KpKP13 Protein target profile

Integration host factor subunit beta

Accession: KP13_04197

Gene: ihfB AHE45428.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQN5
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Length 102
Pocket druggability (P2Rank · AlphaFold DB model) 0.002
Functional annotation 0 EC 7 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. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 225 of 4744 screened genomes (4.7%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.37. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.00.

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
4.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
56.701 Higher values support similarity to known essential genes.
DEG E-value
4.01e-33 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.28 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) 0.002
Structure A0A0H3GQN5
Pocket Pocket 1
Druggability (FPocket) 0.367
Structure A0A0H3GQN5
Pocket Pocket 5
ColabFold model
P2Rank 0.002 · Pocket 1
FPocket 0.588 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 225 / 4744 genomes with a hit
Prevalence 4.7%

Sequence

Primary amino-acid sequence viewer.

MKETGGIMTKSELIERLASQQSHIPAKAVEDAVKEMLEHMASTLAQGERIEIRGFGSFSLHYRAPRTGRNPKTGDKVELEGKYVPHFKPGKELRDRANIYEG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

7
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
  • GO:0030527 The action of a molecule that contributes to the structural integrity of chromatin.
  • GO:0005694 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0006417 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
8 101 Gene3D G3DSA:4.10.520.10 -
8 101 InterPro IPR010992 Integration host factor (IHF)-like DNA-binding domain superfamily
8 98 SMART SM00411 bhlneu
8 98 InterPro IPR000119 Histone-like DNA-binding protein
8 101 Hamap MF_00381 Integration host factor subunit beta [ihfB].
8 101 InterPro IPR005685 Integration host factor, beta subunit
8 101 FunFam G3DSA:4.10.520.10:FF:000003 Integration host factor subunit beta
8 101 NCBIfam TIGR00988 integration host factor subunit beta
8 97 PANTHER PTHR33175 DNA-BINDING PROTEIN HU
8 97 InterPro IPR000119 Histone-like DNA-binding protein
8 96 CDD cd13836 IHF_B
8 98 SUPERFAMILY SSF47729 IHF-like DNA-binding proteins
8 98 InterPro IPR010992 Integration host factor (IHF)-like DNA-binding domain superfamily
8 98 Pfam PF00216 Bacterial DNA-binding protein
54 73 ProSitePatterns PS00045 Bacterial histone-like DNA-binding proteins signature.
54 73 InterPro IPR020816 Histone-like DNA-binding protein, conserved site
66 79 PRINTS PR01727 Prokaryotic integration host factor signature
66 79 InterPro IPR000119 Histone-like DNA-binding protein
48 63 PRINTS PR01727 Prokaryotic integration host factor signature
48 63 InterPro IPR000119 Histone-like DNA-binding protein
82 96 PRINTS PR01727 Prokaryotic integration host factor signature
82 96 InterPro IPR000119 Histone-like DNA-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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.002
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #5
0.367
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_A0A0H3GQN5
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_04197
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GQN5