MTBC Gene Atlas

Rv0849 Resolved · high auto-curated

H37Rv Rv0849 · MTBC0 mtbc0_000904 · 419 aa · 949207–950466 (+) · RefSeq NP_215364.1

Annotation: from legacy to revised

Legacy (H37Rv / Mycobrowser)MFS-type transporter
MTBC0 PGAP re-annotationMFS transporter
Revised (this work)MFS transporter. Pfam: MFS_1 (PF07690.22).

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

Curated reference (UniProt)

UniProt P9WJX5 SwissProt · reviewed · Inferred from homology
UniProt nameUncharacterized MFS-type transporter Rv0849

UniProt still lists this protein as Uncharacterized MFS-type transporter Rv0849; the revised annotation above is ahead of the current UniProt record.

Functional vocabulary (eggNOG-mapper, orthology transfer)

COG category E Amino acid transport and metabolism
G Carbohydrate transport and metabolism
P Inorganic ion transport and metabolism
eggNOG descriptionMajor facilitator superfamily
Orthologous groupCOG0477

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) pseudogene candidate

pN/pS 0.062 · strong purifying
Polymorphic sites (≥ 0.1% of strains) 6 synonymous, 1 missense, 0 nonsense, 3 frameshift
Disruption 3 distinct premature-stop/frameshift site(s); most common in 1.03% of strains (1500) · 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
MFS_1PF07690.22 4.0e-2917–314 Major Facilitator Superfamily

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

Closest characterised functional partner: cysK2 (cysteine synthase CysK), high confidence from genomic context alone (score 995 excluding text-mining).

PartnerProductScoreNo text-miningChannels (≥400)
Rv0848 cysK2 cysteine synthase CysK 999 995 ctx neighborhood:881 cooccurence:735 coexpression:862 textmining:810
Rv0850 Rv0850, (MTV043.43), len: 110 aa. Putative transposase (fragment), similar in part to others e.g. Q45144|Q4514 transposable element IS31831 995 969 ctx neighborhood:801 coexpression:850 textmining:870
Rv0846c mmcO oxidase 946 907 coexpression:843 textmining:455
Rv0847 lpqS lipoprotein LpqS 969 854 ctx neighborhood:472 coexpression:734 textmining:803
Rv2963 integral membrane protein 936 825 coexpression:822 textmining:654
Rv2687c antibiotic ABC transporter permease 667 667 ctx cooccurence:631
Rv1978 hyp hypothetical protein 629 629 ctx cooccurence:629
Rv2686c antibiotic ABC transporter permease 620 620 ctx cooccurence:618
Rv1733c transmembrane protein 469 469 ctx cooccurence:469
Rv3912 rsmA anti-sigma-M factor RsmA 459 449 ctx cooccurence:447
Rv0106 hyp hypothetical protein 428 428 ctx cooccurence:409
Rv2643 arsC arsenic-transport integral membrane protein ArsC 695 106 textmining:673
Rv0190 ricR hyp hypothetical protein 461 82 textmining:438
Rv3000 transmembrane protein 639 77 textmining:625
Rv2641 cadI cadmium inducible protein CadI 655 72 textmining:644

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

  • Legacy H37Rv annotation: MFS-type transporter
  • MTBC0 PGAP product: MFS transporter
  • Pfam (hmmscan --cut_ga): MFS_1 PF07690.22 (E=4e-29)
  • (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 NP_215364.1)
  • Domains: Pfam-A via hmmscan --cut_ga — MFS_1 (PF07690.22)
  • 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 COG0477
  • Curated reference: UniProt P9WJX5 (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 — 19 functional partner(s); context anchor cysK2
  • Primary literature: none located yet; annotation rests on the domain/homology sources above.

Ancestral MTBC0 protein sequence

>mtbc0_000904|Rv0849|
MGARAIFRGFNRPSRVLMINQFGINIGFYMLMPYLADYLAGPLGLAAWAVGLVMGVRNFSQQGMFFVGGTLADRFGYKPLIIAGCLIRTGGFALLVVAQSLPSVLIAAAATGFAGALFNPAVRGYLAAEAGERKIEAFAMFNVFYQSGILLGPLVGLVLLALDFRITVLAAAGVFGLLTVAQLVALPQHRADSEREKTSILQDWRVVVRNRPFLTLAAAMTGCYALSFQIYLALPMQASILMPRNQYLLIAAMFAVSGLVAVGGQLRITRWFAVRWGAERSLVVGATILAASFIPVAVIPNGQRFGVAVAVMALVLSASLLAVASAALFPFEMRAVVALSGDRLVATHYGFYSTIVGVGVLVGNLAIGSLMSAARRLNTDEIVWGGLILVGIVAVAGLRRLDTFTSGSQNMTGRWAAPR