rfe Resolved · high auto-curated
H37Rv Rv1302 · MTBC0 mtbc0_001394 ·
404 aa · 1467334–1468548 (+) ·
RefSeq NP_215818.1
Annotation: from legacy to revised
| Legacy (H37Rv / Mycobrowser) | decaprenyl-phosphate N-acetylglucosaminephosphotransferase |
|---|---|
| MTBC0 PGAP re-annotation | UDP-N-acetylglucosamine--decaprenyl-phosphate N-acetylglucosaminephosphotransferase |
| Revised (this work) | UDP-N-acetylglucosamine--decaprenyl-phosphate N-acetylglucosaminephosphotransferase. Pfam: Glycos_transf_4 (PF00953.27). |
Auto-curated: this verdict and function were generated by rules from PGAP + Pfam + Foldseek and have not been hand-reviewed.
Curated reference (UniProt)
| UniProt |
P9WMW5
SwissProt · reviewed
· Evidence at protein level
|
|---|---|
| UniProt name | Decaprenyl-phosphate N-acetylglucosaminephosphotransferase |
| EC (curated) |
EC 2.7.8.35
|
| Curated function | Involved in the biosynthesis of the disaccharide D-N-acetylglucosamine-L-rhamnose which plays an important role in the mycobacterial cell wall as a linker connecting arabinogalactan and peptidoglycan via a phosphodiester linkage. Catalyzes the transfer of the N-acetylglucosamine-1-phosphate (GlcNAc-1P) moiety from UDP-GlcNAc onto the carrier lipid decaprenyl phosphate (C50-P), yielding GlcNAc-pyrophosphoryl-decaprenyl (GlcNAc-PP-C50). |
Functional vocabulary (eggNOG-mapper, orthology transfer)
| COG category |
M Cell wall / membrane / envelope biogenesis
|
|---|---|
| Preferred name | rfe |
| eggNOG description | PFAM Glycosyl transferase family 4 |
| Orthologous group | COG0472 |
| EC number |
EC 2.7.8.33, EC 2.7.8.35
|
| KEGG orthology |
K02851
|
| Gene Ontology (40) |
GO:0000287, GO:0003674, GO:0003824, GO:0005488, GO:0005575, GO:0005623, GO:0005886, GO:0008150, GO:0008152, GO:0009058, GO:0009059, GO:0009987 +28 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 | 0.765 · relaxed/neutral |
|---|---|
| Polymorphic sites (≥ 0.1% of strains) | 1 synonymous, 2 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_4 | PF00953.27 | 2.9e-37 | 111–274 | Glycosyl transferase family 4 |
Functional interaction network (STRING v12, guilt-by-association)
Closest characterised functional partner: Rv1301 (threonylcarbamoyl-AMP synthase), high confidence from genomic context alone (score 788 excluding text-mining).
| Partner | Product | Score | No text-mining | Channels (≥400) |
|---|---|---|---|---|
Rv3265c wbbL1 |
N-acetylglucosaminyl-diphospho-decaprenol L-rhamnosyltransferase | 989 | 918 | database:900 textmining:877 |
Rv1301 |
threonylcarbamoyl-AMP synthase | 816 | 788 ctx | neighborhood:782 |
Rv1307 atpH |
ATP synthase subunit b/delta | 785 | 785 ctx | neighborhood:674 |
Rv1300 hemK |
release factor glutamine methyltransferase | 777 | 777 ctx | neighborhood:770 |
Rv1299 prfA |
peptide chain release factor PrfA | 772 | 772 ctx | neighborhood:770 |
Rv1298 rpmE |
50S ribosomal protein L31 | 745 | 746 ctx | neighborhood:705 |
Rv2155c murD |
UDP-N-acetylmuramoylalanine--D-glutamate ligase | 748 | 714 | coexpression:698 |
Rv2157c murF |
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | 726 | 689 | coexpression:625 |
Rv1306 atpF |
ATP synthase subunit B | 665 | 665 ctx | neighborhood:620 |
Rv0017c rodA |
cell division protein RodA | 691 | 664 | coexpression:457 |
Rv1308 atpA |
ATP synthase subunit alpha | 651 | 638 ctx | neighborhood:579 |
Rv1018c glmU |
bifunctional UDP-N-acetylglucosamine pyrophosphorylase/glucosamine-1-phosphate N-acetyltransferase | 647 | 608 | database:500 |
Rv1311 atpC |
ATP synthase subunit epsilon | 597 | 598 | coexpression:408 |
Rv2154c ftsW |
lipid II flippase FtsW | 653 | 595 | coexpression:462 |
Rv2153c murG |
UDP-N-acetylglucosamine--N-acetylmuramyl-(pentapeptide) pyrophosphoryl-undecaprenol-N-acetylglucosamine transferase | 776 | 569 | coexpression:477 textmining:503 |
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: decaprenyl-phosphate N-acetylglucosaminephosphotransferase
- MTBC0 PGAP product: UDP-N-acetylglucosamine--decaprenyl-phosphate N-acetylglucosaminephosphotransferase
- Pfam (hmmscan --cut_ga): Glycos_transf_4 PF00953.27 (E=3e-37)
- (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_215818.1)
- Domains: Pfam-A via hmmscan --cut_ga — Glycos_transf_4 (PF00953.27)
- 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
COG0472 - Curated reference: UniProt P9WMW5 (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 —
54 functional partner(s); context anchor
Rv1301 - Primary literature: none located yet; annotation rests on the domain/homology sources above.
Ancestral MTBC0 protein sequence
>mtbc0_001394|Rv1302|rfe MQYGLEVSSDVAGVAGGLLALSYRGAGVPLRELALVGLTAAIITYFATGPVRMLASRLGAVAYPRERDVHVTPTPRMGGLAMFLGIVGAVFLASQLPALTRGFVYSTGMPAVLVAGAVIMGIGLIDDRWGLDALTKFAGQITAASVLVTMGVAWSVLYIPVGGVGTIVLDQASSILLTLALTVSIVNAMNFVDGLDGLAAGLGLITALAICMFSVGLLRDHGGDVLYYPPAVISVVLAGACLGFLPHNFHRAKIFMGDSGSMLIGLMLAAASTTAAGPISQNAYGARDVFALLSPFLLVVAVMFVPMLDLLLAIVRRTRAGRSAFSPDKMHLHHRLLQIGHSHRRVVLIIYLWVGIVAFGAASSIFFNPRDTAAVMLGAIVVAGVATLIPLLRRGDDYYDPDLD