KpATCC43816 Protein target profile

ubiquinone oxidoreductase, Na(+)-translocating, B subunit

Accession: VK055_2326

Gene: AIK80930.1 nqrB 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GSA2
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Length 412
Pocket druggability (P2Rank · AlphaFold DB model) 0.717
Functional annotation 1 EC 7 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.

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.72, FPocket 0.94). Use the 3D pocket comparison to verify whether they identify the same site. 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. Strong predicted binding pocket FPocket selected-pocket score 0.94. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 116 of 4744 screened genomes (2.4%) 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.

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
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
33.579 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
93.71 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) 0.717
Structure A0A0H3GSA2
Pocket Pocket 1
Druggability (FPocket) 0.939
Structure A0A0H3GSA2
Pocket Pocket 2
ColabFold model
P2Rank 0.846 · Pocket 1
FPocket 0.943 · Pocket 27
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 116 / 4744 genomes with a hit
Prevalence 2.4%

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.

MGLKHLIEKLEPHFTHGGKLEKYYPLYEAAATIFYTPGQVTRGAAHVRDAIDLKRMMILVWFAVFPAMFWGMYNVGLQTIPALHKLYGAEQLQQAIANNWHYSVAQWLGVSFSADAGWLSMMTLGAVFFLPIYITVFIVGGFWEVLFAIVRKHEINEGFFVTSILFALIVPPTLPLWQAALGISFGVVIAKEIFGGTGRNFLNPALAGRAFLFFAYPAQISGDLVWTAADGFSGATPLSQWASGGGEALVNVATGVPVSWMDAFLGNIPGSIGEVSTLMIFIGGAIILFGRVASWRIVAGVMIGMIATATLFNVIGSDTNPMFAMPWYWHLVLGGFAFGMMFMATDPVSASFTDKGKWSYGVLIGVMCVLIRVVNPAYPEGMMLAILFANLFAPLFDYLVVQANIKRRKSRG

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:0016655 Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
  • GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
  • GO:0022904 A process in which a series of electron carriers operate together to transfer electrons from donors such as NADH and FADH2 to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
  • 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:0006814 The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
74 117 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
118 146 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
125 147 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
381 401 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
297 315 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
268 290 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
35 411 PANTHER PTHR30578 ELECTRON TRANSPORT COMPLEX PROTEIN RNFD
35 411 InterPro IPR004338 Ion-translocating oxidoreductase NqrB/RnfD
291 296 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
147 157 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 412 PIRSF PIRSF016055 NqrB
1 412 InterPro IPR010966 Na(+)-translocating NADH-quinone reductase subunit B
326 345 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
58 80 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
56 73 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
2 412 Hamap MF_00426 Na(+)-translocating NADH-quinone reductase subunit B [nqrB].
2 412 InterPro IPR010966 Na(+)-translocating NADH-quinone reductase subunit B
376 380 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
159 181 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
297 316 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
178 267 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
346 356 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
402 412 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
379 401 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
357 375 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
268 290 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
316 326 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 55 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
3 408 NCBIfam TIGR01937 NADH:ubiquinone reductase (Na(+)-transporting) subunit B
3 408 InterPro IPR010966 Na(+)-translocating NADH-quinone reductase subunit B
42 405 Pfam PF03116 NQR2, RnfD, RnfE family
42 405 InterPro IPR004338 Ion-translocating oxidoreductase NqrB/RnfD
158 177 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
327 345 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
358 375 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
0.717
Likely same site as FPocket 2 0.8 Å 21 shared residues 95% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.53
Likely same site as FPocket 1 2.0 Å 18 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.27
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Surrounding area
Pocket 4 P2Rank #4
0.088
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Surrounding area
Pocket 5 P2Rank #5
0.087
Likely same site as FPocket 4 3.2 Å 9 shared residues 82% of smaller site
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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 #2
0.939
Likely same site as P2Rank 1 0.8 Å 21 shared residues 95% of smaller site
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Surrounding area
Pocket 2 FPocket #1
0.539
Likely same site as P2Rank 2 2.0 Å 18 shared residues 100% of smaller site
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Surrounding area
Pocket 3 FPocket #4
0.451
Likely same site as P2Rank 5 3.2 Å 9 shared residues 82% 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_A0A0H3GSA2
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2326
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GSA2