KpKP13 Protein target profile

DNA polymerase III subunit delta

Accession: KP13_03334

Gene: AHE45713.1 holA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GTY2
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Length 344
Pocket druggability (P2Rank · AlphaFold DB model) 0.048
Functional annotation 1 EC 5 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. Moderate predicted binding pocket FPocket selected-pocket score 0.62. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 113 of 4744 screened genomes (2.4%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.62) — 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
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
91.14 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) 0.048
Structure A0A0H3GTY2
Pocket Pocket 1
Druggability (FPocket) 0.622
Structure A0A0H3GTY2
Pocket Pocket 4
ColabFold model
P2Rank 0.045 · Pocket 1
FPocket 0.3 · Pocket 17
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 113 / 4744 genomes with a hit
Prevalence 2.4%

Sequence

Primary amino-acid sequence viewer.

MMIRLYPEQLRAQLTEGLRAAYLLLGNDPLLLQESQDAIREAAAAQGFTEHHTFSIDNSTDWQAIFALSQAMSLFASRQTLLLILPENGPNAAINEQLATLVGLLHDDLLLIVRGNKLTKAQENAAWLTALAQRAVQVSCQTPEYAQLPRWLAARAKQHQLQLDDAASQLLCYCYEGNLLALAQALERLALLWPDGKLTLPRVEQAVNDAAHFTPYHWVDALLAGKSKRVLHVLQQLRLEGCEPAILLRTLQRELLLLVTLKRQATHTPLRSLFDKHRVWQNRRQLLSDALTRLSGEQLRQAVTLLTRAELTFKQDYGHDVWPELESLSLLLCHKALADVFIDG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0009360 The DNA polymerase III holoenzyme is a complex that contains 10 different types of subunits. These subunits are organized into 3 functionally essential sub-assemblies: the pol III core, the beta sliding clamp processivity factor and the clamp-loading complex. The pol III core carries out the polymerase and the 3'-5' exonuclease proofreading activities. The polymerase is tethered to the template via the sliding clamp processivity factor. The clamp-loading complex assembles the beta processivity factor onto the primer template and plays a central role in the organization and communication at the replication fork.
  • 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:0003887 Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); DNA-template-directed extension of the 3'-end of a DNA strand by one nucleotide at a time.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0006261 A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
22 191 Pfam PF06144 DNA polymerase III, delta subunit
22 191 InterPro IPR010372 DNA polymerase III delta, N-terminal
143 207 CDD cd18138 HLD_clamp_pol_III_delta
2 211 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
2 211 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
215 344 Gene3D G3DSA:1.20.272.10 -
215 344 FunFam G3DSA:1.20.272.10:FF:000008 DNA polymerase III, delta subunit
144 214 FunFam G3DSA:1.10.8.60:FF:000041 DNA polymerase III subunit delta
215 339 Pfam PF14840 Processivity clamp loader gamma complex DNA pol III C-term
215 339 InterPro IPR032780 DNA polymerase III subunit delta, C-terminal
2 336 PANTHER PTHR34388 DNA POLYMERASE III SUBUNIT DELTA
213 335 SUPERFAMILY SSF48019 post-AAA+ oligomerization domain-like
213 335 InterPro IPR008921 DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal
19 333 NCBIfam TIGR01128 DNA polymerase III subunit delta
19 333 InterPro IPR005790 DNA polymerase III, delta subunit
2 141 Gene3D G3DSA:3.40.50.300 -
2 141 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
144 214 Gene3D G3DSA:1.10.8.60 -
2 141 FunFam G3DSA:3.40.50.300:FF:001093 DNA polymerase III subunit delta

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
0.048
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #4
0.622
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_A0A0H3GTY2
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_03334
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GTY2