Rv3037c Resolved · high auto-curated
H37Rv Rv3037c · MTBC0 - ·
358 aa · 3397214–3398290 (-) ·
RefSeq NP_217553.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | S-adenosylmethionine-dependent methyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | S-adenosylmethionine-dependent methyltransferase. Pfam: Thump_like (PF18096.7). |
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 |
P9WJZ3
SwissProt · reviewed
· Inferred from homology
|
|---|---|
| UniProt name | Uncharacterized S-adenosylmethionine-dependent methyltransferase Rv3037c |
| EC (curated) |
EC 2.1.1.-
|
UniProt still lists this protein as Uncharacterized S-adenosylmethionine-dependent methyltransferase Rv3037c; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
J Translation, ribosomal structure and biogenesis
|
|---|---|
| eggNOG description | DNA repair |
| Orthologous group | COG2263 |
| Gene Ontology (33) |
GO:0001510, GO:0003674, GO:0003824, GO:0006139, GO:0006396, GO:0006725, GO:0006807, GO:0008150, GO:0008152, GO:0008168, GO:0008173, GO:0009451 +21 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) pseudogene candidate
| pN/pS | 0.679 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 6 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 3.03% of strains (4393) · 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 |
|---|---|---|---|---|
Thump_like | PF18096.7 | 3.3e-18 | 281–356 | THUMP domain-like |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: serB2 (phosphoserine phosphatase SerB), medium confidence from genomic context alone (score 539 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3036c TB22.2 hyp |
hypothetical protein | 578 | 578 ctx | neighborhood:578 |
Rv3042c serB2 |
phosphoserine phosphatase SerB | 539 | 539 ctx | neighborhood:472 |
Rv2848c cobB |
cobyrinic acid A,C-diamide synthase | 514 | 514 | coexpression:514 |
Rv3038c hyp |
hypothetical protein | 646 | 504 ctx | neighborhood:493 |
Rv3438 hyp |
hypothetical protein | 494 | 494 ctx | cooccurence:494 |
Rv3041c |
ABC transporter ATP-binding protein | 492 | 493 ctx | neighborhood:490 |
Rv3753c hyp |
hypothetical protein | 492 | 493 ctx | cooccurence:490 |
Rv3039c echA17 |
enoyl-CoA hydratase EchA17 | 491 | 492 ctx | neighborhood:490 |
Rv3040c hyp |
hypothetical protein | 491 | 492 ctx | neighborhood:490 |
Rv2267c stf3 hyp |
hypothetical protein | 466 | 466 ctx | cooccurence:466 |
Rv3311 hyp |
hypothetical protein | 421 | 421 ctx | cooccurence:421 |
Rv2731 hyp |
hypothetical protein | 420 | 421 ctx | cooccurence:419 |
Rv3043c ctaD |
cytochrome C oxidase cytochrome 1 | 409 | 409 ctx | neighborhood:409 |
Rv2446c |
integral membrane protein | 408 | 409 ctx | cooccurence:405 |
Rv2135c hyp |
hypothetical protein | 521 | 191 | 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
- Annotation from H37Rv (no MTBC0 1:1 anchor; H37Rv protein used): S-adenosylmethionine-dependent methyltransferase
- Pfam (hmmscan --cut_ga): Thump_like PF18096.7 (E=3e-18)
- (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_217553.1)
- Domains: Pfam-A via hmmscan --cut_ga — Thump_like (PF18096.7)
- 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
COG2263 - Curated reference: UniProt P9WJZ3 (SwissProt, reviewed; Inferred from homology)
- 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 —
21 functional partner(s); context anchor
serB2 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv3037c| MRARFGDRAPWLVETTLLRRRAAGKLGELCPNVGVSQWLFTDEALQQATAAPVARHRARRLAGRVVHDATCSIGTELAALRELAVRAVGSDIDPVRLAMARHNLAALGMEADLCRADVLHPVTRDAVVVIDPARRSNGRRRFHLADYQPGLGPLLDRYRGRDVVVKCAPGIDFEEVGRLGFEGEIEVISYRGGVREACLWSAGLAGSGIRRRASILDSGEQIGDDEPDDCGVRPAGKWIVDPDGAVVRAGLVRNYGARHGLWQLDPQIAYLSGDRLPPALRGFEVLEQLAFDERRLRQVLSALDCGAAEILVRGVAIDPDALRRRLRLRGSRPLAVVITRIGAGSLSHVTAYVCRPSR