garA Resolved · high auto-curated
H37Rv Rv1827 · MTBC0 mtbc0_001941 ·
162 aa · 2090684–2091172 (+) ·
RefSeq NP_216343.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glycogen accumulation regulator GarA |
|---|---|
| MTBC0 PGAP re-annotation | glycogen accumulation regulator GarA |
| Revised (this work) | Glycogen accumulation regulator GarA. Pfam: Yop-YscD_cpl (PF16697.11), FHA (PF00498.32). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WJA9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glycogen accumulation regulator GarA |
| Curated function | Involved in regulation of glutamate metabolism. Acts as a phosphorylation-dependent molecular switch that modulates the activities of Kgd, Gdh and GltB. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
T Signal transduction mechanisms
|
|---|---|
| Preferred name | garA |
| eggNOG description | Fha domain |
| Orthologous group | COG1716 |
| Gene Ontology (90) |
GO:0003674, GO:0005488, GO:0005515, GO:0005575, GO:0005576, GO:0005618, GO:0005623, GO:0005886, GO:0006109, GO:0006110, GO:0006140, GO:0006464 +78 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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.28% of strains (404) · clonal |
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 |
|---|---|---|---|---|
Yop-YscD_cpl | PF16697.11 | 1.2e-15 | 62–146 | Inner membrane component of T3SS, cytoplasmic domain |
FHA | PF00498.32 | 3.1e-20 | 78–140 | FHA domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pknB (serine/threonine-protein kinase PknB), high confidence from genomic context alone (score 982 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1248c kgd |
multifunctional 2-oxoglutarate dehydrogenase E1 component /2-oxoglutarate dehydrogenase dihydrolipoyllysine-residue succinyltransferase | 999 | 999 | experimental:999 textmining:920 |
Rv0014c pknB |
serine/threonine-protein kinase PknB | 999 | 982 ctx | cooccurence:471 experimental:964 textmining:949 |
Rv1828 |
HTH-type transcriptional regulator | 918 | 912 ctx | neighborhood:882 |
Rv2476c gdh |
NAD-dependent glutamate dehydrogenase | 945 | 906 | experimental:905 textmining:446 |
Rv0410c pknG |
serine/threonine-protein kinase PknG | 995 | 902 | experimental:899 textmining:959 |
Rv1829 hyp |
hypothetical protein | 777 | 766 ctx | neighborhood:763 |
Rv1826 gcvH |
glycine cleavage system protein H | 734 | 735 ctx | neighborhood:727 |
Rv2199c ctaF |
cytochrome c oxidase polypeptide 4 | 729 | 729 | coexpression:729 |
Rv0015c pknA |
serine/threonine-protein kinase PknA | 960 | 701 ctx | cooccurence:467 experimental:443 textmining:873 |
Rv1824 hyp |
hypothetical protein | 696 | 696 ctx | neighborhood:692 |
Rv1364c |
sigma factor regulatory protein | 687 | 686 | coexpression:646 |
Rv2176 pknL |
serine/threonine-protein kinase PknL | 791 | 667 ctx | cooccurence:415 experimental:443 |
Rv1825 hyp |
hypothetical protein | 658 | 658 ctx | neighborhood:653 |
Rv1823 hyp |
hypothetical protein | 657 | 656 ctx | neighborhood:653 |
Rv1822 pgsA2 |
CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase | 642 | 643 ctx | neighborhood:626 |
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: glycogen accumulation regulator GarA
- MTBC0 PGAP product: glycogen accumulation regulator GarA
- Pfam (hmmscan --cut_ga): Yop-YscD_cpl PF16697.11 (E=1e-15), FHA PF00498.32 (E=3e-20)
- (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_216343.1)
- Domains: Pfam-A via hmmscan --cut_ga — Yop-YscD_cpl (PF16697.11), FHA (PF00498.32)
- 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
COG1716 - Curated reference: UniProt P9WJA9 (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 —
78 functional partner(s); context anchor
pknB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001941|Rv1827|garA MTDMNPDIEKDQTSDEVTVETTSVFRADFLSELDAPAQAGTESAVSGVEGLPPGSALLVVKRGPNAGSRFLLDQAITSAGRHPDSDIFLDDVTVSRRHAEFRLENNEFNVVDVGSLNGTYVNREPVDSAVLANGDEVQIGKFRLVFLTGPKQGEDDGSTGGP