Protein profile

VK055_5110

integrase core domain protein

Genome: KpATCC43816

Gene: AIK83636.1 Structure source: AlphaFold + ColabFold UniProt A4GZE2
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Amino acids 300
Annotations 5
Features 12
PDB binders 0
Druggability 0.653

Overview

Basic information about this protein and its source genome.

Accession
VK055_5110
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK83636.1
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:0003676 Binding to a nucleic acid. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). 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:0032196 Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites. For elements that are transcribed as the first step of transposition, the process starts with the transcription of the transposable element, its translation and maturation, and ending with integration into DNA. For elements that are cut out, the process starts with the excision of the donor DNA and integrated into another site.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
26.721
Localization
Cytoplasmic
ColabFold pLDDT
81.57

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 0.653
Structure A4GZE2
Pocket Pocket 2
P2Rank 0.106
Structure A4GZE2
Pocket Pocket 1
ColabFold model
FPocket 0.27 · Pocket 1
P2Rank 0.17 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 9 / 4744 genomes with a hit
Normalized 0.002

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0015074 The process in which a DNA segment is incorporated into another, usually larger, DNA molecule such as a chromosome.
  • GO:0003676 Binding to a nucleic acid.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • 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:0032196 Any process involved in mediating the movement of discrete segments of DNA between nonhomologous sites. For elements that are transcribed as the first step of transposition, the process starts with the transcription of the transposable element, its translation and maturation, and ending with integration into DNA. For elements that are cut out, the process starts with the excision of the donor DNA and integrated into another site.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
101 273 SUPERFAMILY SSF53098 Ribonuclease H-like
101 273 InterPro IPR012337 Ribonuclease H-like superfamily
1 51 ProSiteProfiles PS50531 IS21 transposase-type HTH domain profile.
1 51 InterPro IPR017894 HTH domain, IS21 transposase-type
106 283 Gene3D G3DSA:3.30.420.10 -
106 283 InterPro IPR036397 Ribonuclease H superfamily
99 279 ProSiteProfiles PS50994 Integrase catalytic domain profile.
99 279 InterPro IPR001584 Integrase, catalytic core
101 209 Pfam PF00665 Integrase core domain
101 209 InterPro IPR001584 Integrase, catalytic core
1 289 PANTHER PTHR35004 TRANSPOSASE RV3428C-RELATED
1 287 NCBIfam NF033546 IS21 family transposase

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_A4GZE2
AlphaFold — — full sequence — Viewing
ColabFold VK055_5110
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
6 0.011
17 0.002
24 0.0
26 0.0

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 3.57 0.106
2 3.12 0.084
3 2.99 0.078
4 1.86 0.03
5 1.62 0.022