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2  structures 28  species 0  interactions 32  sequences 3  architectures

Family: PilJ_C (PF18223)

Summary: Pili PilJ C-terminal domain

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.

Pili PilJ C-terminal domain Provide feedback

This is the C-terminal domain of PilJ, a Type IV pilin found in gram-positive Clostridium difficile. Incorporation of PilJ into pili exposes the C-terminal domain of PilJ to create a novel interaction surface. This C-terminal domain is not observed in other Type IV pilin proteins [1].

Literature references

  1. Piepenbrink KH, Maldarelli GA, de la Pena CF, Mulvey GL, Snyder GA, De Masi L, von Rosenvinge EC, Gunther S, Armstrong GD, Donnenberg MS, Sundberg EJ;, J Biol Chem. 2014;289:4334-4345.: Structure of Clostridium difficile PilJ exhibits unprecedented divergence from known type IV pilins. PUBMED:24362261 EPMC:24362261


This tab holds annotation information from the InterPro database.

InterPro entry IPR040599

This is the C-terminal domain of PilJ, a Type IV pilin found in Gram-positive Clostridium difficile. Incorporation of PilJ into pili exposes the C-terminal domain of PilJ to create a novel interaction surface. This C-terminal domain is not observed in other Type IV pilin proteins [ PUBMED:24362261 ].

Domain organisation

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

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Pfam Clan

This family is a member of clan Pilus (CL0327), which has the following description:

This clan contains bacterial and archaeal systems involved in flagellar or twitching motility, adhesion, protein secretion, and DNA uptake, such as type II secretion system (T2SS), the type IV pilus or the competence pilus (Com) [4]. Pili proteins enable the transfer of plasmid between bacteria. The families in this clan adopt an alpha helical structure which is packed against a beta sheet [2-3].

The clan contains the following 15 members:

Arch_flagellin Bundlin ComP_DUS GspH PilA4 Pilin Pilin_GH Pilin_PilX PilJ_C PilM PilS T2SSG T2SSI T2SSJ TcpA

Alignments

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.

  Seed
(7)
Full
(32)
Representative proteomes UniProt
(126)
RP15
(8)
RP35
(27)
RP55
(33)
RP75
(48)
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

  Seed
(7)
Full
(32)
Representative proteomes UniProt
(126)
RP15
(8)
RP35
(27)
RP55
(33)
RP75
(48)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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.

  Seed
(7)
Full
(32)
Representative proteomes UniProt
(126)
RP15
(8)
RP35
(27)
RP55
(33)
RP75
(48)
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...

Trees

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: ECOD:EUF03122
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Smart A
Number in seed: 7
Number in full: 32
Average length of the domain: 95.1 aa
Average identity of full alignment: 21 %
Average coverage of the sequence by the domain: 30.14 %

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 26.7 26.7
Trusted cut-off 26.8 27.1
Noise cut-off 26.3 26.3
Model length: 95
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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

Selections

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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...

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Structures

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 PilJ_C domain has been found. There are 2 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.

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