Rv3829c Resolved · high auto-curated
H37Rv Rv3829c · MTBC0 mtbc0_004058 ·
536 aa · 4327508–4329118 (-) ·
RefSeq NP_218346.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | dehydrogenase |
|---|---|
| MTBC0 PGAP re-annotation | NAD(P)/FAD-dependent oxidoreductase |
| Revised (this work) | NAD(P)/FAD-dependent oxidoreductase. Pfam: NAD_binding_8 (PF13450.13), Amino_oxidase (PF01593.31). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O07794
TrEMBL · unreviewed
· Predicted
|
|---|---|
| UniProt name | Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 2 |
| Curated function | Probable oxidoreductase that may play a role as regulator of mitochondrial function. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| eggNOG description | FAD dependent oxidoreductase |
| Orthologous group | COG1233 |
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) pseudogene candidate
| pN/pS | 0.367 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 12 synonymous, 13 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 24.32% of strains (35314) · 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 |
|---|---|---|---|---|
NAD_binding_8 | PF13450.13 | 3.5e-09 | 8–62 | NAD(P)-binding Rossmann-like domain |
Amino_oxidase | PF01593.31 | 1.8e-09 | 15–328 | Flavin containing amine oxidoreductase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3830c (TetR family transcriptional regulator), high confidence from genomic context alone (score 888 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3830c |
TetR family transcriptional regulator | 959 | 888 ctx | neighborhood:672 cooccurence:670 textmining:653 |
Rv3828c |
resolvase | 775 | 774 ctx | neighborhood:773 |
Rv3827c |
transposase | 775 | 774 ctx | neighborhood:773 |
Rv3397c phyA |
phytoene synthase | 772 | 665 | coexpression:653 |
Rv1635c |
mannosyltransferase | 623 | 623 ctx | cooccurence:623 |
Rv0048c |
membrane protein | 564 | 564 ctx | cooccurence:564 |
Rv0077c |
oxidoreductase | 555 | 555 ctx | cooccurence:541 |
Rv0875c hyp |
hypothetical protein | 553 | 553 ctx | cooccurence:553 |
Rv2407 rnz |
ribonuclease Z | 548 | 546 ctx | cooccurence:541 |
Rv1353c |
HTH-type transcriptional regulator | 545 | 545 ctx | cooccurence:543 |
Rv2079 hyp |
hypothetical protein | 534 | 534 ctx | cooccurence:531 |
Rv1171 hyp |
hypothetical protein | 534 | 534 ctx | cooccurence:533 |
Rv3831 hyp |
hypothetical protein | 531 | 531 ctx | neighborhood:526 |
Rv1346 mbtN |
acyl-[acyl-carrier-protein | 495 | 496 ctx | cooccurence:486 |
Rv1834 lipZ |
hydrolase | 495 | 496 ctx | cooccurence:478 |
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: dehydrogenase
- MTBC0 PGAP product: NAD(P)/FAD-dependent oxidoreductase
- Pfam (hmmscan --cut_ga): NAD_binding_8 PF13450.13 (E=3e-09), Amino_oxidase PF01593.31 (E=2e-09)
- (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_218346.1)
- Domains: Pfam-A via hmmscan --cut_ga — NAD_binding_8 (PF13450.13), Amino_oxidase (PF01593.31)
- 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
COG1233 - Curated reference: UniProt O07794 (TrEMBL, unreviewed; Predicted)
- 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 —
38 functional partner(s); context anchor
Rv3830c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_004058|Rv3829c| MTGYDAIVIGAGHNGLTAAVLLQRAGLRTACLDAKRYAGGMASTVELFDGYRFEIAGSVQFPTSSAVSSELGLDSLPTVDLEVMSVALRGVGDDPVVQFTDPTKMLTHLHRVHGADAVTGMAGLLAWSQAPTRALGRFEAGTLPKSFDEMYACATNEFERSAIDDMLFGSVTDVLDRHFPDREKHGALRGSMTVLAVNTLYRGPATPGSAAALAFGLGVPEGDFVRWKKLRGGIGALTTHLSQLLERTGGEVRLRSKVTEIVVDNSRSSARVRGVRTAAGDTLTSPIVVSAIAPDVTINELIDPAVLPSEIRDRYLRIDHRGSYLQMHFALAQPPAFAAPYQALNDPSMQASMGIFCTPEQVQQQWEDCRRGIVPADPTVVLQIPSLHDPSLAPAGKQAASAFAMWFPIEGGSKYGGYGRAKVEMGQNVIDKITRLAPNFKGSILRYTTFTPKHMGVMFGAPGGDYCHALLHSDQIGPNRPGPKGFIGQPIPIAGLYLGSAGCHGGPGITFIPGYNAARQALADRRAANCCVLSGR