atpB Family assigned · medium auto-curated
H37Rv Rv1304 · MTBC0 mtbc0_001396 ·
250 aa · 1469283–1470035 (+) ·
RefSeq NP_215820.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ATP synthase subunit A |
|---|---|
| MTBC0 PGAP re-annotation | F0F1 ATP synthase subunit A |
| Revised (this work) | F0F1 ATP synthase subunit A. Pfam: ATP-synt_A (PF00119.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPV7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ATP synthase subunit a |
| Curated function | Key component of the proton channel; it plays a direct role in the translocation of protons across the membrane. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | atpB |
| eggNOG description | it plays a direct role in the translocation of protons across the membrane |
| Orthologous group | COG0356 |
| KEGG orthology |
K02108
|
| KEGG pathways |
map00190, map00195, map01100
|
| KEGG modules |
M00157
|
| Gene Ontology (128) |
GO:0003674, GO:0003824, GO:0005215, GO:0005575, GO:0005622, GO:0005623, GO:0005886, GO:0005887, GO:0006139, GO:0006163, GO:0006164, GO:0006725 +116 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 | 0.491 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
ATP-synt_A | PF00119.26 | 1.3e-47 | 31–240 | ATP synthase A chain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: atpH (ATP synthase subunit b/delta), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1307 atpH |
ATP synthase subunit b/delta | 999 | 1000 ctx | neighborhood:778 cooccurence:431 coexpression:999 experimental:999 database:972 textmining:820 |
Rv1311 atpC |
ATP synthase subunit epsilon | 999 | 1000 ctx | neighborhood:664 cooccurence:546 coexpression:861 experimental:928 database:967 textmining:823 |
Rv1305 atpE |
ATP synthase subunit C | 999 | 1000 ctx | neighborhood:813 cooccurence:582 coexpression:957 experimental:997 database:984 textmining:754 |
Rv1310 atpD |
ATP synthase subunit beta | 999 | 1000 ctx | neighborhood:707 cooccurence:735 coexpression:967 experimental:928 database:964 textmining:799 |
Rv1308 atpA |
ATP synthase subunit alpha | 999 | 1000 ctx | neighborhood:738 cooccurence:735 coexpression:958 experimental:928 database:972 textmining:824 |
Rv1309 atpG |
ATP synthase subunit gamma | 999 | 1000 ctx | neighborhood:738 cooccurence:754 coexpression:970 experimental:928 database:962 textmining:829 |
Rv1306 atpF |
ATP synthase subunit B | 999 | 1000 ctx | neighborhood:778 coexpression:949 experimental:997 database:900 textmining:851 |
Rv2193 ctaE |
cytochrome C oxidase subunit III | 992 | 990 | coexpression:890 experimental:916 |
Rv1507c hyp |
hypothetical protein | 984 | 983 | coexpression:730 experimental:829 database:638 |
Rv1303 hyp |
hypothetical protein | 981 | 977 ctx | neighborhood:882 cooccurence:684 coexpression:423 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 972 | 964 | coexpression:964 |
Rv3628 ppa |
inorganic pyrophosphatase | 928 | 918 | database:900 |
Rv2200c ctaC |
cytochrome C oxidase subunit II | 913 | 886 | coexpression:886 |
Rv3152 nuoH |
NADH-quinone oxidoreductase subunit H | 901 | 870 | coexpression:861 |
Rv3157 nuoM |
NADH-quinone oxidoreductase subunit M | 900 | 870 | coexpression:860 |
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 A
- MTBC0 PGAP product: F0F1 ATP synthase subunit A
- Pfam (hmmscan --cut_ga): ATP-synt_A PF00119.26 (E=1e-47)
- (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_215820.1)
- Domains: Pfam-A via hmmscan --cut_ga — ATP-synt_A (PF00119.26)
- 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
COG0356 - Curated reference: UniProt P9WPV7 (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 —
148 functional partner(s); context anchor
atpH - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001396|Rv1304|atpB MTETILAAQIEVGEHHTATWLGMTVNTDTVLSTAIAGLIVIALAFYLRAKVTSTDVPGGVQLFFEAITIQMRNQVESAIGMRIAPFVLPLAVTIFVFILISNWLAVLPVQYTDKHGHTTELLKSAAADINYVLALALFVFVCYHTAGIWRRGIVGHPIKLLKGHVTLLAPINLVEEVAKPISLSLRLFGNIFAGGILVALIALFPPYIMWAPNAIWKAFDLFVGAIQAFIFALLTILYFSQAMELEEEHH