rdgB Family assigned · medium auto-curated
H37Rv Rv1341 · MTBC0 mtbc0_001438 ·
204 aa · 1518275–1518889 (+) ·
RefSeq NP_215857.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | non-canonical purine NTP pyrophosphatase |
|---|---|
| MTBC0 PGAP re-annotation | RdgB/HAM1 family non-canonical purine NTP pyrophosphatase |
| Revised (this work) | RdgB/HAM1 family non-canonical purine NTP pyrophosphatase. Pfam: Ham1p_like (PF01725.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMR7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | dITP/XTP pyrophosphatase |
| EC (curated) |
EC 3.6.1.66
|
| Curated function | Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP. Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA/RNA and avoiding chromosomal lesions. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | rdgB |
| eggNOG description | Pyrophosphatase that catalyzes the hydrolysis of nucleoside triphosphates to their monophosphate derivatives, with a high preference for the non-canonical purine nucleotides XTP (xanthosine triphosphate), dITP (deoxyinosine triphosphate) and ITP. Seems to function as a house-cleaning enzyme that removes non-canonical purine nucleotides from the nucleotide pool, thus preventing their incorporation into DNA RNA and avoiding chromosomal lesions |
| Orthologous group | COG0127 |
| EC number |
EC 3.6.1.66
|
| KEGG orthology |
K02428
|
| KEGG pathways |
map00230
|
| Gene Ontology (55) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0006139, GO:0006725, GO:0006753, GO:0006793, GO:0006796 +43 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 | 0.195 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.24% of strains (352) · 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 |
|---|---|---|---|---|
Ham1p_like | PF01725.22 | 6.5e-59 | 7–195 | Ham1 family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: rphA (ribonuclease PH), high confidence from genomic context alone (score 994 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv1340 rphA |
ribonuclease PH | 993 | 994 ctx | neighborhood:825 fusion:900 coexpression:678 |
Rv3396c guaA |
GMP synthase | 975 | 963 ctx | cooccurence:409 database:900 |
Rv1338 murI |
glutamate racemase | 960 | 960 ctx | neighborhood:632 fusion:890 |
Rv2445c ndkA |
nucleoside diphosphate kinase | 938 | 931 | database:900 |
Rv3411c guaB2 |
inosine-5'-monophosphate dehydrogenase | 935 | 928 | database:900 |
Rv1843c guaB1 |
inosine-5'-monophosphate dehydrogenase | 934 | 927 | database:900 |
Rv3410c guaB3 |
oxidoreductase | 926 | 919 | database:900 |
Rv1021 mazG |
nucleoside triphosphate pyrophosphohydrolase | 916 | 916 | database:900 |
Rv3624c hpt |
hypoxanthine-guanine phosphoribosyltransferase | 911 | 905 | database:900 |
Rv1339 hyp |
hypothetical protein | 821 | 821 ctx | neighborhood:808 |
Rv1336 cysM |
O-phosphoserine sulfhydrylase | 813 | 813 ctx | neighborhood:780 |
Rv1335 cysO |
sulfur carrier protein CysO | 785 | 785 ctx | neighborhood:777 |
Rv1334 mec |
[CysO | 773 | 774 ctx | neighborhood:758 |
Rv0639 nusG |
transcription termination/antitermination protein NusG | 767 | 767 | coexpression:767 |
Rv1333 |
hydrolase | 761 | 762 ctx | neighborhood:758 |
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: non-canonical purine NTP pyrophosphatase
- MTBC0 PGAP product: RdgB/HAM1 family non-canonical purine NTP pyrophosphatase
- Pfam (hmmscan --cut_ga): Ham1p_like PF01725.22 (E=7e-59)
- (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_215857.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ham1p_like (PF01725.22)
- 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
COG0127 - Curated reference: UniProt P9WMR7 (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 —
68 functional partner(s); context anchor
rphA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001438|Rv1341|rdgB MALVTKLLVASRNRKKLAELRRVLDGAGLSGLTLLSLGDVSPLPETPETGVTFEDNALAKARDAFSATGLASVADDSGLEVAALGGMPGVLSARWSGRYGDDAANTALLLAQLCDVPDERRGAAFVSACALVSGSGEVVVRGEWPGTIAREPRGDGGFGYDPVFVPYGDDRTAAQLSPAEKDAVSHRGRALALLLPALRSLATG