Rv0496 Family assigned · medium auto-curated
H37Rv Rv0496 · MTBC0 - ·
328 aa · 586394–587380 (+) ·
RefSeq NP_215010.3
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Contains Ppx-GppA (PF02541.23) domain(s); putative function inferred from the domain architecture. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Annotated on the H37Rv protein: this gene has no 1:1 ancestral MTBC0 anchor (PE/PPE, paralogue, IS element, or otherwise unanchored CDS).
Curated reference (UniProt)
| UniProt |
P9WHV5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Exopolyphosphatase 1 |
| 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 short-chain length polyphosphates as substrates. 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 | ppx1 |
| eggNOG description | 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 (11) |
GO:0003674, GO:0003824, GO:0006793, GO:0008150, GO:0008152, GO:0009987, GO:0016462, GO:0016787, GO:0016817, GO:0016818, GO:0044237
|
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 | 0.556 · 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 |
|---|---|---|---|---|
Ppx-GppA | PF02541.23 | 5.4e-95 | 2–291 | Ppx/GppA phosphatase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0497 (transmembrane protein), high confidence from genomic context alone (score 887 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) |
|---|---|---|---|---|
Rv1026 ppx2 hyp |
hypothetical protein | 963 | 928 | database:900 textmining:514 |
Rv2583c relA |
bifunctional (p)ppGpp synthase/hydrolase RelA | 939 | 912 | database:900 |
Rv0497 |
transmembrane protein | 887 | 887 ctx | neighborhood:881 |
Rv0498 hyp |
hypothetical protein | 864 | 864 ctx | neighborhood:863 |
Rv0499 hyp |
hypothetical protein | 847 | 847 ctx | neighborhood:846 |
Rv0500 proC |
pyrroline-5-carboxylate reductase | 816 | 816 ctx | neighborhood:815 |
Rv2984 ppk1 |
polyphosphate kinase | 968 | 814 ctx | cooccurence:432 coexpression:643 textmining:839 |
Rv0500A |
DNA-binding protein | 717 | 717 ctx | neighborhood:715 |
Rv0495c hyp |
hypothetical protein | 643 | 643 ctx | neighborhood:639 |
Rv1629 polA |
DNA polymerase I | 479 | 480 | coexpression:410 |
Rv0500B |
Rv0500B, len: 33 aa. Conserved hypothetical protein. Basic protein 18 of the 33 aa are Arg or Lys, with strong similarity to AL079345|SCE68_ | 430 | 430 ctx | neighborhood:422 |
Rv0502 hyp |
hypothetical protein | 417 | 416 | |
Rv3232c ppk2 |
polyphosphate kinase | 929 | 414 | textmining:885 |
Rv2603c |
transcriptional regulator | 878 | 104 | textmining:870 |
Rv3301c phoY1 |
phosphate transport system transcriptional regulator PhoY | 659 | 82 | textmining:645 |
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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): hypothetical protein
- Pfam (hmmscan --cut_ga): Ppx-GppA PF02541.23 (E=5e-95)
- (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_215010.3)
- 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 P9WHV5 (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 —
23 functional partner(s); context anchor
Rv0497 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0496| MVDAHRGGHPTPMSSTKATLRLAEATDSSGKITKRGADKLISTIDEFAKIAISSGCAELMAFATSAVRDAENSEDVLSRVRKETGVELQALRGEDESRLTFLAVRRWYGWSAGRILNLDIGGGSLEVSSGVDEEPEIALSLPLGAGRLTREWLPDDPPGRRRVAMLRDWLDAELAEPSVTVLEAGSPDLAVATSKTFRSLARLTGAAPSMAGPRVKRTLTANGLRQLIAFISRMTAVDRAELEGVSADRAPQIVAGALVAEASMRALSIEAVEICPWALREGLILRKLDSEADGTALIESSSVHTSVRAVGGQPADRNAANRSRGSKP