Protein profile

VK055_3165

tyrosine recombinase XerC

Genome: KpATCC43816

Gene: xerC AIK81737.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GH57
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Amino acids 300
Annotations 8
Features 21
PDB binders 0
Druggability 0.444

Overview

Basic information about this protein and its source genome.

Accession
VK055_3165
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
xerC AIK81737.1
Status
annotated
Amino acids
300
Structure source
AlphaFold + ColabFold
GO
GO:0015074 The process in which a DNA segment is incorporated into another, usually larger, DNA molecule such as a chromosome. 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: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: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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 (%)
88.0
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
90.78

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 0.444
Structure A0A0H3GH57
Pocket Pocket 13
P2Rank 0.252
Structure A0A0H3GH57
Pocket Pocket 1
ColabFold model
FPocket 0.419 · Pocket 1
P2Rank 0.369 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 161 / 4744 genomes with a hit
Normalized 0.034

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • GO:0015074 The process in which a DNA segment is incorporated into another, usually larger, DNA molecule such as a chromosome.
  • 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: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: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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • 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: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.

21 records
Show feature table
Start End DB Term Name
115 290 Gene3D G3DSA:1.10.443.10 Intergrase catalytic core
115 290 InterPro IPR013762 Integrase-like, catalytic domain superfamily
7 101 Gene3D G3DSA:1.10.150.130 -
7 101 InterPro IPR010998 Integrase/recombinase, N-terminal
8 296 Hamap MF_01808 Tyrosine recombinase XerC [xerC].
8 296 InterPro IPR023009 Tyrosine recombinase XerC/XerD
4 90 ProSiteProfiles PS51900 Core-binding (CB) domain profile.
4 90 InterPro IPR044068 Core-binding (CB) domain
9 101 SUPERFAMILY SSF47823 lambda integrase-like, N-terminal domain
115 290 FunFam G3DSA:1.10.443.10:FF:000002 Tyrosine recombinase XerC
11 92 Pfam PF02899 Phage integrase, N-terminal SAM-like domain
11 92 InterPro IPR004107 Integrase, SAM-like, N-terminal
118 285 CDD cd00798 INT_XerDC_C
115 282 Pfam PF00589 Phage integrase family
115 282 InterPro IPR002104 Integrase, catalytic domain
111 290 ProSiteProfiles PS51898 Tyrosine recombinase domain profile.
111 290 InterPro IPR002104 Integrase, catalytic domain
109 294 SUPERFAMILY SSF56349 DNA breaking-rejoining enzymes
109 294 InterPro IPR011010 DNA breaking-rejoining enzyme, catalytic core
12 298 NCBIfam TIGR02224 tyrosine recombinase XerC
12 298 InterPro IPR011931 Tyrosine recombinase XerC

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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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_A0A0H3GH57
AlphaFold — — full sequence — Viewing
ColabFold VK055_3165
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
2 0.037
12 0.017
3 0.01
11 0.001

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 6.12 0.252
2 3.05 0.081
3 1.89 0.032
4 1.17 0.009
5 0.92 0.004