Protein target profile

KP13_05556

LysM domain/BON superfamily protein

Genome: KpKP13 Gene: AHE44562.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSY1
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Length 149
Pocket druggability 0.055
Functional annotation 0 EC 1 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. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 73 of 4744 screened genomes (1.5%) have a significant similarity hit. Mixed conservation Core/accessory calls are not fully concordant. Weak predicted binding pocket FPocket selected-pocket score 0.06. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.04.

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
1.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
64.865 Higher values support similarity to known essential genes.
DEG E-value
8.63e-64 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Unknown

Structure confidence

ColabFold pLDDT
91.17 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 0.055
Structure A0A0H3GSY1
Pocket Pocket 2
P2Rank 0.04
Structure A0A0H3GSY1
Pocket Pocket 1
ColabFold model
FPocket 0.155 · Pocket 2
P2Rank 0.066 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 73 / 4744 genomes with a hit
Prevalence 1.5%

Cross-references

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

Sequence

UniProt A0A0H3GSY1

Sequence

Primary amino-acid sequence viewer.

MGLLNFVKEAGEKIWDAVSGDSKEDRAEKLKKHIDGLNLPGAEKVNIDVAEDGTATVTGDVASQEDKEKILVAVGNVTGVGQVSDGVKVTQSGAESRFYTVKSGDTLSAISKAMYGSANEYQRIFEANKPMLTHPDKIYPGQVLIIPAK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
98 147 SMART SM00257 LysM_2
98 147 InterPro IPR018392 LysM domain
24 90 Pfam PF04972 BON domain
24 90 InterPro IPR007055 BON domain
97 146 ProSiteProfiles PS51782 LysM domain profile.
97 146 InterPro IPR018392 LysM domain
96 149 FunFam G3DSA:3.10.350.10:FF:000001 Peptidoglycan-binding protein LysM
97 147 SUPERFAMILY SSF54106 LysM domain
97 147 InterPro IPR036779 LysM domain superfamily
97 146 CDD cd00118 LysM
22 91 ProSiteProfiles PS50914 BON domain profile.
22 91 InterPro IPR007055 BON domain
94 149 Gene3D G3DSA:3.10.350.10 LysM domain
94 149 InterPro IPR036779 LysM domain superfamily
99 147 Pfam PF01476 LysM domain
99 147 InterPro IPR018392 LysM domain

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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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

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.04
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_A0A0H3GSY1
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_05556
ColabFold — — full sequence — Loaded