KpATCC43816 Protein target profile

glycerol-3-phosphate dehydrogenase, anaerobic, Bsubunit

Accession: VK055_4867

Gene: glpB AIK83394.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GVN0
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Length 419
Pocket druggability (P2Rank · AlphaFold DB model) 0.959
Metabolic reactions 2
Chokepoint No
Functional annotation 1 EC 3 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Central metabolic position More central than 99.8% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Review the complete evidence below

Risks to review

Microbiome similarity 72 of 4744 screened genomes (1.5%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.96) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.73, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

Evidence gaps

No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
1.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
40.288 Higher values support similarity to known essential genes.
DEG E-value
4.78e-90 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
95.09 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.959
Structure A0A0H3GVN0
Pocket Pocket 1
Druggability (FPocket) 0.733
Structure A0A0H3GVN0
Pocket Pocket 1
ColabFold model
P2Rank 0.968 · Pocket 1
FPocket 0.78 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 72 / 4744 genomes with a hit
Prevalence 1.5%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: more central than 99.8% of genes in this genome, no human homolog detected.

Relative network centrality 99.8% more central than 99.8% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reactions

2 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MKFDCAIIGGGLAGLLCGLALNQHGLRSVIISRGQSALHFSSASLDLLSALPNGDNVTDVAQGLQQLAEQLPEHPYSRLGAEAVLEYATQAEALLAACGAVMQGDARRPHRRVTPLGTLRPAWLSPLEVPVAPLPSQGACLVGISGFADFQPHLAAAALGQHGVTAAAVEIELPLLDVLRDNPTEFRAANIARVLDDENMWPALHAALLPLAQQYDLLIMPACFGLADDRLYHWLQARLPCPLRLLPTLPPSVPGMRLHSQLQRQFIREGGAWLAGDEVVKISHRQNAVEAVWTRNHGDIALRPRFTVLASGSFFSNGLVATRDSVREPILGLDLHQTLPRESWYQRDFFASQPWQRFGVKTDALLRPLLGGQPFHNLFAIGSLLGGFDAIQLGCGGGVCAVTALHAARQIHALAGGRP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0004368 Catalysis of the reaction: sn-glycerol 3-phosphate + a quinone = glycerone phosphate + a quinol.
  • GO:0009331 An enzyme complex that catalyzes the oxidation of sn-glycerol 3-phosphate to dihydroxyacetone phosphate, with concurrent reduction of flavin adenine dinucleotide (FAD) to FADH2. In E. coli, the complex is either a GlpA-GlpB-GlpC heterotrimer that functions in anaerobic conditions, or a GlpD homodimer that functions in aerobic conditions.
  • GO:0019563 The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
1 4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
3 411 NCBIfam TIGR03378 anaerobic glycerol-3-phosphate dehydrogenase subunit GlpB
3 411 InterPro IPR009158 Glycerol-3-phosphate dehydrogenase, GlpB subunit
1 417 PIRSF PIRSF000141 Anaerobic_G3P_dh
1 417 InterPro IPR009158 Glycerol-3-phosphate dehydrogenase, GlpB subunit
18 22 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
4 399 Pfam PF00890 FAD binding domain
4 399 InterPro IPR003953 FAD-dependent oxidoreductase 2, FAD binding domain
5 17 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 22 Phobius SIGNAL_PEPTIDE Signal peptide region
23 419 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 169 Gene3D G3DSA:3.50.50.60 -
1 169 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
1 412 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
1 412 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
1 415 Hamap MF_00753 Anaerobic glycerol-3-phosphate dehydrogenase subunit B [glpB].
1 415 InterPro IPR009158 Glycerol-3-phosphate dehydrogenase, GlpB subunit

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

Download VMD script Full viewer

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.959
Likely same site as FPocket 1 2.9 Å 38 shared residues 90% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.077
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Surrounding area
Pocket 3 P2Rank #3
0.044
Likely same site as FPocket 15 1.3 Å 7 shared residues 100% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.01
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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1
0.733 Unusual size
Likely same site as P2Rank 1 2.9 Å 38 shared residues 90% of smaller site
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Surrounding area
Pocket 2 FPocket #15
0.275
Likely same site as P2Rank 3 1.3 Å 7 shared residues 100% of smaller site
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Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GVN0
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4867
ColabFold — — full sequence — Loaded

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GVN0

Pathways

BioCyc RXN-15740 BioCyc GLYC3PDEHYDROG-RXN