Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
0  structures 332  species 0  interactions 1343  sequences 3  architectures

Family: SCPU (PF05229)

Summary: Spore Coat Protein U 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.

Spore Coat Protein U domain Provide feedback

This domain is found in a bacterial family of spore coat proteins [1] as well as a family of secreted pili proteins involved in motility and biofilm formation ([2]). This family is distantly related to fimbrial proteins.

Literature references

  1. Gollop R, Inouye M, Inouye S; , J Bacteriol 1991;173:3597-3600.: Protein U, a late-developmental spore coat protein of Myxococcus xanthus, is a secretory protein. PUBMED:1904442 EPMC:1904442

  2. Tomaras AP, Dorsey CW, Edelmann RE, Actis LA; , Microbiology 2003;149:3473-3484.: Attachment to and biofilm formation on abiotic surfaces by Acinetobacter baumannii: involvement of a novel chaperone-usher pili assembly system. PUBMED:14663080 EPMC:14663080


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007893

This domain is found in protein U, a spore coat protein produced at the late stage of development of Myxococcus xanthus. Protein U is produced as a secretory precursor, pro-protein U, which is then secreted across the membrane to assemble on the spore surface [PUBMED:1904442]. This domain is also found in a number of the genes within a conserved polycistronic operon that encodes a novel chaperone-usher pili assembly system. Examples are CsuA/B of Acinetobacter baumannii, and the CsuA, CsuB and CsuE of Vibrio parahaemolyticus and the related genes of Yersinia pestis.

In A. baumannii, csuC and csuE are required in the early steps of the process that that leads to biofilm formation. The conservation of the genes and gene order among unrelated bacteria, suggests that the csu operon is widespread and is involved in surface pilus formation which allows the bacteria to form biofilms on abiotic surfaces, a property that may aid there survival in their natural environment [PUBMED:14663080].

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 Adhesin (CL0204), which has the following description:

This superfamily includes a variety of bacterial adhesins that have a jelly-roll beta-barrel fold [1]. These domains are involved in sugar recognition.

The clan contains the following 7 members:

Adhesin_Dr Collagen_bind Collagen_bind_2 DUF1120 Fimbrial PapG_N SCPU

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(127)
Full
(1343)
Representative proteomes NCBI
(1103)
Meta
(36)
RP15
(48)
RP35
(107)
RP55
(209)
RP75
(336)
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(127)
Full
(1343)
Representative proteomes NCBI
(1103)
Meta
(36)
RP15
(48)
RP35
(107)
RP55
(209)
RP75
(336)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(127)
Full
(1343)
Representative proteomes NCBI
(1103)
Meta
(36)
RP15
(48)
RP35
(107)
RP55
(209)
RP75
(336)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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: Yeats C
Previous IDs: none
Type: Domain
Author: Yeats C
Number in seed: 127
Number in full: 1343
Average length of the domain: 142.70 aa
Average identity of full alignment: 23 %
Average coverage of the sequence by the domain: 81.23 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.4 22.4
Trusted cut-off 22.4 22.5
Noise cut-off 22.2 22.3
Model length: 139
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Show

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...

Loading sunburst data...

Tree controls

Hide

The 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.