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8  structures 1123  species 0  interactions 1619  sequences 5  architectures

Family: ComP_DUS (PF16732)

Summary: Type IV minor pilin ComP, DNA uptake sequence receptor

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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.

Type IV minor pilin ComP, DNA uptake sequence receptor Provide feedback

ComP-DUS is the DNA-uptake sequence receptor of pathogenic Proteobacteria. ComP is a type IV minor pilin -site on the minor type IV pilin, C one of three minor (low abundance) pilins in pathogenic Proteobacteria Neisseria species (with PilV and PilX). These modulate Tfp-mediated properties without affecting Tfp biogenesis. ComP plays a prominent role in competence at the level of DNA uptake. Comp is exposed on the surface of Neisseria filaments, and it is this that recognises homotypic DNA through genus-specific DNA uptake sequence (DUS) motifs [1].

Literature references

  1. Cehovin A, Simpson PJ, McDowell MA, Brown DR, Noschese R, Pallett M, Brady J, Baldwin GS, Lea SM, Matthews SJ, Pelicic V;, Proc Natl Acad Sci U S A. 2013;110:3065-3070.: Specific DNA recognition mediated by a type IV pilin. PUBMED:23386723 EPMC:23386723


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR031982

ComP is a type IV minor pilin which plays a key role in pathogenesis and a DNA uptake sequence (DUS) receptor which is involved in natural transformation in Neisseria species [PUBMED:24385921]. Natural transformation is a process by which competent bacteria take up free DNA and incorporate it into their genomes [PUBMED:24385921]. ComP can bind any DNA, but displays a marked preference for Neisseria DUS motifs, and hence might be directly responsible for selective DNA uptake in Neisseria species [PUBMED:23386723].

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 is a clan contains bacterial pilus subunits and proteins involved in secretion. 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 13 members:

Bundlin ComP_DUS GspH 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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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
(109)
Full
(1619)
Representative proteomes UniProt
(5514)
NCBI
(8382)
Meta
(108)
RP15
(341)
RP35
(1009)
RP55
(1656)
RP75
(2543)
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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
(109)
Full
(1619)
Representative proteomes UniProt
(5514)
NCBI
(8382)
Meta
(108)
RP15
(341)
RP35
(1009)
RP55
(1656)
RP75
(2543)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(109)
Full
(1619)
Representative proteomes UniProt
(5514)
NCBI
(8382)
Meta
(108)
RP15
(341)
RP35
(1009)
RP55
(1656)
RP75
(2543)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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: Pfam-B_19918 (release 27.0), pdb:2m3k-A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 109
Number in full: 1619
Average length of the domain: 93.90 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 64.93 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.3 27.3
Trusted cut-off 27.3 27.3
Noise cut-off 27.2 27.2
Model length: 87
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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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 ComP_DUS domain has been found. There are 8 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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