Protein profile

VK055_1983

bacterial regulatory helix-turn-helix, AraC family protein

Genome: KpATCC43816

Gene: ramA AIK80589.1 Structure source: Experimental + AlphaFold + ColabFold UniProt A0A0H3GPK2|Q48413
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Amino acids 113
Annotations 3
Features 19
PDB binders 0
Druggability 0.267

Overview

Basic information about this protein and its source genome.

Accession
VK055_1983
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
ramA AIK80589.1
Status
annotated
Amino acids
113
Structure source
Experimental + 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)
Y
DEG identity (%)
45.192
DEG E-value
2.04e-32
Localization
Cytoplasmic
ColabFold pLDDT
92.11

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 0.267
Structure A0A0H3GPK2
Pocket Pocket 1
P2Rank 0.027
Structure A0A0H3GPK2
Pocket Pocket 1
ColabFold model
FPocket 0.357 · Pocket 4
P2Rank 0.015 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 80 / 4744 genomes with a hit
Normalized 0.017

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.

19 records
Show feature table
Start End DB Term Name
5 56 Gene3D G3DSA:1.10.10.60 -
4 110 PANTHER PTHR47504 RIGHT ORIGIN-BINDING PROTEIN
59 108 SUPERFAMILY SSF46689 Homeodomain-like
59 108 InterPro IPR009057 Homeobox-like domain superfamily
62 113 Gene3D G3DSA:1.10.10.60 -
59 101 ProSitePatterns PS00041 Bacterial regulatory proteins, araC family signature.
59 101 InterPro IPR018062 HTH domain AraC-type, conserved site
74 89 PRINTS PR00032 AraC bacterial regulatory protein HTH signature
74 89 InterPro IPR020449 Transcription regulator HTH, AraC- type
89 105 PRINTS PR00032 AraC bacterial regulatory protein HTH signature
89 105 InterPro IPR020449 Transcription regulator HTH, AraC- type
6 56 SUPERFAMILY SSF46689 Homeodomain-like
6 56 InterPro IPR009057 Homeobox-like domain superfamily
9 107 ProSiteProfiles PS01124 Bacterial regulatory proteins, araC family DNA-binding domain profile.
9 107 InterPro IPR018060 DNA binding HTH domain, AraC-type
28 106 Pfam PF12833 Helix-turn-helix domain
28 106 InterPro IPR018060 DNA binding HTH domain, AraC-type
22 105 SMART SM00342 aracneu4
22 105 InterPro IPR018060 DNA binding HTH domain, AraC-type

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

2 + 2

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

Entry Method Resolution Chain Coverage Links Status
PDB 7BEF
X-ray 20.00 Å - —
PDBe RCSB PDBj File
Viewing
PDB 7BEG
X-ray 20.00 Å - —
PDBe RCSB PDBj File
Loaded
AlphaFold AF_A0A0H3GPK2
AlphaFold — — full sequence — Loaded
ColabFold VK055_1983
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 25.57 0.907
2 20.31 0.853
3 13.32 0.682
4 12.29 0.646
5 10.98 0.589