KpKP13 Protein target profile

Exu regulon transcriptional regulator

Accession: KP13_02875

Gene: AHE42555.1 exuR 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVZ9
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Length 258
Pocket druggability (P2Rank · AlphaFold DB model) 0.093
Functional annotation 0 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

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. Strong predicted binding pocket FPocket selected-pocket score 0.85. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 102 of 4744 screened genomes (2.2%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.85) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.09.

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
2.2% 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
84.39 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) 0.093
Structure A0A0H3GVZ9
Pocket Pocket 1
Druggability (FPocket) 0.848
Structure A0A0H3GVZ9
Pocket Pocket 14
ColabFold model
P2Rank 0.527 · Pocket 1
FPocket 0.386 · Pocket 19
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 102 / 4744 genomes with a hit
Prevalence 2.2%

Sequence

Primary amino-acid sequence viewer.

MEIIEPRRLYQQLAAELKTRIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIHVISNHPKYQQVADESLEFANYGPFELLQARQLIESNIAEFAATQVTKQDIMKLMEIQEKARNEKCFRDSEWDLQFHVQVALATQNSALAAIVEKMWTQRVHNPYWKKLHEHIDLRTVDNWCDDHDQILKALLRKDPNAAKLAMWQHLENTKQMLFNETSDDFEFNADRYLFAENPVVHLDTAVNGAK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

3
  • 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.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
96 220 SMART SM00895 FCD_2
96 220 InterPro IPR011711 GntR, C-terminal
94 226 SUPERFAMILY SSF48008 GntR ligand-binding domain-like
94 226 InterPro IPR008920 Transcription regulator FadR/GntR, C-terminal
3 77 Gene3D G3DSA:1.10.10.10 -
3 77 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
3 231 PANTHER PTHR43537 TRANSCRIPTIONAL REGULATOR, GNTR FAMILY
7 75 ProSiteProfiles PS50949 GntR-type HTH domain profile.
7 75 InterPro IPR000524 Transcription regulator HTH, GntR
13 72 SMART SM00345 gntr3
13 72 InterPro IPR000524 Transcription regulator HTH, GntR
2 76 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
2 76 InterPro IPR036390 Winged helix DNA-binding domain superfamily
46 62 PRINTS PR00035 GntR bacterial regulatory protein HTH signature
46 62 InterPro IPR000524 Transcription regulator HTH, GntR
32 46 PRINTS PR00035 GntR bacterial regulatory protein HTH signature
32 46 InterPro IPR000524 Transcription regulator HTH, GntR
95 229 Gene3D G3DSA:1.20.120.530 -
95 229 InterPro IPR008920 Transcription regulator FadR/GntR, C-terminal
96 219 Pfam PF07729 FCD domain
96 219 InterPro IPR011711 GntR, C-terminal
9 72 Pfam PF00392 Bacterial regulatory proteins, gntR family
9 72 InterPro IPR000524 Transcription regulator HTH, GntR
95 229 FunFam G3DSA:1.20.120.530:FF:000002 GntR family transcriptional regulator
9 69 CDD cd07377 WHTH_GntR
9 69 InterPro IPR000524 Transcription regulator HTH, GntR

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
0.093
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Surrounding area
Pocket 2 P2Rank #2
0.074
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Surrounding area
Pocket 3 P2Rank #3
0.045
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Surrounding area
Pocket 4 P2Rank #4
0.036
Likely same site as FPocket 14 2.5 Å 6 shared residues 100% of smaller site
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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 #14
0.848
Likely same site as P2Rank 4 2.5 Å 6 shared residues 100% 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_A0A0H3GVZ9
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_02875
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GVZ9