Powering down the Pfam website
On October 5th, we began redirecting traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will remain available at pfam-legacy.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
44  structures 1122  species 0  interactions 1262  sequences 3  architectures

Family: PilP (PF04351)

Summary: Pilus assembly protein, PilP

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Pilus assembly protein, PilP Provide feedback

The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [1].

Literature references

  1. Sakai D, Komano T; , J Bacteriol 2002;184:444-451.: Genes required for plasmid R64 thin-pilus biogenesis: identification and localization of products of the pilK, pilM, pilO, pilP, pilR, and pilT genes. PUBMED:11751821 EPMC:11751821

This tab holds annotation information from the InterPro database.

InterPro entry IPR007446

Bacterial type IV pili are surface filaments critical for diverse biological processes including surface and host cell adhesion, colonisation, biofilm formation, twitching motility, DNA uptake during natural transformation and virulence [ PUBMED:7565110 , PUBMED:27022027 ]. The proteins necessary to form the type IV pili inner-membrane complex, are included in the pilMNOPQ operon which encodes the cytoplasmic actin-like protein PilM, PilN, PilO, the periplasmic lipoprotein PilP and the outer-membrane secretin PilQ. The inner-membrane PilM/N/O/P complex is required for the optimal function of the outer-membrane secretin PilQ. This cluster is highly conserved across the type IV pilus-producing bacterial species, and all of these proteins have been shown to be essential for twitching motility [ PUBMED:19857646 , PUBMED:19857645 ].

The PilP family are periplasmic proteins involved in the biogenesis of type IV pili [ PUBMED:11751821 ]. The N-terminal domain of PilP interacts with the periplasmic regions of PilNO, while the C-terminal beta-domain of PilP interacts with the N0 domain of PilQ, connecting PilO to the secretin PilQ [ PUBMED:23457250 ].

This entry also includes competence protein D (comD) from Haemophilus influenzae which is encoded in the homologous operon comA/B/C/D/E.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

Loading domain graphics...

Pfam Clan

This family is a member of clan PilP (CL0655), which has the following description:

The clan contains the following 3 members:



We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

Representative proteomes UniProt
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

Representative proteomes UniProt

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

Representative proteomes UniProt
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...


This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: COG3168
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Mifsud W
Number in seed: 95
Number in full: 1262
Average length of the domain: 141.9 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 78.1 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.6 25.6
Trusted cut-off 25.7 25.6
Noise cut-off 25.4 25.4
Model length: 147
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


Generate a FASTA-format file

Clear selection

This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

Loading sunburst data...

Tree controls


The tree shows the occurrence of this domain across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the PilP domain has been found. There are 44 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

Loading structure mapping...

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
G3XCX7 View 3D Structure Click here
P31771 View 3D Structure Click here
Q5FAD1 View 3D Structure Click here