nrdB Resolved · high auto-curated
H37Rv Rv0233 · MTBC0 mtbc0_000248 ·
314 aa · 278966–279910 (+) ·
RefSeq NP_214747.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | ribonucleoside-diphosphate reductase subunit beta NrdB |
|---|---|
| MTBC0 PGAP re-annotation | R2-like ligand-binding oxidase |
| Revised (this work) | R2-like ligand-binding oxidase. Pfam: Ribonuc_red_sm (PF00268.28). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WH69
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | R2-like ligand binding oxidase |
| EC (curated) |
EC 1.-.-.-
|
| Curated function | Probable oxidase that might be involved in lipid metabolism. Is not essential for the survival of M.tuberculosis in stress conditions. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
F Nucleotide transport and metabolism
|
|---|---|
| Preferred name | nrdB |
| eggNOG description | ribonucleotide reductase |
| Orthologous group | COG0208 |
| EC number |
EC 1.17.4.1
|
| KEGG orthology |
K00526
|
| KEGG pathways |
map00230, map00240, map01100
|
| KEGG modules |
M00053
|
| Gene Ontology (23) |
GO:0003674, GO:0003824, GO:0005488, GO:0005506, GO:0005515, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0008150, GO:0008152 +11 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 | 0.617 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.12% of strains (180) · 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 |
|---|---|---|---|---|
Ribonuc_red_sm | PF00268.28 | 4.1e-19 | 28–273 | Ribonucleotide reductase, small chain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0232 (transcriptional regulator), high confidence from genomic context alone (score 983 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3051c nrdE |
ribonucleoside-diphosphate reductase subunit alpha | 993 | 985 | coexpression:648 experimental:600 database:900 textmining:604 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 987 | 985 | coexpression:648 experimental:600 database:900 |
Rv0232 |
transcriptional regulator | 982 | 983 ctx | neighborhood:882 coexpression:860 |
Rv3247c tmk |
thymidylate kinase | 913 | 904 | database:900 |
Rv1712 cmk |
cytidylate kinase | 913 | 904 | database:900 |
Rv3048c nrdF2 |
ribonucleoside-diphosphate reductase subunit beta NrdF2 | 956 | 901 | database:900 textmining:581 |
Rv1981c nrdF1 |
ribonucleoside-diphosphate reductase subunit beta NrdF1 | 953 | 901 | database:900 textmining:550 |
Rv2583c relA |
bifunctional (p)ppGpp synthase/hydrolase RelA | 901 | 901 | database:900 |
Rv0733 adk |
adenylate kinase | 940 | 900 | database:900 textmining:432 |
Rv2445c ndkA |
nucleoside diphosphate kinase | 909 | 900 | database:900 |
Rv1617 pykA |
pyruvate kinase | 907 | 900 | database:900 |
Rv1389 gmk |
guanylate kinase | 905 | 900 | database:900 |
Rv3052c nrdI |
NrdI protein | 950 | 884 | coexpression:455 experimental:788 textmining:591 |
Rv3083 mymA |
FAD-containing monooxygenase MymA | 733 | 733 | coexpression:733 |
Rv3086 adhD |
alcohol dehydrogenase D | 730 | 730 | coexpression:730 |
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: ribonucleoside-diphosphate reductase subunit beta NrdB
- MTBC0 PGAP product: R2-like ligand-binding oxidase
- Pfam (hmmscan --cut_ga): Ribonuc_red_sm PF00268.28 (E=4e-19)
- (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_214747.1)
- Domains: Pfam-A via hmmscan --cut_ga — Ribonuc_red_sm (PF00268.28)
- 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
COG0208 - Curated reference: UniProt P9WH69 (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 —
46 functional partner(s); context anchor
Rv0232 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000248|Rv0233|nrdB MTRTRSGSLAAGGLNWASLPLKLFAGGNAKFWDPADIDFTRDRADWEKLSDDERDYATRLCTQFIAGEEAVTEDIQPFMSAMRAEGRLADEMYLTQFAFEEAKHTQVFRMWLDAVGISEDLHRYLDDLPAYRQIFYAELPECLNALSADPSPAAQVRASVTYNHIVEGMLALTGYYAWHKICVERAILPGMQELVRRIGDDERRHMAWGTFTCRRHVAADDANWTVFETRMNELIPLALRLIEEGFALYGDQPPFDLSKDDFLQYSTDKGMRRFGTISNARGRPVAEIDVDYSPAQLEDTFADEDRRTLAAASA