KpATCC43816 Protein target profile

ssDNA and dsDNA binding, ATP binding protein

Accession: VK055_3361

Gene: recF AIK81918.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3H4V2
Length 357
Pocket druggability (P2Rank · AlphaFold DB model) 0.864
Direct ligand evidence 0 51 total records
Functional annotation 0 EC 8 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.

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
3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
93.838 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.76 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) 0.864
Structure A0A0H3H4V2
Pocket Pocket 1
Druggability (FPocket) 0.812
Structure A0A0H3H4V2
Pocket Pocket 2
ColabFold model
P2Rank 0.806 · Pocket 1
FPocket 0.296 · Pocket 25
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 145 / 4744 genomes with a hit
Prevalence 3.1%

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.

MSLSRLLIKDFRNIEHADLALSPGFNFLVGANGSGKTSVLEAIYTLGHGRAFRSLQIGRVIRHEQDAFVLHGRLQGEERETAIGLTKDKQGDSKVRIDGTDGHKVAELAHLMPMQLITPEGFTLLNGGPKYRRAFLDWGCFHNEAGFFTAWSNLKRLVKQRNAALRQVSRYAQLRPWDLELIPLAEQISRWRAEYSAAIVEDMADTCQQFLPEFTLTFSFQRGWEKETDYAEVLERNFERDRMLTYTAHGPHKADFRIRADGAPVEDTLSRGQLKLLMCALRLAQGEFLTRVSGRRCLYLIDDFASELDDARRGLLSSRLKATQSQVFVSAISAEHVMDMSDKNSKMFRVEKGKITD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

8
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0003697 Binding to single-stranded DNA.
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
  • GO:0000731 Synthesis of DNA that proceeds from the broken 3' single-strand DNA end and uses the homologous intact duplex as the template.
  • GO:0006302 The repair of double-strand breaks in DNA via homologous and nonhomologous mechanisms to reform a continuous DNA helix.
  • GO:0009432 An error-prone process for repairing damaged microbial DNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
3 354 Pfam PF02463 RecF/RecN/SMC N terminal domain
3 354 InterPro IPR003395 RecF/RecN/SMC, N-terminal
1 356 PANTHER PTHR32182 DNA REPLICATION AND REPAIR PROTEIN RECF
6 331 Gene3D G3DSA:3.40.50.300 -
6 331 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
117 137 ProSitePatterns PS00617 RecF protein signature 1.
117 137 InterPro IPR018078 DNA-binding, RecF, conserved site
120 297 FunFam G3DSA:1.20.1050.90:FF:000001 DNA replication and repair protein RecF
120 297 Gene3D G3DSA:1.20.1050.90 -
120 297 InterPro IPR042174 DNA-binding RecF, domain 2
1 343 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
1 343 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
298 316 ProSitePatterns PS00618 RecF protein signature 2.
298 316 InterPro IPR018078 DNA-binding, RecF, conserved site
1 355 NCBIfam TIGR00611 DNA replication and repair protein RecF
1 355 InterPro IPR001238 DNA-binding, RecF
1 357 Hamap MF_00365 DNA replication and repair protein RecF [recF].
1 357 InterPro IPR001238 DNA-binding, RecF

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
0.864
Likely same site as FPocket 2 0.9 Å 22 shared residues 96% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.196
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.07
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
0.812 Unusual size
Likely same site as P2Rank 1 0.9 Å 22 shared residues 96% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:30-37
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_A0A0H3H4V2
AlphaFold DB full sequence Viewing
ColabFold VK055_3361
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.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AGS PDB via homolog 523.2 Da · LogP -1.51 · TPSA 262.1 Open detail RCSB PDB
ZINC12360002 ZINC proposed compound · Tanimoto 0.855 Detail ZINC
ZINC12360703 ZINC proposed compound · Tanimoto 0.855 Detail ZINC
ZINC12503599 ZINC proposed compound · Tanimoto 0.855 Detail ZINC
ZINC16546165 ZINC proposed compound · Tanimoto 0.855 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
AGS RCSB PDB Q8RDL3 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.