ppk1 Resolved · high auto-curated
H37Rv Rv2984 · MTBC0 mtbc0_003169 ·
742 aa · 3361163–3363391 (+) ·
RefSeq NP_217500.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | polyphosphate kinase |
|---|---|
| MTBC0 PGAP re-annotation | RNA degradosome polyphosphate kinase |
| Revised (this work) | RNA degradosome polyphosphate kinase. Pfam: PP_kinase_N (PF13089.12), PP_kinase (PF02503.23), PP_kinase_C_1 (PF17941.8), PP_kinase_C (PF13090.13), PLDc_2 (PF13091.13). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WHV9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Polyphosphate kinase |
| EC (curated) |
EC 2.7.4.1
|
| Curated function | Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | ppk |
| eggNOG description | Catalyzes the reversible transfer of the terminal phosphate of ATP to form a long-chain polyphosphate (polyP) |
| Orthologous group | COG0855 |
| EC number |
EC 2.7.4.1
|
| KEGG orthology |
K00937
|
| KEGG pathways |
map00190, map03018
|
| Gene Ontology (61) |
GO:0000287, GO:0001666, GO:0003674, GO:0003824, GO:0005488, GO:0005575, GO:0005623, GO:0005886, GO:0006464, GO:0006468, GO:0006793, GO:0006796 +49 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 | 0.662 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 4 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 |
|---|---|---|---|---|
PP_kinase_N | PF13089.12 | 3.0e-38 | 53–159 | Polyphosphate kinase N-terminal domain |
PP_kinase | PF02503.23 | 1.5e-66 | 168–357 | Polyphosphate kinase middle domain |
PP_kinase_C_1 | PF17941.8 | 8.7e-74 | 386–552 | Polyphosphate kinase C-terminal domain 1 |
PP_kinase_C | PF13090.13 | 2.9e-54 | 559–726 | Polyphosphate kinase C-terminal domain 2 |
PLDc_2 | PF13091.13 | 1.7e-07 | 590–701 | PLD-like domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: ppk2 (polyphosphate kinase), high confidence from genomic context alone (score 954 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3232c ppk2 |
polyphosphate kinase | 994 | 954 ctx | cooccurence:512 database:900 textmining:895 |
Rv3628 ppa |
inorganic pyrophosphatase | 944 | 900 | database:900 textmining:462 |
Rv2985 mutT1 |
8-oxo-dGTP diphosphatase | 824 | 818 ctx | neighborhood:783 |
Rv0819 mshD |
mycothiol acetyltransferase | 815 | 815 ctx | fusion:783 |
Rv0496 ppx1 hyp |
hypothetical protein | 968 | 814 ctx | cooccurence:432 coexpression:643 textmining:839 |
Rv1026 ppx2 hyp |
hypothetical protein | 965 | 793 ctx | cooccurence:406 coexpression:646 textmining:841 |
Rv2983 cofC |
2-phospho-L-lactate guanylyltransferase | 779 | 779 ctx | neighborhood:777 |
Rv2982c gpdA2 |
glycerol-3-phosphate dehydrogenase | 711 | 711 ctx | neighborhood:708 |
Rv1629 polA |
DNA polymerase I | 538 | 495 | coexpression:425 |
Rv2981c ddlA |
D-alanine--D-alanine ligase | 597 | 474 ctx | neighborhood:472 |
Rv2090 |
5'-3' exonuclease | 499 | 265 | |
Rv2702 ppgK |
polyphosphate glucokinase | 424 | 197 | |
Rv0933 pstB |
phosphate ABC transporter ATP-binding protein PstB | 401 | 153 | |
Rv0930 pstA1 |
phosphate ABC transporter permease PstA | 412 | 151 | |
Rv3509c ilvX |
acetohydroxyacid synthase large subunit | 459 | 77 | textmining:439 |
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: polyphosphate kinase
- MTBC0 PGAP product: RNA degradosome polyphosphate kinase
- Pfam (hmmscan --cut_ga): PP_kinase_N PF13089.12 (E=3e-38), PP_kinase PF02503.23 (E=2e-66), PP_kinase_C_1 PF17941.8 (E=9e-74), PP_kinase_C PF13090.13 (E=3e-54), PLDc_2 PF13091.13 (E=2e-07)
- (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_217500.1)
- Domains: Pfam-A via hmmscan --cut_ga — PP_kinase_N (PF13089.12), PP_kinase (PF02503.23), PP_kinase_C_1 (PF17941.8), PP_kinase_C (PF13090.13), PLDc_2 (PF13091.13)
- 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
COG0855 - Curated reference: UniProt P9WHV9 (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 —
28 functional partner(s); context anchor
ppk2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003169|Rv2984|ppk1 MMSNDRKVTEIENSPVTEVRPEEHAWYPDDSALAAPPAATPAAISDQLPSDRYLNRELSWLDFNARVLALAADKSMPLLERAKFLAIFASNLDEFYMVRVAGLKRRDEMGLSVRSADGLTPREQLGRIGEQTQQLASRHARVFLDSVLPALGEEGIYIVTWADLDQAERDRLSTYFNEQVFPVLTPLAVDPAHPFPFVSGLSLNLAVTVRQPEDGTQHFARVKVPDNVDRFVELAAREASEEAAGTEGRTALRFLPMEELIAAFLPVLFPGMEIVEHHAFRITRNADFEVEEDRDEDLLQALERELARRRFGSPVRLEIADDMTESMLELLLRELDVHPGDVIEVPGLLDLSSLWQIYAVDRPTLKDRTFVPATHPAFAERETPKSIFATLREGDVLVHHPYDSFSTSVQRFIEQAAADPNVLAIKQTLYRTSGDSPIVRALIDAAEAGKQVVALVEIKARFDEQANIAWARALEQAGVHVAYGLVGLKTHCKTALVVRREGPTIRRYCHVGTGNYNSKTARLYEDVGLLTAAPDIGADLTDLFNSLTGYSRKLSYRNLLVAPHGIRAGIIDRVEREVAAHRAEGAHNGKGRIRLKMNALVDEQVIDALYRASRAGVRIEVVVRGICALRPGAQGISENIIVRSILGRFLEHSRILHFRAIDEFWIGSADMMHRNLDRRVEVMAQVKNPRLTAQLDELFESALDPCTRCWELGPDGQWTASPQEGHSVRDHQESLMERHRSP