atpF Family assigned · medium auto-curated
H37Rv Rv1306 · MTBC0 mtbc0_001398 ·
171 aa · 1470360–1470875 (+) ·
RefSeq NP_215822.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ATP synthase subunit B |
|---|---|
| MTBC0 PGAP re-annotation | F0F1 ATP synthase subunit B |
| Revised (this work) | F0F1 ATP synthase subunit B. Pfam: ATP-synt_B (PF00430.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPV5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ATP synthase subunit b |
| Curated function | F(1)F(0) ATP synthase produces ATP from ADP in the presence of a proton or sodium gradient. F-type ATPases consist of two structural domains, F(1) containing the extramembraneous catalytic core and F(0) containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation..; FUNCTION: Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | atpF |
| eggNOG description | Component of the F(0) channel, it forms part of the peripheral stalk, linking F(1) to F(0) |
| Orthologous group | COG0711 |
| KEGG orthology |
K02109
|
| KEGG pathways |
map00190, map00195, map01100
|
| KEGG modules |
M00157
|
| Gene Ontology (16) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0005887, GO:0008150, GO:0016020, GO:0016021, GO:0030312, GO:0031224, GO:0031226, GO:0040007 +4 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 | n/a |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 0 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_B | PF00430.24 | 1.8e-32 | 30–160 | ATP synthase B/B' CF(0) |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: atpD (ATP synthase subunit beta), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1310 atpD |
ATP synthase subunit beta | 999 | 1000 ctx | neighborhood:619 coexpression:955 experimental:997 database:900 textmining:799 |
Rv1308 atpA |
ATP synthase subunit alpha | 999 | 1000 ctx | neighborhood:817 coexpression:925 experimental:997 database:900 textmining:854 |
Rv1309 atpG |
ATP synthase subunit gamma | 999 | 1000 ctx | neighborhood:817 coexpression:954 experimental:997 database:900 textmining:823 |
Rv1304 atpB |
ATP synthase subunit A | 999 | 1000 ctx | neighborhood:778 coexpression:949 experimental:997 database:900 textmining:851 |
Rv1307 atpH |
ATP synthase subunit b/delta | 999 | 1000 ctx | neighborhood:882 coexpression:949 experimental:997 database:900 |
Rv1305 atpE |
ATP synthase subunit C | 999 | 1000 ctx | neighborhood:836 coexpression:960 experimental:997 database:900 textmining:648 |
Rv1311 atpC |
ATP synthase subunit epsilon | 999 | 1000 ctx | neighborhood:730 coexpression:943 experimental:870 database:900 textmining:812 |
Rv1303 hyp |
hypothetical protein | 955 | 955 ctx | neighborhood:778 coexpression:731 |
Rv3628 ppa |
inorganic pyrophosphatase | 950 | 945 | coexpression:472 database:900 |
Rv1507c hyp |
hypothetical protein | 930 | 924 | coexpression:670 experimental:773 |
Rv2196 qcrB |
ubiquinol-cytochrome C reductase cytochrome subunit B | 938 | 879 | coexpression:879 textmining:517 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 889 | 817 | coexpression:817 textmining:419 |
Rv0682 rpsL |
30S ribosomal protein S12 | 887 | 776 | coexpression:774 textmining:519 |
Rv0701 rplC |
50S ribosomal protein L3 | 790 | 760 | coexpression:725 |
Rv0710 rpsQ |
30S ribosomal protein S17 | 798 | 743 | coexpression:708 |
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 B
- MTBC0 PGAP product: F0F1 ATP synthase subunit B
- Pfam (hmmscan --cut_ga): ATP-synt_B PF00430.24 (E=2e-32)
- (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_215822.1)
- Domains: Pfam-A via hmmscan --cut_ga — ATP-synt_B (PF00430.24)
- 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
COG0711 - Curated reference: UniProt P9WPV5 (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 —
125 functional partner(s); context anchor
atpD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001398|Rv1306|atpF MGEVSAIVLAASQAAEEGGESSNFLIPNGTFFVVLAIFLVVLAVIGTFVVPPILKVLRERDAMVAKTLADNKKSDEQFAAAQADYDEAMTEARVQASSLRDNARADGRKVIEDARVRAEQQVASTLQTAHEQLKRERDAVELDLRAHVGTMSATLASRILGVDLTASAATR