Rv2025c Family assigned · medium auto-curated
H37Rv Rv2025c · MTBC0 mtbc0_002158 ·
332 aa · 2299363–2300361 (-) ·
RefSeq NP_216541.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | cation efflux system protein |
|---|---|
| MTBC0 PGAP re-annotation | cation diffusion facilitator family transporter |
| Revised (this work) | Cation diffusion facilitator family transporter. Pfam: Cation_efflux (PF01545.27), ZT_dimer (PF16916.12). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGF5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable cation efflux system protein Rv2025c |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | Belongs to the cation diffusion facilitator (CDF) transporter (TC 2.A.4) family |
| Orthologous group | COG0053 |
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 | 1.619 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 9 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 |
|---|---|---|---|---|
Cation_efflux | PF01545.27 | 2.2e-46 | 44–237 | Cation efflux transmembrane domain |
ZT_dimer | PF16916.12 | 1.5e-13 | 242–315 | Cation efflux protein, cytoplasmic domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2026c (universal stress protein), medium confidence from genomic context alone (score 523 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1240 mdh |
malate dehydrogenase | 679 | 679 | coexpression:668 |
Rv0827c kmtR |
HTH-type transcriptional regulator KmtR | 912 | 539 | textmining:817 |
Rv2026c |
universal stress protein | 523 | 523 ctx | neighborhood:517 |
Rv2027c dosT |
two component sensor histidine kinase DosT | 494 | 489 ctx | neighborhood:467 |
Rv2226 hyp |
hypothetical protein | 483 | 484 ctx | cooccurence:479 |
Rv2028c |
universal stress protein | 477 | 478 | |
Rv1712 cmk |
cytidylate kinase | 420 | 420 | coexpression:401 |
Rv0648 |
alpha-mannosidase | 417 | 418 | coexpression:418 |
Rv0846c mmcO |
oxidase | 417 | 380 | |
Rv1674c |
transcriptional regulator | 482 | 304 | |
Rv2856 nicT |
nickel-transport integral membrane protein NicT | 409 | 241 | |
Rv3270 ctpC |
manganese/zinc-exporting P-type ATPase | 610 | 196 | textmining:536 |
Rv3743c ctpJ |
cation transporter ATPase J | 616 | 195 | textmining:544 |
Rv1469 ctpD |
cobalt/nickel-exporting P-type ATPase | 637 | 188 | textmining:572 |
Rv0052 hyp |
hypothetical protein | 447 | 155 |
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: cation efflux system protein
- MTBC0 PGAP product: cation diffusion facilitator family transporter
- Pfam (hmmscan --cut_ga): Cation_efflux PF01545.27 (E=2e-46), ZT_dimer PF16916.12 (E=1e-13)
- (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_216541.1)
- Domains: Pfam-A via hmmscan --cut_ga — Cation_efflux (PF01545.27), ZT_dimer (PF16916.12)
- 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
COG0053 - Curated reference: UniProt P9WGF5 (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 —
22 functional partner(s); context anchor
Rv2026c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002158|Rv2025c| MTHDHAHSRGVPAMIKEIFAPHSHDAADSVDDTLESTAAGIRTVKISLLVLGLTALIQIVIVVMSGSVALAADTIHNFADALTAVPLWIAFALGAKPATRRYTYGFGRVEDLAGSFVVAMITMSAIIAGYEAIARLIHPQQIEHVGWVALAGLVGFIGNEWVALYRIRVGHRIGSAALIADGLHARTDGFTSLAVLCSAGGVALGFPLADPIVGLLITAAILAVLRTAARDVFRRLLDGVDPAMVDAAEQALAARPGVQAVRSVRMRWIGHRLHADAELDVDPALDLAQAHRIAHDAEHELTHTVPKLTTALIHAYPAEHGSSIPDRGRTVE