ppx2 Resolved · high auto-curated
H37Rv Rv1026 · MTBC0 mtbc0_001102 ·
319 aa · 1154356–1155315 (+) ·
RefSeq NP_215542.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | exopolyphosphatase Ppx2 |
| Revised (this work) | Exopolyphosphatase Ppx2. Pfam: Ppx-GppA (PF02541.23). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P96374
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Exopolyphosphatase 2 |
| EC (curated) |
EC 3.6.1.11
|
| Curated function | Degradation of inorganic polyphosphates (polyP). Releases orthophosphate processively from the ends of the polyP chain. Prefers long-chain length polyphosphates as substrates (By similarity). Can also hydrolyze ATP and ADP substrates, but lacks GTPase activity. Cannot hydrolyze pppGpp to ppGpp. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolismP Inorganic ion transport and metabolism
|
|---|---|
| Preferred name | ppx2 |
| eggNOG description | PFAM Ppx GppA phosphatase |
| Orthologous group | COG0248 |
| EC number |
EC 3.6.1.11, EC 3.6.1.40
|
| KEGG orthology |
K01524
|
| KEGG pathways |
map00230
|
| Gene Ontology (8) |
GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0016020, GO:0040007, 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 | 0.097 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 1 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 |
|---|---|---|---|---|
Ppx-GppA | PF02541.23 | 2.0e-88 | 20–315 | Ppx/GppA phosphatase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1024 (membrane protein), high confidence from genomic context alone (score 871 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1025 hyp |
hypothetical protein | 993 | 993 ctx | neighborhood:881 fusion:899 coexpression:500 |
Rv0496 ppx1 hyp |
hypothetical protein | 963 | 928 | database:900 textmining:514 |
Rv2583c relA |
bifunctional (p)ppGpp synthase/hydrolase RelA | 939 | 912 | database:900 |
Rv1024 |
membrane protein | 909 | 871 ctx | neighborhood:861 |
Rv1023 eno |
enolase | 862 | 862 ctx | neighborhood:861 |
Rv2984 ppk1 |
polyphosphate kinase | 965 | 793 ctx | cooccurence:406 coexpression:646 textmining:841 |
Rv1022 lpqU |
lipoprotein LpqU | 764 | 765 ctx | neighborhood:762 |
Rv1021 mazG |
nucleoside triphosphate pyrophosphohydrolase | 686 | 687 ctx | neighborhood:682 |
Rv2538c aroB |
3-dehydroquinate synthase | 646 | 646 ctx | fusion:608 |
Rv1020 mfd |
transcription-repair coupling factor | 615 | 616 ctx | neighborhood:610 |
Rv1629 polA |
DNA polymerase I | 476 | 477 | coexpression:407 |
Rv1571 hyp |
hypothetical protein | 422 | 423 | coexpression:423 |
Rv1019 |
transcriptional regulator | 421 | 422 | |
Rv3232c ppk2 |
polyphosphate kinase | 914 | 283 | textmining:885 |
Rv3301c phoY1 |
phosphate transport system transcriptional regulator PhoY | 666 | 98 | textmining:646 |
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: hypothetical protein
- MTBC0 PGAP product: exopolyphosphatase Ppx2
- Pfam (hmmscan --cut_ga): Ppx-GppA PF02541.23 (E=2e-88)
- (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_215542.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ppx-GppA (PF02541.23)
- 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
COG0248 - Curated reference: UniProt P96374 (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 —
24 functional partner(s); context anchor
Rv1024 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001102|Rv1026|ppx2 MALTRVAAIDCGTNSIRLLIADVGAGLARGELHDVHRETRIVRLGQGVDATGRFAPEAIARTRTALTDYAELLTFHHAERVRMVATSAARDVVNRDVFFAMTADVLGAALPGSAAEVITGAEEAELSFRGAVGELGSAGAPFVVVDLGGGSTEIVLGEHEVVASYSADIGCVRLTERCLHSDPPTLQEVSTARRLVRERLEPALRTVPLELARTWVGLAGTMTTLSALAQSMTAYDAAAIHLSRVPGADLLEVCQRLIGMTRKQRAALAPMHPGRADVIGGGAIVVEELARELRERAGIDQLTVSEHDILDGIALSLAG