Bacterial glycerol uptake and catabolism through glycerol 3-phosphate

A reusable bacterial module for channel-mediated glycerol uptake followed by conversion to dihydroxyacetone phosphate. GlpF facilitates glycerol movement across the cytoplasmic membrane, GlpK traps intracellular glycerol as sn-glycerol 3-phosphate, and FAD-dependent GlpD oxidizes that intermediate to dihydroxyacetone phosphate while reducing the respiratory quinone pool.

MODULE:bacterial_glycerol_uptake_catabolismDRAFTCONCRETEMetabolic Pathwaymodules/bacterial_glycerol_uptake_catabolism.yaml
glycerol catabolic processGO:0019563
GO:0019563
glycerol catabolic process
GO:0019563 captures conversion of glycerol into metabolic intermediates.
PMID:25827416
The glycerol-dependent metabolic persistence of Pseudomonas putida KT2440 reflects the regulatory logic of the GlpR repressor.
The organism-specific study identifies GlpF-mediated uptake, GlpK phosphorylation, and ubiquinone-dependent GlpD oxidation in KT2440.
file:PSEPK/glpF/glpF-ai-review.yaml
PSEPK glpF gene review
Q88NX7 is curated as a plasma-membrane glycerol channel rather than an energy-coupled transporter.
file:PSEPK/glpK/glpK-ai-review.yaml
PSEPK glpK gene review
Q88NX8 is the ATP-dependent glycerol kinase performing the first intracellular reaction.
file:PSEPK/glpD/glpD-ai-review.yaml
PSEPK glpD gene review
Q88NY0 is curated as the FAD-dependent glycerol-3-phosphate:quinone dehydrogenase.

The module starts with extracellular glycerol and ends with dihydroxyacetone phosphate plus reduced quinone. Passive channel transport does not itself consume ATP; phosphorylation by GlpK provides metabolic trapping. Alternative active glycerol transporters, glycerol dehydrogenase routes, phospholipid-derived glycerol 3-phosphate, quinol reoxidation, and downstream glycolysis are outside the boundary. PSEPK-specific transcription and regulation at the glp locus are supporting context, not required parts.

4Nodes
3Parts
0Variant Sets
0Variants
3Annotons
2Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:bacterial_glycerol_uptake_catabolism deep-research report alongside the module YAML.

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 (3/6 grounded genes reviewed)

2 complete review(s) · 2 with deep research · 3 missing review · 1 reviewed but lacking deep research

Gene Review Complete Deep research
glpD Q88NY0 4/5
glpF Q88NX7
glpK Q88NX8
GlpK (Escherichia coli K-12) P0A6F3
GlpF (Escherichia coli K-12) P0AER0
GlpD (Escherichia coli K-12) P13035

Details

Context
bacteriaNCBITaxon:2
Bacterial glycerol uptake and catabolismMetabolic Pathwaybacterial_glycerol_uptake_catabolism
glycerol catabolic processGO:0019563
Context
bacteriaNCBITaxon:2

Connections

GlpF supplies intracellular glycerol to GlpK.
GlpK supplies sn-glycerol 3-phosphate to GlpD.
Part 1: facilitated glycerol uptake
GlpF-dependent glycerol uptakeTransport Stepglpf_glycerol_uptake

Annotons

GlpF glycerol channel activity
glpf_activity
Participant: Family: glycerol-channel PAINT lineage within the aquaporin family
Family:
glycerol-channel PAINT lineage within the aquaporin familyPANTHER:PTHR43829:SF9 The PANTHER subfamily is heterogeneous; the required PAINT node restricts the annoton to the glycerol-channel lineage carrying GO:0015254.
Representative Members: GlpF (Pseudomonas putida KT2440)UniProtKB:Q88NX7 GlpF (Escherichia coli K-12)UniProtKB:P0AER0

Function

glycerol channel activityGO:0015254
Substrates: extracellular glycerol
Products: intracellular glycerol

Processes

glycerol transmembrane transportGO:0015793

Locations

plasma membraneGO:0005886

Facilitates diffusion of glycerol into the cell.

Part 2: glycerol phosphorylation
GlpK-dependent glycerol 3-phosphate formationReactionglpk_glycerol_3_phosphate_formation

Annotons

GlpK glycerol kinase activity
glpk_activity
Participant: Family: glycerol kinase family
Family:
glycerol kinase familyPANTHER:PTHR10196:SF69
Representative Members: GlpK (Pseudomonas putida KT2440)UniProtKB:Q88NX8 GlpK (Escherichia coli K-12)UniProtKB:P0A6F3

Function

glycerol kinase activityGO:0004370
Substrates: glycerol ATP
Products: sn-glycerol 3-phosphate ADP

Processes

glycerol catabolic processGO:0019563

Traps imported glycerol as the phosphorylated GlpD substrate.

Part 3: glycerol 3-phosphate oxidation
GlpD-dependent dihydroxyacetone phosphate formationReactionglpd_dhap_formation

Annotons

GlpD glycerol-3-phosphate:quinone dehydrogenase activity
glpd_activity
Participant: Family: bacterial catabolic GlpD PAINT lineage
Family:
bacterial catabolic GlpD PAINT lineagePANTHER:PTHR11985 The required PAINT node separates the bacterial glycerol-catabolic lineage from mitochondrial shuttle members elsewhere in PTHR11985.
Representative Members: GlpD (Pseudomonas putida KT2440)UniProtKB:Q88NY0 GlpD (Escherichia coli K-12)UniProtKB:P13035

Function

glycerol-3-phosphate dehydrogenase (quinone) activityGO:0004368
Substrates: sn-glycerol 3-phosphate quinone
Products: dihydroxyacetone phosphate quinol

Processes

glycerol-3-phosphate catabolic processGO:0046168

Locations

plasma membraneGO:0005886

Produces DHAP and transfers electrons to the quinone pool.