2e-193–62 Bacterial regulatory helix-turn-helix protein, lysR family
LysR_substratePF03466.26 5.6e-2888–295 LysR substrate binding domain

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv3167c TetR family transcriptional regulator 877 873 coexpression:857
Rv1931c transcriptional regulator 865 860 coexpression:860
Rv0691c mftR mycofactocin biosynthesis transcriptional regulator MftR 856 854 coexpression:836
Rv0377 HTH-type transcriptional regulator 847 848 coexpression:803
Rv1027c kdpE transcriptional regulator KdpE 855 847 coexpression:827
Rv2282c LysR family HTH-type transcriptional regulator 846 847 coexpression:803
Rv1267c embR transcriptional regulator EmbR 851 846 coexpression:846
Rv3055 TetR family transcriptional regulator 851 846 coexpression:801
Rv3263 DNA methylase 843 844 coexpression:820
Rv1359 transcriptional regulator 843 843 coexpression:843
Rv1675c cmr HTH-type transcriptional regulator Cmr 850 842 coexpression:842
Rv1674c transcriptional regulator 850 840 coexpression:837
Rv3830c TetR family transcriptional regulator 842 840 coexpression:820
Rv0494 HTH-type transcriptional regulator 844 837 coexpression:802
Rv1725c hyp hypothetical protein 841 836 coexpression:835

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: oxidative stress response regulatory protein OxyS
  • MTBC0 PGAP product: LysR family transcriptional regulator OxyS
  • Pfam (hmmscan --cut_ga): HTH_1 PF00126.34 (E=1e-19), LysR_substrate PF03466.26 (E=6e-28)
  • (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_214631.1)
  • Domains: Pfam-A via hmmscan --cut_ga — HTH_1 (PF00126.34), LysR_substrate (PF03466.26)
  • 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 COG0583
  • Curated reference: UniProt L7N677 (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)
  • Interaction network: STRING v12.0 (Szklarczyk et al. 2023, doi:10.1093/nar/gkac1000), taxon 83332, CC-BY 4.0 — 87 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000128|Rv0117|oxyS
MLFRQLEYFVAVAQERHFARAAEKCYVSQPALSSAIAKLERELNVTLINRGHSFEGLTREGERLVVWAKRILAEHAAFKAEVDAVRSGITGTLRLGTVPTASTTASLVLSAFCSAHPLAKVQVCSRLAATELYRRLREFELDAVIVHPETQDSDDVDLVPLYEEQYVLLSPADMLPPGTSTLVWRDAAQLPLALLTADMRDRQVIDAAFADHAVSAIPQVETDSVASLFAQVATGNWASIVPHTWLWAMPMSGPTGGEIRAVELVDPVLKAQIALATNALGPGSPVARALITCAQALALNEFFDTQLRGITRRR