Rv2962c Resolved · high auto-curated
H37Rv Rv2962c · MTBC0 mtbc0_003145 ·
449 aa · 3334948–3336297 (-) ·
RefSeq NP_217478.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | PGL/p-HBAD biosynthesis rhamnosyltransferase |
|---|---|
| MTBC0 PGAP re-annotation | PGL/p-HBAD biosynthesis rhamnosyltransferase |
| Revised (this work) | PGL/p-HBAD biosynthesis rhamnosyltransferase. 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 |
P9WN09
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | PGL/p-HBAD biosynthesis rhamnosyltransferase |
| EC (curated) |
EC 2.4.1.-
|
| Curated function | Catalyzes the transfer of the first rhamnosyl residue on p-hydroxybenzoic acid or phenolphthiocerol derivatives to form, after O-methylation at position 2 of the sugar unit, mono-O-methyl-glycosyl-p-hydroxybenzoic acid derivative (p-HBAD I) and 2-O-methyl-rhamnosyl-phenolphthiocerol dimycocerosate (also called mycoside B) during 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 | PFAM UDP-glucuronosyl UDP-glucosyltransferase |
| Orthologous group | COG1819 |
| Gene Ontology (59) |
GO:0003674, GO:0003824, GO:0005575, GO:0005622, GO:0005623, GO:0005886, GO:0006629, GO:0006643, GO:0006664, GO:0008150, GO:0008152, GO:0008194 +47 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 | 1.073 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 3 synonymous, 7 missense, 2 nonsense, 2 frameshift |
| Disruption | 4 distinct premature-stop/frameshift site(s); most common in 8.77% of strains (12738) · convergent |
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 | 8.4e-06 | 283–415 | Glycosyltransferase family 28 C-terminal domain |
UDPGT | PF00201.25 | 5.9e-08 | 293–417 | UDP-glucoronosyl and UDP-glucosyl transferase |
EryCIII-like_C | PF06722.19 | 1.4e-17 | 295–419 | Erythromycin biosynthesis protein CIII-like, C-terminal domain |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv2963 (integral membrane protein), medium confidence from genomic context alone (score 571 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv2963 |
integral membrane protein | 571 | 571 ctx | neighborhood:554 |
Rv1004c |
membrane protein | 539 | 540 ctx | cooccurence:528 |
Rv2959c |
rhamnosyl O-methyltransferase | 598 | 509 | database:500 |
Rv2939 papA5 |
phthiocerol/phthiodiolone dimycocerosyl transferase | 503 | 503 | database:500 |
Rv0304c PPE5 |
PPE family protein PPE5 | 499 | 500 ctx | cooccurence:499 |
Rv2337c hyp |
hypothetical protein | 487 | 487 ctx | cooccurence:471 |
Rv3347c PPE55 |
PPE family protein PPE55 | 473 | 474 ctx | cooccurence:472 |
Rv3350c PPE56 |
PPE family protein PPE56 | 471 | 472 ctx | cooccurence:470 |
Rv0355c PPE8 |
PPE family protein PPE8 | 471 | 471 ctx | cooccurence:471 |
Rv1243c PE_PGRS23 |
PE-PGRS family protein PE_PGRS23 | 462 | 462 ctx | cooccurence:462 |
Rv3343c PPE54 |
PPE family protein PPE54 | 450 | 451 ctx | cooccurence:448 |
Rv0124 PE_PGRS2 |
PE-PGRS family protein PE_PGRS2 | 445 | 445 ctx | cooccurence:445 |
Rv0888 spmT hyp |
hypothetical protein | 441 | 442 ctx | cooccurence:438 |
Rv1651c PE_PGRS30 |
PE-PGRS family protein PE_PGRS30 | 438 | 438 ctx | cooccurence:438 |
Rv1917c PPE34 |
PPE family protein PPE34 | 437 | 437 ctx | cooccurence:436 |
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 rhamnosyltransferase
- MTBC0 PGAP product: PGL/p-HBAD biosynthesis rhamnosyltransferase
- Pfam (hmmscan --cut_ga): Glyco_tran_28_C PF04101.23 (E=8e-06), UDPGT PF00201.25 (E=6e-08), EryCIII-like_C PF06722.19 (E=1e-17)
- (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_217478.1)
- 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 P9WN09 (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 —
50 functional partner(s); context anchor
Rv2963 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_003145|Rv2962c| MRVSCVYATASRWGGPPVASEVRGDAAISTTPDAAPGLAARRRRILFVAEAVTLAHVVRPFALAQSLDPSRYEVHFACDPRYNQLLGPLPFRHHAIHTIPSERFFGNLTQGRFYAMRTLRKYVEADLRVLDEIAPDLVVGDLRISLSVSARLAGIPYIAIANAYWSPYAQRRFPLPDVIWTRLFGVRLVKLLYRLERPLLFALQCMPLNWVRRRHGLSSLGWNLCRIFTDGDHTLYADVPELMPTYDLPANHEYLGPVLWSPAGKPPTWWDSLPTDRPIVYATLGTSGGRNLLQLVLNALAELPVTVIAATAGRSDLKTVPANAFVADYLPGEAAAARSAVVVCNGGSLTTQQALVAGVPVIGVAGNLDQHLNMEAVERAGAGVLLRTERLKSQRVAGAVMQVISRSEYRQAAARLADAFGRDRVGFPQHVENALRLMPENRPRTWLAS