KpKP13 Protein target profile

Recombination protein recR

Accession: KP13_03619

Gene: recR AHE45961.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GKL4
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Length 201
Pocket druggability (P2Rank · AlphaFold DB model) 0.047
Functional annotation 0 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. Strong predicted binding pocket FPocket selected-pocket score 0.97. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 200 of 4744 screened genomes (4.2%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.97) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.05.

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
4.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
43.814 Higher values support similarity to known essential genes.
DEG E-value
1.45e-50 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
95.63 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) 0.047
Structure A0A0H3GKL4
Pocket Pocket 1
Druggability (FPocket) 0.969
Structure A0A0H3GKL4
Pocket Pocket 2
ColabFold model
P2Rank 0.042 · Pocket 1
FPocket 0.641 · Pocket 16
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 200 / 4744 genomes with a hit
Prevalence 4.2%

Sequence

Primary amino-acid sequence viewer.

MQTSPLLTQLMEALRCLPGVGPKSAQRMAFTLLQRDRSGGMRLAQALTRAMSEIGHCADCRTFTEQEVCNICSNPRRQENGQICVVESPADIYAIEQTGQYSGRYFVLMGHLSPLDGIGPDDIGLDRLEQRLEAESITEVILATNPTVEGEATANYIAELCAQYGVDASRIAHGVPVGGELEMVDGTTLSHSLAGRHKITF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

5
  • 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:0046872 Binding to a metal ion.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • 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.
  • GO:0008270 Binding to a zinc ion (Zn).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
81 166 SMART SM00493 toprim5
81 166 InterPro IPR006171 TOPRIM domain
2 199 SUPERFAMILY SSF111304 Recombination protein RecR
2 199 InterPro IPR023627 Recombination protein RecR
81 176 ProSiteProfiles PS50880 Toprim domain profile.
81 176 InterPro IPR006171 TOPRIM domain
81 192 CDD cd01025 TOPRIM_recR
81 192 InterPro IPR034137 RecR, TOPRIM domain
2 197 NCBIfam TIGR00615 recombination mediator RecR
2 197 InterPro IPR000093 DNA recombination protein RecR
41 77 Pfam PF02132 RecR protein
41 77 InterPro IPR023628 Recombination protein RecR, C4-type zinc finger
172 199 Gene3D G3DSA:6.10.250.240 -
1 51 FunFam G3DSA:1.10.8.420:FF:000001 Recombination protein RecR
1 199 Hamap MF_00017 Recombination protein RecR [recR].
1 199 InterPro IPR000093 DNA recombination protein RecR
1 199 PANTHER PTHR30446 RECOMBINATION PROTEIN RECR
77 171 Gene3D G3DSA:3.40.1360.10 -
81 172 Pfam PF13662 Toprim domain
81 172 InterPro IPR006171 TOPRIM domain
77 171 FunFam G3DSA:3.40.1360.10:FF:000001 Recombination protein RecR
57 78 ProSitePatterns PS01300 RecR protein signature.
57 78 InterPro IPR015967 Recombination protein RecR, conserved site
1 51 Gene3D G3DSA:1.10.8.420 RecR Domain 1

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
0.047
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.015
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2
0.969
Show in viewer
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_A0A0H3GKL4
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_03619
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GKL4