Protein target profile

KP13_00802

Autonomous glycyl radical cofactor

Genome: KpKP13 Gene: grcA AHE43167.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GW99
Export view
Length 127
Pocket druggability 0.079
Functional annotation 0 EC 3 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. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 216 of 4744 screened genomes (4.6%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.08.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. 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
4.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
92.126 Higher values support similarity to known essential genes.
DEG E-value
5.76e-86 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
89.35 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 0.079
Structure A0A0H3GW99
Pocket Pocket 2
P2Rank
Structure A0A0H3GW99
Pocket No pockets
ColabFold model
FPocket 0.129 · Pocket 4
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 216 / 4744 genomes with a hit
Prevalence 4.6%

Cross-references

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

Sequence

UniProt A0A0H3GW99

Sequence

Primary amino-acid sequence viewer.

MITGIQITKAANDDLLNSFWLLDSEKGEARCLCAKGGFAEDDVVAVSKLGEIEYREIPVDVKPEVRVEGGQHLNVNVLRRETLLDAVEHPEKYPQLTIRVSGYAVRFNSLTPEQQRDVIARTFTESL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008861 Catalysis of the reaction: acetyl-CoA + formate = CoA + pyruvate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
67 126 PANTHER PTHR30191 FORMATE ACETYLTRANSFERASE
64 126 FunFam G3DSA:3.20.70.20:FF:000002 Autonomous glycyl radical cofactor
5 127 ProSiteProfiles PS51149 Glycine radical domain profile.
5 127 InterPro IPR001150 Glycine radical domain
1 127 Hamap MF_00806 Autonomous glycyl radical cofactor [grcA].
1 127 InterPro IPR011140 Autonomous glycyl radical cofactor GrcA
97 105 ProSitePatterns PS00850 Glycine radical domain signature.
97 105 InterPro IPR019777 Formate C-acetyltransferase glycine radical, conserved site
64 126 SUPERFAMILY SSF51998 PFL-like glycyl radical enzymes
2 127 NCBIfam TIGR04365 autonomous glycyl radical cofactor GrcA
2 127 InterPro IPR011140 Autonomous glycyl radical cofactor GrcA
2 127 PIRSF PIRSF000378 Gly_radicl_YfiD
64 126 Gene3D G3DSA:3.20.70.20 -
16 108 Pfam PF01228 Glycine radical
16 108 InterPro IPR001150 Glycine radical 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

No pockets are loaded yet for the displayed AlphaFold DB model AF_A0A0H3GW99 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_A0A0H3GW99
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_00802
ColabFold — — full sequence — Loaded