Protein target profile

KP13_05476

Lambda repressor-like, DNA-binding domain-containing protein

Genome: KpKP13 Gene: AHE44481.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GNM9
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Length 346
Pocket druggability 0.847
Functional annotation 0 EC 5 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 0.85, P2Rank 0.86). 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. 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. Review the complete evidence below

Risks to review

Microbiome similarity 9 of 4744 screened genomes (0.2%) 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.

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
0.2% 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.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
90.55 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 0.847
Structure A0A0H3GNM9
Pocket Pocket 1
P2Rank 0.86
Structure A0A0H3GNM9
Pocket Pocket 1
ColabFold model
FPocket 0.271 · Pocket 1
P2Rank 0.861 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 9 / 4744 genomes with a hit
Prevalence 0.2%

Cross-references

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

Sequence

UniProt A0A0H3GNM9

Sequence

Primary amino-acid sequence viewer.

MKKIATKITLADIAREARVGVATVDRVLNKRAAVKESTALRVLEAARRLGFTLEQPHYRLAAGKAPVTIRMGFILLQESHSFYLPLARALKREAAPWLPAGQAPVILHFAIDAVEAMAQAIHRLSDEVEVLGLVALDHPLIRHAVARAAARGVRVFTLLSDLSVPQRSGYIGLDNHKAGRTAAWFIERLCRGNGEIGIIIGDNRFTCQESCEISFRSCLREQGKGQQILEPVRSHERADIARTVTEQMLTQYPALQAIYAPCGGVEGIVDALRDSGRQQEIALVCHGPLSDSELALIDGTIDIMLNHRLDEFAAVTLRAMADAASRPHSEVISLPQPFDIITKENM

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • GO:0030246 Binding to a carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
113 337 Gene3D G3DSA:3.40.50.2300 -
2 64 Gene3D G3DSA:1.10.260.40 -
2 64 InterPro IPR010982 Lambda repressor-like, DNA-binding domain superfamily
174 346 Gene3D G3DSA:3.40.50.2300 -
8 62 ProSiteProfiles PS50932 LacI-type HTH domain profile.
8 62 InterPro IPR000843 LacI-type HTH domain
67 345 PANTHER PTHR30036 D-XYLOSE-BINDING PERIPLASMIC PROTEIN
7 80 SMART SM00354 laci3
7 80 InterPro IPR000843 LacI-type HTH domain
70 343 CDD cd06307 PBP1_sugar_binding
9 52 Pfam PF00356 Bacterial regulatory proteins, lacI family
9 52 InterPro IPR000843 LacI-type HTH domain
68 342 SUPERFAMILY SSF53822 Periplasmic binding protein-like I
68 342 InterPro IPR028082 Periplasmic binding protein-like I
11 52 CDD cd01392 HTH_LacI
11 52 InterPro IPR000843 LacI-type HTH domain
115 324 Pfam PF13407 Periplasmic binding protein domain
115 324 InterPro IPR025997 Periplasmic binding protein
10 28 ProSitePatterns PS00356 LacI-type HTH domain signature.
7 63 SUPERFAMILY SSF47413 lambda repressor-like DNA-binding domains
7 63 InterPro IPR010982 Lambda repressor-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.

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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
0.847
Likely same site as P2Rank 1 1.7 Å 20 shared residues 95% of smaller site
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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
0.86
Likely same site as FPocket 1 1.7 Å 20 shared residues 95% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.03
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Surrounding area
Site 3 P2Rank #3
0.006
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Surrounding area
Site 4 P2Rank #4
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_A0A0H3GNM9
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_05476
ColabFold — — full sequence — Loaded