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125  structures 726  species 0  interactions 1997  sequences 11  architectures

Family: PapD_N (PF00345)

Summary: Pili and flagellar-assembly chaperone, PapD N-terminal domain

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

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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 and flagellar-assembly chaperone, PapD N-terminal domain Provide feedback

C2 domain-like beta-sandwich fold. This domain is the n-terminal part of the PapD chaperone protein for pilus and flagellar assembly.

Literature references

  1. Holmgren A, Branden CI; , Nature 1989;342:248-251.: Crystal structure of chaperone protein PapD reveals an immunoglobulin fold. PUBMED:2478891 EPMC:2478891


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016147

Most Gram-negative bacteria possess a supramolecular structure - the pili - on their surface, which mediates attachment to specific receptors. Many interactive subunits are required to assemble pili, but their assembly only takes place after translocation across the cytoplasmic membrane. Periplasmic chaperones assist pili assembly by binding to the subunits, thereby preventing premature aggregation [ PUBMED:8670884 , PUBMED:1683764 ]. Pili chaperones are structurally, and possibly evolutionarily, related to the immunoglobulin superfamily [ PUBMED:1348692 , PUBMED:17082819 ]: they contain two globular domains, with a topology identical to an immunoglobulin fold [ PUBMED:2478891 ].

This entry represents the N-terminal domain.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 PapD-like (CL0556), which has the following description:

This superfamily is characterised by proteins in families involved in ciliary or flagellar function. The families may be acting as chaperones.

The clan contains the following 8 members:

ASH DUF1573 EcpB_C Motile_Sperm PapD-like PapD_N Peptidase_M60_C TMEM131_like_N

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
(74)
Full
(1997)
Representative proteomes UniProt
(35175)
RP15
(140)
RP35
(577)
RP55
(1993)
RP75
(6245)
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
(74)
Full
(1997)
Representative proteomes UniProt
(35175)
RP15
(140)
RP35
(577)
RP55
(1993)
RP75
(6245)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(74)
Full
(1997)
Representative proteomes UniProt
(35175)
RP15
(140)
RP35
(577)
RP55
(1993)
RP75
(6245)
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: Prosite
Previous IDs: pili_assembly; Pili_assembly_N;
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD , Griffiths-Jones SR
Number in seed: 74
Number in full: 1997
Average length of the domain: 121.4 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 50.54 %

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 23.0 23.0
Trusted cut-off 23.0 23.0
Noise cut-off 22.9 22.9
Model length: 125
Family (HMM) version: 23
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 PapD_N domain has been found. There are 125 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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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
A0A077ZDQ9 View 3D Structure Click here
A0A0H3GGZ6 View 3D Structure Click here
A0A0H3GLA1 View 3D Structure Click here
A0A0H3GNA0 View 3D Structure Click here
A0A0H3GSF8 View 3D Structure Click here
A0A0H3GST7 View 3D Structure Click here
A0A0H3GT77 View 3D Structure Click here
A0A0H3H2G9 View 3D Structure Click here
H9L411 View 3D Structure Click here
H9L483 View 3D Structure Click here
P26926 View 3D Structure Click here
P28722 View 3D Structure Click here
P31697 View 3D Structure Click here
P33128 View 3D Structure Click here
P33342 View 3D Structure Click here
P33409 View 3D Structure Click here
P37923 View 3D Structure Click here
P40876 View 3D Structure Click here
P42914 View 3D Structure Click here
P43661 View 3D Structure Click here
P53520 View 3D Structure Click here
P69965 View 3D Structure Click here
P75749 View 3D Structure Click here
P75856 View 3D Structure Click here
P77249 View 3D Structure Click here
P77599 View 3D Structure Click here
P77616 View 3D Structure Click here
Q32DK1 View 3D Structure Click here
Q32HW2 View 3D Structure Click here
Q32IL6 View 3D Structure Click here
Q32JM8 View 3D Structure Click here
Q8X5E4 View 3D Structure Click here
Q8ZJU0 View 3D Structure Click here
Q8ZJV4 View 3D Structure Click here
Q8ZM91 View 3D Structure Click here
Q8ZNN6 View 3D Structure Click here
Q8ZRI0 View 3D Structure Click here
Q8ZRI3 View 3D Structure Click here
Q8ZRK3 View 3D Structure Click here
Q8ZRR5 View 3D Structure Click here