Protein profile

KP13_03460

Transcriptional activator ramA

Genome: KpKP13

Gene: ramA AHE45836.1 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
KP13_03460
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
ramA AHE45836.1
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:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. 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.

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
90.69

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 0.423 · Pocket 1
P2Rank 0.02 · Pocket 1
Core conservation Accessory gene
Roary accessory
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:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

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

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

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 KP13_03460
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer