KpATCC43816 Protein target profile

lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase

Accession: VK055_0077

Gene: AIK78705.1 msbB 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3H045
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Length 324
Pocket druggability (P2Rank · AlphaFold DB model) 0.716
Metabolic reactions 1
Chokepoint Yes
Functional annotation 1 EC 7 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Metabolic chokepoint Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.72, FPocket 0.86). Use the 3D pocket comparison to verify whether they identify the same site. Central metabolic position More central than 92.3% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. Review the complete evidence below

Risks to review

Microbiome similarity 110 of 4744 screened genomes (2.3%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.72) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant.

Evidence gaps

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
2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
83.901 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.92 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) 0.716
Structure A0A0H3H045
Pocket Pocket 1
Druggability (FPocket) 0.86
Structure A0A0H3H045
Pocket Pocket 9
ColabFold model
P2Rank 0.931 · Pocket 1
FPocket 0.817 · Pocket 25
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 110 / 4744 genomes with a hit
Prevalence 2.3%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Attractive metabolic target: catalyzes a producing & consuming chokepoint reaction in Lipopolysaccharide biosynthesis, no isoenzyme backup detected, more central than 92.3% of genes in this genome, no human homolog detected.

Relative network centrality 92.3% more central than 92.3% of genes in this genome
Chokepoint Chokepoint gene
Pathways
Lipopolysaccharide biosynthesis
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

METKKNNIEFIPKFEKSFLLPRYWGAWLGVFAFAGIALTPPSFRDPLLGKLGRLVGRLAKSSRRRAQINLLYCFPEKSEYEREAIIDAMYASAPQAMVMMAELGLRDPQKILARVDWQGKAIIDEMQRNNEKVIFLVPHAWGVDIPAMLMASGGQKMAAMFHNQGNPVFDYVWNTVRRRFGGRMHARNDGIKPFIQSVRQGYWGYYLPDQDHGAEHSEFVDFFATYKATLPAIGRLMKVCRARVVPLFPVYDGKTHRLTVLVRPPMDDLLDADDTTIARRMNEEVEVFVKPHTEQYTWILKLLKTRKPGEIEPYKRKELFPKKK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
CytoplasmicMembrane

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
  • GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
  • GO:0016747 Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
  • GO:0009276 The peptidoglycan layer of the Gram-negative cell envelope. In Gram-negative cells the peptidoglycan is relatively thin (1-2nm) and is linked to the outer membrane by lipoproteins. In Gram-negative cells the peptidoglycan is too thin to retain the primary stain in the Gram staining procedure and therefore cells appear red after Gram stain.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0036104 The chemical reactions and pathways resulting in the formation of Kdo2-lipid A, a lipopolysaccharide (LPS) component.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
112 304 CDD cd07984 LPLAT_LABLAT-like
112 304 InterPro IPR004960 Bacterial lipid A biosynthesis acyltransferase
24 43 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
6 314 PANTHER PTHR30606 LIPID A BIOSYNTHESIS LAUROYL ACYLTRANSFERASE
6 314 InterPro IPR004960 Bacterial lipid A biosynthesis acyltransferase
4 310 Hamap MF_01944 Lipid A biosynthesis myristoyltransferase [lpxM].
4 310 InterPro IPR011921 Lipid A biosynthesis myristoyltransferase
12 305 Pfam PF03279 Bacterial lipid A biosynthesis acyltransferase
12 305 InterPro IPR004960 Bacterial lipid A biosynthesis acyltransferase
1 23 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
44 324 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
10 314 NCBIfam TIGR02208 lauroyl-Kdo(2)-lipid IV(A) myristoyltransferase
10 314 InterPro IPR011921 Lipid A biosynthesis myristoyltransferase
21 43 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
9 314 PIRSF PIRSF026649 MsbB
9 314 InterPro IPR004960 Bacterial lipid A biosynthesis acyltransferase

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
0.716
Likely same site as FPocket 9 1.5 Å 11 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.695
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Surrounding area
Pocket 3 P2Rank #3
0.086
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Surrounding area
Pocket 4 P2Rank #4
0.083
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Surrounding area
Pocket 5 P2Rank #5
0.025
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #9
0.86
Likely same site as P2Rank 1 1.5 Å 11 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #14
0.201 Unusual size
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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_A0A0H3H045
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0077
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3H045

Pathways

KEGG R05075 BioCyc MYRISTOYLACYLTRAN-RXN