atpD Family assigned · medium auto-curated
H37Rv Rv1310 · MTBC0 mtbc0_001402 ·
486 aa · 1474880–1476340 (+) ·
RefSeq NP_215826.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ATP synthase subunit beta |
|---|---|
| MTBC0 PGAP re-annotation | F0F1 ATP synthase subunit beta |
| Revised (this work) | F0F1 ATP synthase subunit beta. Pfam: ATP-synt_ab_N (PF02874.30), ATP-synt_ab (PF00006.32), ATP-synt_VA_C (PF22919.2). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPU5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ATP synthase subunit beta |
| EC (curated) |
EC 7.1.2.2
|
| Curated function | Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | atpD |
| eggNOG description | Produces ATP from ADP in the presence of a proton gradient across the membrane. The catalytic sites are hosted primarily by the beta subunits |
| Orthologous group | COG0055 |
| EC number |
EC 3.6.3.14
|
| KEGG orthology |
K02112
|
| KEGG pathways |
map00190, map00195, map01100
|
| KEGG modules |
M00157
|
| Gene Ontology (16) |
GO:0005575, GO:0005576, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0016020, GO:0030312, 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 | 0.083 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 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_ab_N | PF02874.30 | 5.9e-19 | 23–94 | ATP synthase alpha/beta family, beta-barrel domain |
ATP-synt_ab | PF00006.32 | 2.6e-70 | 151–364 | ATP synthase alpha/beta family, nucleotide-binding domain |
ATP-synt_VA_C | PF22919.2 | 2.2e-15 | 371–435 | C-terminal domain of V and A type ATP synthase |
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:619 coexpression:955 experimental:997 database:900 textmining:799 |
Rv1308 atpA |
ATP synthase subunit alpha | 999 | 1000 ctx | neighborhood:823 coexpression:968 experimental:997 database:984 textmining:518 |
Rv1309 atpG |
ATP synthase subunit gamma | 999 | 1000 ctx | neighborhood:823 cooccurence:774 coexpression:976 experimental:997 database:965 textmining:877 |
Rv1304 atpB |
ATP synthase subunit A | 999 | 1000 ctx | neighborhood:707 cooccurence:735 coexpression:967 experimental:928 database:964 textmining:799 |
Rv1307 atpH |
ATP synthase subunit b/delta | 999 | 1000 ctx | neighborhood:666 coexpression:999 experimental:999 database:968 textmining:818 |
Rv1311 atpC |
ATP synthase subunit epsilon | 999 | 1000 ctx | neighborhood:867 coexpression:976 experimental:928 database:984 textmining:837 |
Rv1305 atpE |
ATP synthase subunit C | 999 | 1000 ctx | neighborhood:613 coexpression:968 experimental:928 database:975 textmining:567 |
Rv1507c hyp |
hypothetical protein | 985 | 984 | coexpression:729 experimental:829 database:661 |
Rv3628 ppa |
inorganic pyrophosphatase | 939 | 930 | database:900 |
Rv3457c rpoA |
DNA-directed RNA polymerase subunit alpha | 933 | 887 | coexpression:844 textmining:438 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 896 | 871 | coexpression:854 |
Rv0685 tuf |
elongation factor Tu | 952 | 869 | coexpression:852 textmining:652 |
Rv0708 rplP |
50S ribosomal protein L16 | 905 | 864 | coexpression:845 |
Rv0721 rpsE |
30S ribosomal protein S5 | 877 | 851 | coexpression:825 |
Rv0667 rpoB |
DNA-directed RNA polymerase subunit beta | 959 | 849 | coexpression:795 textmining:744 |
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 beta
- MTBC0 PGAP product: F0F1 ATP synthase subunit beta
- Pfam (hmmscan --cut_ga): ATP-synt_ab_N PF02874.30 (E=6e-19), ATP-synt_ab PF00006.32 (E=3e-70), ATP-synt_VA_C PF22919.2 (E=2e-15)
- (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_215826.1)
- Domains: Pfam-A via hmmscan --cut_ga — ATP-synt_ab_N (PF02874.30), ATP-synt_ab (PF00006.32), ATP-synt_VA_C (PF22919.2)
- 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
COG0055 - Curated reference: UniProt P9WPU5 (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 —
253 functional partner(s); context anchor
atpF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001402|Rv1310|atpD MTTTAEKTDRPGKPGSSDTSGRVVRVTGPVVDVEFPRGSIPELFNALHAEITFESLAKTLTLEVAQHLGDNLVRTISLQPTDGLVRGVEVIDTGRSISVPVGEGVKGHVFNALGDCLDEPGYGEKFEHWSIHRKPPAFEELEPRTEMLETGLKVVDLLTPYVRGGKIALFGGAGVGKTVLIQEMINRIARNFGGTSVFAGVGERTREGNDLWVELAEANVLKDTALVFGQMDEPPGTRMRVALSALTMAEWFRDEQGQDVLLFIDNIFRFTQAGSEVSTLLGRMPSAVGYQPTLADEMGELQERITSTRGRSITSMQAVYVPADDYTDPAPATTFAHLDATTELSRAVFSKGIFPAVDPLASSSTILDPSVVGDEHYRVAQEVIRILQRYKDLQDIIAILGIDELSEEDKQLVNRARRIERFLSQNMMAAEQFTGQPGSTVPVKETIEAFDRLCKGDFDHVPEQAFFLIGGLDDLAKKAESLGAKL