Rv3230c Resolved · high auto-curated
H37Rv Rv3230c · MTBC0 mtbc0_003439 ·
380 aa · 3629254–3630396 (-) ·
RefSeq NP_217747.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | stearoyl-CoA 9-desaturase electron transfer protein |
|---|---|
| MTBC0 PGAP re-annotation | NADPH oxidoreductase |
| Revised (this work) | NADPH oxidoreductase. Pfam: FAD_binding_6 (PF00970.31), NAD_binding_1 (PF00175.27), Fer2 (PF00111.33). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WNE9
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | NADPH oxidoreductase |
| EC (curated) |
EC 1.-.-.-
|
| Curated function | Is likely involved in the aerobic desaturation system responsible for the synthesis of oleic acid from stearoyl-CoA; oleic acid is a precursor of mycobacterial membrane phospholipids and triglycerides. Is the electron transfer partner for the stearoyl-CoA 9-desaturase DesA3. Catalyzes electron transfer reaction between NADPH and the diiron center of DesA3. Cannot use NADH. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
C Energy production and conversion
|
|---|---|
| eggNOG description | Oxidoreductase FAD-binding domain |
| Orthologous group | COG1018 |
| Gene Ontology (23) |
GO:0000166, GO:0003674, GO:0003824, GO:0005488, GO:0006091, GO:0008150, GO:0008152, GO:0009055, GO:0009987, GO:0016491, GO:0022900, GO:0036094 +11 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 | 0.36 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 5 synonymous, 5 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 |
|---|---|---|---|---|
FAD_binding_6 | PF00970.31 | 1.1e-08 | 88–161 | Oxidoreductase FAD-binding domain |
NAD_binding_1 | PF00175.27 | 2.4e-08 | 173–267 | Oxidoreductase NAD-binding domain |
Fer2 | PF00111.33 | 6.2e-11 | 305–372 | 2Fe-2S iron-sulfur cluster binding domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: desA3 (stearoyl-CoA 9-desaturase), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3229c desA3 |
stearoyl-CoA 9-desaturase | 999 | 1000 ctx | neighborhood:788 fusion:794 cooccurence:766 coexpression:824 database:900 textmining:700 |
Rv0824c desA1 |
acyl-ACP desaturase DesA | 931 | 928 | database:900 |
Rv1094 desA2 |
acyl-ACP desaturase DesA | 930 | 927 | database:900 |
Rv1465 |
nitrogen fixation related protein | 869 | 850 | database:621 |
Rv3025c iscS |
cysteine desulfurase | 855 | 834 | experimental:422 database:621 |
Rv1175c fadH |
NADPH dependent 2,4-dienoyl-CoA reductase FadH | 862 | 812 | experimental:430 database:568 |
Rv0886 fprB |
ferredoxin/ferredoxin--NADP reductase | 867 | 775 | experimental:430 database:568 textmining:436 |
Rv3231c hyp |
hypothetical protein | 952 | 769 ctx | neighborhood:768 textmining:803 |
Rv3858c gltD |
glutamate synthase small subunit | 778 | 752 | experimental:430 database:568 |
Rv3153 nuoI |
NADH-quinone oxidoreductase subunit I | 786 | 751 | experimental:700 |
Rv3106 fprA |
NADPH-ferredoxin reductase FprA | 777 | 751 | experimental:430 database:568 |
Rv3148 nuoD |
NADH-quinone oxidoreductase subunit D | 749 | 733 | experimental:702 |
Rv2940c mas |
multifunctional mycocerosic acid synthase | 808 | 731 | experimental:703 |
Rv3825c pks2 |
phthioceranic/hydroxyphthioceranic acid synthase | 808 | 731 | experimental:703 |
Rv2048c pks12 |
polyketide synthase | 808 | 731 | experimental:703 |
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: stearoyl-CoA 9-desaturase electron transfer protein
- MTBC0 PGAP product: NADPH oxidoreductase
- Pfam (hmmscan --cut_ga): FAD_binding_6 PF00970.31 (E=1e-08), NAD_binding_1 PF00175.27 (E=2e-08), Fer2 PF00111.33 (E=6e-11)
- (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_217747.1)
- Domains: Pfam-A via hmmscan --cut_ga — FAD_binding_6 (PF00970.31), NAD_binding_1 (PF00175.27), Fer2 (PF00111.33)
- 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
COG1018 - Curated reference: UniProt P9WNE9 (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 —
108 functional partner(s); context anchor
desA3 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003439|Rv3230c| MSKKHTTLNASIIDTRRPTVAGADRHPGWHALRKIAARITTPLLPDDYLHLANPLWSARELRGRILGVRRETEDSATLFIKPGWGFSFDYQPGQYIGIGLLVDGRWRWRSYSLTSSPAASGSARMVTVTVKAMPEGFLSTHLVAGVKPGTIVRLAAPQGNFVLPDPAPPLILFLTAGSGITPVMSMLRTLVRRNQITDVVHLHSAPTAADVMFGAELAALAADHPGYRLSVRETRAQGRLDLTRIGQQVPDWRERQTWACGPEGVLNQADKVWSSAGASDRLHLERFAVSKTAPAGAGGTVTFARSGKSVAADAATSLMDAGEGAGVQLPFGCRMGICQSCVVDLVEGHVRDLRTGQRHEPGTRVQTCVSAASGDCVLDI