KpKP13 Protein target profile

Prophage lambda integrase

Accession: KP13_04859

Gene: intE AHE45219.1 3D evidence: ColabFold model
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Length 375
Pocket druggability (P2Rank · ColabFold model) 0.136
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. Structure available ColabFold model

Risks to review

Microbiome similarity 28 of 4744 screened genomes (0.6%) have a significant similarity hit. Mixed conservation Core/accessory calls are not fully concordant. Weak predicted binding pocket FPocket selected-pocket score 0.36. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.14.

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
0.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
59.416 Higher values support similarity to known essential genes.
DEG E-value
5.73e-168 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
91.86 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

ColabFold / curated 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) 0.136
Structure CB_KP13_04859
Pocket Pocket 1
Druggability (FPocket) 0.358
Structure CB_KP13_04859
Pocket Pocket 9
ColabFold model
P2Rank 0.136 · Pocket 1
FPocket 0.358 · Pocket 9
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 28 / 4744 genomes with a hit
Prevalence 0.6%

Sequence

Primary amino-acid sequence viewer.

MAARPRKNNISIPNLYPLFSRKVNKVYWRYKHPITGKFHSLGTDEAEATAIAIEANKRLAEQNTRQILALSDKIATSKGKAITAITWLDRYWKIQEERLATGDIKKNTYKQKAKPVALLKERVGMKLISAVDVRDIAQILDEYISEGQPRMAQVIRSVLIDVFKEAQHAGEVPPGHNPALATKQPRRRITRQRLNLNEWQKIFDIADANHKYMGNAMLLALITGQRLGDISRMKFTDVWDDHLHIEQEKTGSKIAIPLALRCDAINWSLREVIARCRDYAVSPYLVHFLHSTSQAERGAQVKARTLTMNFSKARDKAKIDWGDGTPATFHEQRSLAERLYEAQGINTQKLLGHKSPNQTAQYHDDRGKDWVKVAL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Unknown

Gene Ontology (GO)

4
  • GO:0008907 Catalysis of the integration of one DNA segment into another.
  • 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0015074 The process in which a DNA segment is incorporated into another, usually larger, DNA molecule such as a chromosome.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
1 72 Pfam PF09003 Bacteriophage lambda integrase, Arm DNA-binding domain
1 72 InterPro IPR015094 Integrase, lambda-type, N-terminal DNA-binding
198 371 CDD cd00800 INT_Lambda_C
82 167 ProSiteProfiles PS51900 Core-binding (CB) domain profile.
82 167 InterPro IPR044068 Core-binding (CB) domain
189 375 ProSiteProfiles PS51898 Tyrosine recombinase domain profile.
189 375 InterPro IPR002104 Integrase, catalytic domain
82 189 Gene3D G3DSA:1.10.150.130 -
82 189 InterPro IPR010998 Integrase/recombinase, N-terminal
193 364 Pfam PF00589 Phage integrase family
193 364 InterPro IPR002104 Integrase, catalytic domain
1 68 Gene3D G3DSA:3.30.160.60 Classic Zinc Finger
191 375 Gene3D G3DSA:1.10.443.10 Intergrase catalytic core
191 375 InterPro IPR013762 Integrase-like, catalytic domain superfamily
86 374 SUPERFAMILY SSF56349 DNA breaking-rejoining enzymes
86 374 InterPro IPR011010 DNA breaking-rejoining enzyme, catalytic core
17 60 SUPERFAMILY SSF54171 DNA-binding domain
17 60 InterPro IPR016177 DNA-binding domain superfamily

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
0.136
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Surrounding area
Pocket 2 P2Rank #2
0.049
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Surrounding area
Pocket 3 P2Rank #3
0.018
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Surrounding area
Pocket 4 P2Rank #4
0.004
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #9
0.358
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Surrounding area
Pocket 2 FPocket #1
0.258 Unusual size
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Surrounding area
All structural evidence 0 experimental · 1 predicted

Structural evidence

0 + 1

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
ColabFold KP13_04859
ColabFold — — full sequence — Viewing