Rv2859c Resolved · high auto-curated
H37Rv Rv2859c · MTBC0 mtbc0_003040 ·
308 aa · 3191386–3192312 (-) ·
RefSeq NP_217375.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutamine amidotransferase |
|---|---|
| MTBC0 PGAP re-annotation | gamma-glutamyl-gamma-aminobutyrate hydrolase |
| Revised (this work) | Gamma-glutamyl-gamma-aminobutyrate hydrolase. Pfam: Peptidase_C26 (PF07722.20), GATase (PF00117.35). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O33341
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative glutamine amidotransferase Rv2859c |
| EC (curated) |
EC 2.4.2.-
|
UniProt still lists this protein as Putative glutamine amidotransferase Rv2859c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| eggNOG description | glutamine amidotransferase |
| Orthologous group | COG2071 |
| KEGG orthology |
K07010
|
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) | 2 synonymous, 0 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 |
|---|---|---|---|---|
Peptidase_C26 | PF07722.20 | 3.2e-72 | 66–279 | Peptidase C26 |
GATase | PF00117.35 | 2.6e-13 | 161–282 | Glutamine amidotransferase class-I |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: glnA4 (glutamine synthetase), high confidence from genomic context alone (score 961 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2860c glnA4 |
glutamine synthetase | 963 | 961 ctx | neighborhood:881 cooccurence:459 coexpression:445 |
Rv2857c |
3-oxoacyl-ACP reductase | 927 | 927 ctx | neighborhood:882 |
Rv2858c aldC |
aldehyde dehydrogenase AldC | 928 | 925 ctx | neighborhood:882 |
Rv2861c mapB |
methionine aminopeptidase | 539 | 539 ctx | neighborhood:535 |
Rv0255c cobQ1 |
cobyric acid synthase | 444 | 445 ctx | neighborhood:440 |
Rv1127c ppdK |
pyruvate, phosphate dikinase PpdK | 467 | 442 | |
Rv1878 glnA3 |
glutamine synthetase GlnA | 475 | 440 | coexpression:421 |
Rv2220 glnA1 |
glutamine synthetase | 474 | 440 | coexpression:421 |
Rv2222c glnA2 |
glutamine synthetase | 475 | 439 | coexpression:420 |
Rv2862c hyp |
hypothetical protein | 421 | 421 ctx | neighborhood:419 |
Rv2589 gabT |
4-aminobutyrate aminotransferase | 434 | 402 | |
Rv2047c hyp |
hypothetical protein | 429 | 402 | |
Rv3329 |
aminotransferase | 411 | 389 |
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: glutamine amidotransferase
- MTBC0 PGAP product: gamma-glutamyl-gamma-aminobutyrate hydrolase
- Pfam (hmmscan --cut_ga): Peptidase_C26 PF07722.20 (E=3e-72), GATase PF00117.35 (E=3e-13)
- (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_217375.1)
- Domains: Pfam-A via hmmscan --cut_ga — Peptidase_C26 (PF07722.20), GATase (PF00117.35)
- 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
COG2071 - Curated reference: UniProt O33341 (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 —
13 functional partner(s); context anchor
glnA4 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003040|Rv2859c| MDLSASRSDGGDPLRPASPRLRSPVSDGGDPLRPASPRLRSPVSDGGDPLRPASPRLRSPLGASRPVVGLTAYLEQVRTGVWDIPAGYLPADYFEGITMAGGVAVLLPPQPVDPESVGCVLDSLHALVITGGYDLDPAAYGQEPHPATDHPRPGRDAWEFALLRGALQRGMPVLGICRGTQVLNVALGGTLHQHLPDILGHSGHRAGNGVFTRLPVHTASGTRLAELIGESADVPCYHHQAIDQVGEGLVVSAVDVDGVIEALELPGDTFVLAVQWHPEKSLDDLRLFKALVDAASGYAGRQSQAEPR