KpATCC43816 Protein target profile

narK MFS nitrate/nitrite antiporter

Accession: VK055_0604

Gene: AIK79227.1 narK2 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GTE2
Length 460
Pocket druggability (P2Rank · AlphaFold DB model) 0.968
Direct ligand evidence 0 52 total records
Functional annotation 0 EC 10 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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

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

Structure confidence

ColabFold pLDDT
93.21 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) 0.968
Structure A0A0H3GTE2
Pocket Pocket 1
Druggability (FPocket) 0.794
Structure A0A0H3GTE2
Pocket Pocket 31
ColabFold model
P2Rank 0.95 · Pocket 1
FPocket 0.867 · Pocket 19
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 108 / 4744 genomes with a hit
Prevalence 2.3%

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.

MSVQNDKDNHYLLNNWRPENKAFWENKGQAIARRNLWISVACLLLAFCVWMLFSAVAVNLNKVGFHFTTDQLFLLTALPSLSGAILRVPYSFMVPLFGGRYWTVLSTVILIVPCIWLGVAIQNITTPFWVFIIIALLCGFAGANFASSMGNISFFFPKAKQGSALGVNGGLGNLGVSVMQMVAPAVIFLPLFTFLGVHGVTQPDGSTITLSNAALVWVPLLLLATVAAWFGMNDIAGSKASIRDQLPVLKRPHMWLLSLLYLATFGSFIGFSAGFAMLAKTQFPAVDILKLAFFGPFIGALARSFGGIISDRLGGVRVTLVNFVLMALFTGLLFLTLPGSGSGSFLAFYVVFIGLFLTAGLGSGSTFQMIAVIFRQLTIDSVKQRGGSDEEAQHEAVTDTAAALGFISAIGAIGGFFIPKAFGTSLAMTGSPVGAMKVFFVFYVVCVLVTWLVYGRRKSA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

10 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

10
  • GO:0015707 The directed movement of nitrite into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0015113 Enables the transfer of nitrite (NO2-) ions from one side of a membrane to the other.
  • GO:0015706 The directed movement of nitrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0015112 Enables the transfer of nitrate ions (NO3-) from one side of a membrane to the other.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0022857 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
  • 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:0015291 Enables the transfer of a solute from one side of a membrane to the other, up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by a chemiosmotic source of energy, not direct ATP coupling. Secondary active transporters include symporters and antiporters.
  • GO:0042128 The nitrogen metabolic process that encompasses the uptake of nitrate from the environment and reduction to ammonia, and results in the incorporation of nitrogen derived from nitrate into cellular substances.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

48 records
Show feature table
Start End DB Term Name
128 150 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
36 452 CDD cd17341 MFS_NRT2_like
36 452 InterPro IPR044772 Nitrate transporter
11 454 PANTHER PTHR23515 HIGH-AFFINITY NITRATE TRANSPORTER 2.3
11 454 InterPro IPR044772 Nitrate transporter
43 419 Pfam PF07690 Major Facilitator Superfamily
43 419 InterPro IPR011701 Major facilitator superfamily
396 418 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
233 252 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
214 232 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
288 306 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
307 317 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
178 200 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
171 194 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
36 60 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
346 375 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
277 287 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
72 90 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
195 213 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
318 340 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
313 335 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 460 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains
1 460 InterPro IPR036259 MFS transporter superfamily
345 367 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
341 345 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
36 58 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
419 437 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
128 150 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
253 276 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
91 101 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
34 415 NCBIfam TIGR00886 NarK family nitrate/nitrite MFS transporter
34 415 InterPro IPR004737 Nitrate transporter NarK/NarU-like
376 395 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
102 122 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
123 127 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
61 71 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
438 454 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
14 458 SUPERFAMILY SSF103473 MFS general substrate transporter
14 458 InterPro IPR036259 MFS transporter superfamily
1 35 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
455 460 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
99 121 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
213 232 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 460 FunFam G3DSA:1.20.1250.20:FF:000024 Nitrite extrusion protein NarK
401 418 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
151 170 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
254 276 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
433 455 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.

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
0.968
Likely same site as FPocket 1 5.9 Å 20 shared residues 87% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.33
Likely same site as FPocket 14 0.4 Å 8 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.101
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Surrounding area
Pocket 4 P2Rank #4
0.015
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Surrounding area
Pocket 5 P2Rank #5
0.011
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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 #31
0.794 Unusual size
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Surrounding area
Pocket 2 FPocket #14
0.726
Likely same site as P2Rank 2 0.4 Å 8 shared residues 100% of smaller site
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Surrounding area
Pocket 3 FPocket #1
0.299 Unusual size
Likely same site as P2Rank 1 5.9 Å 20 shared residues 87% of smaller site
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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_A0A0H3GTE2
AlphaFold DB full sequence Viewing
ColabFold VK055_0604
ColabFold full sequence Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
OLA PDB via homolog 282.5 Da · LogP 6.11 · TPSA 37.3 Open detail RCSB PDB
OLC PDB via homolog Detail RCSB PDB
ZINC1501016272 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1501016273 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1501016315 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
OLA RCSB PDB P10903 282.5 Da LogP 6.11 TPSA 37.3 1 viol. ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)O
OLC RCSB PDB P10903 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)O

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.

Cross-references

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