Protein target profile

VK055_2566

transaldolase

Genome: KpATCC43816 Gene: AIK81163.1 tal3 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GMB4
Length 317
Pocket druggability 0.128
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 61 total records
Functional annotation 1 EC 5 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.

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
Hit
Human identity (%)
60.377 Lower values reduce human off-target concern.
Human E-value
2.48e-134
Gut microbiome similarity
4.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
71.565 Higher values support similarity to known essential genes.
DEG E-value
9.51e-166 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Unknown

Structure confidence

ColabFold pLDDT
98.25 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 0.128
Structure A0A0H3GMB4
Pocket Pocket 14
P2Rank 0.612
Structure A0A0H3GMB4
Pocket Pocket 1
ColabFold model
FPocket 0.631 · Pocket 9
P2Rank 0.541 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 199 / 4744 genomes with a hit
Prevalence 4.2%

Cross-references

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

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 98.4% of genes in this genome.

Relative network centrality 98.4% more central than 98.4% 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.

MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILGAAQIPEYRKLIDDAVAWARSQSSDRAQQILDASDKLAVNIGLEILKLIPGRISTEVDARLSYDTEASIAKAKRIIKLYNDAGISNDRILIKLASTWQGIRAAEQLEKEGINCNLTLLFSFAQARACAEAGVFLISPFVGRILDWYKANTDKKEYAPAEDPGVVSVSEIYEYYKQHGYETVVMGASFRNVGEILELAGCDRLTIAPALLKELSESEGAVERKLVYTGEVKARPERITESEFLWQHNQDPMAVDKLAEGIRKFAIDQEKLEKMIDELL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0004801 Catalysis of the reaction: sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate = D-erythrose 4-phosphate + D-fructose 6-phosphate.
  • GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0006098 The metabolic process in which glucose-6-phosphate is oxidized to form carbon dioxide (CO2) and ribulose 5-phosphate, coupled to reduction of NADP+ to NADPH; ribulose 5-P then enters a series of reactions that can yield biosynthetic precursors (ribose-5-phosphate and erythrose-4-phosphate) and glycolytic intermediates (fructose-6-phosphate and glyceraldehyde-3-phosphate).
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
129 146 ProSitePatterns PS00958 Transaldolase active site.
129 146 InterPro IPR018225 Transaldolase, active site
1 316 SUPERFAMILY SSF51569 Aldolase
3 315 PANTHER PTHR10683 TRANSALDOLASE
3 315 InterPro IPR001585 Transaldolase/Fructose-6-phosphate aldolase
2 317 Gene3D G3DSA:3.20.20.70 Aldolase class I
2 317 InterPro IPR013785 Aldolase-type TIM barrel
2 317 Hamap MF_00492 Transaldolase [tal].
2 317 InterPro IPR004730 Transaldolase type 1
31 39 ProSitePatterns PS01054 Transaldolase signature 1.
31 39 InterPro IPR018225 Transaldolase, active site
4 313 CDD cd00957 Transaldolase_TalAB
4 313 InterPro IPR004730 Transaldolase type 1
1 317 FunFam G3DSA:3.20.20.70:FF:000002 Transaldolase
14 313 Pfam PF00923 Transaldolase/Fructose-6-phosphate aldolase
14 313 InterPro IPR001585 Transaldolase/Fructose-6-phosphate aldolase
4 316 NCBIfam TIGR00874 transaldolase
4 316 InterPro IPR004730 Transaldolase type 1

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

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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

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

Site 1 P2Rank #1
0.612
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.156
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.086
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.002
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Surrounding area
Residue sets
UniProt: Active site:132-132 Schiff-base intermediate with substrate
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_A0A0H3GMB4
AlphaFold DB full sequence Viewing
ColabFold VK055_2566
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.

61 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 11 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
44S PDB via homolog 244.1 Da · LogP -2.08 · TPSA 136.7 Open detail RCSB PDB
4Y8 PDB via homolog Detail RCSB PDB
A5P PDB via homolog Detail RCSB PDB
E4P PDB via homolog Detail RCSB PDB
F6R PDB via homolog Detail RCSB PDB

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
44S RCSB PDB P0A870 244.1 Da LogP -2.08 TPSA 136.7 ✓ Ro5 ✓ Clean C1[C@H]([C@@H](O[C@H]1O)[C@@H](COP(=O)(O)O)O)O
4Y8 RCSB PDB P78055 74.1 Da LogP -0.43 TPSA 37.3 ✓ Ro5 ✓ Clean CC(=O)CO
A5P RCSB PDB Q5NFX0 232.1 Da LogP -2.83 TPSA 147.7 1 viol. ✓ Clean C([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)O
E4P RCSB PDB Q9HKI3 200.1 Da LogP -1.98 TPSA 124.3 ✓ Ro5 ✓ Clean C([C@H]([C@H](C=O)O)O)OP(=O)(O)O
F6R RCSB PDB P0A870 260.1 Da LogP -3.26 TPSA 164.8 1 viol. ✓ Clean C([C@H]([C@H]([C@@H](C(=O)CO)O)O)O)OP(=O)(O)O
FLC RCSB PDB Q9HKI3 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
G3P RCSB PDB Q9HKI3 172.1 Da LogP -1.55 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@H](COP(=O)(O)O)O)O
I22 RCSB PDB Q5NFX0 290.2 Da LogP -3.90 TPSA 185.0 1 viol. ✓ Clean C([C@H]([C@H]([C@H]([C@@H](C(=O)CO)O)O)O)O)OP(=…
LW1 RCSB PDB P78055 112.2 Da LogP 1.56 TPSA 17.1 ✓ Ro5 ✓ Clean c1cc(sc1)C=O
LW2 RCSB PDB P78055 186.2 Da LogP 0.73 TPSA 57.5 ✓ Ro5 ✓ Clean CC(=O)[C@H]([C@@H](c1cccs1)O)O
P2D RCSB PDB P78055 100.1 Da LogP 0.55 TPSA 34.1 ✓ Ro5 ✓ Clean CC(=O)CC(=O)C

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.