KpATCC43816 Protein target profile

quinate/shikimate dehydrogenase (Pyrroloquinoline-quinone)

Accession: VK055_0527

Gene: AIK79150.1 quiA 3D evidence: AlphaFold DB model + ColabFold model Metabolism 10 reactions UniProt A0A0H3GTK8
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Length 790
Pocket druggability (P2Rank · AlphaFold DB model) 0.932
Metabolic reactions 10
Chokepoint No
Functional annotation 0 EC 6 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.93, FPocket 0.83). Use the 3D pocket comparison to verify whether they identify the same site. 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 58 of 4744 screened genomes (1.2%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.93) — check the ligand evidence before deprioritizing on off-target risk alone.

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
1.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
40.87 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
93.92 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) 0.932
Structure A0A0H3GTK8
Pocket Pocket 1
Druggability (FPocket) 0.832
Structure A0A0H3GTK8
Pocket Pocket 17
ColabFold model
P2Rank 0.95 · Pocket 1
FPocket 0.999 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 58 / 4744 genomes with a hit
Prevalence 1.2%

Metabolic context

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

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% 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

10 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.

MATGNAPRGFPRILQWLLAGLMLIIGLAVGILGAKLALVGGTLYFALMGVVMVIAAVLIFRNRRGGILLYAVAFIASVIWAISDAGWNYWPLFSRLFALGVLAFLAALVWPFLASPPAKKGPAYGVAAVLAVALAVSFGWMFKSAPLVSATEAVPVKPVAPGEQQKNWAHWGNTTHGDRFAALDQINKQNVNQLQVAWVAHTGDIPQSNGSGAEDQNTPLQIGDTLYVCTPYSKVLALDVDSGKEKWRYDSKSSSPNWQRCRGLGYYADSQAQTAPASGTQPAACSRRLFLPTIDARLIAIDADTGKLCENFGDGGIVDLSVGMGEVKAGYYQQTSTPLVAGNVVVVGGRVADNYSTGEPPGVVRAFDVHTGKLAWAWDPGNPALTGVPPEGQTYTRGTPNVWSAMSYDAKLNLIYLPTGNATPDFFGGERTALDDKYSSSIVAVDATTGQVRWHFQTTHHDLWDFDLPSQPLLYDLPDGKGGTTPVLVQTSKQGMIFMLNRETGEPVAKVEERPVPAGNVKGERYSPTQPYSVGMPMIGNQTLTESDMWGATPIDLLLCRIQFKEMRHQGVFTPPGEDRSLQFPGSLGGMNWGSVSLDPNNSLMFVNDMRLGLANYMVPRAKVAKDASGIEMGIVPMEGTPFGAMRERFLSPLGIPCQKPPFGTMSAVDLKTGKLVWQVPVGTVEDTGPLGIRMHMPIPIGMPTLGASLATQSGLLFLAGTQDFYLRAFDTANGKEIWKSRLPVGSQSGPMTYVSPKTGKQYIIINAGGARQSPDRGDYIIAYALPDHH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

6
  • GO:0016614 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • GO:0048038 Binding to a quinone, any member of a class of diketones derivable from aromatic compounds by conversion of two CH groups into CO groups with any necessary rearrangement of double bonds.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0008876 Catalysis of the reaction: D-glucose + ubiquinone = D-glucono-1,5-lactone + ubiquinol.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

46 records
Show feature table
Start End DB Term Name
164 772 SUPERFAMILY SSF50998 Quinoprotein alcohol dehydrogenase-like
164 772 InterPro IPR011047 Quinoprotein alcohol dehydrogenase-like superfamily
168 786 CDD cd10280 PQQ_mGDH
168 786 InterPro IPR017511 PQQ-dependent membrane bound dehydrogenase
16 37 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
664 751 Pfam PF13360 PQQ-like domain
664 751 InterPro IPR002372 Pyrrolo-quinoline quinone repeat
67 90 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
121 140 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
96 114 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
121 142 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
61 66 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
148 786 Gene3D G3DSA:2.140.10.10 -
92 114 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
43 60 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
36 58 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
17 787 NCBIfam TIGR03074 membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family
17 787 InterPro IPR017511 PQQ-dependent membrane bound dehydrogenase
1 15 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
143 790 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
115 120 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
403 424 ProSitePatterns PS00364 Bacterial quinoprotein dehydrogenases signature 2.
403 424 InterPro IPR001479 Quinoprotein dehydrogenase, conserved site
65 82 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
634 681 SMART SM00564 ire1_9
634 681 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
710 742 SMART SM00564 ire1_9
710 742 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
281 313 SMART SM00564 ire1_9
281 313 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
338 379 SMART SM00564 ire1_9
338 379 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
481 512 SMART SM00564 ire1_9
481 512 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
219 250 SMART SM00564 ire1_9
219 250 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
408 457 SMART SM00564 ire1_9
408 457 InterPro IPR018391 Pyrrolo-quinoline quinone beta-propeller repeat
91 95 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
13 32 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
224 254 Pfam PF01011 PQQ enzyme repeat
224 254 InterPro IPR002372 Pyrrolo-quinoline quinone repeat
440 467 Pfam PF01011 PQQ enzyme repeat
440 467 InterPro IPR002372 Pyrrolo-quinoline quinone repeat
38 42 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
145 770 PANTHER PTHR32303 QUINOPROTEIN ALCOHOL DEHYDROGENASE (CYTOCHROME C)

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.

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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
0.932
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Surrounding area
Pocket 2 P2Rank #2
0.884
Likely same site as FPocket 17 4.5 Å 18 shared residues 95% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.529
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Surrounding area
Pocket 4 P2Rank #4
0.45
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Surrounding area
Pocket 5 P2Rank #5
0.188
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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 #17
0.832
Likely same site as P2Rank 2 4.5 Å 18 shared residues 95% of smaller site
Show in viewer
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_A0A0H3GTK8
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0527
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GTK8

Pathways

BioCyc 1.1.99.25-RXN-QUINATE/UBIQUINONE-6//DEHYDROQUINATE/UBIQUINOL-30.50. BioCyc SHIKIMATE-PQQ-RXN-SHIKIMATE/UBIQUINONE-8//3-DEHYDRO-SHIKIMATE/CPD-9956.53. BioCyc 1.1.99.25-RXN-QUINATE/CPD-3766//DEHYDROQUINATE/MENADIOL.42. BioCyc SHIKIMATE-PQQ-RXN-SHIKIMATE/CPD-9720//3-DEHYDRO-SHIKIMATE/CPD-12126.50. BioCyc 1.1.99.25-RXN-QUINATE/UBIQUINONE-8//DEHYDROQUINATE/CPD-9956.46. BioCyc 1.1.99.25-RXN-QUINATE/CPD-9720//DEHYDROQUINATE/CPD-12126.43. BioCyc SHIKIMATE-PQQ-RXN-SHIKIMATE/CPD-3766//3-DEHYDRO-SHIKIMATE/MENADIOL.49. BioCyc 1.1.99.25-RXN-QUINATE/CPD-9733//DEHYDROQUINATE/CPD-12118.43. BioCyc SHIKIMATE-PQQ-RXN-SHIKIMATE/CPD-9733//3-DEHYDRO-SHIKIMATE/CPD-12118.50. BioCyc SHIKIMATE-PQQ-RXN-SHIKIMATE/UBIQUINONE-6//3-DEHYDRO-SHIKIMATE/UBIQUINOL-30.57.