Summary: Spore Coat Protein U domain
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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
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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
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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
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...
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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 17 members:
Adhesin_Dr AfaD AgI_II_C2 Antig_Caf1 Antigen_C Collagen_bind DUF1120 Fim-adh_lectin FimA Fimbrial FimH_man-bind GramPos_pilinBB PapG_N Saf-Nte_pilin SCPU SdrG_C_C Sgo0707_N2Alignments
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 (54) |
Full (1617) |
Representative proteomes | UniProt (14538) |
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RP15 (147) |
RP35 (583) |
RP55 (1622) |
RP75 (3958) |
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HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (54) |
Full (1617) |
Representative proteomes | UniProt (14538) |
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RP15 (147) |
RP35 (583) |
RP55 (1622) |
RP75 (3958) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | Yeats C |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Yeats C |
Number in seed: | 54 |
Number in full: | 1617 |
Average length of the domain: | 139.5 aa |
Average identity of full alignment: | 23 % |
Average coverage of the sequence by the domain: | 80.49 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 139 | ||||||||||||
Family (HMM) version: | 18 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 SCPU 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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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.
Protein | Predicted structure | External Information |
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Q9HVD9 | View 3D Structure | Click here |
Q9HVE2 | View 3D Structure | Click here |
Q9HVE3 | View 3D Structure | Click here |
Q9HVE4 | View 3D Structure | Click here |