KpATCC43816 Protein target profile

[citrate (pro-3S)-lyase] ligase

Accession: VK055_2541

Gene: AIK81138.1 citC 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GN23
Export view
Length 342
Pocket druggability (P2Rank · AlphaFold DB model) 0.948
Metabolic reactions 1
Chokepoint No
Functional annotation 1 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 90.2% 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. Second pocket predictor agrees P2Rank predicted binding-site probability 0.95. Review the complete evidence below

Risks to review

Microbiome similarity 78 of 4744 screened genomes (1.6%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.95) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant. Weak predicted binding pocket FPocket selected-pocket score 0.21.

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
1.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
50.294 Higher values support similarity to known essential genes.
DEG E-value
1.47e-118 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
92.71 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) 0.948
Structure A0A0H3GN23
Pocket Pocket 1
Druggability (FPocket) 0.209
Structure A0A0H3GN23
Pocket Pocket 23
ColabFold model
P2Rank 0.943 · Pocket 1
FPocket 0.797 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 78 / 4744 genomes with a hit
Prevalence 1.6%

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 90.2% of genes in this genome, no human homolog detected.

Relative network centrality 90.2% more central than 90.2% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

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.

MTLILKRVQLLKDKPRREAIDRFLRQHQLSLEADCEMAIIAEYQQRLVGCGAIAGNVLKCIAIDPSLQGEGLSLKLLTELLTLAYELGRSELFLFTKPCNAALFSGAGFWPIAQAGDRAVLMENSRERLTRYCRQLAMYRQPGRKIGAIVMNANPFTLGHRWLVEQAASQCDWLHLFVVKEDASCFSYHDRFKLIEQGITGIDKVTLHPGSAYLISRATFPGYFLKEQGVVDDCHSQIDLQLFRERLAPALQITHRFVGTEPLCPLTRNYNQRMKSLLEAPGDAPPIEVVELARIEKNGGPVSASRVRELYRQRNWQAVAALVPPGTLSFLMQLAESEHQTA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0016747 Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.
  • 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:0008771 Catalysis of the reaction: ATP + acetate + (citrate (pro-3S)-lyase) (thiol form) = AMP + diphosphate + (citrate (pro-3S)-lyase) (acetyl form).
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
142 342 FunFam G3DSA:3.40.50.620:FF:000071 [Citrate [pro-3S]-lyase] ligase
8 118 Gene3D G3DSA:3.40.630.30 -
145 333 SUPERFAMILY SSF52374 Nucleotidylyl transferase
146 331 SMART SM00764 citrate_ly_lig5
146 331 InterPro IPR013166 Citrate lyase ligase, C-terminal
15 116 SUPERFAMILY SSF55729 Acyl-CoA N-acyltransferases (Nat)
15 116 InterPro IPR016181 Acyl-CoA N-acyltransferase
28 331 CDD cd02169 Citrate_lyase_ligase
28 331 InterPro IPR005216 Citrate lyase ligase
21 103 Pfam PF00583 Acetyltransferase (GNAT) family
21 103 InterPro IPR000182 GNAT domain
1 342 PIRSF PIRSF005751 Acet_citr_lig
1 342 InterPro IPR005216 Citrate lyase ligase
3 339 PANTHER PTHR40599 [CITRATE [PRO-3S]-LYASE] LIGASE
3 339 InterPro IPR005216 Citrate lyase ligase
146 203 NCBIfam TIGR00125 cytidyltransferase-like domain
146 203 InterPro IPR004821 Cytidyltransferase-like domain
5 340 NCBIfam TIGR00124 [citrate (pro-3S)-lyase] ligase
5 340 InterPro IPR005216 Citrate lyase ligase
142 342 Gene3D G3DSA:3.40.50.620 HUPs
142 342 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
146 331 Pfam PF08218 Citrate lyase ligase C-terminal domain
1 127 ProSiteProfiles PS51186 Gcn5-related N-acetyltransferase (GNAT) domain profile.
1 127 InterPro IPR000182 GNAT domain

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.948
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.563
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.021
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.021
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.0
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #23
0.209
Show in viewer
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_A0A0H3GN23
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2541
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GN23

Pathways

KEGG R04449 BioCyc CITC-RXN