Protein target profile

VK055_0392

gluconate 2-dehydrogenase cytochrome c subunit

Genome: KpATCC43816 Gene: AIK79018.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GZ84
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Length 443
Pocket druggability 0.97
Metabolic reactions 2
Chokepoint No
Functional annotation 0 EC 6 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

Central metabolic position More central than 98.2% of genes in this genome. 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. Second pocket predictor agrees P2Rank predicted binding-site probability 1.00. Review the complete evidence below

Risks to review

Microbiome similarity 45 of 4744 screened genomes (0.9%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.97) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.97, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

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
0.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
88.82 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 0.97
Structure A0A0H3GZ84
Pocket Pocket 23
P2Rank 0.998
Structure A0A0H3GZ84
Pocket Pocket 1
ColabFold model
FPocket 0.554 · Pocket 25
P2Rank 0.998 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 45 / 4744 genomes with a hit
Prevalence 0.9%

Cross-references

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

Sequence

UniProt A0A0H3GZ84

Pathways

KEGG R01741 BioCyc RXN-14204 KEGG R01742 BioCyc GLUCONATE-2-DEHYDROGENASE-RXN

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 98.2% of genes in this genome, no human homolog detected.

Relative network centrality 98.2% more central than 98.2% of genes in this genome
Chokepoint Not a chokepoint
Pathways
Pentose phosphate pathway
Catalyzed reactions

2 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MQWLSALVLGALSCAAFAEEAPADSNLIKQGEYLARAGDCVACHTNGKAGKPFAGGLPMETPIGTIYSTNITPDKEHGIGGYTFEEFDDAVRKGVRKDGSTLYPAMPYPSFARISEADMRAMYAYFMHGVEPVNVANKDTDIPWPLSMRWPLAFWRGIFAPTPSDFVANPQVDPVLERGRYLVEGLGHCGACHTPRSLTMQEKALSESEGDDYLAGSNAPIDGWVASSLRGENRDGLGTWSEAELAEFLKTGRNDKSVVFGGMSDVVEHSLQYLSDDDITAIARYLKSLPPRGGKQTPAPVEDSVAKDLWKGNDSKTGAALYVDNCAACHRTDGAGYKRAFPSLKGNPVVQTEDATSLIHIVLTGSTTPAVKDAVSNLTMPSFGWRLDDQQVADVVNFIRTSWGNNAPAVSASDVAKVRKETAAHDEKALGNADISKLPGAGQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0016614 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
  • GO:0005506 Binding to an iron (Fe) ion.
  • GO:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring.
  • GO:0009055 A molecular function representing the directed movement of electrons from one molecular entity to another, typically mediated by electron carriers or acceptors, resulting in the transfer of energy and/or the reduction-oxidation (redox) transformation of chemical species. This activity is fundamental to various biological processes, including cellular respiration and photosynthesis, as well as numerous enzymatic reactions involved in metabolic pathways.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

36 records
Show feature table
Start End DB Term Name
313 403 ProSiteProfiles PS51007 Cytochrome c family profile.
313 403 InterPro IPR009056 Cytochrome c-like domain
1 18 Phobius SIGNAL_PEPTIDE Signal peptide region
174 290 ProSiteProfiles PS51007 Cytochrome c family profile.
174 290 InterPro IPR009056 Cytochrome c-like domain
2 133 Gene3D G3DSA:1.10.760.10 -
2 133 InterPro IPR036909 Cytochrome c-like domain superfamily
152 299 Gene3D G3DSA:1.10.760.10 -
152 299 InterPro IPR036909 Cytochrome c-like domain superfamily
26 130 ProSiteProfiles PS51007 Cytochrome c family profile.
26 130 InterPro IPR009056 Cytochrome c-like domain
7 422 PANTHER PTHR35008 BLL4482 PROTEIN-RELATED
18 153 SUPERFAMILY SSF46626 Cytochrome c
18 153 InterPro IPR036909 Cytochrome c-like domain superfamily
300 429 Gene3D G3DSA:1.10.760.10 -
300 429 InterPro IPR036909 Cytochrome c-like domain superfamily
15 18 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
3 14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
28 125 Pfam PF13442 Cytochrome C oxidase, cbb3-type, subunit III
28 125 InterPro IPR009056 Cytochrome c-like domain
315 399 Pfam PF13442 Cytochrome C oxidase, cbb3-type, subunit III
315 399 InterPro IPR009056 Cytochrome c-like domain
177 295 SUPERFAMILY SSF46626 Cytochrome c
177 295 InterPro IPR036909 Cytochrome c-like domain superfamily
1 18 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
1 23 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
377 399 PRINTS PR00605 Class IC cytochrome C signature
377 399 InterPro IPR008168 Cytochrome c, class IC
324 335 PRINTS PR00605 Class IC cytochrome C signature
324 335 InterPro IPR008168 Cytochrome c, class IC
1 2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
317 423 SUPERFAMILY SSF46626 Cytochrome c
317 423 InterPro IPR036909 Cytochrome c-like domain superfamily
1 436 PIRSF PIRSF000018 Mb_ADH_cytochrome_c
1 436 InterPro IPR014353 Membrane-bound alcohol dehydrogenase, cytochrome c subunit
19 443 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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 · FPocket

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

Site 1 FPocket #23
0.97
Unusual size
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Surrounding area
Site 2 FPocket #12
0.934
Likely same site as P2Rank 2 0.8 Å 24 shared residues 96% of smaller site
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Surrounding area
Site 3 FPocket #9
0.844
Unusual size
Show in viewer
Surrounding area
Site 4 FPocket #27
0.294
Likely same site as P2Rank 5 7.7 Å 10 shared residues 77% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.998
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Surrounding area
Site 2 P2Rank #2
0.93
Likely same site as FPocket 12 0.8 Å 24 shared residues 96% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.358
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Surrounding area
Site 4 P2Rank #4
0.116
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Surrounding area
Site 5 P2Rank #5
0.094
Likely same site as FPocket 27 7.7 Å 10 shared residues 77% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:192-192 covalent
UniProt: Binding site:195-195 covalent
UniProt: Binding site:196-196 axial binding residue
UniProt: Binding site:329-329 covalent
UniProt: Binding site:332-332 covalent
UniProt: Binding site:333-333 axial binding residue
UniProt: Binding site:43-43 covalent
UniProt: Binding site:46-46 covalent
UniProt: Binding site:47-47 axial binding residue
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_A0A0H3GZ84
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0392
ColabFold — — full sequence — Loaded