Protein target profile

KP13_05429

putative HTH-type transcriptional regulator

Genome: KpKP13 Gene: AHE44980.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRQ3

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Length 249

Pocket druggability 0.268

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

Microbiome similarity 96 of 4744 screened genomes (2.0%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.27.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. 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: 2.0% 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.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 93.28 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.268

Structure A0A0H3GRQ3

Pocket Pocket 8

P2Rank 0.828

Structure A0A0H3GRQ3

Pocket Pocket 1

ColabFold model

FPocket 0.09 · Pocket 2

P2Rank 0.7 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 96 / 4744 genomes with a hit

Prevalence 2.0%

Cross-references

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

Sequence

UniProt A0A0H3GRQ3

Sequence

Primary amino-acid sequence viewer.

MNARQQSILQVVIDKGRMSVADLAKMTGVSEVTIRQDLNLLEKQSYLRRTHGYAVPLDSEDVETRMMTHFAIKRELASRAAALVNTGETVFIENGSSNALLARTLAERGDITIITVSSYIAHLLKETPGEVILLGGIYQKRSESMVGPLTRQFIQQVHFSKAFIGIDGWQAETGFTGRDMMRADVVNAVLEKHCEAIILSDSSKFSAVHPYPLGPAGRFNRVITDDRLPDACREQLLRSGLTVDIVPYI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
67	227	SMART	SM01134	DeoRC_2
67	227	SUPERFAMILY	SSF100950	NagB/RpiA/CoA transferase-like
67	227	InterPro	IPR037171	NagB/RpiA transferase-like
2	59	Gene3D	G3DSA:1.10.10.10	-
2	59	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
4	59	Pfam	PF08220	DeoR-like helix-turn-helix domain
4	59	InterPro	IPR001034	DeoR-type HTH domain
22	36	PRINTS	PR00037	LacR bacterial regulatory protein HTH signature
22	36	InterPro	IPR001034	DeoR-type HTH domain
36	54	PRINTS	PR00037	LacR bacterial regulatory protein HTH signature
36	54	InterPro	IPR001034	DeoR-type HTH domain
71	225	Pfam	PF00455	DeoR C terminal sensor domain
71	225	InterPro	IPR014036	DeoR C-terminal sensor domain
4	56	SMART	SM00420	deor2
4	56	InterPro	IPR001034	DeoR-type HTH domain
1	246	NCBIfam	NF040887	DNA-binding transcriptional regulator YciT
2	59	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
2	59	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
1	56	ProSiteProfiles	PS51000	DeoR-type HTH domain profile.
1	56	InterPro	IPR001034	DeoR-type HTH domain
4	38	ProSitePatterns	PS00894	DeoR-type HTH domain signature.
4	38	InterPro	IPR018356	Transcription regulator, HTH DeoR-type, conserved site
3	241	PANTHER	PTHR30363	HTH-TYPE TRANSCRIPTIONAL REGULATOR SRLR-RELATED

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 · FPocket

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

Site 1 FPocket #8

0.268

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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.828

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Surrounding area

Site 2 P2Rank #2

0.139

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Surrounding area

Site 3 P2Rank #3

0.002

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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_A0A0H3GRQ3	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_05429	ColabFold	—	—	full sequence	—	Loaded