KpKP13 Protein target profile

Lipoprotein 34

Accession: KP13_03825

Gene: AHE43309.1 nlpB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWJ5
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Length 310
Pocket druggability (P2Rank · AlphaFold DB model) 0.165
Functional annotation 0 EC 3 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. Moderate predicted binding pocket FPocket selected-pocket score 0.56. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 92 of 4744 screened genomes (1.9%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.56) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.17.

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
1.9% 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
89.53 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) 0.165
Structure A0A0H3GWJ5
Pocket Pocket 1
Druggability (FPocket) 0.558
Structure A0A0H3GWJ5
Pocket Pocket 10
ColabFold model
P2Rank 0.029 · Pocket 1
FPocket 0.518 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 92 / 4744 genomes with a hit
Prevalence 1.9%

Sequence

Primary amino-acid sequence viewer.

MSGDEAYLQASPLSELHAPAGMILPIQVGDYNIPVANSTGAVGKALDIRPPAQPLALVSGARTQFNGDTATLMVENGRSGSLWAQVTSILQAKNYVIAKRDDASQTLNTDWVEWNRLDEDQQYRGRYQISVKPQGYQQAVVVKLVNLEQAGKPVADPASLQRYSTAMLNVISEGLDMNATSAQNAAQRSAGATFDVQSAADDTGLPMLVVRAPFNLVWQRLPGALEKVGMKVTDSTRSQGSMALTYKPLSDSSWQELGARDPQLVSGDYKLQVGDLDNRSSLQFIDPKGHTLTQSQNDALVAVFQAAFNK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
OuterMembrane

Gene Ontology (GO)

3
  • GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
  • GO:0043165 The assembly of an outer membrane of the type formed in Gram-negative bacteria. This membrane is enriched in polysaccharide and protein, and the outer leaflet of the membrane contains specific lipopolysaccharide structures.
  • GO:0051205 The process that results in the incorporation of a protein into a biological membrane. Incorporation in this context means having some part or covalently attached group that is inserted into the the hydrophobic region of one or both bilayers.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

9 records
Show feature table
Start End DB Term Name
67 177 Gene3D G3DSA:3.30.530.50 -
7 308 Pfam PF06804 NlpB/DapX lipoprotein
7 308 InterPro IPR010653 NlpB/DapX lipoprotein
192 310 Gene3D G3DSA:3.30.310.170 Outer membrane protein assembly factor BamC
192 310 InterPro IPR042268 Outer membrane protein assembly factor BamC, C-terminal
1 310 PIRSF PIRSF026343 NlpB
1 310 InterPro IPR014524 Outer membrane protein assembly factor BamC
2 310 Hamap MF_00924 Outer membrane protein assembly factor BamC [bamC].
2 310 InterPro IPR014524 Outer membrane protein assembly factor BamC

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.

Download VMD script Full viewer

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Drag to rotate — click the view, then scroll to zoom.

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
0.165
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.021
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #10
0.558
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_A0A0H3GWJ5
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_03825
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GWJ5