KpKP13 Protein target profile

Tyrosine recombinase xerD

Accession: KP13_02195

Gene: AHE42764.1 xerD 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GV48
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Length 298
Pocket druggability (P2Rank · AlphaFold DB model) 0.131
Functional annotation 0 EC 9 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

Risks to review

Microbiome similarity 193 of 4744 screened genomes (4.1%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.14. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.13.

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
4.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
60.324 Higher values support similarity to known essential genes.
DEG E-value
4.43e-98 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
86.77 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) 0.131
Structure A0A0H3GV48
Pocket Pocket 1
Druggability (FPocket) 0.135
Structure A0A0H3GV48
Pocket Pocket 18
ColabFold model
P2Rank 0.122 · Pocket 1
FPocket 0.186 · Pocket 7
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 193 / 4744 genomes with a hit
Prevalence 4.1%

Sequence

Primary amino-acid sequence viewer.

MKQDLALIEQFLDALWLERNLAENTLSAYRRDLTMLVEWLHHRGLSLASVGSDDLQALLAERQSGGYKATSTARLLSAVRRFFQHLYREKIRPDDPSALLASPKLPQRLPKDLSEAQVERLLQAPLVEQPLELRDKAMLEVLYATGLRVSELVGLTMSDISLRQGVLRVVGKGNKERLVPLGEEAVLWVENYLEYGRPWLLNGVASDVLFPSQRAQQMTRQTFWHRIKHYAVLAGIDSEKLSPHVLRHAFATHLLNHGADLRVVQMLLGHSDLSTTQIYTHVATERLRQLHQQHHPRA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

9
  • 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:0009009 Catalysis of the formation of new phosphodiester bonds between a pair of short, unique target DNA sequences.
  • GO:0015074 The process in which a DNA segment is incorporated into another, usually larger, DNA molecule such as a chromosome.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0009037 Catalysis of the formation of new phosphodiester bonds between a pair of short, unique DNA target sequences; occurs through a phosphotyrosyl intermediate in which the target sequence is first cleaved by the nucleophilic attack by a tyrosine in the active site.
  • GO:0051301 The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
  • GO:0007059 The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
  • GO:0006313 A type of transposition in which a transposable element (transposon) is moved to another part of a genome, either by a cut-and-paste mechanism or a replicative mechanism.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
2 87 ProSiteProfiles PS51900 Core-binding (CB) domain profile.
2 87 InterPro IPR044068 Core-binding (CB) domain
48 292 PANTHER PTHR30349 PHAGE INTEGRASE-RELATED
113 284 Pfam PF00589 Phage integrase family
113 284 InterPro IPR002104 Integrase, catalytic domain
8 90 Pfam PF02899 Phage integrase, N-terminal SAM-like domain
8 90 InterPro IPR004107 Integrase, SAM-like, N-terminal
9 298 NCBIfam TIGR02225 site-specific tyrosine recombinase XerD
9 298 InterPro IPR011932 Tyrosine recombinase XerD
4 298 Hamap MF_01807 Tyrosine recombinase XerD [xerD].
4 298 InterPro IPR011932 Tyrosine recombinase XerD
111 292 FunFam G3DSA:1.10.443.10:FF:000001 Tyrosine recombinase XerD
3 98 Gene3D G3DSA:1.10.150.130 -
3 98 InterPro IPR010998 Integrase/recombinase, N-terminal
3 100 FunFam G3DSA:1.10.150.130:FF:000002 Tyrosine recombinase XerD
6 298 Hamap MF_01808 Tyrosine recombinase XerC [xerC].
6 298 InterPro IPR023009 Tyrosine recombinase XerC/XerD
115 287 CDD cd00798 INT_XerDC_C
111 292 Gene3D G3DSA:1.10.443.10 Intergrase catalytic core
111 292 InterPro IPR013762 Integrase-like, catalytic domain superfamily
7 290 SUPERFAMILY SSF56349 DNA breaking-rejoining enzymes
7 290 InterPro IPR011010 DNA breaking-rejoining enzyme, catalytic core
108 292 ProSiteProfiles PS51898 Tyrosine recombinase domain profile.
108 292 InterPro IPR002104 Integrase, catalytic domain

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
0.131
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.079
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.01
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:148-148
UniProt: Active site:172-172
UniProt: Active site:244-244
UniProt: Active site:247-247
UniProt: Active site:270-270
UniProt: Active site:279-279 O-(3'-phospho-DNA)-tyrosine intermediate
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_A0A0H3GV48
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_02195
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GV48