Protein target profile

KP13_02197

Single-stranded-DNA-specific exonuclease recJ

Genome: KpKP13 Gene: AHE42766.1 recJ 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GY37
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Length 577
Pocket druggability 0.067
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. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.89. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 155 of 4744 screened genomes (3.3%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.07.

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
3.3% 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.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
93.15 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 0.067
Structure A0A0H3GY37
Pocket Pocket 5
P2Rank 0.886
Structure A0A0H3GY37
Pocket Pocket 1
ColabFold model
FPocket 0.504 · Pocket 4
P2Rank 0.715 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 155 / 4744 genomes with a hit
Prevalence 3.3%

Cross-references

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

Sequence

UniProt A0A0H3GY37

Sequence

Primary amino-acid sequence viewer.

MKQQIQLRRREAVDGVELPADLPPLLQRLYASRGVRSAQELERSVKGMLPWTQLTGVEKAVEMLHDAFQKGLHIVVVGDFDADGATSTALSVLALRALGYGNVSYLVPNRFEDGYGLSPEVVDQAHARGAQMIMTVDNGISSHAGVDHAHALGIPVLVTDHHLPGETLPAAEAIVNPNLRDCDFPSKSLAGVGVAFYLMLALRTFLRDKGWFDARGIPAPNLAELLDLVALGTVADVVPLDANNRILTWQGLSRIRAGKCRPGIKALLEIANRDPQKLAASDLGFALGPRLNAAGRLDDMSVGVALLLCDNIGEARVLANELDALNQTRKEIEQGMQAEALTLCQQLERSADTLPGGLAMYHPQWHQGVVGILASRIKERFHRPVIAFAPTGDGTLKGSGRSIQGLHMRDALERLDTLYPGLILKFGGHAMAAGLSLEEARFEEFQQRFGELVTEWLDPALLQGEVVSDGPLAAAEMSMEVAQMLRDAGPWGQMFPEPLFDGRFRLLQQRLVGERHLKVMVEPVDGGPLLDGIAFNVDTSIWPDNGVREVQLAYKLDINEFRGNRSLQLIIDHLWPN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0008409 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 5' end.
  • GO:0003676 Binding to a nucleic acid.
  • GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
  • GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
24 573 NCBIfam TIGR00644 single-stranded-DNA-specific exonuclease RecJ
24 573 InterPro IPR004610 Bacterial RecJ exonuclease
50 326 FunFam G3DSA:3.90.1640.30:FF:000001 Single-stranded-DNA-specific exonuclease RecJ
327 456 FunFam G3DSA:3.10.310.30:FF:000001 Single-stranded-DNA-specific exonuclease recJ
469 572 Pfam PF17768 RecJ OB domain
469 572 InterPro IPR041122 RecJ, OB domain
207 577 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
188 206 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
315 335 Coils Coil Coil
322 452 Pfam PF02272 DHHA1 domain
322 452 InterPro IPR003156 DHHA1 domain
327 456 Gene3D G3DSA:3.10.310.30 -
73 233 Pfam PF01368 DHH family
73 233 InterPro IPR001667 DDH domain
50 326 Gene3D G3DSA:3.90.1640.30 -
48 465 SUPERFAMILY SSF64182 DHH phosphoesterases
48 465 InterPro IPR038763 DHH phosphoesterase superfamily
1 187 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 576 PANTHER PTHR30255 SINGLE-STRANDED-DNA-SPECIFIC EXONUCLEASE RECJ

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

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.886
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Surrounding area
Site 2 P2Rank #2
0.296
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Surrounding area
Site 3 P2Rank #3
0.058
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Surrounding area
Site 4 P2Rank #4
0.034
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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_A0A0H3GY37
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_02197
ColabFold — — full sequence — Loaded