MTBC Gene Atlas

lprC Family assigned · low

H37Rv Rv1275 · MTBC0 mtbc0_001365 · 180 aa · 1433734–1434276 (+) · RefSeq NP_215791.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)lipoprotein LprC
MTBC0 PGAP re-annotationDUF3558 domain-containing protein
Revised (this work)Lipoprotein of the Lpr (LprB/LprC) family. RefSeq product 'lipoprotein LprC'.

Curated reference (UniProt)

UniProt O86337 TrEMBL · unreviewed · Evidence at protein level
UniProt namePossible lipoprotein LprC

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category J Translation, ribosomal structure and biogenesis
Preferred namelprC
eggNOG descriptionProtein of unknown function (DUF3558)
Orthologous groupCOG1188

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 0.677 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 1 synonymous, 2 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
DUF3558PF12079.14 1.8e-2916–177 Protein of unknown function (DUF3558)

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

Closest characterised functional partner: lprB (lipoprotein LprB), high confidence from genomic context alone (score 994 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv1274 lprB lipoprotein LprB 999 994 ctx neighborhood:882 cooccurence:774 coexpression:802 textmining:852
Rv2904c rplS 50S ribosomal protein L19 875 875 coexpression:404 experimental:788
Rv1643 rplT 50S ribosomal protein L20 797 797 experimental:787
Rv3456c rplQ 50S ribosomal protein L17 810 796 experimental:787
Rv2441c rpmA 50S ribosomal protein L27 792 793 experimental:787
Rv2442c rplU 50S ribosomal protein L21 791 792 experimental:787
Rv3443c rplM 50S ribosomal protein L13 791 791 experimental:788
Rv0704 rplB 50S ribosomal protein L2 790 789 experimental:787
Rv0719 rplF 50S ribosomal protein L6 789 789 experimental:787
Rv0706 rplV 50S ribosomal protein L22 789 789 experimental:788
Rv0701 rplC 50S ribosomal protein L3 789 789 experimental:787
Rv1642 rpmI 50S ribosomal protein L35 789 789 experimental:787
Rv0714 rplN 50S ribosomal protein L14 789 789 experimental:788
Rv0716 rplE 50S ribosomal protein L5 789 789 experimental:787
Rv0720 rplR 50S ribosomal protein L18 788 789 experimental:787

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

  • Foldseek vs AFDB-SwissProt: lipoprotein LprB, TM 0.59, E 6e-6
  • Structural homology vs AlphaFold-Swiss-Prot (Foldseek; 542k curated SwissProt structures), project 'Still unknown gene function' phase13, 2026-06-10. Fold/family-level, not a demonstrated function.

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_215791.1)
  • Domains: Pfam-A via hmmscan --cut_ga — DUF3558 (PF12079.14)
  • 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 COG1188
  • Curated reference: UniProt O86337 (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 — 196 functional partner(s); context anchor lprB
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_001365|Rv1275|lprC
MRRVLVGAAALITALLVLTGCTKSISGTAVKAGGAGVPRNNNSQERYPNLLKECEVLTTDILAKTVGADPLDIQSTFVGAICRWQAANPAGLIDITRFWFEQGSLSNERKVAEGLKYQVETRAIQGVDSIVMRTGDPNGACGVASDAAGVVGWWVNPQAPGIDACGQAIKLMELTLATNA