KpATCC43816 Protein target profile

urease subunit beta

Accession: VK055_4195

Gene: ureB2 AIK82740.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A422ZKQ5
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Length 146
Pocket druggability (FPocket · AlphaFold DB model) 0.103
Metabolic reactions 2
Chokepoint No
Functional annotation 1 EC 3 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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

Main supporting evidence

Central metabolic position More central than 90.4% of genes in this genome. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 68 of 4744 screened genomes (1.4%) have a significant similarity hit. Mixed conservation Core/accessory calls are not fully concordant. Weak predicted binding pocket FPocket selected-pocket score 0.10.

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
1.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
47.959 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
90.21 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)
Structure A0A422ZKQ5
Pocket No pockets
Druggability (FPocket) 0.103
Structure A0A422ZKQ5
Pocket Pocket 1
ColabFold model
FPocket 0.094 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 68 / 4744 genomes with a hit
Prevalence 1.4%

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 90.4% of genes in this genome, no human homolog detected.

Relative network centrality 90.4% more central than 90.4% 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.

MKKQSNTSETMVKKVETGVPVGGYVLADSPITFNEGRSITTVHVKNTGDRPIQVGSHFHFFEANKALEFERSKAFGKRLNITATTAIRFEPGDAITVELIPFSGQQVVYGFNNLVDGWVGNASGIQGDAPEDILNNAIKHGFKSVS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0043419 The chemical reactions and pathways resulting in the breakdown of urea, the water soluble compound O=C-(NH2)2.
  • GO:0035550 A multiprotein nickel-containing complex that possesses urease activity (catalysis of the hydrolysis of urea to ammonia and carbon dioxide).
  • GO:0009039 Catalysis of the reaction: urea + 2 H2O + H+ = hydrogencarbonate + 2 NH4+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
12 122 PANTHER PTHR33569 UREASE
22 117 Pfam PF00699 Urease beta subunit
22 117 InterPro IPR002019 Urease, beta subunit-like
19 146 Gene3D G3DSA:2.10.150.10 Urease, beta subunit
19 146 InterPro IPR036461 Urease, beta subunit superfamily
22 123 SUPERFAMILY SSF51278 Urease, beta-subunit
22 123 InterPro IPR036461 Urease, beta subunit superfamily
19 119 Hamap MF_01954 Urease subunit beta [ureB].
19 119 InterPro IPR002019 Urease, beta subunit-like
22 119 NCBIfam TIGR00192 urease subunit beta
22 119 InterPro IPR002019 Urease, beta subunit-like
22 119 CDD cd00407 Urease_beta

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

No pockets are loaded yet for the displayed AlphaFold DB model AF_A0A422ZKQ5 structure. Run experimental pocket backfill to show FPocket/P2Rank overlays on this structure.

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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'.
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_A0A422ZKQ5
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4195
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A422ZKQ5

Pathways

KEGG R00131 BioCyc UREASE-RXN BioCyc RXN-24539