gatB Family assigned · medium auto-curated
H37Rv Rv3009c · MTBC0 mtbc0_003198 ·
509 aa · 3388573–3390102 (-) ·
RefSeq NP_217525.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B |
|---|---|
| MTBC0 PGAP re-annotation | Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB |
| Revised (this work) | Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB. Pfam: GatB_N (PF02934.21), GatB_Yqey (PF02637.24). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WN61
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B |
| 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 | gatB |
| 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 | COG0064 |
| EC number |
EC 6.3.5.6, EC 6.3.5.7
|
| KEGG orthology |
K02434
|
| KEGG pathways |
map00970, map01100
|
| Gene Ontology (41) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0006082, GO:0006139, GO:0006399, GO:0006520, GO:0006725, GO:0006807, GO:0008150 +29 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 | 0.187 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 9 synonymous, 5 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 |
|---|---|---|---|---|
GatB_N | PF02934.21 | 1.8e-109 | 28–321 | GatB/GatE catalytic domain |
GatB_Yqey | PF02637.24 | 2.0e-38 | 360–504 | GatB domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: gatA (glutamyl-tRNA(GLN) amidotransferase subunit A), high confidence from genomic context alone (score 999 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3011c gatA |
glutamyl-tRNA(GLN) amidotransferase subunit A | 999 | 999 ctx | neighborhood:578 cooccurence:774 coexpression:646 experimental:629 database:900 textmining:616 |
Rv3012c gatC |
glutamyl-tRNA(GLN) amidotransferase subunit C | 999 | 999 ctx | neighborhood:578 coexpression:757 experimental:928 database:900 textmining:439 |
Rv2572c aspS |
aspartate--tRNA ligase | 993 | 989 ctx | fusion:850 coexpression:644 experimental:790 textmining:478 |
Rv3375 amiD |
amidase | 980 | 969 ctx | cooccurence:774 coexpression:646 experimental:629 textmining:411 |
Rv2363 amiA2 |
amidase | 970 | 968 ctx | cooccurence:772 coexpression:646 experimental:629 |
Rv1263 amiB2 |
amidase AmiB | 970 | 968 ctx | cooccurence:772 coexpression:646 experimental:629 |
Rv3175 |
amidase | 970 | 968 ctx | cooccurence:770 coexpression:648 experimental:629 |
Rv2888c amiC |
amidase AmiC | 969 | 967 ctx | cooccurence:762 coexpression:647 experimental:629 |
Rv1307 atpH |
ATP synthase subunit b/delta | 888 | 889 | coexpression:874 |
Rv2992c gltS |
glutamate--tRNA ligase | 926 | 879 | coexpression:407 experimental:790 textmining:416 |
Rv3396c guaA |
GMP synthase | 909 | 826 | coexpression:813 textmining:500 |
Rv3010c pfkA |
6-phosphofructokinase | 881 | 801 ctx | neighborhood:743 textmining:431 |
Rv1650 pheT |
phenylalanine--tRNA ligase subunit beta | 786 | 710 | coexpression:645 |
Rv2146c |
transmembrane protein | 660 | 660 | coexpression:649 |
Rv0709 rpmC |
50S ribosomal protein L29 | 655 | 649 | coexpression:648 |
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: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B
- MTBC0 PGAP product: Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase subunit GatB
- Pfam (hmmscan --cut_ga): GatB_N PF02934.21 (E=2e-109), GatB_Yqey PF02637.24 (E=2e-38)
- (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_217525.1)
- Domains: Pfam-A via hmmscan --cut_ga — GatB_N (PF02934.21), GatB_Yqey (PF02637.24)
- 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
COG0064 - Curated reference: UniProt P9WN61 (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 —
85 functional partner(s); context anchor
gatA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003198|Rv3009c|gatB MTVAAGAAKAAGAELLDYDEVVARFQPVLGLEVHVELSTATKMFCGCTTTFGGEPNTQVCPVCLGLPGSLPVLNRAAVESAIRIGLALNCEIVPWCRFARKNYFYPDMPKNYQISQYDEPIAINGYLDAPLEDGTTWRVEIERAHMEEDTGKLTHIGSETGRIHGATGSLIDYNRAGVPLIEIVTKPIVGAGARAPQIARSYVTALRDLLRALDVSDVRMDQGSMRCDANVSLKPAGTTEFGTRTETKNVNSLKSVEVAVRYEMQRQGAILASGGRITQETRHFHEAGYTSAGRTKETAEDYRYFPEPDLEPVAPSRELVERLRQTIPELPWLSRRRIQQEWGVSDEVMRDLVNAGAVELVAATVEHGASSEAARAWWGNFLAQKANEAGIGLDELAITPAQVAAVVALVDEGKLSNSLARQVVEGVLAGEGEPEQVMTARGLALVRDDSLTQAAVDEALAANPDVADKIRGGKVAAAGAIVGAVMKATRGQADAARVRELVLEACGQG