efpA Resolved · high auto-curated
H37Rv Rv2846c · MTBC0 mtbc0_003025 ·
530 aa · 3173705–3175297 (-) ·
RefSeq NP_217362.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | MFS-type transporter EfpA |
|---|---|
| MTBC0 PGAP re-annotation | multidrug efflux MFS transporter EfpA |
| Revised (this work) | Multidrug efflux MFS transporter EfpA. 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 |
P9WJY5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized MFS-type transporter EfpA |
UniProt still lists this protein as Uncharacterized MFS-type transporter EfpA; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolismG Carbohydrate transport and metabolismP Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | efpA |
| eggNOG description | Major facilitator superfamily |
| Orthologous group | COG0477 |
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.618 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 5 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
MFS_1 | PF07690.22 | 3.7e-44 | 61–449 | Major Facilitator Superfamily |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cysG (multifunctional uroporphyrin-III C-methyltransferase/precorrin-2 oxidase/ferrochelatase), high confidence from genomic context alone (score 854 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2847c cysG |
multifunctional uroporphyrin-III C-methyltransferase/precorrin-2 oxidase/ferrochelatase | 854 | 854 ctx | neighborhood:853 |
Rv3801c fadD32 |
long-chain-fatty-acid--AMP ligase FadD32 | 823 | 770 | coexpression:770 |
Rv2845c proS |
proline--tRNA ligase | 740 | 740 ctx | neighborhood:736 |
Rv2247 accD6 |
acetyl-/propionyl-CoA carboxylase subunit beta | 830 | 731 | coexpression:731 |
Rv2246 kasB |
3-oxoacyl-ACP synthase 2 | 756 | 729 | coexpression:729 |
Rv2245 kasA |
3-oxoacyl-ACP synthase 1 | 876 | 716 | coexpression:716 textmining:584 |
Rv2848c cobB |
cobyrinic acid A,C-diamide synthase | 708 | 708 ctx | neighborhood:708 |
Rv2849c cobO |
cob(I)alamin adenosyltransferase | 708 | 708 ctx | neighborhood:708 |
Rv2851c |
GCN5-like N-acetyltransferase | 699 | 700 ctx | neighborhood:698 |
Rv2850c |
magnesium chelatase | 699 | 700 ctx | neighborhood:698 |
Rv2852c mqo |
malate:quinone oxidoreductase | 672 | 673 ctx | neighborhood:668 |
Rv2854 hyp |
hypothetical protein | 584 | 569 ctx | neighborhood:569 |
Rv2855 mtr |
mycothione reductase | 580 | 565 ctx | neighborhood:565 |
Rv0412c glnX |
membrane protein | 533 | 533 | coexpression:533 |
Rv2243 fabD |
malonyl CoA-acyl carrier protein transacylase | 564 | 442 | coexpression:441 |
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 EfpA
- MTBC0 PGAP product: multidrug efflux MFS transporter EfpA
- Pfam (hmmscan --cut_ga): MFS_1 PF07690.22 (E=4e-44)
- (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_217362.1)
- 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 P9WJY5 (SwissProt, reviewed; 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 —
41 functional partner(s); context anchor
cysG - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003025|Rv2846c|efpA MTALNDTERAVRNWTAGRPHRPAPMRPPRSEETASERPSRYYPTWLPSRSFIAAVIAIGGMQLLATMDSTVAIVALPKIQNELSLSDAGRSWVITAYVLTFGGLMLLGGRLGDTIGRKRTFIVGVALFTISSVLCAVAWDEATLVIARLSQGVGSAIASPTGLALVATTFPKGPARNAATAVFAAMTAIGSVMGLVVGGALTEVSWRWAFLVNVPIGLVMIYLARTALRETNKERMKLDATGAILATLACTAAVFAFSIGPEKGWMSGITIGSGLVALAAAVAFVIVERTAENPVVPFHLFRDRNRLVTFSAILLAGGVMFSLTVCIGLYVQDILGYSALRAGVGFIPFVIAMGIGLGVSSQLVSRFSPRVLTIGGGYLLFGAMLYGSFFMHRGVPYFPNLVMPIVVGGIGIGMAVVPLTLSAIAGVGFDQIGPVSAIALMLQSLGGPLVLAVIQAVITSRTLYLGGTTGPVKFMNDVQLAALDHAYTYGLLWVAGAAIIVGGMALFIGYTPQQVAHAQEVKEAIDAGEL