MTBC Gene Atlas

Rv1019 Family assigned · medium auto-curated

H37Rv Rv1019 · MTBC0 mtbc0_001095 · 197 aa · 1145652–1146245 (+) · RefSeq NP_215535.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)transcriptional regulator
MTBC0 PGAP re-annotationTetR/AcrR family transcriptional regulator
Revised (this work)TetR/AcrR family transcriptional regulator. Pfam: TetR_N (PF00440.30), TetR_C_46 (PF21943.2).

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

Curated reference (UniProt)

UniProt P96381 TrEMBL · unreviewed · Evidence at protein level
UniProt nameProbable transcriptional regulatory protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category K Transcription
Preferred nameicaR
eggNOG descriptionTranscriptional regulator
Orthologous groupCOG1309

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 n/a
Polymorphic sites (≥ 0.1% of strains) 0 synonymous, 1 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
TetR_NPF00440.30 1.3e-1614–54 Bacterial regulatory proteins, tetR family
TetR_C_46PF21943.2 3.7e-0980–183 Tetracyclin repressor-like, C-terminal domain

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv1152 transcriptional regulator 850 845 coexpression:845
Rv0038 hyp hypothetical protein 841 841 coexpression:841
Rv0653c transcriptional regulator 823 824 coexpression:772
Rv1985c lysG HTH-type transcriptional regulator 824 821 coexpression:799
Rv2788 sirR transcriptional repressor SirR 820 818 coexpression:817
Rv1725c hyp hypothetical protein 816 812 coexpression:812
Rv0117 oxyS oxidative stress response regulatory protein OxyS 811 804 coexpression:780
Rv0691c mftR mycofactocin biosynthesis transcriptional regulator MftR 807 802 coexpression:802
Rv3183 higA3 transcriptional regulator 802 802 coexpression:802
Rv3263 DNA methylase 802 802 coexpression:802
Rv3855 ethR HTH-type transcriptional repressor EthR 799 799 coexpression:799
Rv1773c transcriptional regulator 805 798 coexpression:798
Rv1776c transcriptional regulator 798 798 coexpression:798
Rv1359 transcriptional regulator 798 798 coexpression:798
Rv3736 AraC/XylS family transcriptional regulator 800 797 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: transcriptional regulator
  • MTBC0 PGAP product: TetR/AcrR family transcriptional regulator
  • Pfam (hmmscan --cut_ga): TetR_N PF00440.30 (E=1e-16), TetR_C_46 PF21943.2 (E=4e-09)
  • (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_215535.1)
  • Domains: Pfam-A via hmmscan --cut_ga — TetR_N (PF00440.30), TetR_C_46 (PF21943.2)
  • 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 COG1309
  • Curated reference: UniProt P96381 (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 — 58 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001095|Rv1019|
MTGTERRHQLIGIARSLFAERGYDGTSIEEIAQRANVSKPVVYEHFGGKEGLYAVVVDREMSALLDGITSSLTNNRSRVRVERVALALLTYVEERTDGFRIMIRDSPASISSGTYSSLLNDAVSQVSSILAGDFARRGLDPDLAPLYAQALVGSVSMTAQWWLDAREPKKEVVAAHLVNLVWNGLTHLEADPRLQDE