arsB2 Resolved · high auto-curated
H37Rv Rv3578 · MTBC0 mtbc0_003797 ·
413 aa · 4043819–4045060 (+) ·
RefSeq NP_218095.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | arsenic transport integral membrane protein ArsB |
|---|---|
| MTBC0 PGAP re-annotation | arsenic transport integral membrane protein ArsB |
| Revised (this work) | Arsenic transport integral membrane protein ArsB. Pfam: ArsB (PF02040.21), CitMHS (PF03600.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YCG9
TrEMBL · unreviewed
· Inferred from homology
|
|---|---|
| UniProt name | Possible arsenical pump integral membrane protein ArsB2 |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | arsB |
| eggNOG description | Arsenical pump membrane protein |
| 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 | 0.853 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.45% of strains (649) · 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 | 2.5e-23 | 3–399 | Arsenical pump membrane protein |
CitMHS | PF03600.23 | 2.4e-33 | 24–343 | Citrate transporter |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lppH (lipoprotein LppH), medium confidence from genomic context alone (score 583 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3577 hyp |
hypothetical protein | 875 | 875 ctx | neighborhood:867 |
Rv3576 lppH |
lipoprotein LppH | 584 | 583 ctx | neighborhood:581 |
Rv1885c |
chorismate mutase | 490 | 490 ctx | cooccurence:486 |
Rv3575c |
LacI family transcriptional regulator | 475 | 447 ctx | neighborhood:444 |
Rv2655c |
prophage protein | 440 | 441 ctx | cooccurence:437 |
Rv0053 rpsF |
30S ribosomal protein S6 | 408 | 409 | coexpression:407 |
Rv0067c |
transcriptional regulator | 424 | 184 | |
Rv1226c |
transmembrane protein | 422 | 183 | |
Rv2643 arsC |
arsenic-transport integral membrane protein ArsC | 400 | 161 | |
Rv1282c oppC |
oligopeptide ABC transporter permease OppC | 429 | 101 |
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 ArsB
- MTBC0 PGAP product: arsenic transport integral membrane protein ArsB
- Pfam (hmmscan --cut_ga): ArsB PF02040.21 (E=3e-23), CitMHS PF03600.23 (E=2e-33)
- (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_218095.1)
- Domains: Pfam-A via hmmscan --cut_ga — ArsB (PF02040.21), CitMHS (PF03600.23)
- 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 I6YCG9 (TrEMBL, unreviewed; 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 —
10 functional partner(s); context anchor
lppH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003797|Rv3578|arsB2 MTLAVALILLAVVLGFAVARPRGWPEAAAAVPAAVILLAIGAISPQQAMAQVSGLARVVAFLGAVLVLAKLCDDEGLFEAAGAAMARASAESHRLLRQVFAVSAAITAALCLDATVVLLTPVVLATVRRLRTPVRPYAYATAHLANAASLLLPVSNLTNLLAYHGAGISFTKFTLLMALPWLSAVAAVYVVFRWFFARDLRVVPDRQQLKPAPRLPMFVLVVVALTLGGFAVAESVGLAPTWAALAGAAVLALRSLRRGHTSVLRIARAVNVSFLVFVLALGVVVHAVMLNGMAARMSAVLPTGSGLPALLGIAALAAVLANVVNNLPATLVLVPLVAAGGPAAVLAVLLGVNIGPNLTYAGSLSNLLWRGVLRRHNVDASVGEYTRLGLCTVPAALAMAVLALWASAQVLGI