Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | trans-aconitate methyltransferase |
|---|
| MTBC0 PGAP re-annotation | trans-aconitate 2-methyltransferase |
|---|
| Revised (this work) | Trans-aconitate 2-methyltransferase. Pfam: Methyltransf_23 (PF13489.13), FtsJ (PF01728.26), MTS (PF05175.21), Methyltransf_31 (PF13847.13), Methyltransf_25 (PF13649.13), Methyltransf_11 (PF08241.19), Methyltransf_12 (PF08242.19). |
|---|
Auto-curated: this verdict and function were generated by rules from
PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WGA3
SwissProt · reviewed
· Evidence at protein level
|
|---|
| UniProt name | Probable trans-aconitate 2-methyltransferase |
|---|
| EC (curated) |
EC 2.1.1.144
|
|---|
| Curated function | Catalyzes the S-adenosylmethionine monomethyl esterification of trans-aconitate. |
|---|
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|
| Preferred name | tam |
|---|
| eggNOG description | Catalyzes the S-adenosylmethionine monomethyl esterification of trans-aconitate |
|---|
| Orthologous group | COG4106 |
|---|
| EC number |
EC 2.1.1.144
|
|---|
| KEGG orthology |
K00598
|
|---|
| Gene Ontology (23) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0008150, GO:0008152, GO:0008168, GO:0008757, GO:0016740, GO:0016741 +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 |
0.273 · purifying
|
|---|
| Polymorphic sites (≥ 0.1% of strains) |
5 synonymous, 4 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 |
|---|
Methyltransf_23 | PF13489.13 |
5.9e-13 | 13–146 |
Methyltransferase domain |
FtsJ | PF01728.26 |
3.0e-05 | 20–95 |
FtsJ-like methyltransferase |
MTS | PF05175.21 |
3.6e-05 | 22–100 |
Methyltransferase small domain |
Methyltransf_31 | PF13847.13 |
4.3e-07 | 30–127 |
Methyltransferase domain |
Methyltransf_25 | PF13649.13 |
1.7e-13 | 33–119 |
Methyltransferase domain |
Methyltransf_11 | PF08241.19 |
4.8e-12 | 34–123 |
Methyltransferase domain |
Methyltransf_12 | PF08242.19 |
7.2e-10 | 34–121 |
Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|
Rv0293c hyp |
hypothetical protein |
778 |
778 ctx |
neighborhood:777 |
Rv2628 hyp |
hypothetical protein |
627 |
47 |
textmining:625 |
Rv0987 |
adhesion component ABC transporter permease |
652 |
46 |
textmining:651 |
Rv3019c esxR |
ESAT-6 like protein EsxR |
541 |
44 |
textmining:540 |
Rv1769 hyp |
hypothetical protein |
870 |
41 |
textmining:870 |
Rv0988 hyp |
hypothetical protein |
803 |
41 |
textmining:803 |
Rv0289 espG3 |
ESX-3 secretion-associated protein EspG3 |
548 |
41 |
textmining:548 |
Rv0291 mycP3 |
membrane-anchored mycosin MycP |
511 |
41 |
textmining:511 |
Rv3879c espK |
ESX-1 secretion-associated protein EspK |
412 |
41 |
textmining:412 |
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: trans-aconitate methyltransferase
- MTBC0 PGAP product: trans-aconitate 2-methyltransferase
- Pfam (hmmscan --cut_ga): Methyltransf_23 PF13489.13 (E=6e-13), FtsJ PF01728.26 (E=3e-05), MTS PF05175.21 (E=4e-05), Methyltransf_31 PF13847.13 (E=4e-07), Methyltransf_25 PF13649.13 (E=2e-13), Methyltransf_11 PF08241.19 (E=5e-12), Methyltransf_12 PF08242.19 (E=7e-10)
- (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_214808.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_23 (PF13489.13), FtsJ (PF01728.26), MTS (PF05175.21), Methyltransf_31 (PF13847.13), Methyltransf_25 (PF13649.13), Methyltransf_11 (PF08241.19), Methyltransf_12 (PF08242.19)
- 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
COG4106
- Curated reference: UniProt
P9WGA3
(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 —
9 functional partner(s)
- Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_000313|Rv0294|tam
MWDPDVYLAFSGHRNRPFYELVSRVGLERARRVVDLGCGPGHLTRYLARRWPGAVIEALDSSPEMVAAAAERGIDATTGDLRDWKPKPDTDVVVSNAALHWVPEHSDLLVRWVDELAPGSWIAVQIPGNFETPSHAAVRALARREPYAKLMRDIPFRVGAVVQSPAYYAELLMDTGCKVDVWETTYLHQLTGEHPVLDWITGSALVPVRERLSDESWQQFRQELIPLLNDAYPPRADGSTIFPFRRLFMVAEVGGARRSGG
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