Rv3679 Family assigned · medium auto-curated
H37Rv Rv3679 · MTBC0 mtbc0_003899 ·
340 aa · 4142606–4143628 (+) ·
RefSeq NP_218196.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | anion transporter ATPase |
|---|---|
| MTBC0 PGAP re-annotation | ArsA family ATPase |
| Revised (this work) | ArsA family ATPase. Pfam: ArsA_ATPase (PF02374.22), CbiA (PF01656.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WKX5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ATPase BagA |
| EC (curated) |
EC 3.6.1.-
|
| Curated function | Component of the heterodimeric BagAB ATPase complex, whose two subunits are actively involved in ATP hydrolysis. The ATPase activity is required to mediate resistance against nitric oxide (NO) and elevated levels of glycerol. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | arsA_2 |
| eggNOG description | PFAM Anion-transporting ATPase |
| Orthologous group | COG0003 |
| Gene Ontology (8) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, GO:0044464, GO:0071944
|
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 | 0.214 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 3 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 |
|---|---|---|---|---|
ArsA_ATPase | PF02374.22 | 2.1e-15 | 22–181 | Anion-transporting ATPase |
CbiA | PF01656.30 | 1.6e-07 | 26–241 | CobQ/CobB/MinD/ParA nucleotide binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3680 (anion transporter ATPase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3680 |
anion transporter ATPase | 999 | 1000 ctx | neighborhood:882 experimental:999 database:900 |
Rv3678A hyp |
hypothetical protein | 785 | 785 ctx | neighborhood:783 |
Rv3678c hyp |
hypothetical protein | 781 | 781 ctx | neighborhood:774 |
Rv3677c |
beta lactamase | 783 | 776 ctx | neighborhood:774 |
Rv0487 hyp |
hypothetical protein | 759 | 759 ctx | cooccurence:758 |
Rv2185c TB16.3 hyp |
hypothetical protein | 720 | 720 ctx | cooccurence:708 |
Rv0857 hyp |
hypothetical protein | 715 | 716 ctx | cooccurence:715 |
Rv0854 hyp |
hypothetical protein | 697 | 697 ctx | cooccurence:686 |
Rv0244c fadE5 |
acyl-CoA dehydrogenase FadE5 | 684 | 685 ctx | cooccurence:682 |
Rv0474 |
HTH-type transcriptional regulator | 665 | 665 ctx | cooccurence:663 |
Rv1467c fadE15 |
acyl-CoA dehydrogenase | 651 | 652 ctx | cooccurence:647 |
Rv0501 galE2 |
UDP-glucose 4-epimerase GalE | 630 | 630 ctx | cooccurence:627 |
Rv0502 hyp |
hypothetical protein | 624 | 624 ctx | cooccurence:619 |
Rv3662c hyp |
hypothetical protein | 585 | 585 ctx | cooccurence:582 |
Rv1691 hyp |
hypothetical protein | 578 | 556 | database:410 |
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: anion transporter ATPase
- MTBC0 PGAP product: ArsA family ATPase
- Pfam (hmmscan --cut_ga): ArsA_ATPase PF02374.22 (E=2e-15), CbiA PF01656.30 (E=2e-07)
- (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_218196.1)
- Domains: Pfam-A via hmmscan --cut_ga — ArsA_ATPase (PF02374.22), CbiA (PF01656.30)
- 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
COG0003 - Curated reference: UniProt P9WKX5 (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 —
29 functional partner(s); context anchor
Rv3680 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003899|Rv3679| MVATTSSGGSSVGWPSRLSGVRLHLVTGKGGTGKSTIAAALALTLAAGGRKVLLVEVEGRQGIAQLFDVPPLPYQELKIATAERGGQVNALAIDIEAAFLEYLDMFYNLGIAGRAMRRIGAVEFATTIAPGLRDVLLTGKIKETVVRLDKNKLPVYDAIVVDAPPTGRIARFLDVTKAVSDLAKGGPVHAQSEGVVKLLHSNQTAIHLVTLLEALPVQETLEAIEELAQMELPIGSVIVNRNIPAHLEPQDLAKAAEGEVDADSVRAGLLTAGVKLPDADFAGLLTETIQHATRITARAEIAQQLDALQVPRLELPTVSDGVDLGSLYELSESLAQQGVR