KpATCC43816 Protein target profile

DNA repair RadC family protein

Accession: VK055_3491

Gene: AIK82047.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3H4I9
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Length 218
Pocket druggability (P2Rank · AlphaFold DB model) 0.165
Functional annotation 0 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

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. Strong predicted binding pocket FPocket selected-pocket score 0.70. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 133 of 4744 screened genomes (2.8%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.70) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.17.

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
2.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
72.558 Higher values support similarity to known essential genes.
DEG E-value
2.64e-119 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
91.53 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) 0.165
Structure A0A0H3H4I9
Pocket Pocket 1
Druggability (FPocket) 0.7
Structure A0A0H3H4I9
Pocket Pocket 14
ColabFold model
P2Rank 0.191 · Pocket 1
FPocket 0.474 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 133 / 4744 genomes with a hit
Prevalence 2.8%

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.

MENLMPREKMLQYGIETLTDVELLALFLRVGTRRQDVLSYAQALLQRFGSLYALLSADKAQLIAVDGLGLAKYAQLKGIAELARRYFSSQLVEEAALVTPSMTREFLQSQLTEEEREIFMVIFLDNQNRVLKHSRLFSGTLSHVEVHPREIVREAIKVNAAAVILAHNHPSGSPEPSQADRLITERVIKCCRFMEIRVLDHLVIGRGAYVSFAERGWI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

3
  • GO:0046872 Binding to a metal ion.
  • GO:0008237 Catalysis of the hydrolysis of peptide bonds 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:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
38 81 Gene3D G3DSA:1.10.150.20 -
167 172 ProSitePatterns PS01302 Uncharacterized protein family UPF0758 signature.
167 172 InterPro IPR020891 Uncharacterised protein family UPF0758, conserved site
95 217 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase, domain 2
5 218 NCBIfam TIGR00608 DNA repair protein RadC
5 218 InterPro IPR001405 Uncharacterised protein family UPF0758
96 218 ProSiteProfiles PS50249 MPN domain profile.
96 218 InterPro IPR037518 MPN domain
99 216 Pfam PF04002 RadC-like JAB domain
99 216 InterPro IPR025657 RadC-like JAB domain
2 218 Hamap MF_00018 UPF0758 protein YicR [yicR].
2 218 InterPro IPR022820 Uncharacterised protein family UPF0758, YicR subfamily
147 183 SUPERFAMILY SSF102712 JAB1/MPN domain
104 213 CDD cd08071 MPN_DUF2466
104 213 InterPro IPR025657 RadC-like JAB domain
14 81 SUPERFAMILY SSF47781 RuvA domain 2-like
14 81 InterPro IPR010994 RuvA domain 2-like
2 218 PANTHER PTHR30471 DNA REPAIR PROTEIN RADC
2 218 InterPro IPR001405 Uncharacterised protein family UPF0758
5 74 Pfam PF20582 UPF0758 N-terminal
5 74 InterPro IPR046778 UPF0758, N-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.

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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
0.165
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Surrounding area
Pocket 2 P2Rank #2
0.062
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Surrounding area
Pocket 3 P2Rank #3
0.026
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Surrounding area
Pocket 4 P2Rank #4
0.01
Likely same site as FPocket 1 1.9 Å 9 shared residues 100% of smaller site
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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 #14
0.7
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Surrounding area
Pocket 2 FPocket #1
0.562
Likely same site as P2Rank 4 1.9 Å 9 shared residues 100% of smaller site
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Surrounding area
Pocket 3 FPocket #7
0.217
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Surrounding area
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_A0A0H3H4I9
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_3491
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3H4I9