Genome KpATCC43816

Protein target profile

PTS IIA-like nitrogen-regulatory protein PtsN

Accession: VK055_3863

Gene: ptsN AIK82413.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GZ03

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Length 161

Pocket druggability (P2Rank) 0.041

Functional annotation 0 EC 5 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

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: 2.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 91.925 Higher values support similarity to known essential genes.
DEG E-value: 2.3600000000000002e-107 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 91.38 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) 0.041

Structure A0A0H3GZ03

Pocket Pocket 1

Druggability (FPocket) 0.976

Structure A0A0H3GZ03

Pocket Pocket 1

ColabFold model

P2Rank 0.089 · Pocket 1

FPocket 0.98 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 127 / 4744 genomes with a hit

Prevalence 2.7%

Cross-references

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

Sequence

UniProt A0A0H3GZ03

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MNNDSALQLSNVLNQECTRSQVHCQSKKRALEIISELAAKQLSLPPQVVFEAILTREKMGSTGIGNGIAIPHGKLEEDTLRAVGVFVQLETPIAFDAIDNQPVDLLFALLVPADQTKTHLHTLSLVAKRLADKAICRRLRAAQSDEELYEIITEAGSSDDA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0009401 The uptake and phosphorylation of specific carbohydrates from the extracellular environment; uptake and phosphorylation are coupled, making the PTS a link between the uptake and metabolism of sugars; phosphoenolpyruvate is the original phosphate donor; phosphoenolpyruvate passes the phosphate via a signal transduction pathway, to enzyme 1 (E1), which in turn passes it on to the histidine protein, HPr; the next step in the system involves sugar-specific membrane-bound complex, enzyme 2 (EII), which transports the sugar into the cell; it includes the sugar permease, which catalyzes the transport reactions; EII is usually divided into three different domains, EIIA, EIIB, and EIIC.
GO:0008982 Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + sugar(out) = protein histidine + sugar phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
GO:0030295 Binds to and increases the activity of a protein kinase, an enzyme which phosphorylates a protein.

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	161	FunFam	G3DSA:3.40.930.10:FF:000003	PTS IIA-like nitrogen regulatory protein PtsN
11	155	ProSiteProfiles	PS51094	PTS_EIIA type-2 domain profile.
11	155	InterPro	IPR002178	PTS EIIA type-2 domain
13	152	CDD	cd00211	PTS_IIA_fru
13	152	InterPro	IPR002178	PTS EIIA type-2 domain
12	154	Pfam	PF00359	Phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 2
12	154	InterPro	IPR002178	PTS EIIA type-2 domain
8	154	NCBIfam	TIGR01419	PTS IIA-like nitrogen regulatory protein PtsN
8	154	InterPro	IPR006320	Phosphotransferase system, IIA-like nitrogen-regulatory protein PtsN
8	156	PANTHER	PTHR47738	PTS SYSTEM FRUCTOSE-LIKE EIIA COMPONENT-RELATED
8	154	SUPERFAMILY	SSF55804	Phoshotransferase/anion transport protein
8	154	InterPro	IPR016152	Phosphotransferase/anion transporter
57	73	ProSitePatterns	PS00372	PTS EIIA domains phosphorylation site signature 2.
57	73	InterPro	IPR002178	PTS EIIA type-2 domain
1	160	Gene3D	G3DSA:3.40.930.10	-
1	160	InterPro	IPR016152	Phosphotransferase/anion transporter

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

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

Pocket 1 P2Rank #1

0.041

Likely same site as FPocket 1 6.3 Å 7 shared residues 100% of smaller site

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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1

0.976 Unusual size

Likely same site as P2Rank 1 6.3 Å 7 shared residues 100% of smaller site

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_A0A0H3GZ03	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_3863	ColabFold	—	—	full sequence	—	Loaded