KpATCC43816 Protein target profile

bacterial regulatory, luxR family protein

Accession: VK055_5099

Gene: AIK83625.1 3D evidence: ColabFold model Metabolism Not in network

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Length 133

Pocket druggability (P2Rank · ColabFold model) 0.007

Functional annotation 0 EC 2 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

Risks to review

Mixed conservation Core/accessory calls are not fully concordant. Weak predicted binding pocket FPocket selected-pocket score 0.13. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.01.

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: 0.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 63.52 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

ColabFold / curated 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) 0.007

Structure CB_VK055_5099

Pocket Pocket 1

Druggability (FPocket) 0.127

Structure CB_VK055_5099

Pocket Pocket 13

ColabFold model

P2Rank 0.007 · Pocket 1

FPocket 0.127 · Pocket 13

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 0 / 4744 genomes with a hit

Prevalence 0.0%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MNHKISIKEYSYLKKIGSPVFFILNTNCKVNSTLIGINIIDAHEAILILKDIMLSLFNGGKQLDYKPINLTKKESFVLRLYIDGLSLTQISEKIAIRKKTLLTHTRNILNKTGVKHHNHLNILKNILGIHLAY

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization: Unknown

Gene Ontology (GO)

GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
69	120	Pfam	PF00196	Bacterial regulatory proteins, luxR family
69	120	InterPro	IPR000792	Transcription regulator LuxR, C-terminal
54	123	SUPERFAMILY	SSF46894	C-terminal effector domain of the bipartite response regulators
54	123	InterPro	IPR016032	Signal transduction response regulator, C-terminal effector
70	84	PRINTS	PR00038	LuxR bacterial regulatory protein HTH signature
70	84	InterPro	IPR000792	Transcription regulator LuxR, C-terminal
100	112	PRINTS	PR00038	LuxR bacterial regulatory protein HTH signature
100	112	InterPro	IPR000792	Transcription regulator LuxR, C-terminal
84	100	PRINTS	PR00038	LuxR bacterial regulatory protein HTH signature
84	100	InterPro	IPR000792	Transcription regulator LuxR, C-terminal
42	127	Gene3D	G3DSA:1.10.10.10	-
42	127	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily

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

0.007

Show in viewer

Surrounding area

All structural evidence 0 experimental · 1 predicted

Structural evidence

0 + 1

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
ColabFold VK055_5099	ColabFold	—	—	full sequence	—	Viewing