KpATCC43816 Protein target profile

cobyric acid synthase CobQ

Accession: VK055_4342

Gene: cobQ AIK82887.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GXK7
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Length 507
Pocket druggability (P2Rank · AlphaFold DB model) 0.868
Metabolic reactions 1
Chokepoint Yes
Functional annotation 0 EC 3 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.

Main supporting evidence

Metabolic chokepoint Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Central metabolic position More central than 91.3% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Review the complete evidence below

Risks to review

Microbiome similarity 219 of 4744 screened genomes (4.6%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.87) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.79, 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
4.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
43.687 Higher values support similarity to known essential genes.
DEG E-value
1.4699999999999998e-128 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
92.47 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) 0.868
Structure A0A0H3GXK7
Pocket Pocket 1
Druggability (FPocket) 0.788
Structure A0A0H3GXK7
Pocket Pocket 2
ColabFold model
P2Rank 0.905 · Pocket 1
FPocket 0.53 · Pocket 39
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 219 / 4744 genomes with a hit
Prevalence 4.6%

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing & consuming chokepoint reaction in Porphyrin metabolism, no isoenzyme backup detected, more central than 91.3% of genes in this genome, no human homolog detected.

Relative network centrality 91.3% more central than 91.3% of genes in this genome
Chokepoint Chokepoint gene
Pathways
Porphyrin metabolism
Catalyzed reaction

1 reaction 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.

MTLAVMLQGTASDVGKSVLVAGLCRIFHQDGLRTAPFKSQNMALNSGITPDGKEMGRAQIFQAEAAGIAPDVRMNPILLKPTSDRQAQVVLMGQVATSMDAVSYHQYKPRLREQILAVYQSLAGEYEALVLEGAGSPAEINLRDRDIVNMGMAEMAQCPVILVADIDRGGVFAAIYGTLALLQPQERARVKGVIINKFRGDVALLRSGIEQIEALTGVPVLGVMPWLDVDLEDEDGVALQAGKYHRTDRRDIDIAVVHLPHIANFTDFNALAAQPDVRVRYVRDPQALADADLVILPGSKNTLGDLCWLRESGMAHAVEQARQRKVPLLGICGGYQMLGETIIDEVESGLGAQPGLGVLKTVTHFAQHKTTTQVQATLGSALPDWLADAAGLRVSGYEIHMGETRREAGCPPLLQLHKAGQAVDDGAISDDGLAFGTYLHGLFDSDAFTRALLNGLRQRKGLAPLDSALEYARYKTRQFDRLAEAMREHIAIDKIYAIMRQHQEPLC

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

3
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0009236 The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
  • GO:0015420 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: vitamin B12(out) + ATP + H2O = ADP + an vitamin B12(in) + H+ + phosphate. Vitamin B12 is alkylcob(III)alamin.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
251 396 Gene3D G3DSA:3.40.50.880 -
251 396 InterPro IPR029062 Class I glutamine amidotransferase-like
4 225 CDD cd05389 CobQ_N
4 225 InterPro IPR047045 Cobyric acid synthase, N-terminal domain
1 502 Hamap MF_00028 Cobyric acid synthase [cobQ].
1 502 InterPro IPR004459 Cobyric acid synthase CobQ
1 500 PANTHER PTHR21343 DETHIOBIOTIN SYNTHETASE
253 447 Pfam PF07685 CobB/CobQ-like glutamine amidotransferase domain
253 447 InterPro IPR011698 CobB/CobQ-like glutamine amidotransferase
254 453 CDD cd01750 GATase1_CobQ
254 453 InterPro IPR033949 Cobyric acid synthase, glutamine amidotransferase type 1
254 456 SUPERFAMILY SSF52317 Class I glutamine amidotransferase-like
254 456 InterPro IPR029062 Class I glutamine amidotransferase-like
253 462 ProSiteProfiles PS51273 Glutamine amidotransferase type 1 domain profile.
1 234 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
1 234 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
5 228 Pfam PF13500 AAA domain
4 237 Gene3D G3DSA:3.40.50.300 -
4 237 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
251 448 ProSiteProfiles PS51274 CobBQ-type GATase domain profile.
5 493 NCBIfam TIGR00313 cobyric acid synthase CobQ
5 493 InterPro IPR004459 Cobyric acid synthase CobQ

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
0.868
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Surrounding area
Pocket 2 P2Rank #2
0.449
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Surrounding area
Pocket 3 P2Rank #3
0.167
Likely same site as FPocket 37 3.3 Å 12 shared residues 71% of smaller site
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Surrounding area
Pocket 4 P2Rank #4
0.124
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Surrounding area
Pocket 5 P2Rank #5
0.066
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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
0.788 Unusual size
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Surrounding area
Pocket 2 FPocket #37
0.349
Likely same site as P2Rank 3 3.3 Å 12 shared residues 71% of smaller site
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Surrounding area
Pocket 3 FPocket #1
0.293
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Surrounding area
Residue sets
UniProt: Active site:332-332 Nucleophile
UniProt: Active site:440-440
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_A0A0H3GXK7
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4342
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GXK7

Pathways

KEGG R05225 BioCyc R345-RXN