gadB Resolved · high auto-curated
H37Rv Rv3432c · MTBC0 mtbc0_003651 ·
460 aa · 3876258–3877640 (-) ·
RefSeq NP_217949.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutamate decarboxylase GadB |
|---|---|
| MTBC0 PGAP re-annotation | glutamate decarboxylase |
| Revised (this work) | Glutamate decarboxylase. Pfam: Pyridoxal_deC (PF00282.26). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YG46
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glutamate decarboxylase |
| EC (curated) |
EC 4.1.1.15
|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
E Amino acid transport and metabolism
|
|---|---|
| Preferred name | gadB |
| eggNOG description | Belongs to the group II decarboxylase family |
| Orthologous group | COG0076 |
| EC number |
EC 4.1.1.15
|
| KEGG orthology |
K01580
|
| KEGG pathways |
map00250, map00410, map00430, map00650, map01100, map01110, map01120, map02024, map04727, map04940
|
| KEGG modules |
M00027
|
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 | 0.077 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 13 synonymous, 3 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 |
|---|---|---|---|---|
Pyridoxal_deC | PF00282.26 | 1.0e-68 | 41–380 | Pyridoxal-dependent decarboxylase conserved domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nnr (bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase), high confidence from genomic context alone (score 906 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3602c panC |
pantothenate synthetase | 946 | 943 | coexpression:421 database:900 |
Rv2589 gabT |
4-aminobutyrate aminotransferase | 947 | 926 | database:900 |
Rv1187 rocA |
pyrroline-5-carboxylate dehydrogenase RocA | 921 | 917 | database:900 |
Rv0147 |
aldehyde dehydrogenase | 921 | 917 | database:900 |
Rv3293 pcd |
piperideine-6-carboxylic acid dehydrogenase | 921 | 917 | database:900 |
Rv0223c |
aldehyde dehydrogenase | 921 | 917 | database:900 |
Rv0768 aldA |
aldehyde dehydrogenase AldA | 921 | 916 | database:900 |
Rv1878 glnA3 |
glutamine synthetase GlnA | 911 | 906 | database:900 |
Rv3433c nnr |
bifunctional ADP-dependent (S)-NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase | 910 | 906 ctx | neighborhood:829 coexpression:408 |
Rv2860c glnA4 |
glutamine synthetase | 910 | 905 | database:900 |
Rv2220 glnA1 |
glutamine synthetase | 936 | 904 | database:900 |
Rv2222c glnA2 |
glutamine synthetase | 917 | 904 | database:900 |
Rv3859c gltB |
glutamate synthase large subunit | 964 | 903 | database:900 textmining:644 |
Rv2394 ggtB |
gamma-glutamyltranspeptidase precursor GgtB | 912 | 901 | database:900 |
Rv0773c ggtA |
bifunctional cephalosporin acylase/gamma-glutamyltranspeptidase | 911 | 901 | database:900 |
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: glutamate decarboxylase GadB
- MTBC0 PGAP product: glutamate decarboxylase
- Pfam (hmmscan --cut_ga): Pyridoxal_deC PF00282.26 (E=1e-68)
- (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_217949.1)
- Domains: Pfam-A via hmmscan --cut_ga — Pyridoxal_deC (PF00282.26)
- 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
COG0076 - Curated reference: UniProt I6YG46 (TrEMBL, unreviewed; 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 —
73 functional partner(s); context anchor
nnr - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003651|Rv3432c|gadB MSRSHPSVPAHSIAPAYTGRMFTAPVPALRMPDESMDPEAAYRFIHDELMLDGSSRLNLATFVTTWMDPEAEKLMAETFDKNMIDKDEYPATAAIEARCVSMVADLFHAEGLRDHDPTSATGVSTIGSSEAVMLGGLALKWRWRQRVGSWKGRMPNLVMGSNVQVVWEKFCRYFDVEPRYLPMERGRYVITPEQVLAAVDENTIGVVAILGTTYTGELEPIAEICAALDKLAAGGGVDVPVHVDAASGGFVVPFLHPDLVWDFRLPRVVSINVSGHKYGLTYPGVGFVVWRGPEHLPEDLVFRVNYLGGDMPTFTLNFSRPGNQVVGQYYNFLRLGRDGYTKVMQALSHTARWLGDQLREVDHCEVISDGSAIPVVSFRLAGDRGYTEFDVSHELRTFGWQVPAYTMPDNATDVAVLRIVVREGLSADLARALHDDAVTALAALDKVKPGGHFDAQHFAH