Protein profile

KP13_02195

Tyrosine recombinase xerD

Genome: KpKP13

Gene: AHE42764.1 xerD Structure source: AlphaFold + ColabFold UniProt A0A0H3GV48
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Amino acids 298
Annotations 9
Features 24
PDB binders 0
Druggability 0.135

Overview

Basic information about this protein and its source genome.

Accession
KP13_02195
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42764.1 xerD
Status
annotated
Amino acids
298
Structure source
AlphaFold + ColabFold
GO
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.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
60.324
DEG E-value
4.43e-98
Localization
Cytoplasmic
ColabFold pLDDT
86.77

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.135
Structure A0A0H3GV48
Pocket Pocket 18
P2Rank 0.131
Structure A0A0H3GV48
Pocket Pocket 1
ColabFold model
FPocket 0.186 · Pocket 7
P2Rank 0.122 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 193 / 4744 genomes with a hit
Normalized 0.041

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GV48
AlphaFold — — full sequence — Viewing
ColabFold KP13_02195
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 2.94 0.094
2 1.87 0.037