MTBC Gene Atlas

Rv1973 Family assigned · low

H37Rv Rv1973 · MTBC0 mtbc0_002089 · 160 aa · 2236281–2236763 (+) · RefSeq NP_216489.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)Mce associated membrane protein
MTBC0 PGAP re-annotationhypothetical protein
Revised (this work)Outer-membrane protein (OMP) of the mycobacterial cell envelope. RefSeq leaves it of unknown function. Predicted as a beta-barrel OMP and experimentally localised to the outer membrane (detected in the membrane fraction and surface-accessible to proteinase K), tripling the count of known Mtb OMPs (Song 2008). Precise function unfixed.

Curated reference (UniProt)

UniProt P9WJ77 SwissProt · reviewed · Inferred from homology
UniProt nameOuter membrane protein Rv1973

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category O Post-translational modification, protein turnover, chaperones
eggNOG descriptionHeat shock 70 kDa protein
Orthologous groupCOG0443
KEGG orthology K18481
KEGG modules M00670
Gene Ontology (11) GO:0005575, GO:0005623, GO:0009279, GO:0016020, GO:0019867, GO:0030312, GO:0030313, GO:0031975, GO:0044462, GO:0044464, GO:0071944

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 1.136 · relaxed/neutral
Polymorphic sites (≥ 0.1% of strains) 1 synonymous, 3 missense, 0 nonsense, 1 frameshift
Disruption 1 distinct premature-stop/frameshift site(s); most common in 0.14% of strains (202) · 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)

No Pfam-A domain above the gathering threshold (or not yet scanned).

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

Closest characterised functional partner: Rv1972 (Mce associated membrane protein), high confidence from genomic context alone (score 992 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv1972 Mce associated membrane protein 991 992 ctx neighborhood:800 cooccurence:762 coexpression:836
Rv1966 mce3A Mce family protein Mce3A 986 982 ctx neighborhood:715 cooccurence:737 coexpression:785
Rv1970 lprM Mce family lipoprotein LprM 989 978 ctx neighborhood:715 cooccurence:655 coexpression:798 textmining:518
Rv1971 mce3F Mce family protein Mce3F 976 976 ctx neighborhood:721 cooccurence:608 coexpression:801
Rv1968 mce3C Mce family protein Mce3C 990 974 ctx neighborhood:717 cooccurence:633 coexpression:772 textmining:657
Rv1975 hyp hypothetical protein 963 962 ctx neighborhood:739 coexpression:780
Rv1967 mce3B Mce family protein Mce3B 960 961 ctx neighborhood:714 cooccurence:502 coexpression:746
Rv1974 membrane protein 943 944 ctx neighborhood:763 coexpression:772
Rv1969 mce3D Mce family protein Mce3D 940 941 ctx neighborhood:715 cooccurence:705
Rv1965 yrbE3B integral membrane protein 842 843 ctx neighborhood:715
Rv1964 yrbE3A integral membrane protein 794 793 ctx neighborhood:705
Rv0492c GMC-type oxidoreductase 770 761 database:536
Rv1363c membrane protein 760 760 ctx cooccurence:726
Rv3825c pks2 phthioceranic/hydroxyphthioceranic acid synthase 765 738 experimental:470 database:508
Rv2048c pks12 polyketide synthase 762 734 experimental:470 database:508

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

  • Beta-barrel outer-membrane protein; experimentally localised to outer membrane (Song 2008, PMID 18439872)
  • 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_216489.1)
  • Domains: Pfam-A via hmmscan --cut_ga — none above threshold
  • 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 COG0443
  • Curated reference: UniProt P9WJ77 (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 — 284 functional partner(s); context anchor Rv1972
  • Primary literature: Song H, Sandie R, Wang Y, Andrade-Navarro MA, Niederweis M (2008). Identification of outer membrane proteins of Mycobacterium tuberculosis Tuberculosis (Edinb) 88(6):526-44. doi:10.1016/j.tube.2008.02.004 PMID:18439872

Ancestral MTBC0 protein sequence

>mtbc0_002089|Rv1973|
MSWSRVIAYGLLPGLALALTCGAGLLKWQDGAVRDAAVARAESVRAATDGTTALLSYRPDTVQHDLESARSRLTGTFLDAYTQLTHDVVIPGAQQKQISAVATVAAAASVSTSADRAVVLLFVNQTITVGKDAPTTAASSVRVTLDNINGRWLISQFEPI