Protein target profile

VK055_4805

tRNA pseudouridine(38-40) synthase

Genome: KpATCC43816 Gene: truA AIK83332.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GR85
Export view
Length 270
Pocket druggability 0.919
Metabolic reactions 1
Chokepoint No
Functional annotation 1 EC 6 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.92. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Low human similarity A human hit was flagged, but identity is only 28.333% - a weak match, lower risk than a close homolog. This target also has a predicted binding pocket (FPocket 0.92) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 209 of 4744 screened genomes (4.4%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.92) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.29.

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
Hit
Human identity (%)
28.333 Lower values reduce human off-target concern.
Human E-value
2.55e-06
Gut microbiome similarity
4.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
68.846 Higher values support similarity to known essential genes.
DEG E-value
1.27e-136 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.97 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 0.919
Structure A0A0H3GR85
Pocket Pocket 17
P2Rank 0.288
Structure A0A0H3GR85
Pocket Pocket 1
ColabFold model
FPocket 0.555 · Pocket 11
P2Rank 0.348 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 209 / 4744 genomes with a hit
Prevalence 4.4%

Cross-references

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

Sequence

UniProt A0A0H3GR85

Pathways

KEGG R03020 BioCyc TRNA-PSEUDOURIDINE-SYNTHASE-I-RXN

Metabolic context

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

Explore metabolic network
Relative network centrality 0.0% more central than 0.0% 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.

MSEMEQQPICKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETRAQRKDAAWTLGVNANLPGDIAVRWVKHVPADFHARFSATARRYRYVIYNHRLRPAVLSHGVTHFHQPLDAERMQRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRYGAYVVVDIKANAFVHHMVRNIVGSLMEVGAGNQPESWMAELLAAKDRTLAAATAKAEGLYLVSVDYPAHYDLPVLPMGPLFLAD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0009451 The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
  • GO:0001522 The intramolecular conversion of uridine to pseudouridine within an RNA molecule.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0009982 Catalysis of the reaction: a uridine in RNA = a pseudouridine in RNA. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5.
  • GO:0160147 Catalysis of the reaction: uridine(38/39/40) in tRNA = pseudouridine(38/39/40) in tRNA. Modifies uridine(38), uridine(39) and/or uridine(40) in tRNA.
  • GO:0031119 The intramolecular conversion of uridine to pseudouridine in a tRNA molecule.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
8 113 Gene3D G3DSA:3.30.70.580 -
8 113 InterPro IPR020094 Pseudouridine synthase TruA/RsuA/RluB/E/F, N-terminal
9 113 FunFam G3DSA:3.30.70.580:FF:000001 tRNA pseudouridine synthase A
114 251 FunFam G3DSA:3.30.70.660:FF:000001 tRNA pseudouridine synthase A
151 253 Pfam PF01416 tRNA pseudouridine synthase
151 253 InterPro IPR020097 Pseudouridine synthase I, TruA, alpha/beta domain
17 111 Pfam PF01416 tRNA pseudouridine synthase
17 111 InterPro IPR020097 Pseudouridine synthase I, TruA, alpha/beta domain
10 252 PANTHER PTHR11142 PSEUDOURIDYLATE SYNTHASE
10 252 InterPro IPR001406 Pseudouridine synthase I, TruA
11 247 NCBIfam TIGR00071 tRNA pseudouridine(38-40) synthase TruA
11 247 InterPro IPR001406 Pseudouridine synthase I, TruA
9 264 SUPERFAMILY SSF55120 Pseudouridine synthase
9 264 InterPro IPR020103 Pseudouridine synthase, catalytic domain superfamily
10 259 PIRSF PIRSF001430 PSU-A
10 259 InterPro IPR001406 Pseudouridine synthase I, TruA
14 252 CDD cd02570 PseudoU_synth_EcTruA
14 252 InterPro IPR001406 Pseudouridine synthase I, TruA
10 252 Hamap MF_00171 tRNA pseudouridine synthase A [truA].
114 251 Gene3D G3DSA:3.30.70.660 -
114 251 InterPro IPR020095 Pseudouridine synthase I, TruA, C-terminal

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 · FPocket

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

Site 1 FPocket #17
0.919
Likely same site as P2Rank 3 1.4 Å 11 shared residues 100% of smaller site
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.288
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.151
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.062
Likely same site as FPocket 17 1.4 Å 11 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.031
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.008
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:60-60 Nucleophile
UniProt: Binding site:118-118
UniProt: Site:110-110 Interaction with tRNA
UniProt: Site:126-126 Interaction with tRNA
UniProt: Site:139-139 Interaction with tRNA
UniProt: Site:58-58 Interaction with tRNA; Important for base-flipping
UniProt: Site:78-78 Interaction with tRNA
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_A0A0H3GR85
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4805
ColabFold — — full sequence — Loaded