yjcE Resolved · high auto-curated
H37Rv Rv2287 · MTBC0 - ·
542 aa · 2559703–2561331 (+) ·
RefSeq NP_216803.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | Na(+)/H(+) transporter |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Na(+)/H(+) transporter. Pfam: Na_H_Exchanger (PF00999.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WJI3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized Na(+)/H(+) exchanger Rv2287 |
UniProt still lists this protein as Uncharacterized Na(+)/H(+) exchanger Rv2287; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | yjcE |
| eggNOG description | Sodium hydrogen exchanger |
| Orthologous group | COG0025 |
| KEGG orthology |
K03316
|
| Gene Ontology (70) |
GO:0003674, GO:0005215, GO:0005451, GO:0005575, GO:0005623, GO:0005886, GO:0006810, GO:0006811, GO:0006812, GO:0006813, GO:0006814, GO:0006873 +58 more
|
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 | 0.23 · 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 |
|---|---|---|---|---|
Na_H_Exchanger | PF00999.27 | 4.4e-63 | 23–417 | Sodium/hydrogen exchanger, transmembrane |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: cdh (CDP-diacylglycerol pyrophosphatase), high confidence from genomic context alone (score 784 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2288 hyp |
hypothetical protein | 786 | 786 ctx | neighborhood:781 |
Rv2289 cdh |
CDP-diacylglycerol pyrophosphatase | 784 | 784 ctx | neighborhood:781 |
Rv3696c glpK |
glycerol kinase | 608 | 591 | database:518 |
Rv2286c hyp |
hypothetical protein | 565 | 565 ctx | neighborhood:559 |
Rv0200 |
transmembrane protein | 524 | 503 | database:435 |
Rv2290 lppO |
lipoprotein LppO | 502 | 502 ctx | neighborhood:499 |
Rv1973 |
Mce associated membrane protein | 522 | 501 | database:435 |
Rv1363c |
membrane protein | 522 | 501 | database:435 |
Rv2390c hyp |
hypothetical protein | 522 | 501 | database:435 |
Rv0199 |
membrane protein | 522 | 500 | database:435 |
Rv1362c |
membrane protein | 522 | 500 | database:435 |
Rv1972 |
Mce associated membrane protein | 522 | 500 | database:435 |
Rv0178 |
Mce associated membrane protein | 521 | 499 | database:435 |
Rv3492c |
Mce associated protein | 520 | 498 | database:435 |
Rv0177 |
Mce associated protein | 519 | 497 | database:435 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): Na(+)/H(+) transporter
- Pfam (hmmscan --cut_ga): Na_H_Exchanger PF00999.27 (E=4e-63)
- (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_216803.1)
- Domains: Pfam-A via hmmscan --cut_ga — Na_H_Exchanger (PF00999.27)
- 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
COG0025 - Curated reference: UniProt P9WJI3 (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 —
25 functional partner(s); context anchor
cdh - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2287|yjcE MNGRRTIGEDGLVFGLVVIVALVAAVVVGTVLGHRYRVGPPVLLILSGSLLGLIPRFGDVQIDGEVVLLLFLPAILYWESMNTSFREIRWNLRVIVMFSIGLVIATAVAVSWTARALGMESHAAAVLGAVLSPTDAAAVAGLAKRLPRRALTVLRGESLINDGTALVLFAVTVAVAEGAAGIGPAALVGRFVVSYLGGIMAGLLVGGLVTLLRRRIDAPLEEGALSLLTPFAAFLLAQSLKCSGVVAVLVSALVLTYVGPTVIRARSRLQAHAFWDIATFLINGSLWVFVGVQIPGAIDHIAGEDGGLPRATVLALAVTGVVIATRIAWVQATTVLGHTVDRVLKKPTRHVGFRQRCVTSWAGFRGAVSLAAALAVPMTTNSGAPFPDRNLIIFVVSVVILVTVLVQGTSLPTVVRWARMPEDVAHANELQLARTRSAQAALDALPTVADELGVAPDLVKHLEKEYEERAVLVMADGADSATSDLAERNDLVRRVRLGVLQHQRQAVTTLRNQNLIDDIVLRELQAAMDLEEVQLLDPADAE