MTBC Gene Atlas

mtc28 Family assigned · medium

H37Rv Rv0040c · MTBC0 mtbc0_000045 · 310 aa · 42532–43464 (-) · RefSeq NP_214554.2

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)hypothetical protein
MTBC0 PGAP re-annotationLpqN/LpqT family lipoprotein
Revised (this work)Cell-envelope lipoprotein of the LpqN/LpqT family (Pfam Lpp-LpqN, PF10738). Members are anchored to the mycobacterial envelope; the specific physiological role of this locus is not established here.

Curated reference (UniProt)

UniProt P9WIM9 SwissProt · reviewed · Evidence at protein level
UniProt nameProline-rich 28 kDa antigen

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category S Function unknown
Preferred namemtc28
eggNOG descriptionProbable lipoprotein LpqN
Orthologous group2APGE
Gene Ontology (2) GO:0005575, GO:0005576

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 1.001 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 3 synonymous, 8 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
Lpp-LpqNPF10738.16 1.5e-66103–270 Probable lipoprotein LpqN

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

Closest characterised functional partner: Rv0039c (transmembrane protein), high confidence from genomic context alone (score 794 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.

PartnerProductScoreNo text-miningChannels (≥400)
Rv3810 pirG cell surface protein 812 812 coexpression:812
Rv0312 hyp hypothetical protein 812 812 coexpression:812
Rv2721c hyp hypothetical protein 803 803 coexpression:803
Rv1477 ripA peptidoglycan endopeptidase RipA 810 800 coexpression:800
Rv0039c transmembrane protein 794 794 ctx neighborhood:785
Rv1158c hyp hypothetical protein 748 748 coexpression:748
Rv1478 ripB peptidoglycan endopeptidase RipB 738 738 coexpression:738
Rv1566c ripD hyp hypothetical protein 747 734 coexpression:734
Rv0041 leuS leucine--tRNA ligase 731 732 ctx neighborhood:730
Rv0888 spmT hyp hypothetical protein 703 703 coexpression:703
Rv1157c hyp hypothetical protein 414 415 coexpression:415
Rv1754c hyp hypothetical protein 415 386
Rv1926c mpt63 immunogenic protein Mpt63 547 46 textmining:545
Rv3279c birA bifunctional biotin operon repressor/biotin--[acetyl-CoA-carboxylase 659 44 textmining:658
Rv3221c TB7.3 acetyl-CoA carboxylase biotin carboxyl carrier protein subunit 808 42 textmining:808

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

  • MTBC0 PGAP product: 'LpqN/LpqT family lipoprotein'
  • Pfam (hmmscan --cut_ga): Lpp-LpqN PF10738 (E=1.5e-66)

ESM Atlas signal (exploratory)

Ancestral protein hash 1f4cb89e38667edbbb0f4d2ccec8f10a. SAE features are orienting indices, not validated domains.

#IndexActivationInterpretation
13621 1.17 Secretory pathway signal motifs
211966 1.16 Low-cysteine small/charged soluble tracts
315441 1.13 Catalysis-adjacent beta-strand micro-motifs
46474 1.12 Acidic/disulfide loops and catalytic Asp/His
5777 1.11 N-terminal targeting signals
61070 0.89 Exposed amphipathic alpha helices
77087 0.70 Extracellular low-complexity repeats
813555 0.68 Small-residue low-complexity tracts

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_214554.2)
  • Domains: Pfam-A via hmmscan --cut_ga — Lpp-LpqN (PF10738.16)
  • 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 2APGE
  • Curated reference: UniProt P9WIM9 (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 — 15 functional partner(s); context anchor Rv0039c
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000045|Rv0040c|mtc28
MIQIARTWRVFAGGMATGFIGVVLVTAGKASADPLLPPPPIPAPVSAPATVPPVQNLTALPGGSSNRFSPAPAPAPIASPIPVGAPGSTAVPPLPPPVTPAISGTLRDHLREKGVKLEAQRPHGFKALDITLPMPPRWTQVPDPNVPDAFVVIADRLGNSVYTSNAQLVVYRLIGDFDPAEAITHGYIDSQKLLAWQTTNASMANFDGFPSSIIEGTYRENDMTLNTSRRHVIATSGADKYLVSLSVTTALSQAVTDGPATDAIVNGFQVVAHAAPAQAPAPAPGSAPVGLPGQAPGYPPAGTLTPVPPR