Rv2954c Resolved · high auto-curated
H37Rv Rv2954c · MTBC0 mtbc0_003136 ·
241 aa · 3327841–3328566 (-) ·
RefSeq NP_217470.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | [2%2C4-di-O-methyl-alpha-L-fucopyranosyl-(1->3)-alpha-L-rhamnopyranosyl-(1->3)-2-O-methyl-alpha-L-rhamnopyranosyl] dimycocerosyl phenol-phthiocerol 3'''-O-methyltransferase |
| Revised (this work) | [2%2C4-di-O-methyl-alpha-L-fucopyranosyl-(1->3)-alpha-L-rhamnopyranosyl-(1->3)-2-O-methyl-alpha-L-rhamnopyranosyl] dimycocerosyl phenol-phthiocerol 3'''-O-methyltransferase. Pfam: Methyltransf_23 (PF13489.13), Methyltransf_9 (PF08003.18), 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.
Curated reference (UniProt)
| UniProt |
I6X5U4
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Methyltransferase type 12 domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
Q Secondary metabolites biosynthesis, transport and catabolism
|
|---|---|
| Preferred name | rsmJ |
| eggNOG description | methyltransferase activity |
| Orthologous group | COG0500 |
| EC number |
EC 2.1.1.197, EC 2.1.1.242
|
| KEGG orthology |
K02169, K15984
|
| KEGG pathways |
map00780, map01100
|
| KEGG modules |
M00572
|
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 | 1.009 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 3 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.11% of strains (165) · 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 |
|---|---|---|---|---|
Methyltransf_23 | PF13489.13 | 4.1e-08 | 34–131 | Methyltransferase domain |
Methyltransf_9 | PF08003.18 | 9.4e-06 | 37–153 | Protein of unknown function (DUF1698) |
Methyltransf_25 | PF13649.13 | 5.6e-11 | 43–125 | Methyltransferase domain |
Methyltransf_12 | PF08242.19 | 1.9e-11 | 44–125 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 1.0e-09 | 44–125 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: iniB (isoniazid inducible protein IniB), high confidence from genomic context alone (score 784 excluding text-mining). This association is the citable seed of a function hypothesis for this hypothetical protein.
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0341 iniB |
isoniazid inducible protein IniB | 784 | 784 ctx | cooccurence:770 |
Rv2955c hyp |
hypothetical protein | 968 | 780 ctx | neighborhood:460 database:500 textmining:864 |
Rv1004c |
membrane protein | 778 | 779 ctx | cooccurence:771 |
Rv3347c PPE55 |
PPE family protein PPE55 | 774 | 774 ctx | cooccurence:772 |
Rv2209 |
integral membrane protein | 774 | 774 ctx | cooccurence:773 |
Rv0355c PPE8 |
PPE family protein PPE8 | 774 | 774 ctx | cooccurence:773 |
Rv1917c PPE34 |
PPE family protein PPE34 | 773 | 774 ctx | cooccurence:771 |
Rv0304c PPE5 |
PPE family protein PPE5 | 773 | 773 ctx | cooccurence:771 |
Rv3343c PPE54 |
PPE family protein PPE54 | 773 | 773 ctx | cooccurence:770 |
Rv3350c PPE56 |
PPE family protein PPE56 | 773 | 773 ctx | cooccurence:772 |
Rv1452c PE_PGRS28 |
PE-PGRS family protein PE_PGRS28 | 772 | 772 ctx | cooccurence:772 |
Rv2490c PE_PGRS43 |
PE-PGRS family protein PE_PGRS43 | 771 | 771 ctx | cooccurence:771 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 770 | 770 ctx | cooccurence:770 |
Rv2082 hyp |
hypothetical protein | 768 | 768 ctx | cooccurence:761 |
Rv0305c PPE6 |
PPE family protein PPE6 | 767 | 768 ctx | cooccurence:765 |
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: hypothetical protein
- MTBC0 PGAP product: [2%2C4-di-O-methyl-alpha-L-fucopyranosyl-(1->3)-alpha-L-rhamnopyranosyl-(1->3)-2-O-methyl-alpha-L-rhamnopyranosyl] dimycocerosyl phenol-phthiocerol 3'''-O-methyltransferase
- Pfam (hmmscan --cut_ga): Methyltransf_23 PF13489.13 (E=4e-08), Methyltransf_9 PF08003.18 (E=9e-06), Methyltransf_25 PF13649.13 (E=6e-11), Methyltransf_12 PF08242.19 (E=2e-11), Methyltransf_11 PF08241.19 (E=1e-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_217470.1)
- Domains: Pfam-A via hmmscan --cut_ga — Methyltransf_23 (PF13489.13), Methyltransf_9 (PF08003.18), 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
COG0500 - Curated reference: UniProt I6X5U4 (TrEMBL, unreviewed; 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 —
138 functional partner(s); context anchor
iniB - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003136|Rv2954c| MRLPGMLRPTAERHFHSIFYLRHNARRQEHLATLGLDLGNKSVLEVGAGIGDHTQFFLDRGCKVLCTEPRGENLDVIRQRFGSNPNVTVDHLDLDGDLPAEAHQYDVVYCYGVLYHLSRPAEALAWMCDRAVDLLLLETCVSYSGEDEPFLVSERASSPSQAITGTGCRPSRVWVMNRLREKMPHVYVTATQPRHRQFPLDWRANGPIASTGLARAVFVASRAPLNLPTLVEELPMVQRRC