atpC Family assigned · medium auto-curated
H37Rv Rv1311 · MTBC0 mtbc0_001403 ·
121 aa · 1476354–1476719 (+) ·
RefSeq NP_215827.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ATP synthase subunit epsilon |
|---|---|
| MTBC0 PGAP re-annotation | F0F1 ATP synthase subunit epsilon |
| Revised (this work) | F0F1 ATP synthase subunit epsilon. Pfam: ATP-synt_DE_N (PF02823.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPV1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ATP synthase epsilon chain |
| Curated function | Produces ATP from ADP in the presence of a proton gradient across the membrane. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | atpC |
| eggNOG description | Produces ATP from ADP in the presence of a proton gradient across the membrane |
| Orthologous group | COG0355 |
| KEGG orthology |
K02114
|
| KEGG pathways |
map00190, map00195, map01100
|
| KEGG modules |
M00157
|
| Gene Ontology (95) |
GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005886, GO:0006139, GO:0006163, GO:0006164, GO:0006725, GO:0006753, GO:0006754, GO:0006793 +83 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 | 0.11 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 1 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 |
|---|---|---|---|---|
ATP-synt_DE_N | PF02823.22 | 1.5e-23 | 4–84 | ATP synthase, Delta/Epsilon chain, beta-sandwich domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: atpF (ATP synthase subunit B), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1306 atpF |
ATP synthase subunit B | 999 | 1000 ctx | neighborhood:730 coexpression:943 experimental:870 database:900 textmining:812 |
Rv1309 atpG |
ATP synthase subunit gamma | 999 | 1000 ctx | neighborhood:812 cooccurence:500 coexpression:973 experimental:997 database:965 textmining:838 |
Rv1308 atpA |
ATP synthase subunit alpha | 999 | 1000 ctx | neighborhood:812 coexpression:967 experimental:928 database:984 textmining:804 |
Rv1310 atpD |
ATP synthase subunit beta | 999 | 1000 ctx | neighborhood:867 coexpression:976 experimental:928 database:984 textmining:837 |
Rv1305 atpE |
ATP synthase subunit C | 999 | 1000 ctx | neighborhood:738 cooccurence:436 coexpression:958 experimental:997 database:970 textmining:569 |
Rv1307 atpH |
ATP synthase subunit b/delta | 999 | 1000 ctx | neighborhood:750 coexpression:999 experimental:999 database:980 textmining:819 |
Rv1304 atpB |
ATP synthase subunit A | 999 | 1000 ctx | neighborhood:664 cooccurence:546 coexpression:861 experimental:928 database:967 textmining:823 |
Rv1507c hyp |
hypothetical protein | 985 | 984 | coexpression:730 experimental:829 database:662 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 956 | 933 | coexpression:918 |
Rv3628 ppa |
inorganic pyrophosphatase | 924 | 925 | database:900 |
Rv1312 hyp |
hypothetical protein | 881 | 881 ctx | neighborhood:881 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 899 | 859 | coexpression:827 |
Rv3456c rplQ |
50S ribosomal protein L17 | 883 | 854 | coexpression:854 |
Rv3150 nuoF |
NADH-quinone oxidoreductase subunit F | 883 | 834 | coexpression:834 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 886 | 827 | coexpression:804 |
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: ATP synthase subunit epsilon
- MTBC0 PGAP product: F0F1 ATP synthase subunit epsilon
- Pfam (hmmscan --cut_ga): ATP-synt_DE_N PF02823.22 (E=2e-23)
- (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_215827.1)
- Domains: Pfam-A via hmmscan --cut_ga — ATP-synt_DE_N (PF02823.22)
- 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
COG0355 - Curated reference: UniProt P9WPV1 (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 —
162 functional partner(s); context anchor
atpF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001403|Rv1311|atpC MAELNVEIVAVDRNIWSGTAKFLFTRTTVGEIGILPRHIPLVAQLVDDAMVRVEREGEKDLRIAVDGGFLSVTEEGVSILAESAEFESEIDEAAAKQDSESDDPRIAARGRARLRAVGAID