Protein profile

KP13_01889

Prepilin peptidase-dependent protein D

Genome: KpKP13

Gene: ppdD AHE46329.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GNA9
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Amino acids 143
Annotations 5
Features 18
PDB binders 0
Druggability 0.28

Overview

Basic information about this protein and its source genome.

Accession
KP13_01889
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
ppdD AHE46329.1
Status
annotated
Amino acids
143
Structure source
AlphaFold + ColabFold
GO
GO:0015627 A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of proteins into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane. Proteins using the Type II pathway are transported across the cytoplasmic membrane by the Sec or Tat complex. GO:0015628 The process in which proteins are secreted across the outer membrane of Gram-negative bacteria by the type II secretion system. Proteins using this pathway are first translocated across the cytoplasmic membrane via the Sec or Tat pathways. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0044096 A short filamentous structure on the surface of a bacterial cell distinguished from other pili by post-translational N-methylation of the pilin monomers. GO:0043107 Any process involved in the controlled movement of a bacterial cell which is dependent on the presence of type IV pili. Includes social gliding motility and twitching motility.

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 (%)
0.0
Localization
Unknown
ColabFold pLDDT
91.79

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 0.28
Structure A0A0H3GNA9
Pocket Pocket 3
P2Rank
Structure A0A0H3GNA9
Pocket No pockets
ColabFold model
FPocket 0.301 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 95 / 4744 genomes with a hit
Normalized 0.02

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:0015627 A large protein complex, containing 12-15 subunits, that spans the cell envelope of Gram-negative bacteria and mediates the movement of proteins into the extracellular environment. The complex includes a component in the cytoplasm, an inner membrane subcomplex that reaches into the periplasmic compartment and a secretion pore in the outer membrane. Proteins using the Type II pathway are transported across the cytoplasmic membrane by the Sec or Tat complex.
  • GO:0015628 The process in which proteins are secreted across the outer membrane of Gram-negative bacteria by the type II secretion system. Proteins using this pathway are first translocated across the cytoplasmic membrane via the Sec or Tat pathways.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0044096 A short filamentous structure on the surface of a bacterial cell distinguished from other pili by post-translational N-methylation of the pilin monomers.
  • GO:0043107 Any process involved in the controlled movement of a bacterial cell which is dependent on the presence of type IV pili. Includes social gliding motility and twitching motility.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
31 143 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
4 27 NCBIfam TIGR02532 prepilin-type N-terminal cleavage/methylation domain
4 27 InterPro IPR012902 Prokaryotic N-terminal methylation site
7 113 SUPERFAMILY SSF54523 Pili subunits
7 113 InterPro IPR045584 Pilin-like
12 30 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
5 25 ProSitePatterns PS00409 Prokaryotic N-terminal methylation site.
5 25 InterPro IPR012902 Prokaryotic N-terminal methylation site
8 139 Gene3D G3DSA:3.30.700.10 Glycoprotein, Type 4 Pilin
6 31 PRINTS PR00813 Bacterial general secretion pathway protein G signature
6 31 InterPro IPR000983 Bacterial general secretion pathway protein G-type pilin
42 60 PRINTS PR00813 Bacterial general secretion pathway protein G signature
42 60 InterPro IPR000983 Bacterial general secretion pathway protein G-type pilin
3 117 PANTHER PTHR30093 GENERAL SECRETION PATHWAY PROTEIN G
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 25 Pfam PF07963 Prokaryotic N-terminal methylation motif
1 25 InterPro IPR012902 Prokaryotic N-terminal methylation site

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

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_A0A0H3GNA9
AlphaFold — — full sequence — Viewing
ColabFold KP13_01889
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
3 0.28