Rv2957 Resolved · high auto-curated
H37Rv Rv2957 · MTBC0 mtbc0_003139 ·
275 aa · 3330645–3331472 (+) ·
RefSeq NP_217473.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PGL/p-HBAD biosynthesis glycosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | PGL/p-HBAD biosynthesis glycosyltransferase |
| Revised (this work) | PGL/p-HBAD biosynthesis glycosyltransferase. Pfam: Glyco_tranf_2_3 (PF13641.13), 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.
Curated reference (UniProt)
| UniProt |
P9WMX7
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PGL/p-HBAD biosynthesis glycosyltransferase Rv2957 |
| EC (curated) |
EC 2.4.1.-
|
| Curated function | Involved in glycosylation steps downstream of mono-O-methyl-glycosyl-p-hydroxybenzoic acid derivative (p-HBAD I) and 2-O-methyl-rhamnosyl-phenolphthiocerol dimycocerosate (mycoside B) during the p-hydroxybenzoic acid derivatives (p-HBAD) and glycosylated phenolphthiocerol dimycocerosates (PGL) biosynthesis. |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| eggNOG description | Involved in glycosylation steps downstream of mono-O- methyl-glycosyl-p-hydroxybenzoic acid derivative (p-HBAD I) and 2- O-methyl-rhamnosyl-phenolphthiocerol dimycocerosate (mycoside B) during the p-hydroxybenzoic acid derivatives (p-HBAD) and glycosylated phenolphthiocerol dimycocerosates (PGL) biosynthesis |
| Orthologous group | COG0463 |
| Gene Ontology (24) |
GO:0003674, GO:0003824, GO:0006629, GO:0006643, GO:0006664, GO:0008150, GO:0008152, GO:0008610, GO:0009058, GO:0009247, GO:0009987, GO:0016740 +12 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)
| pN/pS | 0.953 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 2 synonymous, 5 missense, 1 nonsense, 0 frameshift |
| Disruption | 1 distinct premature-stop/frameshift site(s); most common in 0.30% of strains (431) · 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 |
|---|---|---|---|---|
Glyco_tranf_2_3 | PF13641.13 | 1.6e-09 | 23–142 | Glycosyltransferase like family 2 |
Glycos_transf_2 | PF00535.33 | 7.1e-26 | 26–147 | Glycosyl transferase family 2 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1516c (sugar transferase), high confidence from genomic context alone (score 766 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2956 hyp |
hypothetical protein | 987 | 961 ctx | neighborhood:601 coexpression:820 database:500 textmining:688 |
Rv1516c |
sugar transferase | 766 | 766 ctx | cooccurence:752 |
Rv1520 |
sugar transferase | 760 | 761 ctx | cooccurence:747 |
Rv1512 epiA |
nucleotide-sugar epimerase EpiA | 910 | 551 ctx | cooccurence:465 textmining:809 |
Rv2955c hyp |
hypothetical protein | 728 | 541 ctx | neighborhood:427 textmining:434 |
Rv2958c |
PGL/p-HBAD biosynthesis glycosyltransferase | 902 | 501 | database:500 textmining:812 |
Rv2954c hyp |
hypothetical protein | 670 | 434 | textmining:441 |
Rv0112 gca |
GDP-mannose 4,6-dehydratase | 427 | 409 | |
Rv3784 |
dTDP-glucose 4,6-dehydratase | 431 | 406 | |
Rv1511 gmdA |
GDP-D-mannose dehydratase GmdA | 619 | 324 | textmining:460 |
Rv3347c PPE55 |
PPE family protein PPE55 | 502 | 295 | |
Rv1135c PPE16 |
PPE family protein PPE16 | 434 | 246 | |
Rv2959c |
rhamnosyl O-methyltransferase | 538 | 212 | textmining:439 |
Rv3125c PPE49 |
PPE family protein PPE49 | 561 | 141 | textmining:511 |
Rv1543 |
oxidoreductase | 462 | 92 | textmining:432 |
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: PGL/p-HBAD biosynthesis glycosyltransferase
- MTBC0 PGAP product: PGL/p-HBAD biosynthesis glycosyltransferase
- Pfam (hmmscan --cut_ga): Glyco_tranf_2_3 PF13641.13 (E=2e-09), Glycos_transf_2 PF00535.33 (E=7e-26)
- (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_217473.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyco_tranf_2_3 (PF13641.13), 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
COG0463 - Curated reference: UniProt P9WMX7 (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 —
21 functional partner(s); context anchor
Rv1516c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003139|Rv2957| MVQTKRYAGLTAANTKKVAMAAPMFSIIIPTLNVAAVLPACLDSIARQTCGDFELVLVDGGSTDETLDIANIFAPNLGERLIIHRDTDQGVYDAMNRGVDLATGTWLLFLGADDSLYEADTLARVAAFIGEHEPSDLVYGDVIMRSTNFRWGGAFDLDRLLFKRNICHQAIFYRRGLFGTIGPYNLRYRVLADWDFNIRCFSNPALVTRYMHVVVASYNEFGGLSNTIVDKEFLKRLPMSTRLGIRLVIVLVRRWPKVISRAMVMRTVISWRRRR