desA3 Resolved · high auto-curated
H37Rv Rv3229c · MTBC0 - ·
427 aa · 3605751–3607034 (-) ·
RefSeq YP_177948.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | stearoyl-CoA 9-desaturase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Stearoyl-CoA 9-desaturase. Pfam: FA_desaturase (PF00487.31). |
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 |
P9WNZ3
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | NADPH-dependent stearoyl-CoA 9-desaturase |
| EC (curated) |
EC 1.14.19.n4
|
| 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. Catalyzes the conversion of stearoyl-CoA to oleoyl-CoA by introduction of a cis double bond between carbons 9 and 10 of the acyl chain. Requires the electron transfer partner Rv3230c to pass two electrons from NADPH to its active site diiron center. Is also able to catalyze the 9-desaturation of palmitoyl-CoA to palmitoleoyl-CoA. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
I Lipid transport and metabolism
|
|---|---|
| Preferred name | desA3 |
| eggNOG description | fatty acid desaturase |
| Orthologous group | COG3239 |
| EC number |
EC 1.14.19.3
|
| KEGG orthology |
K00508
|
| KEGG pathways |
map00591, map01100
|
| Gene Ontology (39) |
GO:0001676, GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0006082, GO:0006629, GO:0006631, GO:0006633, GO:0008150, GO:0008152 +27 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 | 0.234 · purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 8 synonymous, 6 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 |
|---|---|---|---|---|
FA_desaturase | PF00487.31 | 8.4e-34 | 69–339 | Fatty acid desaturase |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3230c (stearoyl-CoA 9-desaturase electron transfer protein), high confidence from genomic context alone (score 1000 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3230c |
stearoyl-CoA 9-desaturase electron transfer protein | 999 | 1000 ctx | neighborhood:788 fusion:794 cooccurence:766 coexpression:824 database:900 textmining:700 |
Rv0824c desA1 |
acyl-ACP desaturase DesA | 974 | 924 | database:900 textmining:679 |
Rv1094 desA2 |
acyl-ACP desaturase DesA | 987 | 923 | database:900 textmining:838 |
Rv3231c hyp |
hypothetical protein | 710 | 710 ctx | neighborhood:709 |
Rv3234c tgs3 |
diacyglycerol O-acyltransferase | 536 | 526 ctx | neighborhood:435 |
Rv0241c htdX |
3-hydroxyacyl-thioester dehydratase HtdX | 527 | 526 ctx | cooccurence:515 |
Rv3233c |
Rv3233c, (MTCY20B11.08c), len: 196 aa. Possible triacylglycerol synthase (See Daniel et al., 2004), similar to C-terminus of Q9RIU8|SCM11.13 | 522 | 512 ctx | neighborhood:435 |
Rv2777c hyp |
hypothetical protein | 508 | 509 ctx | cooccurence:493 |
Rv3232c ppk2 |
polyphosphate kinase | 455 | 451 ctx | neighborhood:448 |
Rv0242c fabG4 |
3-oxoacyl-ACP reductase FabG | 460 | 439 ctx | cooccurence:402 |
Rv3252c alkB |
transmembrane alkane 1-monooxygenase AlkB | 438 | 439 ctx | cooccurence:435 |
Rv0243 fadA2 |
acetyl-CoA acetyltransferase FadA | 546 | 435 ctx | cooccurence:419 |
Rv1814 erg3 |
membrane-bound C-5 sterol desaturase | 578 | 298 | textmining:425 |
Rv3140 fadE23 |
acyl-CoA dehydrogenase FadE23 | 444 | 298 | |
Rv2524c fas |
fatty acid synthase | 477 | 208 |
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): stearoyl-CoA 9-desaturase
- Pfam (hmmscan --cut_ga): FA_desaturase PF00487.31 (E=8e-34)
- (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 YP_177948.1)
- Domains: Pfam-A via hmmscan --cut_ga — FA_desaturase (PF00487.31)
- 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
COG3239 - Curated reference: UniProt P9WNZ3 (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 —
21 functional partner(s); context anchor
Rv3230c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3229c|desA3 MAITDVDVFAHLTDADIENLAAELDAIRRDVEESRGERDARYIRRTIAAQRALEVSGRLLLAGSSRRLAWWTGALTLGVAKIIENMEIGHNVMHGQWDWMNDPEIHSSTWEWDMSGSSKHWRYTHNFVHHKYTNILGMDDDVGYGMLRVTRDQRWKRYNIFNVVWNTILAIGFEWGVALQHLEIGKIFKGRADREAAKTRLREFSAKAGRQVFKDYVAFPALTSLSPGATYRSTLTANVVANVIRNVWSNAVIFCGHFPDGAEKFTKTDMIGEPKGQWYLRQMLGSANFNAGPALRFMSGNLCHQIEHHLYPDLPSNRLHEISVRVREVCDRYDLPYTTGSFLVQYGKTWRTLAKLSLPDKYLRDNADDAPETRSERMFAGLGPGFAGADPVTGRRRGLKTAIAAVRGRRRSKRMAKSVTEPDDLAA