MTBC Gene Atlas

ptrp Family assigned · medium

H37Rv Rv0538 · MTBC0 mtbc0_000567 · 548 aa · 633591–635237 (+) · RefSeq NP_215052.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)membrane protein
MTBC0 PGAP re-annotationhypothetical protein
Revised (this work)Proline-threonine repetitive protein (PTRP), an M. tuberculosis-complex-specific cell-wall protein with tandem amino-acid repeats; a serologically immunodominant antigen expressed in vivo during (pre)clinical TB. Molecular/enzymatic function unknown. RefSeq leaves it 'membrane protein'.

Curated reference (UniProt)

UniProt O06404 TrEMBL · unreviewed · Evidence at protein level
UniProt namePossible conserved membrane protein

Functional vocabulary (eggNOG-mapper, orthology transfer)

Orthologous group2DJHP

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 0.656 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 6 synonymous, 10 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
DUF7159PF23717.2 3.4e-272–213 Family of unknown function (DUF7159)

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

Closest characterised functional partner: Rv0539 (dolichyl-phosphate sugar synthase), high confidence from genomic context alone (score 810 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv0539 dolichyl-phosphate sugar synthase 810 810 ctx neighborhood:804
Rv0540 hyp hypothetical protein 806 806 ctx neighborhood:804
Rv3903c cpnT hyp hypothetical protein 795 782 ctx cooccurence:773
Rv2164c hyp hypothetical protein 772 773 ctx cooccurence:767
Rv1775 hyp hypothetical protein 761 762 ctx cooccurence:761
Rv3909 hyp hypothetical protein 760 760 ctx cooccurence:744
Rv2113 integral membrane protein 755 755 ctx cooccurence:752
Rv0339c iniR transcriptional regulator 762 753 ctx cooccurence:744
Rv3835 hyp hypothetical protein 752 753 ctx cooccurence:749
Rv1024 membrane protein 744 745 ctx cooccurence:741
Rv1648 transmembrane protein 744 745 ctx cooccurence:744
Rv2843 hyp hypothetical protein 743 744 ctx cooccurence:742
Rv2264c hyp hypothetical protein 742 742 ctx cooccurence:738
Rv3879c espK ESX-1 secretion-associated protein EspK 744 736 ctx cooccurence:735
Rv3788 hyp hypothetical protein 725 726 ctx cooccurence:724

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

  • Cell-wall protein with proline-threonine tandem repeats; MTBC-specific (Singh 2009, PMID 19604115)
  • Immunodominant antigen expressed in preclinical TB (Singh 2001, PMID 11349098)
  • Pfam DUF7159
  • Curated from the literature crible (project 'Still unknown gene function', 2026-06-09)

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_215052.1)
  • Domains: Pfam-A via hmmscan --cut_ga — DUF7159 (PF23717.2)
  • 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 2DJHP
  • Curated reference: UniProt O06404 (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 — 136 functional partner(s); context anchor Rv0539
  • Primary literature: Singh KK, Sharma N, Vargas D, Liu Z, Belisle JT, Potharaju V, Wanchu A, Behera D, Laal S (2009). Peptides of a novel Mycobacterium tuberculosis-specific cell wall protein for immunodiagnosis of tuberculosis J Infect Dis 200(4):571-81. doi:10.1086/603539 PMID:19604115
  • Primary literature: Singh KK, Zhang X, Patibandla AS, Chien P Jr, Laal S (2001). Antigens of Mycobacterium tuberculosis expressed during preclinical tuberculosis: serological immunodominance of proteins with repetitive amino acid sequences Infect Immun 69(6):4185-91. doi:10.1128/IAI.69.6.4185-4191.2001 PMID:11349098

Ancestral MTBC0 protein sequence

>mtbc0_000567|Rv0538|ptrp
MDVALGVAVTDRVARLALVDSAAPGTVIDQFVLDVAEHPVEVLTETVVGTDRSLAGENHRLVATRLCWPDQAKADELQHALQDSGVHDVAVISEAQAATALVGAAHAGSAVLLVGDETATLSVVGDPDAPPTMVAVAPVAGADATSTVDTLMARLGDQALAPGDVFLVGRSAEHTTVLADQLRAASTMRVQTPDDPTFALARGAAMAAGAATMAHPALVADATTSLPPAEAGQSGSEGEQLAYSQASDYELLPVDEYEEHDEYGAAADRSAPLSRRSLLIGNAVVAFAVIGFASLAVAVAVTIRPTAASKPVEGHQNAQPGKFMPLLPTQQQAPVPPPPPDDPTAGFQGGTIPAVQNVVPRPGTSPGVGGTPASPAPEAPAVPGVVPAPVPIPVPIIIPPFPGWQPGMPTIPTAPPTTPVTTSATTPPTTPPTTPVTTPPTTPPTTPVTTPPTTPPTTPVTTPPTTVAPTTVAPTTVAPTTVAPTTVAPATATPTTVAPQPTQQPTQQPTQQMPTQQQTVAPQTVAPAPQPPSGGRNGSGGGDLFGGF