chaA Resolved · high auto-curated
H37Rv Rv1607 · MTBC0 mtbc0_001713 ·
360 aa · 1818145–1819227 (+) ·
RefSeq NP_216123.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ionic transporter integral membrane protein ChaA |
|---|---|
| MTBC0 PGAP re-annotation | calcium:proton antiporter |
| Revised (this work) | Calcium:proton antiporter. Pfam: Na_Ca_ex (PF01699.30). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O53910
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable ionic transporter integral membrane protein ChaA |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | chaA |
| eggNOG description | Sodium/calcium exchanger protein |
| Orthologous group | COG0387 |
| KEGG orthology |
K07300
|
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 | 0.958 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 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 |
|---|---|---|---|---|
Na_Ca_ex | PF01699.30 | 1.3e-15 | 216–358 | Sodium/calcium exchanger protein |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: vapC21 (ribonuclease VapC21), medium confidence from genomic context alone (score 502 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2757c vapC21 |
ribonuclease VapC21 | 502 | 502 ctx | cooccurence:499 |
Rv1605 hisF |
imidazole glycerol phosphate synthase subunit HisF | 489 | 490 ctx | neighborhood:482 |
Rv1604 impA |
inositol-monophosphatase ImpA | 485 | 486 ctx | neighborhood:473 |
Rv1606 hisI |
phosphoribosyl-AMP cyclohydrolase | 484 | 485 ctx | neighborhood:474 |
Rv1603 hisA |
1-(5-phosphoribosyl)-5-((5-phosphoribosylamino)methylideneamino)imidazole-4-carboxamide isomerase | 505 | 480 ctx | neighborhood:472 |
Rv1602 hisH |
imidazole glycerol phosphate synthase subunit HisH | 474 | 475 ctx | neighborhood:467 |
Rv1599 hisD |
histidinol dehydrogenase | 474 | 474 ctx | neighborhood:466 |
Rv0529 ccsA |
cytochrome C-type biogenesis protein CcsA | 474 | 474 | coexpression:474 |
Rv1601 hisB |
imidazole glycerol-phosphate dehydratase | 471 | 471 ctx | neighborhood:467 |
Rv1600 hisC1 |
histidinol-phosphate aminotransferase | 457 | 457 ctx | neighborhood:452 |
Rv3335c yhjD |
integral membrane protein | 446 | 447 | coexpression:429 |
Rv2707 hyp |
hypothetical protein | 440 | 441 | coexpression:423 |
Rv0229c vapC51 hyp |
hypothetical protein | 440 | 440 ctx | cooccurence:439 |
Rv2323c hyp |
hypothetical protein | 427 | 427 | coexpression:424 |
Rv3846 sodA |
superoxide dismutase | 422 | 423 | coexpression:423 |
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: ionic transporter integral membrane protein ChaA
- MTBC0 PGAP product: calcium:proton antiporter
- Pfam (hmmscan --cut_ga): Na_Ca_ex PF01699.30 (E=1e-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_216123.1)
- Domains: Pfam-A via hmmscan --cut_ga — Na_Ca_ex (PF01699.30)
- 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
COG0387 - Curated reference: UniProt O53910 (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 —
22 functional partner(s); context anchor
vapC21 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001713|Rv1607|chaA MLKRVPWTVVLPSLAFVALVLTWGKQIGPVVGLLAAVLLAGAVLAAVNHAEVVAARVGEPFGSLVLAVAVTTIEVALIVALMVSGGDDAATLARDTVFAAVMITTNGIAGLSLLLGSLRYGVTLFNPHGSGAALATVTTLATLSLVLPTFTTSQSGPELSPGQLIFAGAASLGLYVLFLFTQTVRHRDFFLPVAQKGAVEDDSHADPPSTRAALLSLGLLLVALVAVVGLAKVESPVIEEVVSAAGFPQSFVGVVIATLVLLPETLAAARAARQGRLQTSLNLAYGSAMASIGLTIPTIALASLWLSGPLQLGLGAIQLVLLVLTVVVSVLTVVPGRATRLQGEVHLVLLAAYLFLAVVP