Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | 4-aminobutyrate aminotransferase |
|---|
| MTBC0 PGAP re-annotation | 4-aminobutyrate--2-oxoglutarate transaminase |
|---|
| Revised (this work) | 4-aminobutyrate--2-oxoglutarate transaminase. Pfam: Aminotran_3 (PF00202.28). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WQ79
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | 4-aminobutyrate aminotransferase |
|---|
| EC (curated) |
EC 2.6.1.19, EC 2.6.1.22
|
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|
| Preferred name | gabT |
|---|
| eggNOG description | Belongs to the class-III pyridoxal-phosphate-dependent aminotransferase family |
|---|
| Orthologous group | COG0160 |
|---|
| EC number |
EC 2.6.1.19, EC 2.6.1.22
|
|---|
| KEGG orthology |
K07250
|
|---|
| KEGG pathways |
map00250, map00280, map00410, map00640, map00650, map01100, map01120
|
|---|
| KEGG modules |
M00027
|
|---|
| Gene Ontology (6) |
GO:0005575, GO:0005623, GO:0005886, GO:0016020, 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 |
0.242 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
3 synonymous, 2 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 |
|---|
Aminotran_3 | PF00202.28 |
3.5e-135 | 37–445 |
Aminotransferase class-III |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv3293 pcd |
piperideine-6-carboxylic acid dehydrogenase |
937 |
933 |
database:900 |
Rv0147 |
aldehyde dehydrogenase |
937 |
933 |
database:900 |
Rv0234c gabD1 |
succinate-semialdehyde dehydrogenase |
937 |
933 |
database:900 |
Rv0753c mmsA |
methylmalonate-semialdehyde dehydrogenase |
937 |
932 |
database:900 |
Rv0223c |
aldehyde dehydrogenase |
937 |
932 |
database:900 |
Rv1731 gabD2 |
succinate-semialdehyde dehydrogenase |
937 |
932 |
database:900 |
Rv0768 aldA |
aldehyde dehydrogenase AldA |
937 |
932 |
database:900 |
Rv3432c gadB |
glutamate decarboxylase GadB |
947 |
926 |
database:900 |
Rv0860 fadB |
fatty oxidation protein FadB |
918 |
912 |
database:900 |
Rv0751c mmsB |
3-hydroxyisobutyrate dehydrogenase |
900 |
901 |
database:900 |
Rv3601c panD |
aspartate 1-decarboxylase |
910 |
900 |
database:900 |
Rv3602c panC |
pantothenate synthetase |
905 |
900 |
database:900 |
Rv3667 acs |
acetyl-CoAsynthetase |
836 |
819 |
database:800 |
Rv0408 pta |
phosphate acetyltransferase |
827 |
809 |
database:800 |
Rv0973c accA2 |
acetyl/propionyl-CoA carboxylase subuit alpha |
813 |
804 |
database:800 |
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: 4-aminobutyrate aminotransferase
- MTBC0 PGAP product: 4-aminobutyrate--2-oxoglutarate transaminase
- Pfam (hmmscan --cut_ga): Aminotran_3 PF00202.28 (E=3e-135)
- (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_217105.1)
- Domains: Pfam-A via hmmscan --cut_ga — Aminotran_3 (PF00202.28)
- 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
COG0160
- Curated reference: UniProt
P9WQ79
(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)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002756|Rv2589|gabT
MASLQQSRRLVTEIPGPASQALTHRRAAAVSSGVGVTLPVFVARAGGGIVEDVDGNRLIDLGSGIAVTTIGNSSPRVVDAVRTQVAEFTHTCFMVTPYEGYVAVAEQLNRITPGSGPKRSVLFNSGAEAVENAVKIARSYTGKPAVVAFDHAYHGRTNLTMALTAKSMPYKSGFGPFAPEIYRAPLSYPYRDGLLDKQLATNGELAAARAIGVIDKQVGANNLAALVIEPIQGEGGFIVPAEGFLPALLDWCRKNHVVFIADEVQTGFARTGAMFACEHEGPDGLEPDLICTAKGIADGLPLSAVTGRAEIMNAPHVGGLGGTFGGNPVACAAALATIATIESDGLIERARQIERLVTDRLTTLQAVDDRIGDVRGRGAMIAVELVKSGTTEPDAGLTERLATAAHAAGVIILTCGMFGNIIRLLPPLTIGDELLSEGLDIVCAILADL
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