Rv2423 Resolved · high auto-curated
H37Rv Rv2423 · MTBC0 mtbc0_002580 ·
348 aa · 2743865–2744911 (+) ·
RefSeq NP_216939.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | hypothetical protein |
|---|---|
| MTBC0 PGAP re-annotation | class I SAM-dependent methyltransferase |
| Revised (this work) | Class I SAM-dependent methyltransferase. Pfam: MTS (PF05175.21), Methyltransf_23 (PF13489.13), TehB (PF03848.21), Methyltransf_25 (PF13649.13), 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 |
P71925
TrEMBL · unreviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Methyltransferase domain-containing protein |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
H Coenzyme transport and metabolism
|
|---|---|
| eggNOG description | Methyltransferase type 12 |
| Orthologous group | COG2242 |
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 | 1.283 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 8 missense, 0 nonsense, 1 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.26% of strains (372) · 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 |
|---|---|---|---|---|
MTS | PF05175.21 | 5.4e-05 | 139–250 | Methyltransferase small domain |
Methyltransf_23 | PF13489.13 | 1.8e-07 | 143–258 | Methyltransferase domain |
TehB | PF03848.21 | 4.2e-05 | 148–248 | Tellurite resistance protein TehB |
Methyltransf_25 | PF13649.13 | 3.8e-09 | 150–245 | Methyltransferase domain |
Methyltransf_11 | PF08241.19 | 2.4e-05 | 151–250 | Methyltransferase domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3435c (transmembrane protein), high confidence from genomic context alone (score 768 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) |
|---|---|---|---|---|
Rv2066 cobIJ |
bifunctional S-adenosyl-L-methionine-precorrin-2 methyl transferase/precorrin-3 methylase | 965 | 943 | coexpression:932 textmining:418 |
Rv2067c hyp |
hypothetical protein | 776 | 777 ctx | cooccurence:773 |
Rv3899c hyp |
hypothetical protein | 772 | 772 ctx | cooccurence:771 |
Rv3435c |
transmembrane protein | 767 | 768 ctx | cooccurence:767 |
Rv3166c hyp |
hypothetical protein | 765 | 765 ctx | cooccurence:756 |
Rv2079 hyp |
hypothetical protein | 764 | 764 ctx | cooccurence:763 |
Rv0048c |
membrane protein | 752 | 753 ctx | cooccurence:751 |
Rv3887c eccD2 |
ESX-2 secretion system protein EccD | 747 | 747 ctx | cooccurence:747 |
Rv0977 PE_PGRS16 |
PE-PGRS family protein PE_PGRS16 | 734 | 734 ctx | cooccurence:734 |
Rv3843c |
transmembrane protein | 722 | 723 ctx | cooccurence:722 |
Rv2939 papA5 |
phthiocerol/phthiodiolone dimycocerosyl transferase | 718 | 718 ctx | cooccurence:718 |
Rv1359 |
transcriptional regulator | 715 | 715 ctx | cooccurence:715 |
Rv1904 hyp |
hypothetical protein | 708 | 709 ctx | cooccurence:708 |
Rv1795 eccD5 |
ESX-5 type VII secretion system protein EccD | 706 | 706 ctx | cooccurence:706 |
Rv2065 cobH |
precorrin-8X methylmutase | 727 | 691 | coexpression:673 |
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: class I SAM-dependent methyltransferase
- Pfam (hmmscan --cut_ga): MTS PF05175.21 (E=5e-05), Methyltransf_23 PF13489.13 (E=2e-07), TehB PF03848.21 (E=4e-05), Methyltransf_25 PF13649.13 (E=4e-09), Methyltransf_11 PF08241.19 (E=2e-05)
- (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_216939.1)
- Domains: Pfam-A via hmmscan --cut_ga — MTS (PF05175.21), Methyltransf_23 (PF13489.13), TehB (PF03848.21), Methyltransf_25 (PF13649.13), 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
COG2242 - Curated reference: UniProt P71925 (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 —
80 functional partner(s); context anchor
Rv3435c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_002580|Rv2423| MDNLPIESAESTRLAKAAMTRRFYTRSVVKGEITLPAVPSMIDEYVTMCAGLFAGVGRKFSDEELAHLRAVLQGQLAEAYAASQRSTIVISYNAPMGPTLHYQVRAQWRTVAQEYENWIATREPPLFGTEPDARVWALANEAADPTTHRVLEIGAGTGRNALALARRGHPVDVVEMTPKFADIIRSDAERDSLDVRVIMRDVFSTMDDLRQDYQLMVLSEVVPDFRTTQQLRNLFELAAQCLAPGARLVFNAFLANGDYAPDQAAREFGQQMYTGMCTRAEMSAAAAGLPLELVADDSVYDYEKTHLPPGAWPPTSWYADWIRGLDVFTTNVESCPIEMRWLVFQRRR