atpG Family assigned · medium auto-curated
H37Rv Rv1309 · MTBC0 mtbc0_001401 ·
305 aa · 1473923–1474840 (+) ·
RefSeq NP_215825.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ATP synthase subunit gamma |
|---|---|
| MTBC0 PGAP re-annotation | F0F1 ATP synthase subunit gamma |
| Revised (this work) | F0F1 ATP synthase subunit gamma. Pfam: ATP-synt (PF00231.25). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WPU9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | ATP synthase gamma chain |
| Curated function | Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| Preferred name | atpG |
| eggNOG description | Produces ATP from ADP in the presence of a proton gradient across the membrane. The gamma chain is believed to be important in regulating ATPase activity and the flow of protons through the CF(0) complex |
| Orthologous group | COG0224 |
| KEGG orthology |
K02115
|
| 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 | 2.7 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 | PF00231.25 | 6.1e-96 | 4–301 | ATP synthase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: atpC (ATP synthase subunit epsilon), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1311 atpC |
ATP synthase subunit epsilon | 999 | 1000 ctx | neighborhood:812 cooccurence:500 coexpression:973 experimental:997 database:965 textmining:838 |
Rv1305 atpE |
ATP synthase subunit C | 999 | 1000 ctx | neighborhood:783 coexpression:958 experimental:997 database:963 textmining:626 |
Rv1304 atpB |
ATP synthase subunit A | 999 | 1000 ctx | neighborhood:738 cooccurence:754 coexpression:970 experimental:928 database:962 textmining:829 |
Rv1307 atpH |
ATP synthase subunit b/delta | 999 | 1000 ctx | neighborhood:817 coexpression:999 experimental:999 database:964 textmining:932 |
Rv1308 atpA |
ATP synthase subunit alpha | 999 | 1000 ctx | neighborhood:882 fusion:697 cooccurence:774 coexpression:973 experimental:997 database:965 textmining:916 |
Rv1310 atpD |
ATP synthase subunit beta | 999 | 1000 ctx | neighborhood:823 cooccurence:774 coexpression:976 experimental:997 database:965 textmining:877 |
Rv1306 atpF |
ATP synthase subunit B | 999 | 1000 ctx | neighborhood:817 coexpression:954 experimental:997 database:900 textmining:823 |
Rv3628 ppa |
inorganic pyrophosphatase | 947 | 940 | coexpression:414 database:900 |
Rv2195 qcrA |
ubiquinol-cytochrome C reductase rieske iron-sulfur subunit | 934 | 926 | coexpression:916 |
Rv0707 rpsC |
30S ribosomal protein S3 | 889 | 880 | coexpression:860 |
Rv3459c rpsK |
30S ribosomal protein S11 | 878 | 872 | coexpression:855 |
Rv0708 rplP |
50S ribosomal protein L16 | 887 | 871 | coexpression:851 |
Rv0718 rpsH |
30S ribosomal protein S8 | 865 | 855 | coexpression:832 |
Rv3458c rpsD |
30S ribosomal protein S4 | 875 | 850 | coexpression:830 |
Rv0716 rplE |
50S ribosomal protein L5 | 849 | 849 | coexpression:845 |
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 gamma
- MTBC0 PGAP product: F0F1 ATP synthase subunit gamma
- Pfam (hmmscan --cut_ga): ATP-synt PF00231.25 (E=6e-96)
- (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_215825.1)
- Domains: Pfam-A via hmmscan --cut_ga — ATP-synt (PF00231.25)
- 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
COG0224 - Curated reference: UniProt P9WPU9 (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 —
204 functional partner(s); context anchor
atpC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001401|Rv1309|atpG MAATLRELRGRIRSAGSIKKITKAQELIATSRIARAQARLESARPYAFEITRMLTTLAAEAALDHPLLVERPEPKRAGVLVVSSDRGLCGAYNANIFRRSEELFSLLREAGKQPVLYVVGRKAQNYYSFRNWNITESWMGFSEQPTYENAAEIASTLVDAFLLGTDNGEDQRSDSGEGVDELHIVYTEFKSMLSQSAEAHRIAPMVVEYVEEDIGPRTLYSFEPDATMLFESLLPRYLTTRVYAALLESAASELASRQRAMKSATDNADDLIKALTLMANRERQAQITQEISEIVGGANALAEAR