KpATCC43816 Protein target profile

stationary phase translation inhibitor and ribosome stability factor

Accession: VK055_4581

Gene: AIK83119.1 yfiA 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GWB1
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Length 102
Pocket druggability (FPocket · AlphaFold DB model) 0.15
Functional annotation 0 EC 4 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

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 141 of 4744 screened genomes (3.0%) have a significant similarity hit. Mixed conservation Core/accessory calls are not fully concordant. Weak predicted binding pocket FPocket selected-pocket score 0.15.

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
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
88.43 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)
Structure A0A0H3GWB1
Pocket No pockets
Druggability (FPocket) 0.15
Structure A0A0H3GWB1
Pocket Pocket 2
ColabFold model
FPocket 0.053 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 141 / 4744 genomes with a hit
Prevalence 3.0%

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.

MEITPAIRQHVADRLAKLDKWQTHLINPHIILSKEPQGFIADATINTPNGHLVASARHEDMYAAINELINKLERQLNKVQHKGEARRAATSVKEAGFVEEEE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

4
  • GO:0044238 The chemical reactions and pathways involving those compounds which are formed as a part of the normal anabolic and catabolic processes. These processes take place in most, if not all, cells of the organism.
  • GO:0022627 The small subunit of a ribosome located in the cytosol.
  • GO:0043024 Binding to a small ribosomal subunit.
  • GO:0045900 Any process that stops, prevents, or reduces the frequency, rate or extent of translational elongation.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
1 97 FunFam G3DSA:3.30.160.100:FF:000002 Ribosome-associated translation inhibitor RaiA
1 88 NCBIfam TIGR00741 ribosome-associated translation inhibitor RaiA
1 88 InterPro IPR003489 Ribosome hibernation promoting factor/RaiA
1 96 Gene3D G3DSA:3.30.160.100 -
1 96 InterPro IPR036567 Ribosome hibernation promotion factor-like
1 96 SUPERFAMILY SSF69754 Ribosome binding protein Y (YfiA homologue)
82 96 MobiDBLite mobidb-lite consensus disorder prediction
1 82 Pfam PF02482 Sigma 54 modulation protein / S30EA ribosomal protein
1 82 InterPro IPR003489 Ribosome hibernation promoting factor/RaiA
1 82 CDD cd00552 RaiA
82 102 MobiDBLite mobidb-lite consensus disorder prediction
55 82 Coils Coil Coil
1 88 PANTHER PTHR33231 30S RIBOSOMAL PROTEIN

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

No pockets are loaded yet for the displayed AlphaFold DB model AF_A0A0H3GWB1 structure. Run experimental pocket backfill to show FPocket/P2Rank overlays on this structure.

Loading 3D structure...

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

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'.
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_A0A0H3GWB1
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4581
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GWB1