nrdH Resolved · high auto-curated
H37Rv Rv3053c · MTBC0 mtbc0_003245 ·
79 aa · 3436029–3436268 (-) ·
RefSeq NP_217569.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | glutaredoxin electron transport protein NrdH |
|---|---|
| MTBC0 PGAP re-annotation | redoxin NrdH |
| Revised (this work) | Redoxin NrdH. Pfam: Glutaredoxin (PF00462.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6YB06
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Glutaredoxin-like protein NrdH |
| Curated function | Electron transport system for the ribonucleotide reductase system NrdEF. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| Preferred name | nrdH |
| eggNOG description | (Glutaredoxin-like protein) NrdH |
| Orthologous group | COG0695 |
| KEGG orthology |
K06191
|
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 | 0.0 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 0 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 |
|---|---|---|---|---|
Glutaredoxin | PF00462.31 | 6.1e-16 | 3–61 | Glutaredoxin |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: nrdE (ribonucleoside-diphosphate reductase subunit alpha), high confidence from genomic context alone (score 997 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3051c nrdE |
ribonucleoside-diphosphate reductase subunit alpha | 998 | 997 ctx | neighborhood:564 cooccurence:772 coexpression:872 database:614 textmining:696 |
Rv3052c nrdI |
NrdI protein | 999 | 995 ctx | neighborhood:833 cooccurence:772 coexpression:887 textmining:798 |
Rv0570 nrdZ |
vitamin B12-dependent ribonucleoside-diphosphate reductase | 878 | 864 | database:614 |
Rv3048c nrdF2 |
ribonucleoside-diphosphate reductase subunit beta NrdF2 | 971 | 861 ctx | cooccurence:773 textmining:801 |
Rv1981c nrdF1 |
ribonucleoside-diphosphate reductase subunit beta NrdF1 | 924 | 826 ctx | cooccurence:772 textmining:585 |
Rv3050c |
AsnC family transcriptional regulator | 755 | 756 ctx | neighborhood:625 |
Rv2204c hyp |
hypothetical protein | 757 | 737 | coexpression:728 |
Rv0038 hyp |
hypothetical protein | 697 | 662 | database:643 |
Rv0137c msrA |
peptide methionine sulfoxide reductase MsrA | 578 | 513 | experimental:484 |
Rv1307 atpH |
ATP synthase subunit b/delta | 470 | 470 | coexpression:408 |
Rv3206c moeB1 |
adenylyltransferase/sulfurtransferase MoeZ | 455 | 432 | |
Rv2048c pks12 |
polyketide synthase | 432 | 251 | |
Rv3303c lpdA |
NAD(P)H quinone reductase LpdA | 407 | 198 | |
Rv3913 trxB2 |
thioredoxin reductase | 593 | 196 | textmining:515 |
Rv0233 nrdB |
ribonucleoside-diphosphate reductase subunit beta NrdB | 549 | 191 | textmining:466 |
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: glutaredoxin electron transport protein NrdH
- MTBC0 PGAP product: redoxin NrdH
- Pfam (hmmscan --cut_ga): Glutaredoxin PF00462.31 (E=6e-16)
- (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_217569.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glutaredoxin (PF00462.31)
- 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
COG0695 - Curated reference: UniProt I6YB06 (TrEMBL, unreviewed; 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 —
28 functional partner(s); context anchor
nrdE - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003245|Rv3053c|nrdH MTVTVYTKPACVQCSATSKALDKQGIAYQKVDISLDSEARDYVMALGYLQAPVVVAGNDHWSGFRPDRIKALAGAALTA