KpATCC43816 Protein target profile

DNA repair protein RecO

Accession: VK055_4611

Gene: AIK83145.1 recO 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3H1L1
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Length 245
Pocket druggability (P2Rank · AlphaFold DB model) 0.178
Direct ligand evidence 0 52 total records
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. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 2 structural and 0 bioactivity records.

Risks to review

Microbiome similarity 139 of 4744 screened genomes (2.9%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.69) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.69, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.18.

Evidence coverage

Core evidence streams are available for this target.
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
2.9% 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.

Structure confidence

ColabFold pLDDT
91.42 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) 0.178
Structure A0A0H3H1L1
Pocket Pocket 1
Druggability (FPocket) 0.686
Structure A0A0H3H1L1
Pocket Pocket 1
ColabFold model
P2Rank 0.273 · Pocket 1
FPocket 0.735 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 139 / 4744 genomes with a hit
Prevalence 2.9%

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.

MDGWQRAFVLHSRPWSETSLMLDVFTEESGRVRLVAKGARSKRSNLKGALQPFTPLLVRFGGRGEVKTLRSAEAVSLALPLSGITLYSGLYVNELISRVLEHETRFSELFFDYLHCIQALAGASGSPEPALRRFELALLGHLGYGVDFLHCAGSGEPVDDTMTYRYREEKGFIASLVIDNNTFTGHHLKALASREFPDVDTLRAAKRFTRIALKPYLGGKPLKSRELFRQFMPARKARADNTNND

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

4
  • 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: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:0043590 The region of a bacterial cell to which the DNA is confined.
  • GO:0006302 The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
83 226 Pfam PF02565 Recombination protein O C terminal
83 226 InterPro IPR003717 Recombination protein O, RecO
4 75 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
4 75 InterPro IPR012340 Nucleic acid-binding, OB-fold
79 241 Gene3D G3DSA:1.20.1440.120 -
79 241 InterPro IPR042242 Recombination protein O, C-terminal
1 78 FunFam G3DSA:2.40.50.140:FF:000074 DNA repair protein RecO
1 231 Hamap MF_00201 DNA repair protein RecO [recO].
1 231 InterPro IPR003717 Recombination protein O, RecO
1 78 Gene3D G3DSA:2.40.50.140 -
1 78 InterPro IPR012340 Nucleic acid-binding, OB-fold
86 168 SUPERFAMILY SSF57863 ArfGap/RecO-like zinc finger
86 168 InterPro IPR037278 ARFGAP/RecO-like zinc finger
1 234 PANTHER PTHR33991 DNA REPAIR PROTEIN RECO
1 234 InterPro IPR003717 Recombination protein O, RecO
5 76 Pfam PF11967 Recombination protein O N terminal
5 76 InterPro IPR022572 DNA replication/recombination mediator RecO, N-terminal
5 230 NCBIfam TIGR00613 DNA repair protein RecO
5 230 InterPro IPR003717 Recombination protein O, RecO

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
0.178
Likely same site as FPocket 1 2.6 Å 13 shared residues 93% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.686 Unusual size
Likely same site as P2Rank 1 2.6 Å 13 shared residues 93% of smaller site
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_A0A0H3H1L1
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4611
ColabFold — — full sequence — Loaded

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CPS PDB via homolog 614.9 Da · LogP 2.88 · TPSA 147.0 Open detail RCSB PDB
MLT PDB via homolog Detail RCSB PDB
ZINC72399572 ZINC proposed compound · Tanimoto 0.733 Detail ZINC
ZINC1889002139 ZINC proposed compound · Tanimoto 0.703 Detail ZINC
ZINC1889002140 ZINC proposed compound · Tanimoto 0.703 Detail ZINC

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
CPS RCSB PDB
3Q8D
P0A7H3 614.9 Da LogP 2.88 TPSA 147.0 1 viol. ✓ Clean C[C@H](CCC(=O)NCCC[N+](C)(C)CCCS(=O)(=O)[O-])[C…
MLT RCSB PDB
3Q8D
P0A7H3 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.

Cross-references

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

Sequence

UniProt A0A0H3H1L1