Rv3520c Resolved · high auto-curated
H37Rv Rv3520c · MTBC0 - ·
347 aa · 3956325–3957368 (-) ·
RefSeq NP_218037.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | coenzyme F420-dependent oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Coenzyme F420-dependent oxidoreductase. Pfam: Bac_luciferase (PF00296.27). |
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 |
O53565
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Putative coenzyme F420-dependent oxidoreductase Rv3520c |
| EC (curated) |
EC 1.-.-.-
|
UniProt still lists this protein as Putative coenzyme F420-dependent oxidoreductase Rv3520c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | F420-dependent oxidoreductase |
| Orthologous group | COG2141 |
| Gene Ontology (8) |
GO:0005575, GO:0005618, GO:0005623, GO:0005886, GO:0016020, GO:0030312, GO:0044464, GO:0071944
|
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 | 0.509 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.13% of strains (188) · 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 |
|---|---|---|---|---|
Bac_luciferase | PF00296.27 | 6.1e-72 | 17–328 | Luciferase-like monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0940c (oxidoreductase), high confidence from genomic context alone (score 870 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0940c |
oxidoreductase | 870 | 870 ctx | neighborhood:544 cooccurence:726 |
Rv3521 hyp |
hypothetical protein | 986 | 822 ctx | neighborhood:771 textmining:928 |
Rv3522 ltp4 |
lipid transfer protein | 943 | 815 ctx | neighborhood:760 textmining:705 |
Rv3523 ltp3 |
lipid carrier protein | 953 | 790 ctx | neighborhood:748 textmining:787 |
Rv3262 fbiB |
coenzyme F420:L-glutamate ligase | 786 | 773 ctx | cooccurence:742 |
Rv3547 ddn |
deazaflavin-dependent nitroreductase | 781 | 768 ctx | cooccurence:768 |
Rv3178 |
nitroreductase | 773 | 760 ctx | cooccurence:758 |
Rv1261c hyp |
hypothetical protein | 759 | 760 ctx | cooccurence:758 |
Rv3261 fbiA |
2-phospho-L-lactate transferase | 763 | 750 ctx | cooccurence:741 |
Rv1558 hyp |
hypothetical protein | 750 | 741 ctx | cooccurence:738 |
Rv1855c |
oxidoreductase | 728 | 729 ctx | cooccurence:716 |
Rv0132c fgd2 |
F420-dependent glucose-6-phosphate dehydrogenase | 727 | 727 ctx | cooccurence:726 |
Rv2893 |
oxidoreductase | 734 | 724 ctx | cooccurence:724 |
Rv2161c hyp |
hypothetical protein | 719 | 720 ctx | cooccurence:709 |
Rv0953c |
oxidoreductase | 633 | 633 ctx | cooccurence:633 |
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): coenzyme F420-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): Bac_luciferase PF00296.27 (E=6e-72)
- (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_218037.1)
- Domains: Pfam-A via hmmscan --cut_ga — Bac_luciferase (PF00296.27)
- 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
COG2141 - Curated reference: UniProt O53565 (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 —
27 functional partner(s); context anchor
Rv0940c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3520c| MEAGMKLGLQLGYWGAQPPQNHAELVAAAEDAGFDTVFTAEAWGSDAYTPLAWWGSSTQRVRLGTSVIQLSARTPTACAMAALTLDHLSGGRHILGLGVSGPQVVEGWYGQRFPKPLARTREYIDIVRQVWARESPVTSAGPHYRLPLTGEGTTGLGKALKPITHPLRADIPIMLGAEGPKNVALAAEICDGWLPIFYSPRMAGMYNEWLDEGFARPGARRSREDFEICATAQVVITDDRAAAFAGIKPFLALYMGGMGAEETNFHADVYRRMGYTQVVDEVTKLFRSGRKDEAAEIIPDELVDDAVIVGDIDHVRKQMAVWEAAGVTMMVVTAGSAEQVRDLAALV