nrdR Family assigned · medium auto-curated
H37Rv Rv2718c · MTBC0 mtbc0_002892 ·
154 aa · 3052828–3053292 (-) ·
RefSeq NP_217234.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | transcriptional regulator NrdR |
|---|---|
| MTBC0 PGAP re-annotation | transcriptional regulator NrdR |
| Revised (this work) | Transcriptional regulator NrdR. Pfam: Zn_ribbon_NrdR (PF22811.3), ATP-cone (PF03477.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WIZ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Transcriptional repressor NrdR |
| Curated function | Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR-boxes. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
K Transcription
|
|---|---|
| Preferred name | nrdR |
| eggNOG description | Negatively regulates transcription of bacterial ribonucleotide reductase nrd genes and operons by binding to NrdR- boxes |
| Orthologous group | COG1327 |
| KEGG orthology |
K07738
|
| Gene Ontology (8) |
GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0044424, GO:0044444, GO:0044464
|
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 | 0.344 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
Zn_ribbon_NrdR | PF22811.3 | 5.5e-21 | 1–42 | Transcriptional repressor NrdR-like, N-terminal domain |
ATP-cone | PF03477.22 | 3.3e-18 | 47–132 | ATP cone domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: lexA (repressor LexA), high confidence from genomic context alone (score 770 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2720 lexA |
repressor LexA | 799 | 770 ctx | neighborhood:667 |
Rv2719c chiZ |
membrane protein | 760 | 761 ctx | neighborhood:747 |
Rv2717c hyp |
hypothetical protein | 724 | 724 ctx | neighborhood:720 |
Rv1409 ribG |
bifunctional riboflavin biosynthesis diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino) uracil reductas | 746 | 517 | textmining:496 |
Rv0422c thiD |
hydroxymethylpyrimidine/phosphomethylpyrimidine kinase | 419 | 420 | coexpression:419 |
Rv1901 cinA |
competence damage-inducible protein CinA | 414 | 414 | |
Rv1629 polA |
DNA polymerase I | 448 | 275 | |
Rv1415 ribA2 |
bifunctional riboflavin biosynthesis GTP cyclohydrolase II/3,4-dihydroxy-2-butanone 4-phosphate synthase | 437 | 205 | |
Rv1940 ribA1 |
riboflavin biosynthesis protein RibA | 436 | 203 | |
Rv3051c nrdE |
ribonucleoside-diphosphate reductase subunit alpha | 507 | 177 | textmining:426 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 415 | 146 | |
Rv3053c nrdH |
glutaredoxin electron transport protein NrdH | 665 | 125 | textmining:633 |
Rv3242c hyp |
hypothetical protein | 701 | 106 | textmining:680 |
Rv1314c |
cob(I)yrinic acid a,c-diamide adenosyltransferase | 440 | 99 | textmining:405 |
Rv1981c nrdF1 |
ribonucleoside-diphosphate reductase subunit beta NrdF1 | 408 | 94 |
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: transcriptional regulator NrdR
- MTBC0 PGAP product: transcriptional regulator NrdR
- Pfam (hmmscan --cut_ga): Zn_ribbon_NrdR PF22811.3 (E=5e-21), ATP-cone PF03477.22 (E=3e-18)
- (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_217234.1)
- Domains: Pfam-A via hmmscan --cut_ga — Zn_ribbon_NrdR (PF22811.3), ATP-cone (PF03477.22)
- 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
COG1327 - Curated reference: UniProt P9WIZ1 (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 —
31 functional partner(s); context anchor
lexA - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002892|Rv2718c|nrdR MHCPFCRHPDSRVIDSRETDEGQAIRRRRSCPECGRRFTTVETAVLAVVKRSGVTEPFSREKVISGVRRACQGRQVDDDALNLLAQQVEDSVRAAGSPEIPSHDVGLAILGPLRELDEVAYLRFASVYRSFSSADDFAREIEALRAHRNLSAHS