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.
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 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
-
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
HOMSTRAD: | pili_assembly |
PROSITE: | PDOC00552 |
SCOP: | 3dpa |
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.
Cellular component | outer membrane-bounded periplasmic space (GO:0030288) |
Biological process | cell wall organization (GO:0071555) |
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 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_NAlignments
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 | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 | |||||||
Gzipped |
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
Seed source: | Prosite |
Previous IDs: | pili_assembly; Pili_assembly_N; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
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
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 125 | ||||||||||||
Family (HMM) version: | 23 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
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...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
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.
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.
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.