arsC Family assigned · medium auto-curated
H37Rv Rv2643 · MTBC0 mtbc0_002813 ·
498 aa · 2990471–2991967 (+) ·
RefSeq NP_217159.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | arsenic-transport integral membrane protein ArsC |
|---|---|
| MTBC0 PGAP re-annotation | ACR3 family arsenite efflux transporter |
| Revised (this work) | ACR3 family arsenite efflux transporter. Pfam: SBF (PF01758.22), LMWPc (PF01451.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X4W4
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable arsenic-transport integral membrane protein ArsC |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | arsB |
| eggNOG description | arsenical-resistance protein |
| Orthologous group | COG0394 |
| EC number |
EC 1.20.4.1
|
| KEGG orthology |
K03325, K03741
|
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 | 1.495 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 8 missense, 0 nonsense, 2 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 0.65% of strains (951) · 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 |
|---|---|---|---|---|
SBF | PF01758.22 | 1.1e-60 | 62–258 | Sodium Bile acid symporter family |
LMWPc | PF01451.28 | 6.6e-15 | 366–491 | Low molecular weight phosphotyrosine protein phosphatase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2642 (ArsR family transcriptional regulator), high confidence from genomic context alone (score 940 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2642 |
ArsR family transcriptional regulator | 954 | 940 ctx | neighborhood:882 |
Rv2641 cadI |
cadmium inducible protein CadI | 965 | 817 ctx | neighborhood:756 textmining:820 |
Rv2640c |
ArsR family transcriptional regulator | 851 | 802 ctx | neighborhood:687 |
Rv0324 |
transcriptional regulator | 805 | 729 ctx | neighborhood:479 |
Rv1674c |
transcriptional regulator | 804 | 728 ctx | neighborhood:479 |
Rv2874 dipZ |
integral membrane C-type cytochrome biogenesis protein DipZ | 772 | 554 ctx | neighborhood:544 textmining:510 |
Rv1471 trxB1 |
thioredoxin | 657 | 542 | experimental:438 |
Rv3914 trxC |
thioredoxin TrxC | 647 | 529 | experimental:438 |
Rv1470 trxA |
thioredoxin TrxA | 645 | 526 | experimental:438 |
Rv1324 |
thioredoxin | 643 | 523 | experimental:438 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 585 | 523 | |
Rv1527c pks5 |
polyketide synthase | 585 | 523 | |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 584 | 522 | |
Rv2933 ppsC |
phthiocerol synthesis polyketide synthase type I PpsC | 584 | 522 | |
Rv2048c pks12 |
polyketide synthase | 584 | 522 |
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 ArsC
- MTBC0 PGAP product: ACR3 family arsenite efflux transporter
- Pfam (hmmscan --cut_ga): SBF PF01758.22 (E=1e-60), LMWPc PF01451.28 (E=7e-15)
- (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_217159.1)
- Domains: Pfam-A via hmmscan --cut_ga — SBF (PF01758.22), LMWPc (PF01451.28)
- 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
COG0394 - Curated reference: UniProt I6X4W4 (TrEMBL, unreviewed; 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 —
81 functional partner(s); context anchor
Rv2642 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002813|Rv2643|arsC MTETVTRTAAPAVVGKLSTLDRFLPVWIGSAMAAGLLLGRWIPGLHTALEGVQLDGISLPIALGLLIMMYPVLAKVRYDRLDTVTGDRKLLLSSLLLNWVLGPALMFALAWLLLADLPEYRTGLIIVGLARCIAMVIIWNDLACGDREAAAVLVALNSIFQVAMFAALGWFYLSVLPGWLGLEQTTIATSPWQIAKSVLIFLGIPLLAGYLSRRIGEKTKGRNWYESRFLPKVGPWALYGLLFTIVILFALQGDQITGRPLDVARIALPLLAYFAIMWVGGYLLGAALRLGYRRTTTLAFTAASNNFELAIAVAIATYGATSGQALAGVVGPLIEVPVLVGLVYVSLALRNRLAGPNATHDADKPSVLFVCVHNAGRSQMAAGLLTHLAGDRIEVRSAGTEPAGQVNPTAVAAMAEMGIDITANAPTLLTGGQVQSSDVVITMGCGDACPYFPGVSYRNWKLPDPAGQPLDVVRMIRDDIADRVQALIAELLATAKTR