MTBC Gene Atlas

PE_PGRS34 Family assigned · medium auto-curated

H37Rv Rv1840c · MTBC0 - · 515 aa · 2087971–2089518 (-) · RefSeq YP_177847.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)PE-PGRS family protein PE_PGRS34
MTBC0 PGAP re-annotation—
Revised (this work)PE-PGRS family protein PE_PGRS34. Pfam: PE (PF00934.26), PGRS (PF21526.3).

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

Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).

Curated reference (UniProt)

UniProt P9WIF3 SwissProt · reviewed · Inferred from homology
UniProt nameUncharacterized PE-PGRS family protein PE_PGRS34

UniProt still lists this protein as Uncharacterized PE-PGRS family protein PE_PGRS34; the revised annotation above is ahead of the current UniProt record.

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category I Lipid transport and metabolism
eggNOG descriptionPE family
Orthologous groupCOG0657

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 0.351 · purifying
Polymorphic sites (≥ 0.1% of strains) 9 synonymous, 8 missense, 0 nonsense, 2 frameshift
Disruption 2 distinct premature-stop/frameshift site(s); most common in 0.94% of strains (1362) · clonal

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
PEPF00934.26 3.0e-334–93 PE family
PGRSPF21526.3 1.6e-10114–179 PGRS repeats

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

PartnerProductScoreNo text-miningChannels (≥400)
Rv2442c rplU 50S ribosomal protein L21 929 923 coexpression:666 experimental:773
Rv2412 rpsT 30S ribosomal protein S20 929 922 coexpression:661 experimental:773
Rv3443c rplM 50S ribosomal protein L13 926 920 coexpression:656 experimental:773
Rv1642 rpmI 50S ribosomal protein L35 925 919 coexpression:647 experimental:773
Rv2909c rpsP 30S ribosomal protein S16 924 918 coexpression:652 experimental:773
Rv0979A rpmF 50S ribosomal protein L32 924 917 coexpression:651 experimental:773
Rv2904c rplS 50S ribosomal protein L19 923 916 coexpression:646 experimental:773
Rv2785c rpsO 30S ribosomal protein S15 923 916 coexpression:647 experimental:773
Rv0682 rpsL 30S ribosomal protein S12 922 916 coexpression:646 experimental:773
Rv2441c rpmA 50S ribosomal protein L27 914 910 coexpression:605 experimental:773
Rv3458c rpsD 30S ribosomal protein S4 913 909 coexpression:609 experimental:773
Rv1643 rplT 50S ribosomal protein L20 908 903 coexpression:575 experimental:773
Rv3459c rpsK 30S ribosomal protein S11 905 902 coexpression:585 experimental:773
Rv3456c rplQ 50S ribosomal protein L17 906 900 coexpression:578 experimental:773
Rv3442c rpsI 30S ribosomal protein S9 905 897 coexpression:557 experimental:773

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

  • Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): PE-PGRS family protein PE_PGRS34
  • Pfam (hmmscan --cut_ga): PE PF00934.26 (E=3e-33), PGRS PF21526.3 (E=2e-10)
  • (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 YP_177847.1)
  • Domains: Pfam-A via hmmscan --cut_ga — PE (PF00934.26), PGRS (PF21526.3)
  • 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 COG0657
  • Curated reference: UniProt P9WIF3 (SwissProt, reviewed; 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 — 118 functional partner(s)
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>H37Rv|Rv1840c|PE_PGRS34
MSFVVAAPEVVVAAASDLAGIGSAIGAANAAAAVPTMGVLAAGADEVSAAVADLFGAHAQAYQALSAQAALFHEQFVHAMTAGAGAYAGAEAADAAALDVLNGPFQALFGRPLIGDGANGAPGQPGGPGGLLYGNGGNGGNGGIGQPGGAGGDAGLIGNGGNGGIGGPGATGLAGGAGGVGGLLFGDGGNGGAGGLGTGPVGATGGIGGPGGAAVGLFGHGGAGGAGGLGKAGFAGGAGGTGGTGGLLYGNGGNGGNVPSGAADGGAGGDARLIGNGGDGGSVGAAPTGIGNGGNGGNGGWLYGDGGSGGSTLQGFSDGGTGGNAGMFGDGGNGGFSFFDGNGGDGGTGGTLIGNGGDGGNSVQTDGFLRGHGGDGGNAVGLIGNGGAGGAGSAGTGVFAPGGGSGGNGGNGALLVGNGGAGGSGGPTQIPSVAVPVTGAGGTGGNGGTAGLIGNGGNGGAAGVSGDGTPGTGGNGGYAQLIGDGGDGGPGDSGGPGGSGGTGGTLAGQNGSPGG