KpATCC43816 Protein target profile

YbeY

Accession: VK055_1847

Gene: ybeY AIK80453.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GPX7
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Length 157
Pocket druggability (P2Rank · AlphaFold DB model) 0.791
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.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.49. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.79. Review the complete evidence below

Risks to review

Microbiome similarity 182 of 4744 screened genomes (3.8%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.79) — check the ligand evidence before deprioritizing on off-target risk alone.

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
3.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
89.172 Higher values support similarity to known essential genes.
DEG E-value
4.81e-102 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
93.88 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) 0.791
Structure A0A0H3GPX7
Pocket Pocket 1
Druggability (FPocket) 0.493
Structure A0A0H3GPX7
Pocket Pocket 3
ColabFold model
P2Rank 0.821 · Pocket 1
FPocket 0.447 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 182 / 4744 genomes with a hit
Prevalence 3.8%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSQVILDLQLACEETSGLPDEALFQRWVDAVIPPFQEESELTIRLVDVAESHELNLTYRGKDKPTNVLSFPFEAPPGIEMPLLGDLIICRQVVEQEASEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEGLETEIMLALGYEDPYISEKIAE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
  • GO:0004222 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0004521 Catalysis of the cleavage of ester linkages within ribonucleic acid by creating internal breaks.
  • GO:0008270 Binding to a zinc ion (Zn).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
16 147 NCBIfam TIGR00043 rRNA maturation RNase YbeY
16 147 InterPro IPR002036 Endoribonuclease YbeY
5 148 Hamap MF_00009 Endoribonuclease YbeY [ybeY].
5 148 InterPro IPR002036 Endoribonuclease YbeY
1 155 Gene3D G3DSA:3.40.390.30 Metalloproteases ("zincins"), catalytic domain
1 155 InterPro IPR023091 Metalloprotease catalytic domain superfamily, predicted
15 154 PANTHER PTHR46986 ENDORIBONUCLEASE YBEY, CHLOROPLASTIC
15 154 InterPro IPR002036 Endoribonuclease YbeY
114 124 ProSitePatterns PS01306 Uncharacterized protein family UPF0054 signature.
114 124 InterPro IPR020549 Endoribonuclease YbeY, conserved site
21 142 Pfam PF02130 Endoribonuclease YbeY
21 142 InterPro IPR002036 Endoribonuclease YbeY
3 151 SUPERFAMILY SSF55486 Metalloproteases ("zincins"), catalytic 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

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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
0.791
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #3
0.493
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:114-114
UniProt: Binding site:118-118
UniProt: Binding site:124-124
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_A0A0H3GPX7
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_1847
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GPX7