panD Resolved · high auto-curated
H37Rv Rv3601c · MTBC0 mtbc0_003819 ·
139 aa · 4067566–4067985 (-) ·
RefSeq NP_218118.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | aspartate 1-decarboxylase |
|---|---|
| MTBC0 PGAP re-annotation | aspartate 1-decarboxylase |
| Revised (this work) | Aspartate 1-decarboxylase. Pfam: Asp_decarbox (PF02261.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIL3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Aspartate 1-decarboxylase |
| EC (curated) |
EC 4.1.1.11
|
| Curated function | Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine..; FUNCTION: Overexpression of wild-type protein confers resistance to pyrazinoic acid (POA), the active form of the anti-tuberculosis prodrug pyrazinamide (PZA). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| Preferred name | panD |
| eggNOG description | Catalyzes the pyruvoyl-dependent decarboxylation of aspartate to produce beta-alanine |
| Orthologous group | COG0853 |
| EC number |
EC 4.1.1.11
|
| KEGG orthology |
K01579
|
| KEGG pathways |
map00410, map00770, map01100, map01110
|
| KEGG modules |
M00119
|
| Gene Ontology (62) |
GO:0003674, GO:0003824, GO:0004068, GO:0005575, GO:0005618, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006082, GO:0006520, GO:0006522 +50 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 | 0.509 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
Asp_decarbox | PF02261.23 | 4.4e-50 | 1–113 | Aspartate decarboxylase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: panC (pantothenate synthetase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3602c panC |
pantothenate synthetase | 999 | 1000 ctx | neighborhood:882 cooccurence:678 coexpression:967 database:900 textmining:942 |
Rv3600c coaX |
type III pantothenate kinase | 987 | 979 ctx | neighborhood:882 coexpression:827 textmining:421 |
Rv2225 panB |
3-methyl-2-oxobutanoate hydroxymethyltransferase | 981 | 944 ctx | cooccurence:581 coexpression:852 textmining:691 |
Rv3603c hyp |
hypothetical protein | 940 | 915 ctx | neighborhood:881 |
Rv0768 aldA |
aldehyde dehydrogenase AldA | 929 | 901 | database:900 |
Rv0223c |
aldehyde dehydrogenase | 929 | 901 | database:900 |
Rv3293 pcd |
piperideine-6-carboxylic acid dehydrogenase | 923 | 901 | database:900 |
Rv0147 |
aldehyde dehydrogenase | 910 | 901 | database:900 |
Rv2589 gabT |
4-aminobutyrate aminotransferase | 910 | 900 | database:900 |
Rv3432c gadB |
glutamate decarboxylase GadB | 906 | 900 | database:900 |
Rv1595 nadB |
L-aspartate oxidase | 845 | 830 | database:800 |
Rv0357c purA |
adenylosuccinate synthetase | 810 | 811 | database:800 |
Rv1380 pyrB |
aspartate carbamoyltransferase | 803 | 804 | database:800 |
Rv1538c ansA |
L-aparaginase | 875 | 802 | database:800 |
Rv1658 argG |
argininosuccinate synthase | 801 | 802 | 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: aspartate 1-decarboxylase
- MTBC0 PGAP product: aspartate 1-decarboxylase
- Pfam (hmmscan --cut_ga): Asp_decarbox PF02261.23 (E=4e-50)
- (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_218118.1)
- Domains: Pfam-A via hmmscan --cut_ga — Asp_decarbox (PF02261.23)
- 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
COG0853 - Curated reference: UniProt P9WIL3 (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 —
98 functional partner(s); context anchor
panC - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003819|Rv3601c|panD MLRTMLKSKIHRATVTCADLHYVGSVTIDADLMDAADLLEGEQVTIVDIDNGARLVTYAITGERGSGVIGINGAAAHLVHPGDLVILIAYATMDDARARTYQPRIVFVDAYNKPIDMGHDPAFVPENAGELLDPRLGVG