atpH Family assigned · medium auto-curated
H37Rv Rv1307 · MTBC0 mtbc0_001399 ·
446 aa · 1470882–1472222 (+) ·
RefSeq NP_215823.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ATP synthase subunit b/delta |
|---|---|
| MTBC0 PGAP re-annotation | F0F1 ATP synthase subunit B/delta |
| Revised (this work) | F0F1 ATP synthase subunit B/delta. Pfam: ATP-synt_B (PF00430.24), OSCP (PF00213.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPV3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ATP synthase subunit b-delta [Includes: 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 (By similarity)..; FUNCTION: This fusion protein includes a component of the F(0) channel (subunit b) and of the F(1) subunit (subunit delta). Two. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | atpH |
| eggNOG description | 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 |
| Orthologous group | COG0711 |
| KEGG orthology |
K02109, K02113
|
| KEGG pathways |
map00190, map00195, map01100
|
| KEGG modules |
M00157
|
| Gene Ontology (10) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0030312, GO:0040007, 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 | 0.961 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 8 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 | 4.1e-19 | 3–132 | ATP synthase B/B' CF(0) |
OSCP | PF00213.24 | 5.9e-28 | 277–441 | ATP synthase delta (OSCP) subunit |
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:882 coexpression:949 experimental:997 database:900 |
Rv1309 atpG |
ATP synthase subunit gamma | 999 | 1000 ctx | neighborhood:817 coexpression:999 experimental:999 database:964 textmining:932 |
Rv1308 atpA |
ATP synthase subunit alpha | 999 | 1000 ctx | neighborhood:817 coexpression:999 experimental:999 database:983 textmining:897 |
Rv1310 atpD |
ATP synthase subunit beta | 999 | 1000 ctx | neighborhood:666 coexpression:999 experimental:999 database:968 textmining:818 |
Rv1311 atpC |
ATP synthase subunit epsilon | 999 | 1000 ctx | neighborhood:750 coexpression:999 experimental:999 database:980 textmining:819 |
Rv1305 atpE |
ATP synthase subunit C | 999 | 1000 ctx | neighborhood:836 coexpression:999 experimental:999 database:976 textmining:749 |
Rv1304 atpB |
ATP synthase subunit A | 999 | 1000 ctx | neighborhood:778 cooccurence:431 coexpression:999 experimental:999 database:972 textmining:820 |
Rv1507c hyp |
hypothetical protein | 999 | 1000 | coexpression:974 experimental:999 database:650 |
Rv0702 rplD |
50S ribosomal protein L4 | 997 | 996 | coexpression:996 textmining:468 |
Rv0716 rplE |
50S ribosomal protein L5 | 996 | 996 | coexpression:996 |
Rv0708 rplP |
50S ribosomal protein L16 | 997 | 995 | coexpression:995 textmining:469 |
Rv0706 rplV |
50S ribosomal protein L22 | 997 | 995 | coexpression:995 textmining:406 |
Rv2889c tsf |
elongation factor EF-Ts | 997 | 995 | coexpression:994 textmining:453 |
Rv0718 rpsH |
30S ribosomal protein S8 | 996 | 995 | coexpression:995 |
Rv0703 rplW |
50S ribosomal protein L23 | 996 | 995 | coexpression:995 |
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/delta
- MTBC0 PGAP product: F0F1 ATP synthase subunit B/delta
- Pfam (hmmscan --cut_ga): ATP-synt_B PF00430.24 (E=4e-19), OSCP PF00213.24 (E=6e-28)
- (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_215823.1)
- Domains: Pfam-A via hmmscan --cut_ga — ATP-synt_B (PF00430.24), OSCP (PF00213.24)
- 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 P9WPV3 (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 —
306 functional partner(s); context anchor
atpF - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001399|Rv1307|atpH MSTFIGQLFGFAVIVYLVWRFIVPLVGRLMSARQDTVRQQLADAAAAADRLAEASQAHTKALEDAKSEAHRVVEEARTDAERIAEQLEAQADVEAERIKMQGARQVDLIRAQLTRQLRLELGHESVRQARELVRNHVADQAQQSATVDRFLDQLDAMAPATADVDYPLLAKMRSASRRALTSLVDWFGTMAQDLDHQGLTTLAGELVSVARLLDREAVVTRYLTVPAEDATPRIRLIERLVSGKVGAPTLEVLRTAVSKRWSANSDLIDAIEHVSRQALLELAERAGQVDEVEDQLFRFSRILDVQPRLAILLGDCAVPAEGRVRLLRKVLERADSTVNPVVVALLSHTVELLRGQAVEEAVLFLAEVAVARRGEIVAQVGAAAELSDAQRTRLTEVLSRIYGHPVTVQLHIDAALLGGLSIAVGDEVIDGTLSSRLAAAEARLPD