Rv0539 Resolved · high auto-curated
H37Rv Rv0539 · MTBC0 - ·
210 aa · 631743–632375 (+) ·
RefSeq NP_215053.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | dolichyl-phosphate sugar synthase |
|---|---|
| MTBC0 PGAP re-annotation | — |
| Revised (this work) | Dolichyl-phosphate sugar synthase. Pfam: Glycos_transf_2 (PF00535.33). |
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 |
P9WMY1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Uncharacterized glycosyltransferase Rv0539 |
| EC (curated) |
EC 2.4.-.-
|
UniProt still lists this protein as Uncharacterized glycosyltransferase Rv0539; the revised annotation above is ahead of the current UniProt record.
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | PFAM Glycosyl transferase family 2 |
| Orthologous group | COG1215 |
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 | 0.13 · strong purifying |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 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)
| Pfam | Accession | i-Evalue | Residues | Description |
|---|---|---|---|---|
Glycos_transf_2 | PF00535.33 | 5.7e-20 | 2–147 | Glycosyl transferase family 2 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv0218 (transmembrane protein), high confidence from genomic context alone (score 877 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv0540 hyp |
hypothetical protein | 997 | 985 ctx | neighborhood:882 fusion:499 cooccurence:766 textmining:870 |
Rv0218 |
transmembrane protein | 877 | 877 ctx | neighborhood:521 cooccurence:753 |
Rv0536 galE3 |
UDP-glucose 4-epimerase GalE | 978 | 835 ctx | cooccurence:771 textmining:874 |
Rv0538 |
membrane protein | 810 | 810 ctx | neighborhood:804 |
Rv0541c |
integral membrane protein | 971 | 793 ctx | cooccurence:741 textmining:870 |
Rv0535 pnp |
5'-methylthioadenosine phosphorylase | 936 | 533 ctx | cooccurence:416 textmining:870 |
Rv0219 |
transmembrane protein | 507 | 507 ctx | cooccurence:443 |
Rv3631 |
transferase | 911 | 346 | textmining:870 |
Rv0091 mtn |
5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase | 810 | 53 | textmining:808 |
Rv2855 mtr |
mycothione reductase | 660 | 41 | textmining:661 |
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): dolichyl-phosphate sugar synthase
- Pfam (hmmscan --cut_ga): Glycos_transf_2 PF00535.33 (E=6e-20)
- (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_215053.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glycos_transf_2 (PF00535.33)
- 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
COG1215 - Curated reference: UniProt P9WMY1 (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 —
10 functional partner(s); context anchor
Rv0218 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>H37Rv|Rv0539| MLPCLNEEESLPAVLAAIPAGYRALVVDNNSTDDTATVAARHGAQVVVEPRPGYGSAVHAGVLAATTPIVAVIDADGSMDAGDLPKLVAELDKGADLVTGRRRPVAGLHWPWVARVGTVVMSWRLRTRHRLPVHDIAPMRVARREALLDLGVVDRRSGYPLELLVRAAAAGWRVVELDVSYGPRTGGKSKVSGSLRGSIIAILDFWKVIS