Protein target profile

KP13_01133

putative HTH-type transcriptional regulator

Genome: KpKP13 Gene: AHE44712.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GPK6
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Length 313
Pocket druggability 0.985
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

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.98, P2Rank 0.83). Use the 3D pocket comparison to verify whether they identify the same site. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Strong predicted binding pocket FPocket selected-pocket score 0.98. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.83. Review the complete evidence below

Risks to review

Microbiome similarity 3 of 4744 screened genomes (0.1%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.98) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant.

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
0.1% 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
86.69 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 0.985
Structure A0A0H3GPK6
Pocket Pocket 1
P2Rank 0.832
Structure A0A0H3GPK6
Pocket Pocket 1
ColabFold model
FPocket 0.865 · Pocket 1
P2Rank 0.741 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 3 / 4744 genomes with a hit
Prevalence 0.1%

Cross-references

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

Sequence

UniProt A0A0H3GPK6

Sequence

Primary amino-acid sequence viewer.

MYAVLMKQMLYLKMLAWLEDNIYCNPAIDDLALYMGYSRRFVYDVFYQYGQLPIGQYIRLRRLTIAAVSLRLTRQPIAAIAWQLSYDSPQTFSREFKKRFSLSPREYRCAAHWDTAKLLKKFHPDGESLPLARFFSLPEQVYYGYPMKYELRLSDLVLQSTAKTSIRQKVDRFFTAGGGSLSVLSDYAAASKNELNVEVNAFVGCHEAGKLPPALAMNSSLTTRSGLYVGVEFYGSWSRYARLSSDLYMELLPSLGVSRRDGYDIECFITRHAEGEEAGDRRYRVRYFIPVTLSAAGLRSDSGSGSGPAPGRS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
  • 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.

18 records
Show feature table
Start End DB Term Name
25 108 SMART SM00342 aracneu4
25 108 InterPro IPR018060 DNA binding HTH domain, AraC-type
61 110 SUPERFAMILY SSF46689 Homeodomain-like
61 110 InterPro IPR009057 Homeobox-like domain superfamily
31 108 Pfam PF12833 Helix-turn-helix domain
31 108 InterPro IPR018060 DNA binding HTH domain, AraC-type
127 294 Gene3D G3DSA:3.20.80.10 Regulatory factor, effector binding domain
127 294 InterPro IPR011256 Regulatory factor, effector binding domain superfamily
11 112 Gene3D G3DSA:1.10.10.60 -
12 110 ProSiteProfiles PS01124 Bacterial regulatory proteins, araC family DNA-binding domain profile.
12 110 InterPro IPR018060 DNA binding HTH domain, AraC-type
77 92 PRINTS PR00032 AraC bacterial regulatory protein HTH signature
77 92 InterPro IPR020449 Transcription regulator HTH, AraC- type
92 108 PRINTS PR00032 AraC bacterial regulatory protein HTH signature
92 108 InterPro IPR020449 Transcription regulator HTH, AraC- type
207 291 SUPERFAMILY SSF55136 Probable bacterial effector-binding domain
207 291 InterPro IPR011256 Regulatory factor, effector binding domain superfamily
7 269 PANTHER PTHR47504 RIGHT ORIGIN-BINDING PROTEIN

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 #1
0.985
Likely same site as P2Rank 1 1.8 Å 26 shared residues 96% of smaller site
Unusual size
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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
0.832
Likely same site as FPocket 1 1.8 Å 26 shared residues 96% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.236
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Surrounding area
Site 3 P2Rank #3
0.158
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_A0A0H3GPK6
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_01133
ColabFold — — full sequence — Loaded