Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | pyruvate, phosphate dikinase PpdK |
|---|
| MTBC0 PGAP re-annotation | pyruvate%2C phosphate dikinase |
|---|
| Revised (this work) | Pyruvate%2C phosphate dikinase. Pfam: PPDK_N (PF01326.25), PEP-utilizers (PF00391.30). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O06579
TrEMBL · unreviewed
· Evidence at protein level
|
|---|
| UniProt name | Probable pyruvate, phosphate dikinase PpdK |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
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 |
0.352 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
5 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 |
|---|
PPDK_N | PF01326.25 |
2.9e-21 | 91–258 |
Pyruvate phosphate dikinase, AMP/ATP-binding domain |
PEP-utilizers | PF00391.30 |
7.8e-21 | 389–458 |
PEP-utilising enzyme, mobile domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv1126c hyp |
hypothetical protein |
948 |
948 ctx |
neighborhood:882 coexpression:404 |
Rv2455c korA |
2-oxoglutarate oxidoreductase subunit KorA |
947 |
913 |
database:900 textmining:418 |
Rv2332 mez |
malate oxidoreductase |
917 |
906 |
database:900 |
Rv1023 eno |
enolase |
917 |
906 |
database:900 |
Rv2967c pca |
pyruvate carboxylase |
914 |
906 |
database:900 |
Rv2454c korB |
2-oxoglutarate oxidoreductase subunit KorB |
915 |
904 |
database:900 |
Rv2496c bkdB |
3-methyl-2-oxobutanoate dehydrogenase subunit beta |
913 |
904 |
database:900 |
Rv2497c bkdA |
3-methyl-2-oxobutanoate dehydrogenase subunit alpha |
911 |
904 |
database:900 |
Rv1617 pykA |
pyruvate kinase |
924 |
901 |
database:900 |
Rv2241 aceE |
pyruvate dehydrogenase E1 component |
911 |
901 |
database:900 |
Rv0694 mftD |
mycofactocin system heme/flavin oxidoreductase MftD |
906 |
901 |
database:900 |
Rv0211 pckA |
phosphoenolpyruvate carboxykinase |
934 |
900 |
database:900 |
Rv1872c lldD2 |
L-lactate dehydrogenase |
906 |
900 |
database:900 |
Rv1449c tkt |
transketolase |
837 |
815 |
database:800 |
Rv0946c pgi |
glucose-6-phosphate isomerase |
835 |
813 |
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: pyruvate, phosphate dikinase PpdK
- MTBC0 PGAP product: pyruvate%2C phosphate dikinase
- Pfam (hmmscan --cut_ga): PPDK_N PF01326.25 (E=3e-21), PEP-utilizers PF00391.30 (E=8e-21)
- (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_215643.1)
- Domains: Pfam-A via hmmscan --cut_ga — PPDK_N (PF01326.25), PEP-utilizers (PF00391.30)
- 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
COG0574
- Curated reference: UniProt
O06579
(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 —
43 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001210|Rv1127c|ppdK
MTRITRANGCPDGTLENAVVALDGGANYPREILGNKGHGIDMMRRHHLPVPPAFCITTEVGVRYLAAPESTIAAIWDDVLDRMSWLETETSCTFGRGPNPLLVSVRSGATQSMPGMMDTILDVGMTDAVERVLARPGAADFAHDTRRRFTSMYRRIVGSAGPITDDPYAQLRASIEAVFASWNSPRAVAYRDHHGLDDQGGTAVVVQAMVFGNLTANSGAGVLSSRNPITGANEPFGEWLPGGQGDDVVSGLVAVAPITALRDQQPAVYDQLMAAARSLERMAGDVQEIEFTVEDSQLWLLQTRGAERSAQAAVRLALQLHHEGLIDDTETLRRVTPTHIETLLRPSLQPETRLAAPLLAKGLPACPGVVSGTAYTEVDEALDAADRGEPVILVRDHTRPEDVMGMLAAQGIVTEVGGAASHAAVVSRELGRVAVVGCGPGVAAALAGKEITVDGYEGEVRQGVLALSAWSESDTPELRELADIAQRISS
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