KpKP13 Protein target profile

Nitrite extrusion protein 1

Accession: KP13_04713

Gene: narK AHE44022.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GZJ1
Length 462
Pocket druggability (P2Rank · AlphaFold DB model) 0.961
Direct ligand evidence 0 52 total records
Functional annotation 0 EC 10 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.

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

Structure confidence

ColabFold pLDDT
92.6 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) 0.961
Structure A0A0H3GZJ1
Pocket Pocket 1
Druggability (FPocket) 0.818
Structure A0A0H3GZJ1
Pocket Pocket 28
ColabFold model
P2Rank 0.958 · Pocket 1
FPocket 0.529 · Pocket 15
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 109 / 4744 genomes with a hit
Prevalence 2.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSQSSLPEKANRSVITDWRPEDPEFWQQRGHRVASRNLWISVPCLLLAFCVWMLFSAVAVNLNKVGFQFTTDQLFMLTALPALSGALLRVPYAFMVPLFGGRRWTAFSTGIMIVPCVWLGFAVQDTSTPFSIFVIISLLCGFAGANFASSMANISFFFPKAKQGGALGVNGGLGNMGVSVMQLVAPLVVSISIFAVFGGNGSEQPDGSMLYLENAAWIWVPFLIIFTLAAWFFMNDLSASKASLSEQLPVLKRLHLWIMALLYLATFGSFIGFSAGFAMLSKTQFPDVQILHYAFFGPFIGALARSMGGAISDRLGGTRVTLVNFVVMAVFCALLFLTLPTNGQGGNFIAFFAVFMVLFLTAGLGSASTFQMISVIFRKLTMDRVKAQGGSEAQAMREAATDTAAALGFISAIGAIGGFFIPKAFGISLDLTGSPAGAMKVFLVFYIACVVITWAVYGRKRQ

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:0015112 Enables the transfer of nitrate ions (NO3-) 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: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: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:0055085 The process in which a solute is transported across a lipid bilayer, 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.

51 records
Show feature table
Start End DB Term Name
93 103 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
459 462 Coils Coil Coil
74 92 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
279 289 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
458 462 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
125 129 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
173 196 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
348 370 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
338 348 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
404 421 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
436 458 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
63 73 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
132 154 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
288 307 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
197 215 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 37 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
349 377 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
216 235 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
38 454 CDD cd17341 MFS_NRT2_like
38 454 InterPro IPR044772 Nitrate transporter
36 418 NCBIfam TIGR00886 NarK family nitrate/nitrite MFS transporter
36 418 InterPro IPR004737 Nitrate transporter NarK/NarU-like
130 152 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
426 436 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
290 308 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
378 403 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
309 319 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
320 337 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
235 253 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
174 196 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
15 461 SUPERFAMILY SSF103473 MFS general substrate transporter
15 461 InterPro IPR036259 MFS transporter superfamily
104 124 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
38 62 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
104 122 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 462 FunFam G3DSA:1.20.1250.20:FF:000024 Nitrite extrusion protein NarK
38 60 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
45 422 Pfam PF07690 Major Facilitator Superfamily
45 422 InterPro IPR011701 Major facilitator superfamily
404 425 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
216 234 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
254 278 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
256 278 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
75 97 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
437 457 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 462 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains
1 462 InterPro IPR036259 MFS transporter superfamily
18 457 PANTHER PTHR23515 HIGH-AFFINITY NITRATE TRANSPORTER 2.3
18 457 InterPro IPR044772 Nitrate transporter
320 338 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
153 172 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.

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
0.961
Likely same site as FPocket 35 5.8 Å 24 shared residues 77% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.329
Likely same site as FPocket 28 1.7 Å 9 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.065
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Surrounding area
Pocket 4 P2Rank #4
0.049
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Surrounding area
Pocket 5 P2Rank #5
0.038
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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 #28
0.818
Likely same site as P2Rank 2 1.7 Å 9 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #31
0.787
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Surrounding area
Pocket 3 FPocket #35
0.689 Unusual size
Likely same site as P2Rank 1 5.8 Å 24 shared residues 77% of smaller site
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Surrounding area
Pocket 4 FPocket #22
0.464
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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_A0A0H3GZJ1
AlphaFold DB full sequence Viewing
ColabFold KP13_04713
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.