Rv3238c Family assigned · low auto-curated
H37Rv Rv3238c · MTBC0 mtbc0_003446 ·
244 aa · 3635807–3636541 (-) ·
RefSeq NP_217755.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | integral membrane protein |
|---|---|
| MTBC0 PGAP re-annotation | isoprenylcysteine carboxylmethyltransferase family protein |
| Revised (this work) | Isoprenylcysteine carboxylmethyltransferase family protein. |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
O05883
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Methanethiol S-methyltransferase |
| EC (curated) |
EC 2.1.1.334
|
| Curated function | Catalyzes the methylation of methanethiol (MeSH) to yield dimethylsulphide (DMS). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
O Post-translational modification, protein turnover, chaperones
|
|---|---|
| eggNOG description | NnrU protein |
| Orthologous group | COG2020 |
| EC number |
EC 2.1.1.334
|
| KEGG orthology |
K21310
|
| KEGG pathways |
map00920
|
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 | 0.081 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 4 synonymous, 1 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)
No Pfam-A domain above the gathering threshold (or not yet scanned).
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv3236c (integral membrane transport protein), high confidence from genomic context alone (score 718 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3248c sahH |
adenosylhomocysteinase | 822 | 823 | database:800 |
Rv3283 sseA |
thiosulfate sulfurtransferase SseA | 807 | 807 | database:800 |
Rv2458 mmuM |
homocysteine S-methyltransferase MmuM | 807 | 807 | database:800 |
Rv0815c cysA2 |
thiosulfate sulfurtransferase CysA | 806 | 806 | database:800 |
Rv2291 sseB |
thiosulfate sulfurtransferase SseB | 806 | 806 | database:800 |
Rv2124c metH |
methionine synthase | 806 | 806 | database:800 |
Rv1077 cbs |
cystathionine beta-synthase | 805 | 805 | database:800 |
Rv3340 metC |
O-acetylhomoserine sulfhydrylase | 801 | 801 | database:800 |
Rv2294 |
cystathionine beta-lyase | 800 | 801 | database:800 |
Rv0075 |
aminotransferase | 800 | 801 | database:800 |
Rv0391 metZ |
O-succinylhomoserine sulfhydrylase | 800 | 800 | database:800 |
Rv1079 metB |
cystathionine gamma-synthase | 800 | 800 | database:800 |
Rv1133c metE |
5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase | 800 | 800 | database:800 |
Rv3237c hyp |
hypothetical protein | 760 | 761 ctx | neighborhood:759 |
Rv3236c |
integral membrane transport protein | 718 | 718 ctx | neighborhood:706 |
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: integral membrane protein
- MTBC0 PGAP product: isoprenylcysteine carboxylmethyltransferase family protein
- (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_217755.1)
- Domains: Pfam-A via hmmscan --cut_ga — none above threshold
- 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
COG2020 - Curated reference: UniProt O05883 (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 —
23 functional partner(s); context anchor
Rv3236c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003446|Rv3238c| MKRYLTIIYGAASYLVFLVAFGYAIGFVGDVVVPRTVDHAIAAPIGQAVVVNLVLLGVFAVQHSVMARQGFKRWWTRFVPPSIERSTYVLLASVALLLLYWQWRTMPAVIWDVRQPAGRVALWALFWLGWATVLTSTFMINHFELFGLRQVYLAWRGKPYTEIGFQAHLLYRWVRHPIMLGFVVAFWATPMMTAGHLLFAIGATGYILVALQFEERDLLAALGDQYRDYRREVSMLLPWPHRHT