Rv3359 Resolved · high auto-curated
H37Rv Rv3359 · MTBC0 mtbc0_003574 ·
396 aa · 3798052–3799242 (+) ·
RefSeq NP_217876.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | oxidoreductase |
|---|---|
| MTBC0 PGAP re-annotation | NADH:flavin oxidoreductase |
| Revised (this work) | NADH:flavin oxidoreductase. Pfam: Oxidored_FMN (PF00724.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O50388
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Possible oxidoreductase |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | NADH flavin oxidoreductase |
| Orthologous group | COG1902 |
| EC number |
EC 1.8.1.20
|
| KEGG orthology |
K22347
|
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 | 0.351 · 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 |
|---|---|---|---|---|
Oxidored_FMN | PF00724.27 | 1.0e-42 | 11–248 | NADH:flavin oxidoreductase / NADH oxidase family |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: folD (bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase), high confidence from genomic context alone (score 739 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3356c folD |
bifunctional methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase | 754 | 739 ctx | neighborhood:738 |
Rv3355c |
integral membrane protein | 739 | 739 ctx | neighborhood:738 |
Rv3358 relK |
toxin RelK | 666 | 666 ctx | neighborhood:661 |
Rv3357 relJ |
antitoxin RelJ | 665 | 664 ctx | neighborhood:661 |
Rv0310c hyp |
hypothetical protein | 596 | 575 ctx | cooccurence:512 |
Rv3169 hyp |
hypothetical protein | 564 | 565 ctx | cooccurence:561 |
Rv1747 |
ABC transporter ATP-binding protein/permease | 558 | 536 ctx | neighborhood:536 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 545 | 517 | experimental:484 |
Rv3360 hyp |
hypothetical protein | 509 | 509 ctx | neighborhood:506 |
Rv0770 |
oxidoreductase | 491 | 492 | |
Rv3552 |
CoA-transferase subunit beta | 483 | 481 ctx | cooccurence:470 |
Rv3168 |
aminoglycoside phosphotransferase | 457 | 457 ctx | cooccurence:415 |
Rv0771 |
4-carboxymuconolactone decarboxylase | 475 | 454 ctx | cooccurence:438 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 496 | 452 | experimental:431 |
Rv1162 narH |
nitrate reductase subunit beta | 451 | 452 | experimental:449 |
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: NADH:flavin oxidoreductase
- Pfam (hmmscan --cut_ga): Oxidored_FMN PF00724.27 (E=1e-42)
- (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_217876.1)
- Domains: Pfam-A via hmmscan --cut_ga — Oxidored_FMN (PF00724.27)
- 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
COG1902 - Curated reference: UniProt O50388 (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 —
19 functional partner(s); context anchor
folD - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003574|Rv3359| MAPGSCEAPDVFNPAKLGPLTLRNRVIKAATFEARTPDALVTDDLIEYHRLPAAGGVAMTTVAYCAVSPGGRTGGNQIWMRPHAVPGLRRLTEAIHAEGAAISAQIGHAGPVADARSNQATALAPVRFFNPIAMRFAQKATREDIDDVLAAHAHAARLAVDAGFDAVEIHLGHNYLASAFLSPLLNRRDDEFGGSLQNRAKVARGLVMAVRRAVRQQVAVTAKLNMTDGIRGGITVDEALTTARWLQDDGGLDAIELTAGSSLVNPMYLFRGDAPVKEFAAAFKPPLRWGIRMTGHRFFREYPYRDAYLLREARLFRAELTIPLILLGGITNRTTMDLAMAEGFEFVAMARALLAEPDLVNRIAAEGSQVRSACTHCNQCMATIYRRTHCVVTGAP