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7  structures 905  species 1  interaction 1395  sequences 11  architectures

Family: DotU (PF09850)

Summary: Type VI secretion system protein DotU

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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.

Type VI secretion system protein DotU Provide feedback

DotU is a family of Gram-negative bacterial proteins that form part of the membrane-joining complex of the type VI secretion system. DotU binds tightly to IcmF and together they are tethered to the inner membrane at one end and the peptidoglycan layer at the other; they interact with Lip1 which then tethers the peptidoglycan layer to the outer membrane [1].

Literature references

  1. Filloux A;, F1000Prime Rep. 2013;5:52.: The rise of the Type VI secretion system. PUBMED:24381728 EPMC:24381728


This tab holds annotation information from the InterPro database.

InterPro entry IPR017732

At least two distinct groups of proteins, often encoded by adjacent genes, show sequence similarity due to homology between type IV secretion systems and type VI secretion systems. One is the IcmF family (INTERPRO). The other group is the DotU family, which includes DotU from the Legionella pneumophila type IV secretion system. Many members of this protein family from type VI secretion systems have an additional C-terminal domain with OmpA/MotB homology 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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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
(146)
Full
(1395)
Representative proteomes UniProt
(11193)
NCBI
(18660)
Meta
(31)
RP15
(123)
RP35
(480)
RP55
(1341)
RP75
(3412)
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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
(146)
Full
(1395)
Representative proteomes UniProt
(11193)
NCBI
(18660)
Meta
(31)
RP15
(123)
RP35
(480)
RP55
(1341)
RP75
(3412)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(146)
Full
(1395)
Representative proteomes UniProt
(11193)
NCBI
(18660)
Meta
(31)
RP15
(123)
RP35
(480)
RP55
(1341)
RP75
(3412)
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: COGs (COG3455)
Previous IDs: DUF2077;
Type: Family
Sequence Ontology: SO:0100021
Author: COGs, Finn RD , Sammut SJ
Number in seed: 146
Number in full: 1395
Average length of the domain: 201.10 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 59.95 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.7 21.7
Trusted cut-off 21.7 21.7
Noise cut-off 21.6 21.6
Model length: 205
Family (HMM) version: 10
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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Interactions

There is 1 interaction for this family. More...

DotU

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 DotU domain has been found. There are 7 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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