Protein profile

VK055_5122

bacterial regulatory helix-turn-helix, AraC family protein

Genome: KpATCC43816

Gene: ybtA AIK83648.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GSA3
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Amino acids 319
Annotations 3
Features 17
PDB binders 0
Druggability 0.92

Overview

Basic information about this protein and its source genome.

Accession
VK055_5122
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
ybtA AIK83648.1
Status
annotated
Amino acids
319
Structure source
AlphaFold + ColabFold
GO
GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding. GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons. GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

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 (%)
29.126
Localization
Cytoplasmic
ColabFold pLDDT
86.39

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 0.92
Structure A0A0H3GSA3
Pocket Pocket 1
P2Rank 0.961
Structure A0A0H3GSA3
Pocket Pocket 1
ColabFold model
FPocket 0.595 · Pocket 4
P2Rank 0.963 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 6 / 4744 genomes with a hit
Normalized 0.001

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
  • GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
233 316 SMART SM00342 aracneu4
233 316 InterPro IPR018060 DNA binding HTH domain, AraC-type
212 318 Gene3D G3DSA:1.10.10.60 -
285 300 PRINTS PR00032 AraC bacterial regulatory protein HTH signature
285 300 InterPro IPR020449 Transcription regulator HTH, AraC- type
300 316 PRINTS PR00032 AraC bacterial regulatory protein HTH signature
300 316 InterPro IPR020449 Transcription regulator HTH, AraC- type
239 317 Pfam PF12833 Helix-turn-helix domain
239 317 InterPro IPR018060 DNA binding HTH domain, AraC-type
270 317 SUPERFAMILY SSF46689 Homeodomain-like
270 317 InterPro IPR009057 Homeobox-like domain superfamily
220 318 ProSiteProfiles PS01124 Bacterial regulatory proteins, araC family DNA-binding domain profile.
220 318 InterPro IPR018060 DNA binding HTH domain, AraC-type
270 312 ProSitePatterns PS00041 Bacterial regulatory proteins, araC family signature.
270 312 InterPro IPR018062 HTH domain AraC-type, conserved site
10 318 PANTHER PTHR47893 REGULATORY PROTEIN PCHR
212 318 FunFam G3DSA:1.10.10.60:FF:000253 Transcriptional regulator, AraC family

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_A0A0H3GSA3
AlphaFold — — full sequence — Viewing
ColabFold VK055_5122
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
1 0.92

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 31.9 0.941
2 6.59 0.334
3 0.84 0.003