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121  structures 945  species 0  interactions 1639  sequences 22  architectures

Family: Pilin (PF00114)

Summary: Pilin (bacterial filament)

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

This is the Wikipedia entry entitled "Pilin". More...

Pilin Edit Wikipedia article

Pilin refers to a class of fibrous proteins that have a characteristic fold and are found in pilus structures in bacteria. Bacterial pili are used in the exchange of geneic material during bacterial conjugation, and a short pilus called a fimbrium is used as a cell adhesion mechanism. Although not all bacteria have pili or fimbriae, bacterial pathogens often use their fimbriae to attach to host cells. In gram-negative bacteria, where pili are more common, individual pilin molecules are linked by noncovalent protein-protein interactions, while gram-positive bacteria often have polymerized pilin[1].

Pilin proteins themselves are α+β proteins characterized by a very long N-terminal alpha helix. Many pilins are post-translationally modified by glycosylation or phosphorylation. The assembly of a complete pilus relies on interactions between the N-terminal helices of the individual monomers. The pilus structure sequesters the helices in the center of the fiber lining a central pore, while antiparallel beta sheets occupy the exterior of the fiber[2]. The exact mechanism of pilus assembly from monomers is not known, although chaperone proteins have been identified for some types of pili[3] and specific amino acids required for proper pilus formation have been isolated[4].

References

  1. ^ Telford JL, Barocchi MA, Margarit I, Rappuoli R, Grandi G. (2006). Pili in gram-positive pathogens. Nat Rev Microbiol 4(7):509-19.
  2. ^ Forest KT, Tainer JA. (1997). Type-4 pilus-structure: outside to inside and top to bottom--a minireview. Gene 192(1):165-9.
  3. ^ Jones CH, Pinkner JS, Nicholes AV, Slonim LN, Abraham SN, Hultgren SJ. (1993). FimC is a periplasmic PapD-like chaperone that directs assembly of type 1 pili in bacteria. Proc Natl Acad Sci USA 90(18):8397-401.
  4. ^ Mu XQ, Jiang ZG, Bullitt E. (2005). Localization of a critical interface for helical rod formation of bacterial adhesion P-pili. J Mol Biol 346(1):13-20.

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Pilin (bacterial filament) Provide feedback

Proteins with only the short N-terminal methylation site are not separated from the noise. The Prosite pattern detects those better.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001082

Pilin is a component of type IV pilus (T4P), a polar flexible filament, which consists of a single polypeptide chain arranged in a helical configuration of five subunits per turn, which is involved cell adhesion, microcolony formation, twitching motility and transformation [ PUBMED:31431558 , PUBMED:10850981 ]. Gram-negative bacteria produce pilin which is characterised by the presence of a very short leader peptide of 6 to 7 residues, followed by a methylated N-terminal phenylalanine residue and by a highly conserved sequence of about 24 hydrophobic residues, of the NMePhe type pilin [ PUBMED:2898203 , PUBMED:3118043 ].

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 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...

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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
(140)
Full
(1639)
Representative proteomes UniProt
(10050)
RP15
(269)
RP35
(804)
RP55
(1661)
RP75
(3206)
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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
(140)
Full
(1639)
Representative proteomes UniProt
(10050)
RP15
(269)
RP35
(804)
RP55
(1661)
RP75
(3206)
Alignment:
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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
(140)
Full
(1639)
Representative proteomes UniProt
(10050)
RP15
(269)
RP35
(804)
RP55
(1661)
RP75
(3206)
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: pilin;
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL
Number in seed: 140
Number in full: 1639
Average length of the domain: 112.8 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 66.03 %

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 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 109
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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

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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 Pilin domain has been found. There are 121 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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