dTDP-L-rhamnose biosynthesis

Species-neutral bacterial module for synthesis of the activated sugar dTDP-L-rhamnose from alpha-D-glucose 1-phosphate. The pathway proceeds through dTDP-glucose formation, dTDP-glucose 4,6-dehydration, dTDP-4-dehydrorhamnose 3,5-epimerization, and final NADPH-dependent reduction to dTDP-L-rhamnose. The module represents the soluble nucleotide-sugar supply pathway and treats downstream O-antigen, LPS, and specialized-polysaccharide assembly reactions as consumers, not as part of the biosynthetic module itself.

MODULE:dtdp_l_rhamnose_biosynthesisDRAFTCONCRETEMetabolic Pathwaymodules/dtdp_l_rhamnose_biosynthesis.yaml
dTDP-rhamnose biosynthetic processGO:0019305
GO:0019305
dTDP-rhamnose biosynthetic process
GO:0019305 captures biosynthesis of dTDP-rhamnose, the process annotated on the PSEPK RmlC/RfbC epimerases and RfbD/PP_0500 reductases.
KEGG:ppu00523
Pseudomonas putida KT2440 polyketide sugar unit biosynthesis bucket
The local PSEPK ppu00523 batch contains rmlC, PP_0500, rfbC, rfbD and also pulls in the adjacent rfbA/rffG early-step genes from ppu00525.
KEGG:ppu00525
Pseudomonas putida KT2440 acarbose/validamycin bucket
The ppu00525 bucket contributes the early dTDP-glucose formation and dTDP-glucose 4,6-dehydration steps in PSEPK, rather than a literal acarbose or validamycin pathway.
file:PSEPK/rfbA/rfbA-uniprot.txt
UniProtKB entry for PSEPK rfbA
Q88LZ3 is a glucose-1-phosphate thymidylyltransferase.
file:PSEPK/rffG/rffG-uniprot.txt
UniProtKB entry for PSEPK rffG
Q88LZ1 is a dTDP-glucose 4,6-dehydratase.
file:PSEPK/rfbC/rfbC-uniprot.txt
UniProtKB entry for PSEPK rfbC
Q88LZ4 is a dTDP-4-dehydrorhamnose 3,5-epimerase.
file:PSEPK/rfbD/rfbD-uniprot.txt
UniProtKB entry for PSEPK rfbD
Q88LZ2 is a dTDP-4-dehydrorhamnose reductase.

First-pass PSEPK interpretation: the PP_1782-PP_1785 rfbC-rfbA-rfbD-rffG cluster encodes a complete dTDP-L-rhamnose route, while rmlC/PP_0500 provide additional epimerase/reductase paralogs. Keep downstream O-antigen and other glycan assembly terms as product-use context rather than module-level molecular functions.

5Nodes
4Parts
0Variant Sets
0Variants
6Annotons
3Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✓ present

  • dtdp_l_rhamnose_biosynthesis-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Gene-review completeness (6/6 grounded genes reviewed)

6 complete review(s) · 3 with deep research · 0 missing review · 3 reviewed but lacking deep research

Gene Review Complete Deep research
PP_0500 Q88QJ2 ✓ ✓ ✓
rfbA Q88LZ3 ✓ ✓ ✗
rfbC Q88LZ4 ✓ ✓ ✓
rfbD Q88LZ2 ✓ ✓ ✗
rffG Q88LZ1 ✓ ✓ ✓
rmlC Q88R69 ✓ ✓ ✗

Details

Context
bacteriaNCBITaxon:2
cytosolGO:0005829
dTDP-L-rhamnose biosynthesisMetabolic Pathwaydtdp_l_rhamnose_biosynthesis
dTDP-rhamnose biosynthetic processGO:0019305
Context
bacteriaNCBITaxon:2
cytosolGO:0005829

Connections

RfbA supplies dTDP-glucose for RffG dehydration.
RffG supplies the deoxy-keto dTDP-sugar for RmlC/RfbC.
The epimerase step supplies dTDP-4-dehydro-beta-L-rhamnose.
Part 1: dTDP-glucose formation
Glucose-1-phosphate thymidylyltransferaseReactionrfba_thymidylyltransferase_step

Annotons

rfbA: glucose-1-phosphate thymidylyltransferase
rfba_glucose_1_phosphate_thymidylyltransferase
Participant: Family: glucose-1-phosphate thymidylyltransferase family
Family:
glucose-1-phosphate thymidylyltransferase familyPANTHER:PTHR43532
Representative Members: PSEPK rfbA exemplarUniProtKB:Q88LZ3

Function

glucose-1-phosphate thymidylyltransferase activityGO:0008879
Substrates: dTTP alpha-D-glucose 1-phosphate
Products: dTDP-alpha-D-glucose diphosphate

Processes

dTDP-rhamnose biosynthetic processGO:0019305

Activates glucose 1-phosphate as dTDP-glucose for downstream deoxy-sugar conversion.

