Summary: Pili and flagellar-assembly chaperone, PapD N-terminal domain
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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.
Internal database links
|SCOOP:||Urease_beta DUF1043 DUF2400|
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.
This entry represents the N-terminal domain of pili assembly chaperone, and has a beta-sandwich fold consisting of seven strands in two sheets with a Greek key topology.
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)|
- the number of sequences which exhibit this architecture
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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 6 members:ASH DUF1573 Motile_Sperm PapD-like PapD_N TMEM131_like
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the UniProtKB sequence database using the family HMM
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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Curation and family details
|Previous IDs:||pili_assembly; Pili_assembly_N;|
|Author:||Finn RD, Griffiths-Jones SR|
|Number in seed:||88|
|Number in full:||645|
|Average length of the domain:||121.30 aa|
|Average identity of full alignment:||27 %|
|Average coverage of the sequence by the domain:||49.84 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|Download:||download the raw HMM for this family|
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There are 19 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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 107 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 seqence.
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