umaA Resolved · high auto-curated
H37Rv Rv0469 · MTBC0 - ·
286 aa · 559888–560748 (+) ·
RefSeq YP_177729.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | mycolic acid synthase UmaA |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Mycolic acid synthase UmaA. Pfam: CMAS (PF02353.27), Methyltransf_23 (PF13489.13), Methyltransf_25 (PF13649.13), Methyltransf_12 (PF08242.19), Methyltransf_11 (PF08241.19). |
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 |
Q6MX39
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | S-adenosylmethionine-dependent methyltransferase UmaA |
| EC (curated) |
EC 2.1.1.-
|
| Curated function | Methyltransferase that modifies short-chain fatty acids. In vitro, catalyzes the transfer of the methyl group from S-adenosyl-L-methionine (SAM) to the double bond of phospholipid-linked oleic acid to produce tuberculostearic acid (10-methylstearic-acid or TSA). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | umaA |
| eggNOG description | synthase |
| Orthologous group | COG2230 |
| EC number |
EC 2.1.1.79
|
| KEGG orthology |
K00574
|
| Gene Ontology (22) |
GO:0003674, GO:0003824, GO:0005575, GO:0005623, GO:0005886, GO:0006629, GO:0008150, GO:0008152, GO:0008168, GO:0008610, GO:0008757, GO:0008825 +10 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 | 0.625 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (155) · 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 |
|---|---|---|---|---|
CMAS | PF02353.27 | 1.8e-112 | 6–282 | Mycolic acid cyclopropane synthetase |
Methyltransf_23 | PF13489.13 | 9.1e-10 | 59–187 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 4.4e-09 | 68–161 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 2.2e-08 | 68–162 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 5.6e-06 | 68–164 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: fadB2 (3-hydroxybutyryl-CoA dehydrogenase), medium confidence from genomic context alone (score 563 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0468 fadB2 |
3-hydroxybutyryl-CoA dehydrogenase | 649 | 563 ctx | neighborhood:537 |
Rv0467 icl1 |
isocitrate lyase | 438 | 397 | |
Rv0447c ufaA1 |
cyclopropane-fatty-acyl-phospholipid synthase UfaA | 459 | 302 | |
Rv1752 hyp |
hypothetical protein | 528 | 71 | textmining:513 |
Rv2488c |
LuxR family transcriptional regulator | 420 | 59 | textmining:409 |
Rv0386 |
transcriptional regulator | 417 | 54 | textmining:409 |
Rv0472c |
HTH-type transcriptional regulator | 532 | 53 | textmining:527 |
Rv0824c desA1 |
acyl-ACP desaturase DesA | 443 | 53 | textmining:436 |
Rv0373c |
carbon monoxyde dehydrogenase large subunit | 414 | 50 | textmining:409 |
Rv0195 |
two component transcriptional regulator | 412 | 47 | textmining:409 |
Rv2751 hyp |
hypothetical protein | 630 | 44 | textmining:629 |
Rv0725c hyp |
hypothetical protein | 630 | 44 | textmining:629 |
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): mycolic acid synthase UmaA
- Pfam (hmmscan --cut_ga): CMAS PF02353.27 (E=2e-112), Methyltransf_23 PF13489.13 (E=9e-10), Methyltransf_25 PF13649.13 (E=4e-09), Methyltransf_12 PF08242.19 (E=2e-08), Methyltransf_11 PF08241.19 (E=6e-06)
- (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_177729.1)
- Domains: Pfam-A via hmmscan --cut_ga — CMAS (PF02353.27), Methyltransf_23 (PF13489.13), Methyltransf_25 (PF13649.13), Methyltransf_12 (PF08242.19), Methyltransf_11 (PF08241.19)
- 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
COG2230 - Curated reference: UniProt Q6MX39 (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 —
12 functional partner(s); context anchor
fadB2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0469|umaA MTELRPFYEESQSIYDVSDEFFSLFLDPTMAYTCAYFEREDMTLEEAQNAKFDLALDKLHLEPGMTLLDIGCGWGGGLQRAIENYDVNVIGITLSRNQFEYSKAKLAKIPTERSVQVRLQGWDEFTDKVDRIVSIGAFEAFKMERYAAFFERSYDILPDDGRMLLHTILTYTQKQMHEMGVKVTMSDVRFMKFIGEEIFPGGQLPAQEDIFKFAQAADFSVEKVQLLQQHYARTLNIWAANLEANKDRAIALQSEEIYNKYMHYLTGCEHFFRKGISNVGQFTLTK