Part 2: dTDP-glucose dehydration
dTDP-glucose 4,6-dehydrataseReactionrffg_dtdp_glucose_dehydratase_step

Annotons

rffG: dTDP-glucose 4,6-dehydratase
rffg_dtdp_glucose_dehydratase
Participant: Family: dTDP-glucose 4,6-dehydratase family
Family:
dTDP-glucose 4,6-dehydratase familyPANTHER:PTHR43000
Representative Members: PSEPK rffG exemplarUniProtKB:Q88LZ1

Function

dTDP-glucose 4,6-dehydratase activityGO:0008460
Substrates: dTDP-alpha-D-glucose
Products: dTDP-4-dehydro-6-deoxy-alpha-D-glucose water
Cofactors: NAD+

Processes

dTDP-rhamnose biosynthetic processGO:0019305

Converts dTDP-glucose to the 4-keto-6-deoxy intermediate used by the RmlC/RfbC epimerase step.

Part 3: 3,5-epimerization
dTDP-4-dehydrorhamnose 3,5-epimeraseReactionrmlc_rfbc_epimerase_step

Annotons

rmlC: dTDP-4-dehydrorhamnose 3,5-epimerase
rmlc_epimerase
Participant: Family: dTDP-4-dehydrorhamnose 3,5-epimerase family
Family:
dTDP-4-dehydrorhamnose 3,5-epimerase familyPANTHER:PTHR21047
Representative Members: PSEPK rmlC exemplarUniProtKB:Q88R69

Function

dTDP-4-dehydrorhamnose 3,5-epimerase activityGO:0008830
Substrates: dTDP-4-dehydro-6-deoxy-alpha-D-glucose
Products: dTDP-4-dehydro-beta-L-rhamnose

Processes

dTDP-rhamnose biosynthetic processGO:0019305

Locations

cytosolGO:0005829

Epimerizes the deoxy-keto sugar nucleotide toward the L-rhamnose stereochemistry.

rfbC: dTDP-4-dehydrorhamnose 3,5-epimerase
rfbc_epimerase
Participant: Family: dTDP-4-dehydrorhamnose 3,5-epimerase family
Family:
dTDP-4-dehydrorhamnose 3,5-epimerase familyPANTHER:PTHR21047
Representative Members: PSEPK rfbC exemplarUniProtKB:Q88LZ4

Function

dTDP-4-dehydrorhamnose 3,5-epimerase activityGO:0008830
Substrates: dTDP-4-dehydro-6-deoxy-alpha-D-glucose
Products: dTDP-4-dehydro-beta-L-rhamnose

Processes

dTDP-rhamnose biosynthetic processGO:0019305

Locations

cytosolGO:0005829

Cluster-encoded paralog for the same epimerase step.

Part 4: final reduction to dTDP-L-rhamnose
dTDP-4-dehydrorhamnose reductaseReactionrfbd_pp0500_reductase_step

Annotons

rfbD: dTDP-4-dehydrorhamnose reductase
rfbd_reductase
Participant: Family: dTDP-4-dehydrorhamnose reductase family
Family:
dTDP-4-dehydrorhamnose reductase familyPANTHER:PTHR10491
Representative Members: PSEPK rfbD exemplarUniProtKB:Q88LZ2

Function

dTDP-4-dehydrorhamnose reductase activityGO:0008831
Substrates: dTDP-4-dehydro-beta-L-rhamnose NADPH
Products: dTDP-beta-L-rhamnose NADP+

Processes

dTDP-rhamnose biosynthetic processGO:0019305

Locations

cytosolGO:0005829

Cluster-encoded reductase that completes dTDP-L-rhamnose synthesis.

PP_0500: dTDP-4-dehydrorhamnose reductase
pp0500_reductase
Participant: Family: dTDP-4-dehydrorhamnose reductase family
Family:
dTDP-4-dehydrorhamnose reductase familyPANTHER:PTHR10491
Representative Members: PSEPK PP_0500 exemplarUniProtKB:Q88QJ2

Function

dTDP-4-dehydrorhamnose reductase activityGO:0008831
Substrates: dTDP-4-dehydro-beta-L-rhamnose NADPH
Products: dTDP-beta-L-rhamnose NADP+

Processes

dTDP-rhamnose biosynthetic processGO:0019305

Locations

cytosolGO:0005829

Additional reductase paralog that can complete the same final nucleotide-sugar step.