Rv3030 Family assigned · medium auto-curated
H37Rv Rv3030 · MTBC0 mtbc0_003221 ·
274 aa · 3410411–3411235 (+) ·
RefSeq NP_217546.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | S-adenosylmethionine-dependent methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | methyltransferase domain-containing protein |
| Revised (this work) | Methyltransferase domain-containing protein. Pfam: Methyltransf_23 (PF13489.13), 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 |
P9WJZ1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Probable S-adenosylmethionine-dependent methyltransferase Rv3030 |
| EC (curated) |
EC 2.1.1.-
|
| Curated function | Probable S-adenosylmethionine-dependent methyltransferase required for the 6-O-methylation of the polysaccharide backbone of 6-O-methylglucosyl lipopolysaccharides (MGLP). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| eggNOG description | Methyltransferase |
| Orthologous group | COG2227 |
| EC number |
EC 2.1.1.222, EC 2.1.1.64
|
| KEGG orthology |
K00568
|
| KEGG pathways |
map00130, map01100, map01110
|
| KEGG modules |
M00117
|
| Gene Ontology (21) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005737, GO:0005829, GO:0005886, GO:0008150, GO:0008152, GO:0008168, GO:0008757 +9 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 | 1.027 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 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 |
|---|---|---|---|---|
Methyltransf_23 | PF13489.13 | 2.0e-12 | 53–197 | Methyltransferase domain |
Methyltransf_31 | PF13847.13 | 1.3e-11 | 64–161 | Methyltransferase domain |
Methyltransf_25 | PF13649.13 | 1.4e-18 | 65–153 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 8.5e-23 | 66–156 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 1.7e-09 | 66–155 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3031 (1,4-alpha-glucan-branching protein), high confidence from genomic context alone (score 957 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3031 |
1,4-alpha-glucan-branching protein | 991 | 957 ctx | neighborhood:881 cooccurence:553 textmining:809 |
Rv3032 |
glycogen synthase | 991 | 936 ctx | neighborhood:827 cooccurence:641 textmining:875 |
Rv3029c fixA |
electron transfer flavoprotein subunit beta | 750 | 750 ctx | neighborhood:748 |
Rv3038c hyp |
hypothetical protein | 744 | 742 ctx | cooccurence:706 |
Rv3028c fixB |
electron transfer flavoprotein subunit alpha | 729 | 729 ctx | neighborhood:718 |
Rv2186c hyp |
hypothetical protein | 707 | 696 ctx | cooccurence:695 |
Rv3034c |
acetyltransferase | 953 | 648 ctx | cooccurence:635 textmining:873 |
Rv2418c octT hyp |
hypothetical protein | 925 | 622 ctx | cooccurence:607 textmining:812 |
Rv3032A hyp |
hypothetical protein | 585 | 585 ctx | neighborhood:585 |
Rv2695 hyp |
hypothetical protein | 458 | 459 ctx | cooccurence:456 |
Rv3025c iscS |
cysteine desulfurase | 411 | 411 | |
Rv1208 gpgS |
glucosyl-3-phosphoglycerate synthase | 919 | 185 | textmining:906 |
Rv0187 |
O-methyltransferase | 648 | 103 | textmining:624 |
Rv2419c gpgP |
glucosyl-3-phosphoglycerate phosphatase | 803 | 54 | textmining:801 |
Rv2417c |
DegV domain-containing protein | 437 | 49 | textmining:433 |
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: S-adenosylmethionine-dependent methyltransferase
- MTBC0 PGAP product: methyltransferase domain-containing protein
- Pfam (hmmscan --cut_ga): Methyltransf_23 PF13489.13 (E=2e-12), Methyltransf_31 PF13847.13 (E=1e-11), Methyltransf_25 PF13649.13 (E=1e-18), Methyltransf_11 PF08241.19 (E=8e-23), Methyltransf_12 PF08242.19 (E=2e-09)
- (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_217546.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_23 (PF13489.13), 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
COG2227 - Curated reference: UniProt P9WJZ1 (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 —
16 functional partner(s); context anchor
Rv3031 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003221|Rv3030| MCAFVPHVPRHSRGDNPPSASTASPAVLTLTGERTIPDLDIENYWFRRHQVVYQRLAPRCTARDVLEAGCGEGYGADLIACVARQVIAVDYDETAVAHVRSRYPRVEVMQANLAELPLPDASVDVVVNFQVIEHLWDQARFVRECARVLRGSGLLMVSTPNRITFSPGRDTPINPFHTRELNADELTSLLIDAGFVDVAMCGLFHGPRLRDMDARHGGSIIDAQIMRAVAGAPWPPELAADVAAVTTADFEMVAAGHDRDIDDSLDLIAIAVRP