KpATCC43816 Protein target profile

tRNA 2-selenouridine synthase

Accession: VK055_2071

Gene: AIK80676.1 selU 3D evidence: AlphaFold DB model + ColabFold model Metabolism 8 reactions UniProt A0A0H3GKN1
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Length 358
Pocket druggability (P2Rank · AlphaFold DB model) 0.852
Metabolic reactions 8
Chokepoint Yes
Functional annotation 1 EC 3 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

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 90.5% 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 83 of 4744 screened genomes (1.7%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.85) — 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 0.35.

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
1.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
96.33 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) 0.852
Structure A0A0H3GKN1
Pocket Pocket 1
Druggability (FPocket) 0.346
Structure A0A0H3GKN1
Pocket Pocket 16
ColabFold model
P2Rank 0.915 · Pocket 1
FPocket 0.842 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 83 / 4744 genomes with a hit
Prevalence 1.7%

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing chokepoint reaction, no isoenzyme backup detected, more central than 90.5% of genes in this genome, no human homolog detected.

Relative network centrality 90.5% more central than 90.5% of genes in this genome
Chokepoint Chokepoint gene
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 reactions

8 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.

MTNGTDYRAILASDTPLIDVRAPVEFSQSAMPAAINLPLMNDEERAAVGTCYKRQGPEAALALGHKLVQGDLRASRTQAWLEACARYPHGYLCCARGGQRSHIVQQWLKEAGVDYPLIVGGYKALRQAAIQATDELVQRPIVLIGGCTGNGKTQLVCSRPDGIDLEGLAHHRGSSFGRTLQDQHPQATFENHLAVSLLKKAEQQTRWVLEDEGHMIGANHLPESLRLRMAQSPLAVVEDPFDVRLERLREEYFDRMYRDFIAAYGEEKGWQAYGEYLHHGLFAIRRRLGLQRFAQLTERLDEALVQQQRTASTEAHFAWLVPLLEEYYDPMYRYQLGKKAGKILFRGSWQEVAAWLAK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0043828 Catalysis of the reaction: 5-methylaminomethyl-2-thiouridine + selenophosphate = 5-methylaminomethyl-2-selenouridine + phosphate (at the wobble position in tRNA).
  • GO:0002098 The process in which a uridine at position 34 of a tRNA is post-transcriptionally modified. The wobble nucleoside of the tRNA sequence (position 34) corresponds to the first position of the anticodon.
  • GO:0016765 Catalysis of the transfer of an alkyl or aryl (but not methyl) group from one compound (donor) to another (acceptor).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
1 358 Hamap MF_01622 tRNA 2-selenouridine synthase [selU].
1 358 InterPro IPR017582 tRNA 2-selenouridine synthase
7 131 Gene3D G3DSA:3.40.250.10 -
7 131 InterPro IPR036873 Rhodanese-like domain superfamily
3 357 PANTHER PTHR30401 TRNA 2-SELENOURIDINE SYNTHASE
3 357 InterPro IPR017582 tRNA 2-selenouridine synthase
1 131 SMART SM00450 rhod_4
1 131 InterPro IPR001763 Rhodanese-like domain
6 153 SUPERFAMILY SSF52821 Rhodanese/Cell cycle control phosphatase
6 153 InterPro IPR036873 Rhodanese-like domain superfamily
2 131 FunFam G3DSA:3.40.250.10:FF:000009 tRNA 2-selenouridine/geranyl-2-thiouridine synthase
11 134 ProSiteProfiles PS50206 Rhodanese domain profile.
11 134 InterPro IPR001763 Rhodanese-like domain
5 129 CDD cd01520 RHOD_YbbB
14 342 NCBIfam TIGR03167 tRNA 2-selenouridine(34) synthase MnmH
14 342 InterPro IPR017582 tRNA 2-selenouridine synthase

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
0.852
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Surrounding area
Pocket 2 P2Rank #2
0.362
Likely same site as FPocket 16 1.3 Å 17 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.241
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Surrounding area
Pocket 4 P2Rank #4
0.229
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Surrounding area
Pocket 5 P2Rank #5
0.029
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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 #16
0.346 Unusual size
Likely same site as P2Rank 2 1.3 Å 17 shared residues 100% of smaller site
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Surrounding area
Residue sets
UniProt: Active site:94-94 S-selanylcysteine intermediate
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_A0A0H3GKN1
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2071
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GKN1

Pathways

BioCyc RXN-20762 BioCyc RXN-24092 BioCyc RXN-24091 BioCyc RXN-24090 BioCyc RXN0-2281 BioCyc RXN-20755 BioCyc RXN-20757 BioCyc RXN-20756