pdc Resolved · high auto-curated
H37Rv Rv0853c · MTBC0 mtbc0_000908 ·
560 aa · 952587–954269 (-) ·
RefSeq NP_215368.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | alpha-keto-acid decarboxylase |
|---|---|
| MTBC0 PGAP re-annotation | alpha-keto-acid decarboxylase |
| Revised (this work) | Alpha-keto-acid decarboxylase. Pfam: TPP_enzyme_N (PF02776.24), TPP_enzyme_M (PF00205.29), TPP_enzyme_C (PF02775.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WG37
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Alpha-keto-acid decarboxylase |
| EC (curated) |
EC 4.1.1.-
|
| Curated function | Decarboxylates branched-chain and aromatic alpha-keto acids to aldehydes. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
G Carbohydrate transport and metabolismH Coenzyme transport and metabolism
|
|---|---|
| Preferred name | pdc |
| eggNOG description | Belongs to the TPP enzyme family |
| Orthologous group | COG3961 |
| EC number |
EC 4.1.1.74
|
| KEGG orthology |
K04103, K21431
|
| KEGG pathways |
map00380, map01100
|
| Gene Ontology (12) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005886, GO:0016020, GO:0016829, GO:0016830, GO:0016831, 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 | 0.697 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 10 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (160) · clonal |
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 |
|---|---|---|---|---|
TPP_enzyme_N | PF02776.24 | 1.3e-28 | 15–124 | Thiamine pyrophosphate enzyme, N-terminal TPP binding domain |
TPP_enzyme_M | PF00205.29 | 1.3e-08 | 210–326 | Thiamine pyrophosphate enzyme, central domain |
TPP_enzyme_C | PF02775.27 | 1.4e-20 | 403–539 | Thiamine pyrophosphate enzyme, C-terminal TPP binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: far (fatty-acid-CoA racemase), medium confidence from genomic context alone (score 576 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0856 hyp |
hypothetical protein | 707 | 707 ctx | neighborhood:706 |
Rv0854 hyp |
hypothetical protein | 624 | 624 ctx | neighborhood:618 |
Rv1862 adhA |
alcohol dehydrogenase A | 635 | 586 | database:500 |
Rv0855 far |
fatty-acid-CoA racemase | 576 | 576 ctx | neighborhood:571 |
Rv0363c fba |
fructose-bisphosphate aldolase | 591 | 529 | coexpression:420 |
Rv2683 hyp |
hypothetical protein | 512 | 512 | coexpression:453 |
Rv3086 adhD |
alcohol dehydrogenase D | 547 | 510 | database:500 |
Rv0857 hyp |
hypothetical protein | 429 | 429 ctx | neighborhood:427 |
Rv1437 pgk |
phosphoglycerate kinase | 514 | 406 | coexpression:406 |
Rv1023 eno |
enolase | 472 | 381 | |
Rv0946c pgi |
glucose-6-phosphate isomerase | 467 | 337 | |
Rv2332 mez |
malate oxidoreductase | 418 | 332 | |
Rv1438 tpi |
triosephosphate isomerase | 418 | 320 | |
Rv3002c ilvN |
acetolactate synthase small subunit | 745 | 317 | textmining:643 |
Rv0189c ilvD |
dihydroxy-acid dehydratase | 687 | 252 | textmining:599 |
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: alpha-keto-acid decarboxylase
- MTBC0 PGAP product: alpha-keto-acid decarboxylase
- Pfam (hmmscan --cut_ga): TPP_enzyme_N PF02776.24 (E=1e-28), TPP_enzyme_M PF00205.29 (E=1e-08), TPP_enzyme_C PF02775.27 (E=1e-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_215368.1)
- Domains: Pfam-A via hmmscan --cut_ga — TPP_enzyme_N (PF02776.24), TPP_enzyme_M (PF00205.29), TPP_enzyme_C (PF02775.27)
- 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
COG3961 - Curated reference: UniProt P9WG37 (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 —
30 functional partner(s); context anchor
far - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000908|Rv0853c|pdc MTPQKSDACSDPVYTVGDYLLDRLAELGVSEIFGVPGDYNLQFLDHIVAHPTIRWVGSANELNAGYAADGYGRLRGMSAVVTTFGVGELSVTNAIAGSYAEHVPVVHIVGGPTKDAQGTRRALHHSLGDGDFEHFLRISREITCAQANLMPATAGREIDRVLSEVREQKRPGYILLSSDVARFPTEPPAAPLPRYPGGTSPRALSLFTKAAIELIADHQLTVLADLLVHRLQAVKELEALLAADVVPHATLMWGKSLLDESSPNFLGIYAGAASAERVRAAIEGAPVLVTAGVVFTDMVSGFFSQRIDPARTIDIGQYQSSVADQVFAPLEMSAALQALATILTGRGISSPPVVPPPAEPPPAMPARDEPLTQQMVWDRVCSALTPGNVVLADQGTSFYGMADHRLPQGVTFIGQPLWGSIGYTLPAAVGAAVAHPDRRTVLLIGDGAAQLTVQELGTFSREGLSPVIVVVNNDGYTVERAIHGETAPYNDIVSWNWTELPSALGVTNHLAFRAQTYGQLDDALTVAAARRDRMVLVEVVLPRLEIPRLLGQLVGSMAPQ