Rv3178 Resolved · high auto-curated
H37Rv Rv3178 · MTBC0 - ·
119 aa · 3546438–3546797 (+) ·
RefSeq NP_217694.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | nitroreductase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Nitroreductase. Pfam: F420H2_quin_red (PF04075.21). |
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 |
O53328
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Putative F420H(2)-dependent quinone reductase Rv3178 |
| EC (curated) |
EC 1.1.98.-
|
| Curated function | Involved in a F420-dependent anti-oxidant mechanism that protects M.tuberculosis against oxidative stress and bactericidal agents. Catalyzes the F420H(2)-dependent two-electron reduction of quinones to dihydroquinones, thereby preventing the formation of cytotoxic semiquinones obtained by the one-electron reduction pathway. Since menaquinone is the sole quinone electron carrier in the respiratory chain in M.tuberculosis, the physiological electron acceptor for Fqr-mediated F420H(2) oxidation is therefore likely to be the endogenous menaquinone found in the membrane fraction of M.tuberculosis. |
UniProt still lists this protein as Putative F420H(2)-dependent quinone reductase Rv3178; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
P Inorganic ion transport and metabolism
|
|---|---|
| eggNOG description | F420H(2)-dependent quinone reductase |
| Orthologous group | COG0748 |
| Gene Ontology (24) |
GO:0003674, GO:0005488, GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0008150, GO:0008152, GO:0016020, GO:0030312, GO:0031406, GO:0036094 +12 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 | 1.035 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 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 |
|---|---|---|---|---|
F420H2_quin_red | PF04075.21 | 1.6e-29 | 11–117 | F420H(2)-dependent quinone reductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0044c (oxidoreductase), high confidence from genomic context alone (score 760 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0044c |
oxidoreductase | 774 | 760 ctx | cooccurence:759 |
Rv3520c |
coenzyme F420-dependent oxidoreductase | 773 | 760 ctx | cooccurence:758 |
Rv3261 fbiA |
2-phospho-L-lactate transferase | 869 | 753 ctx | cooccurence:746 textmining:493 |
Rv0407 fgd1 |
F420-dependent glucose-6-phosphate dehydrogenase | 953 | 745 ctx | cooccurence:745 textmining:824 |
Rv1855c |
oxidoreductase | 749 | 734 ctx | cooccurence:732 |
Rv2951c |
phthiodiolone/phenolphthiodiolone dimycocerosates ketoreductase | 740 | 724 ctx | cooccurence:724 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 836 | 717 ctx | cooccurence:707 textmining:446 |
Rv0132c fgd2 |
F420-dependent glucose-6-phosphate dehydrogenase | 731 | 715 ctx | cooccurence:712 |
Rv2983 cofC |
2-phospho-L-lactate guanylyltransferase | 740 | 709 ctx | cooccurence:700 |
Rv3093c |
oxidoreductase | 702 | 684 ctx | cooccurence:684 |
Rv0940c |
oxidoreductase | 685 | 665 ctx | cooccurence:663 |
Rv2161c hyp |
hypothetical protein | 676 | 656 ctx | cooccurence:653 |
Rv3177 |
peroxidase | 651 | 652 ctx | neighborhood:526 |
Rv0791c hyp |
hypothetical protein | 670 | 649 ctx | cooccurence:647 |
Rv3072c hyp |
hypothetical protein | 659 | 638 ctx | cooccurence:638 |
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): nitroreductase
- Pfam (hmmscan --cut_ga): F420H2_quin_red PF04075.21 (E=2e-29)
- (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_217694.1)
- Domains: Pfam-A via hmmscan --cut_ga — F420H2_quin_red (PF04075.21)
- 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
COG0748 - Curated reference: UniProt O53328 (SwissProt, reviewed; Inferred from homology)
- 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 —
34 functional partner(s); context anchor
Rv0044c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3178| MRLGAGFRKPVPTLLLEHRSRKSGKNFVAPLLYITDRNNVIVVASALGQAENPQWYRNLPPNPDTHIQIGSDRRPVRAVVASSDERARLWPRPVDAYADFDSCQSWTERGIPVIILRPR