ceoC Resolved · high auto-curated
H37Rv Rv2692 · MTBC0 - ·
220 aa · 3010024–3010686 (+) ·
RefSeq YP_177901.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | TRK system potassium uptake protein CeoC |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | TRK system potassium uptake protein CeoC. Pfam: NAD_binding_7 (PF13241.13), F420_oxidored (PF03807.24), TrkA_N (PF02254.25), ApbA (PF02558.23), NAD_binding_10 (PF13460.13), TrkA_C (PF02080.27). |
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 |
P9WFZ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Trk system potassium uptake protein TrkA |
| Curated function | Part of a potassium transport system. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | ceoC |
| eggNOG description | Trk system potassium uptake protein |
| Orthologous group | COG0569 |
| KEGG orthology |
K03499
|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 synonymous, 2 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 |
|---|---|---|---|---|
NAD_binding_7 | PF13241.13 | 5.5e-06 | 2–87 | Putative NAD(P)-binding |
F420_oxidored | PF03807.24 | 2.3e-05 | 2–84 | NADP oxidoreductase coenzyme F420-dependent |
TrkA_N | PF02254.25 | 2.2e-27 | 3–118 | TrkA-N domain |
ApbA | PF02558.23 | 1.7e-05 | 3–39 | Ketopantoate reductase PanE/ApbA |
NAD_binding_10 | PF13460.13 | 1.5e-06 | 7–77 | NAD(P)H-binding |
TrkA_C | PF02080.27 | 1.2e-11 | 149–216 | TrkA-C domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ceoB (TRK system potassium uptake protein CeoB), high confidence from genomic context alone (score 931 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2691 ceoB |
TRK system potassium uptake protein CeoB | 951 | 931 ctx | neighborhood:882 |
Rv2690c |
integral membrane protein | 914 | 911 ctx | neighborhood:741 cooccurence:665 |
Rv2694c hyp |
hypothetical protein | 718 | 718 ctx | cooccurence:717 |
Rv2689c hyp |
hypothetical protein | 686 | 685 ctx | neighborhood:684 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 672 | 672 | coexpression:574 |
Rv0260c |
transcriptional regulator | 592 | 583 | coexpression:452 |
Rv0511 hemD |
uroporphyrin-III C-methyltransferase | 480 | 480 | coexpression:450 |
Rv3323c moaX |
MoaD-MoaE fusion protein MoaX | 464 | 463 | coexpression:458 |
Rv3119 moaE1 |
molybdopterin synthase catalytic subunit 1 | 461 | 462 | coexpression:461 |
Rv0866 moaE2 |
molybdopterin synthase catalytic subunit 2 | 461 | 462 | coexpression:461 |
Rv1631 coaE |
dephospho-CoA kinase CoaE | 449 | 450 | coexpression:418 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA | 400 | 213 | |
Rv3237c hyp |
hypothetical protein | 508 | 91 | textmining:481 |
Rv3200c |
transmembrane cation transporter | 482 | 47 | textmining:479 |
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): TRK system potassium uptake protein CeoC
- Pfam (hmmscan --cut_ga): NAD_binding_7 PF13241.13 (E=5e-06), F420_oxidored PF03807.24 (E=2e-05), TrkA_N PF02254.25 (E=2e-27), ApbA PF02558.23 (E=2e-05), NAD_binding_10 PF13460.13 (E=2e-06), TrkA_C PF02080.27 (E=1e-11)
- (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 YP_177901.1)
- Domains: Pfam-A via hmmscan --cut_ga — NAD_binding_7 (PF13241.13), F420_oxidored (PF03807.24), TrkA_N (PF02254.25), ApbA (PF02558.23), NAD_binding_10 (PF13460.13), TrkA_C (PF02080.27)
- 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
COG0569 - Curated reference: UniProt P9WFZ3 (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 —
14 functional partner(s); context anchor
ceoB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv2692|ceoC MKVAVAGAGAVGRSVTRELVENGHDITLIERNPDHLDAAAIPEAHWRLGDACELSLLESIHLEEFDVVVAATGDDKVNVVLSLLAKTEFAVPRVVARVNDPRNEWLFNDAWGVDVAVSTPRMLASLIEEAVTIGDLVRLMEFRTGQANLVEITLPDNTPWGGKPVRKLQLPRDAALVTILRGPRVIVPEADEPLEGGDELLFVAVTEAEEELSRLLLPSM