gatA Family assigned · medium auto-curated
H37Rv Rv3011c · MTBC0 mtbc0_003200 ·
494 aa · 3391259–3392743 (-) ·
RefSeq NP_217527.2
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutamyl-tRNA(GLN) amidotransferase subunit A |
|---|---|
| MTBC0 PGAP re-annotation | Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA |
| Revised (this work) | Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA. Pfam: Amidase (PF01425.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQA1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glutamyl-tRNA(Gln) amidotransferase subunit A |
| EC (curated) |
EC 6.3.5.7
|
| Curated function | Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln) (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | gatA |
| eggNOG description | Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in organisms which lack glutaminyl-tRNA synthetase. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln) |
| Orthologous group | COG0154 |
| EC number |
EC 6.3.5.6, EC 6.3.5.7
|
| KEGG orthology |
K02433
|
| KEGG pathways |
map00970, map01100
|
| Gene Ontology (2) |
GO:0008150, GO:0040007
|
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 | 0.421 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 7 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 |
|---|---|---|---|---|
Amidase | PF01425.27 | 9.5e-162 | 25–476 | Amidase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gatC (glutamyl-tRNA(GLN) amidotransferase subunit C), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3012c gatC |
glutamyl-tRNA(GLN) amidotransferase subunit C | 999 | 999 ctx | neighborhood:881 coexpression:663 experimental:629 database:900 |
Rv3009c gatB |
aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B | 999 | 999 ctx | neighborhood:578 cooccurence:774 coexpression:646 experimental:629 database:900 textmining:616 |
Rv3010c pfkA |
6-phosphofructokinase | 688 | 676 ctx | neighborhood:662 |
Rv2572c aspS |
aspartate--tRNA ligase | 771 | 639 | experimental:405 |
Rv3013 hyp |
hypothetical protein | 639 | 639 ctx | neighborhood:637 |
Rv2992c gltS |
glutamate--tRNA ligase | 716 | 601 | experimental:549 |
Rv2029c pfkB |
6-phosphofructokinase PfkB | 517 | 516 | coexpression:514 |
Rv3014c ligA |
DNA ligase A | 510 | 510 | coexpression:428 |
Rv1307 atpH |
ATP synthase subunit b/delta | 505 | 506 | coexpression:489 |
Rv1407 fmu |
16S rRNA m5C967 methyltransferase | 460 | 460 | coexpression:419 |
Rv0018c pstP |
phosphoserine/threonine phosphatase PstP | 459 | 459 | coexpression:407 |
Rv1380 pyrB |
aspartate carbamoyltransferase | 454 | 455 | coexpression:437 |
Rv2727c miaA |
tRNA delta(2)-isopentenylpyrophosphate transferase | 447 | 446 ctx | fusion:444 |
Rv1385 pyrF |
orotidine 5'-phosphate decarboxylase | 444 | 445 | coexpression:426 |
Rv2150c ftsZ |
cell division protein FtsZ | 439 | 440 | coexpression:440 |
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: glutamyl-tRNA(GLN) amidotransferase subunit A
- MTBC0 PGAP product: Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatA
- Pfam (hmmscan --cut_ga): Amidase PF01425.27 (E=1e-161)
- (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_217527.2)
- Domains: Pfam-A via hmmscan --cut_ga — Amidase (PF01425.27)
- 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
COG0154 - Curated reference: UniProt P9WQA1 (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 —
50 functional partner(s); context anchor
gatC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003200|Rv3011c|gatA MTDIIRSDAATLAAKIAIKEVSSAEITRACLDQIEATDETYHAFLHVAADEALAAAAAVDKQVAAGEPLPSALAGVPLALKDVFTTSDMPTTCGSKILEGWRSPYDATLTARLRAAGIPILGKTNMDEFAMGSSTENSAYGPTRNPWNLDRVPGGSGGGSAAALAAFQAPLAIGSDTGGSIRQPAALTATVGVKPTYGTVSRYGLVACASSLDQGGPCARTVLDTALLHQVIAGHDPRDSTSVDAEVPDVVGAARAGAVGDLRGVRVGVVRQLHGGEGYQPGVLASFEAAVEQLTALGAEVSEVDCPHFDHALAAYYLILPSEVSSNLARFDAMRYGLRVGDDGTRSAEEVMAMTRAAGFGPEVKRRIMIGTYALSAGYYDAYYNQAQKVRTLIARDLDAAYRSVDVLVSPTTPTTAFRLGEKVDDPLAMYLFDLCTLPLNLAGHCGMSVPSGLSPDDGLPVGLQIMAPALADDRLYRVGAAYEAARGPLLSAI