Rv2958c Resolved · high auto-curated
H37Rv Rv2958c · MTBC0 mtbc0_003141 ·
428 aa · 3331889–3333175 (-) ·
RefSeq NP_217474.1
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_tran_28_C (PF04101.23), UDPGT (PF00201.25), EryCIII-like_C (PF06722.19). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WFR1
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PGL/p-HBAD biosynthesis glycosyltransferase Rv2958c |
| 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 |
C Energy production and conversionG Carbohydrate transport and metabolism
|
|---|---|
| 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 | COG1819 |
| Gene Ontology (60) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005886, GO:0006629, GO:0006643, GO:0006664, GO:0008150, GO:0008152, GO:0008194 +48 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 | 2.808 · diversifying/relaxed |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 7 missense, 1 nonsense, 1 frameshift |
| Disruption | 2 distinct premature-stop/frameshift site(s); most common in 11.47% of strains (16651) · 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_tran_28_C | PF04101.23 | 8.7e-08 | 269–402 | Glycosyltransferase family 28 C-terminal domain |
UDPGT | PF00201.25 | 3.0e-10 | 281–406 | UDP-glucoronosyl and UDP-glucosyl transferase |
EryCIII-like_C | PF06722.19 | 1.3e-16 | 284–407 | Erythromycin biosynthesis protein CIII-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2959c (rhamnosyl O-methyltransferase), high confidence from genomic context alone (score 814 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2959c |
rhamnosyl O-methyltransferase | 979 | 814 ctx | neighborhood:529 database:500 textmining:891 |
Rv2932 ppsB |
phthiocerol synthesis polyketide synthase type I PpsB | 554 | 531 | |
Rv2957 |
PGL/p-HBAD biosynthesis glycosyltransferase | 902 | 501 | database:500 textmining:812 |
Rv3137 hisN |
histidinol-phosphatase | 457 | 458 | coexpression:458 |
Rv2276 cyp121 |
cytochrome P450 Cyp121 | 453 | 432 | experimental:403 |
Rv3121 cyp141 |
cytochrome P450 Cyp141 | 450 | 429 | experimental:403 |
Rv1394c cyp132 |
cytochrome P450 Cyp132 | 450 | 429 | experimental:403 |
Rv3518c cyp142 |
cytochrome P450 monooxygenase Cyp142 | 449 | 428 | experimental:403 |
Rv1785c cyp143 |
cytochrome P450 Cyp143 | 449 | 428 | experimental:403 |
Rv0766c cyp123 |
cytochrome P450 Cyp123 | 449 | 428 | experimental:403 |
Rv2268c cyp128 |
cytochrome P450 Cyp128 | 449 | 428 | experimental:403 |
Rv3059 cyp136 |
cytochrome P450 Cyp136 | 447 | 426 | experimental:403 |
Rv1666c cyp139 |
cytochrome P450 Cyp139 | 447 | 426 | experimental:403 |
Rv0136 cyp138 |
cytochrome P450 Cyp138 | 447 | 426 | experimental:403 |
Rv1880c cyp140 |
cytochrome P450 Cyp140 | 447 | 426 | experimental:403 |
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_tran_28_C PF04101.23 (E=9e-08), UDPGT PF00201.25 (E=3e-10), EryCIII-like_C PF06722.19 (E=1e-16)
- (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_217474.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glyco_tran_28_C (PF04101.23), UDPGT (PF00201.25), EryCIII-like_C (PF06722.19)
- 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
COG1819 - Curated reference: UniProt P9WFR1 (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 —
43 functional partner(s); context anchor
Rv2959c - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003141|Rv2958c| MEETSVAGDPGPDAGTSTAPNAAPEPVARRQRILFVGEAATLAHVVRPFVLARSLDPSRYEVHFACDPRFNKLLGPLPFPHHPIHTVPSEEVLLKIAQGRLFYNTRTLRKYIAADRKILNEIAPDVVVGDNRLSLSVSARLAGIPYIAIANAYWSPQARRRFPLPDVPWTRFFGVRPVSILYRLYRPLIFALYCLPLNWLRRKHGLSSLGWDLCRIFTDGDYTLYADVPELVPTYNLPANHRYLGPVLWSPDVKPPTWWHSLPTDRPIIYATLGSSGGKNLLQVVLNALADLPVTVIAATAGRNHLKNVPANAFVADYLPGEAAAARSAVVLCNGGSPTTQQALAAGVPVIGLPSNMDQHLNMEALERAGAGVLLRTERLNTEGVAAAVKQVLSGAEFRQAARRLAEAFGPDFAGFPQHIESALRLVC