MTBC Gene Atlas

mgtC Family assigned · medium auto-curated

H37Rv Rv1811 · MTBC0 mtbc0_001923 · 234 aa · 2071454–2072158 (+) · RefSeq NP_216327.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)Mg2+ transport P-type ATPase MgtC
MTBC0 PGAP re-annotationMgtC/SapB family protein
Revised (this work)MgtC/SapB family protein. Pfam: MgtC (PF02308.22), MgtC_SapB_C (PF21770.4).

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

Curated reference (UniProt)

UniProt I6YBN6 TrEMBL · unreviewed · Inferred from homology
UniProt namePossible Mg2+ transport P-type ATPase C MgtC

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category S Function unknown
Preferred namemgtC
eggNOG descriptionthought to be involved in Mg2 transport (import) may act as an accessory protein for MgtB so mediating magnesium influx into the cytosol catalytic activity ATP H(2)O mg(2 )(out) ADP phosphate mg(2 )(in)
Orthologous groupCOG1285
KEGG orthology K07507

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 0.884 · 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
MgtCPF02308.22 5.0e-3413–133 MgtC family
MgtC_SapB_CPF21770.4 1.7e-24149–225 MGTC/SAPB C-terminal domain

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv1624c membrane protein 689 659 coexpression:648
Rv1810 hyp hypothetical protein 568 569 ctx neighborhood:508
Rv0425c ctpH metal cation transporting ATPase H 548 520 coexpression:413
Rv1997 ctpF cation transporter ATPase F 546 518 coexpression:410
Rv0908 ctpE metal cation transporter ATPase E 545 517 coexpression:409
Rv0107c ctpI cation-transporter ATPase I 545 517 coexpression:409
Rv3432c gadB glutamate decarboxylase GadB 438 415 coexpression:415
Rv1809 PPE33 PPE family protein PPE33 430 381
Rv1607 chaA ionic transporter integral membrane protein ChaA 465 207
Rv1115 hyp hypothetical protein 401 46

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: Mg2+ transport P-type ATPase MgtC
  • MTBC0 PGAP product: MgtC/SapB family protein
  • Pfam (hmmscan --cut_ga): MgtC PF02308.22 (E=5e-34), MgtC_SapB_C PF21770.4 (E=2e-24)
  • (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_216327.1)
  • Domains: Pfam-A via hmmscan --cut_ga — MgtC (PF02308.22), MgtC_SapB_C (PF21770.4)
  • 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 COG1285
  • Curated reference: UniProt I6YBN6 (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 — 10 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001923|Rv1811|mgtC
MQTLTVADFALRLAVGVGCGAIIGLERQWRARMAGLRTNALVATGATLFVLYAVATEDSSPTRVASYVVSGIGFLGGGVILREGFNVRGLNTAATLWCSAAVGVLAASGHLVFTLIGTGTIVAVHLLGRPLGRLVDRDNAVEDEGLQPYQVRVICRPKAETYVRAHIVQRTSSNDITLRGIRTGPAGDDNITLTAHLLMVGHTPAKLERLVAELSLQPGVYAVHWYAGEHAQAE