arsB1 Resolved · high auto-curated
H37Rv Rv2685 · MTBC0 - ·
428 aa · 3001983–3003269 (+) ·
RefSeq YP_177899.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | arsenic-transport integral membrane protein ArsB |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Arsenic-transport integral membrane protein ArsB. Pfam: CitMHS (PF03600.23), ArsB (PF02040.21), NhaB (PF06450.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WPD7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized transporter Rv2685 |
UniProt still lists this protein as Uncharacterized transporter Rv2685; 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 | arsB1 |
| 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 | 0.748 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 4 missense, 2 nonsense, 4 frameshift |
| Disruption | 6 distinct premature-stop/frameshift site(s); most common in 2.24% of strains (3255) · convergent |
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 |
|---|---|---|---|---|
CitMHS | PF03600.23 | 9.3e-86 | 13–366 | Citrate transporter |
ArsB | PF02040.21 | 3.0e-15 | 20–422 | Arsenical pump membrane protein |
NhaB | PF06450.19 | 7.7e-09 | 144–386 | Bacterial Na+/H+ antiporter B (NhaB) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: arsA (arsenic-transport integral membrane protein ArsA), medium confidence from genomic context alone (score 636 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2683 hyp |
hypothetical protein | 898 | 899 ctx | neighborhood:606 cooccurence:728 |
Rv2684 arsA |
arsenic-transport integral membrane protein ArsA | 637 | 636 ctx | neighborhood:577 |
Rv2682c dxs1 |
1-deoxy-D-xylulose 5-phosphate synthase | 420 | 421 ctx | neighborhood:412 |
Rv0053 rpsF |
30S ribosomal protein S6 | 409 | 410 | coexpression:408 |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 405 | 161 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): arsenic-transport integral membrane protein ArsB
- Pfam (hmmscan --cut_ga): CitMHS PF03600.23 (E=9e-86), ArsB PF02040.21 (E=3e-15), NhaB PF06450.19 (E=8e-09)
- (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 YP_177899.1)
- Domains: Pfam-A via hmmscan --cut_ga — CitMHS (PF03600.23), ArsB (PF02040.21), NhaB (PF06450.19)
- 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 P9WPD7 (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 —
5 functional partner(s); context anchor
arsA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2685|arsB1 MSIIAITVFVAGYALIASDRVSKTRVALTCAAIMVGAGIVGSDDVFYSHEAGIDWDVIFLLLGMMIIVSVLRHTGVFEYVAIWAVKRANAAPLRIMILLVLVTALGSALLDNVTTVLLIAPVTLLVCDRLGVNSTPFLVAEVFASNVGGAATLVGDPPNIIIASRAGLTFNDFLIHMAPAVLVVMIALIGLLPWLLGSVTAEPDRVADVLSLNEREAIHDRGLLIKCGVVLVLVFAAFIAHPVLHIQPSLVALLGAGVLVRFSGLERSDYLSSVEWDTLLFFAGLFVMVGALVKTGVVEQLARAATELTGGNELLTVGLILGISAPVSGIIDNIPYVATMTPIVTELVAAMPGHVHPDTFWWALALSADFGGNLTAVAASANVVMLGIARRSGTPISFWKFTRKGAVVTAVSLVLSAVYLWLRYFVFG