Rv2781c Resolved · high auto-curated
H37Rv Rv2781c · MTBC0 mtbc0_002960 ·
344 aa · 3110365–3111399 (-) ·
RefSeq NP_217297.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | nitronate monooxygenase |
| Revised (this work) | Nitronate monooxygenase. Pfam: NMO (PF03060.22). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
I6X5C5
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable nitronate monooxygenase |
| Curated function | Nitronate monooxygenase that uses molecular oxygen to catalyze the oxidative denitrification of alkyl nitronates. Acts on propionate 3-nitronate (P3N), the presumed physiological substrate. Probably functions in the detoxification of P3N, a metabolic poison produced by plants and fungi as a defense mechanism. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
S Function unknown
|
|---|---|
| Preferred name | yrpB |
| eggNOG description | 2-nitropropane dioxygenase |
| Orthologous group | COG2070 |
| EC number |
EC 1.13.12.16
|
| KEGG orthology |
K00459
|
| KEGG pathways |
map00910
|
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 | 0.365 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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 |
|---|---|---|---|---|
NMO | PF03060.22 | 1.4e-125 | 7–339 | Nitronate monooxygenase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: pepR (zinc protease), high confidence from genomic context alone (score 850 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0021c hyp |
hypothetical protein | 929 | 930 | database:900 |
Rv0267 narU |
nitrite extrusion protein NarU | 909 | 909 | database:900 |
Rv0261c narK3 |
nitrate/nitrite transporter | 909 | 908 | database:900 |
Rv1737c narK2 |
nitrate/nitrite transporter | 909 | 908 | database:900 |
Rv2329c narK1 |
nitrate/nitrite transporter | 908 | 908 | database:900 |
Rv1164 narI |
nitrate reductase subunit gamma | 903 | 904 | database:900 |
Rv1162 narH |
nitrate reductase subunit beta | 902 | 903 | database:900 |
Rv1161 narG |
nitrate reductase subunit alpha | 901 | 902 | database:900 |
Rv1736c narX |
nitrate reductase-like protein NarX | 901 | 901 | database:900 |
Rv0252 nirB |
nitrite reductase large subunit NirB | 900 | 900 | database:900 |
Rv0253 nirD |
nitrite reductase small subunit NirD | 900 | 900 | database:900 |
Rv2782c pepR |
zinc protease | 850 | 850 ctx | neighborhood:802 |
Rv2783c gpsI |
bifunctional guanosine pentaphosphate synthetase/polyribonucleotide nucleotidyltransferase | 807 | 807 ctx | neighborhood:802 |
Rv2524c fas |
fatty acid synthase | 782 | 748 | coexpression:712 |
Rv2784c lppU |
lipoprotein LppU | 679 | 678 ctx | neighborhood:675 |
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: oxidoreductase
- MTBC0 PGAP product: nitronate monooxygenase
- Pfam (hmmscan --cut_ga): NMO PF03060.22 (E=1e-125)
- (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_217297.1)
- Domains: Pfam-A via hmmscan --cut_ga — NMO (PF03060.22)
- 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
COG2070 - Curated reference: UniProt I6X5C5 (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 —
45 functional partner(s); context anchor
pepR - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002960|Rv2781c| MVLGFWDIAVPIVGAPMAGGPSTPALAAAVSNAGGLGFVAGGYLSADRLADDIAAARAATTGPIGANLFVPQPSVADWAQLEYYADELEEVAEYYHTEVGQPVYGDDDDWVRKLEVVADVRPEVVSFTFGAPPPDVVQRLSALGLLVSITVTSVYEAGVAIAAGADSLVVQGPAAGGHRGTFAPDMEPGTESLHQLLDRIGSAHDVPLVAAGGLGTAEDVAAVLRRGAIAAQVGTALLLADEAGTNAAHRAALKNPEFDATLVTRAFSGRYARGLANNFTRLLDHVAPLGYPEVHQMTKPIRAAAVQADDPHGTNLWAGSAHRKTRPGPAADIIASLTPDVCSA