MTBC Gene Atlas

lpqZ Family assigned · medium auto-curated

H37Rv Rv1244 · MTBC0 mtbc0_001333 · 286 aa · 1395301–1396161 (+) · RefSeq NP_215760.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)lipoprotein LpqZ
MTBC0 PGAP re-annotationglycine betaine ABC transporter substrate-binding protein
Revised (this work)Glycine betaine ABC transporter substrate-binding protein. Pfam: OpuAC (PF04069.18).

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

Curated reference (UniProt)

UniProt O50459 TrEMBL · unreviewed · Evidence at protein level
UniProt nameProbable lipoprotein LpqZ

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category M Cell wall / membrane / envelope biogenesis
Preferred namelpqZ
eggNOG descriptionABC-type glycine betaine transport system
Orthologous groupCOG1732
KEGG orthology K02002
KEGG pathways map02010
KEGG modules M00208

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 1.151 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 4 synonymous, 12 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
OpuACPF04069.18 4.1e-2033–281 Substrate binding domain of ABC-type glycine betaine transport system

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

Closest characterised functional partner: proV (glycine betaine/carnitine/choline/L-proline ABC transporter ATP-binding protein ProV), high confidence from genomic context alone (score 889 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv3758c proV glycine betaine/carnitine/choline/L-proline ABC transporter ATP-binding protein ProV 902 889 ctx cooccurence:500 coexpression:726
Rv1234 transmembrane protein 790 791 coexpression:705
Rv3759c proX glycine betaine/carnitine/choline/L-proline ABC transporter substrate-binding lipoprotein ProX 789 789 ctx cooccurence:684
Rv3757c proW glycine betaine/carnitine/choline/L-proline ABC transporter permease ProW 802 781 ctx cooccurence:511 coexpression:516
Rv3756c proZ glycine betaine/carnitine/choline/L-proline ABC transporter permease ProZ 783 762 ctx cooccurence:469 coexpression:516
Rv1240 mdh malate dehydrogenase 595 596 ctx neighborhood:544
Rv1239c corA magnesium and cobalt transport transmembrane protein CorA 549 549 ctx neighborhood:544
Rv1836c hyp hypothetical protein 536 537 ctx cooccurence:530
Rv3390 lpqD lipoprotein LpqD 516 517 ctx cooccurence:516
Rv3492c Mce associated protein 514 514 ctx cooccurence:509
Rv3810 pirG cell surface protein 512 512 ctx cooccurence:508
Rv1243c PE_PGRS23 PE-PGRS family protein PE_PGRS23 507 507 ctx neighborhood:507
Rv0479c membrane protein 475 476 ctx cooccurence:473
Rv3527 hyp hypothetical protein 472 472 ctx cooccurence:472
Rv0441c hyp hypothetical protein 464 464 ctx cooccurence:449

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: lipoprotein LpqZ
  • MTBC0 PGAP product: glycine betaine ABC transporter substrate-binding protein
  • Pfam (hmmscan --cut_ga): OpuAC PF04069.18 (E=4e-20)
  • (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_215760.1)
  • Domains: Pfam-A via hmmscan --cut_ga — OpuAC (PF04069.18)
  • 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 COG1732
  • Curated reference: UniProt O50459 (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 — 38 functional partner(s); context anchor proV
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001333|Rv1244|lpqZ
MRITRILALLLAVLLAVSGVAGCSADTGDRHPELVVGSTPDSEAMLLAAIYVAALRSYGFAAHAETAADPVAKLDSGAFTVVPAFTGQMLQTLQPDASVRSDAQVYRAIVSALPEGIAAGDYTTAAEDKPALVVTQSTAKAWGGGDLSELPSHCRGLLVGRVAGAHTPAAVGPCRLPAPREFRNDATMFAALRAGQLVAAWTTTADPDIPADLIMLTDGKPALIRAENIVPLYRRNALTERQLLAVNEVAGVLDTTALIGMRRQVAAGADPAAVAAGWLAEHPLGR