KpKP13 Protein target profile

DNA-binding protein H-NS

Accession: KP13_04701

Gene: AHE44035.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GUZ5
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Length 135
Pocket druggability (FPocket · AlphaFold DB model) 0.96
Functional annotation 0 EC 11 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

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 0.96. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 122 of 4744 screened genomes (2.6%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.96) — 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
2.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
94.074 Higher values support similarity to known essential genes.
DEG E-value
2.6500000000000002e-79 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
85.48 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)
Structure A0A0H3GUZ5
Pocket No pockets
Druggability (FPocket) 0.96
Structure A0A0H3GUZ5
Pocket Pocket 1
ColabFold model
FPocket 0.954 · Pocket 7
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 122 / 4744 genomes with a hit
Prevalence 2.6%

Cross-references

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

Sequence

UniProt A0A0H3GUZ5

Sequence

Primary amino-acid sequence viewer.

MSEALKILNNIRTLRAQARECTLETLEEMLEKLEVVVNERREEENAAAAEIEERTRKLQQYREMLIADGIDPNELLSTMAAVKAGTKTKRAARPAKYSYVDENGETKTWTGQGRTPAVIKKAMDEQGKSLDDFLI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

11 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

11
  • GO:0030527 The action of a molecule that contributes to the structural integrity of chromatin.
  • 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:0046983 The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0009295 The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.
  • GO:0032993 A macromolecular complex containing both protein and DNA molecules.
  • GO:0003681 Binding to DNA in a bent conformation.
  • GO:0001217 A DNA-binding transcription factor activity that represses or decreases the transcription of specific gene sets.
  • GO:0003680 Binding to a DNA structure formed by the minor groove of adenine-thymine-rich DNA regions. Examples of proteins having this function are AT-rich interaction domain (ARID)-containing proteins.
  • GO:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
1 83 FunFam G3DSA:1.10.287.1050:FF:000001 DNA-binding protein
91 135 Gene3D G3DSA:4.10.430.10 -
91 135 InterPro IPR037150 Histone-like protein H-NS, C-terminal domain superfamily
22 135 PANTHER PTHR38097 -
87 135 SMART SM00528 hnsneu2
87 135 InterPro IPR027444 Histone-like protein H-NS, C-terminal domain
16 46 Coils Coil Coil
93 135 SUPERFAMILY SSF81273 H-NS histone-like proteins
33 127 Pfam PF00816 H-NS histone family
33 127 InterPro IPR001801 Histone-like protein H-NS
2 58 SUPERFAMILY SSF81273 H-NS histone-like proteins
1 83 Gene3D G3DSA:1.10.287.1050 -
1 83 InterPro IPR027454 Histone-like protein H-NS, N-terminal
91 135 FunFam G3DSA:4.10.430.10:FF:000001 DNA-binding protein
1 135 PIRSF PIRSF002096 HnS
1 135 InterPro IPR001801 Histone-like protein H-NS

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 (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1
0.96 Unusual size
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_A0A0H3GUZ5
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_04701
ColabFold — — full sequence — Loaded