arsA Family assigned · medium auto-curated
H37Rv Rv2684 · MTBC0 mtbc0_002858 ·
429 aa · 3023029–3024318 (+) ·
RefSeq NP_217200.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | arsenic-transport integral membrane protein ArsA |
|---|---|
| MTBC0 PGAP re-annotation | ArsB/NhaD family transporter |
| Revised (this work) | ArsB/NhaD family transporter. Pfam: ArsB (PF02040.21), CitMHS (PF03600.23), Na_sulph_symp (PF00939.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPD9
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized transporter Rv2684 |
UniProt still lists this protein as Uncharacterized transporter Rv2684; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | arsA |
| eggNOG description | transport of arsenical compounds across the membrane (export) arsenic resistance by an export mechanism. responsible for the translocation of the substrate across the membrane |
| Orthologous group | COG1055 |
| KEGG orthology |
K03893
|
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 | 0.649 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.17% of strains (242) · 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
ArsB | PF02040.21 | 3.1e-19 | 5–422 | Arsenical pump membrane protein |
CitMHS | PF03600.23 | 2.3e-85 | 13–367 | Citrate transporter |
Na_sulph_symp | PF00939.26 | 3.1e-08 | 230–421 | Sodium:sulfate symporter transmembrane region |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: arsB1 (arsenic-transport integral membrane protein ArsB), medium confidence from genomic context alone (score 636 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2683 hyp |
hypothetical protein | 950 | 950 ctx | neighborhood:801 cooccurence:723 |
Rv2685 arsB1 |
arsenic-transport integral membrane protein ArsB | 637 | 636 ctx | neighborhood:577 |
Rv2682c dxs1 |
1-deoxy-D-xylulose 5-phosphate synthase | 543 | 543 ctx | neighborhood:542 |
Rv0053 rpsF |
30S ribosomal protein S6 | 411 | 412 | coexpression:410 |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 405 | 161 | |
Rv0125 pepA |
serine protease PepA | 572 | 51 | textmining:568 |
Rv1607 chaA |
ionic transporter integral membrane protein ChaA | 461 | 51 | textmining:456 |
Rv0527 ccdA |
cytochrome C-type biogenesis protein CcdA | 438 | 45 | textmining:436 |
Rv2608 PPE42 |
PPE family protein PPE42 | 445 | 44 | textmining:444 |
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: arsenic-transport integral membrane protein ArsA
- MTBC0 PGAP product: ArsB/NhaD family transporter
- Pfam (hmmscan --cut_ga): ArsB PF02040.21 (E=3e-19), CitMHS PF03600.23 (E=2e-85), Na_sulph_symp PF00939.26 (E=3e-08)
- (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_217200.1)
- Domains: Pfam-A via hmmscan --cut_ga — ArsB (PF02040.21), CitMHS (PF03600.23), Na_sulph_symp (PF00939.26)
- 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
COG1055 - Curated reference: UniProt P9WPD9 (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 —
9 functional partner(s); context anchor
arsB1 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002858|Rv2684|arsA MSVVAVTIFVAAYVLIASDRVNKTMVALTGAAAVVVLPVITSHDIFYSHDTGIDWDVIFLLVGMMIIVGVLRQTGVFEYTAIWAAKRARGSPLRIMILLVLVSALASALLDNVTTVLLIAPVTLLVCDRLNINTTSFLMAEVFASNIGGAATLVGDPPNIIVASRAGLTFNDFMLHLTPLVVIVLIALIAVLPRLFGSITVEADRIADVMALDEGEAIRDRGLLVKCGAVLVLVFAAFVAHPVLHIQPSLVALLGAGMLIVVSGLTRSEYLSSVEWDTLLFFAGLFIMVGALVKTGVVNDLARAATQLTGGNIVATAFLILGVSAPISGIIDNIPYVATMTPLVAELVAVMGGQPSTDTPWWALALGADFGGNLTAIGASANVVMLGIARRAGAPISFWEFTRKGAVVTAVSIALAAIYLWLRYFVLLH