gatC Family assigned · medium auto-curated
H37Rv Rv3012c · MTBC0 mtbc0_003201 ·
99 aa · 3392740–3393039 (-) ·
RefSeq NP_217528.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutamyl-tRNA(GLN) amidotransferase subunit C |
|---|---|
| MTBC0 PGAP re-annotation | Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC |
| Revised (this work) | Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC. Pfam: GatC (PF02686.21). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN59
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glutamyl-tRNA(Gln) amidotransferase subunit C |
| EC (curated) |
EC 6.3.5.-
|
| Curated function | Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) (By similarity). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| Preferred name | gatC |
| eggNOG description | Allows the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp- tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln) |
| Orthologous group | COG0721 |
| EC number |
EC 6.3.5.6, EC 6.3.5.7
|
| KEGG orthology |
K02435
|
| KEGG pathways |
map00970, map01100
|
| Gene Ontology (6) |
GO:0005575, GO:0005618, GO:0005623, GO:0030312, 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 | 0.335 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 1 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 |
|---|---|---|---|---|
GatC | PF02686.21 | 7.8e-20 | 20–91 | Glu-tRNAGln amidotransferase C subunit |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gatB (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3009c gatB |
aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B | 999 | 999 ctx | neighborhood:578 coexpression:757 experimental:928 database:900 textmining:439 |
Rv3011c gatA |
glutamyl-tRNA(GLN) amidotransferase subunit A | 999 | 999 ctx | neighborhood:881 coexpression:663 experimental:629 database:900 |
Rv1307 atpH |
ATP synthase subunit b/delta | 925 | 923 | coexpression:915 |
Rv3375 amiD |
amidase | 913 | 903 | coexpression:649 experimental:629 |
Rv2363 amiA2 |
amidase | 905 | 899 | coexpression:656 experimental:629 |
Rv2888c amiC |
amidase AmiC | 898 | 892 | coexpression:648 experimental:629 |
Rv1263 amiB2 |
amidase AmiB | 897 | 891 | coexpression:649 experimental:629 |
Rv3175 |
amidase | 896 | 890 | coexpression:645 experimental:629 |
Rv2572c aspS |
aspartate--tRNA ligase | 985 | 871 | experimental:836 textmining:895 |
Rv2753c dapA |
4-hydroxy-tetrahydrodipicolinate synthase | 736 | 721 | coexpression:698 |
Rv3010c pfkA |
6-phosphofructokinase | 668 | 668 ctx | neighborhood:624 |
Rv0651 rplJ |
50S ribosomal protein L10 | 679 | 667 | coexpression:666 |
Rv2056c rpsN2 |
30S ribosomal protein S14 | 664 | 665 | coexpression:665 |
Rv0717 rpsN1 |
30S ribosomal protein S14 | 663 | 664 | coexpression:664 |
Rv0641 rplA |
50S ribosomal protein L1 | 656 | 656 | coexpression:652 |
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 C
- MTBC0 PGAP product: Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatC
- Pfam (hmmscan --cut_ga): GatC PF02686.21 (E=8e-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_217528.1)
- Domains: Pfam-A via hmmscan --cut_ga — GatC (PF02686.21)
- 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
COG0721 - Curated reference: UniProt P9WN59 (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 —
55 functional partner(s); context anchor
gatB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003201|Rv3012c|gatC MSQISRDEVAHLARLARLALTETELDSFAGQLDAILTHVSQIQAVDVTGVQATDNPLKDVNVTRPDETVPCLTQRQVLDQAPDAVDGRFAVPQILGDEQ