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8  structures 9  species 1  interaction 48  sequences 1  architecture

Family: DUF576 (PF04507)

Summary: Csa1 family

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.

"DUF" families are annotated with the Domain of unknown function Wikipedia article. This is a general article, with no specific information about individual Pfam DUFs. If you have information about this particular DUF, please let us know using the "Add annotation" button below.

Csa1 family Provide feedback

This family contains several uncharacterised staphylococcal proteins. These proteins have been called conserved staphylococcal antigens (Csa) [1].

Literature references

  1. Schluepen C, Malito E, Marongiu A, Schirle M, McWhinnie E, Lo Surdo P, Biancucci M, Falugi F, Nardi-Dei V, Marchi S, Fontana MR, Lombardi B, De Falco MG, Rinaudo CD, Spraggon G, Nissum M, Bagnoli F, Grandi G, Bottomley MJ, Liberatori S;, Biochem J. 2013;455:273-284.: Mining the bacterial unknown proteome: identification and characterization of a novel family of highly conserved protective antigens in Staphylococcus aureus. PUBMED:23895222 EPMC:23895222


This tab holds annotation information from the InterPro database.

InterPro entry IPR007595

This family contains several uncharacterised proteins mostly from staphylococcal. These proteins have been called conserved staphylococcal antigens (Csa) [PUBMED:23895222].

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 LolA_LolB (CL0048), which has the following description:

Gram-negative bacteria lipoproteins are anchored to the periplasmic surface of the inner or outer membrane depending on the sorting signal, which is the residue at position 2 of the polypeptide. Five Lol proteins are involved in the sorting and membrane localisation of lipoprotein. An ATP-binding cassette (ABC) transporter, LolCDE, releases outer membrane-specific lipoproteins from the inner membrane, causing the formation of a complex between the released lipoproteins and the periplasmic molecular chaperone LolA. When this complex interacts with outer membrane receptor LolB, the lipoproteins are transferred from LolA to LolB and then localised to the outer membrane. The structures of LolA and LolB are remarkably similar to each other. Both have a hydrophobic cavity consisting of an unclosed beta-barrel and an alpha-helical lid [1,2].

The clan contains the following 16 members:

DUF1329 DUF1571 DUF2092 DUF3108 DUF3261 DUF4292 DUF4412 DUF576 LolA LolA_2 LolA_like LolB LppX_LprAFG MucB_RseB Porph_ging VioE

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
(23)
Full
(48)
Representative proteomes UniProt
(919)
NCBI
(8230)
Meta
(0)
RP15
(2)
RP35
(15)
RP55
(50)
RP75
(83)
Jalview View  View  View  View  View  View  View  View   
HTML View  View               
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
(23)
Full
(48)
Representative proteomes UniProt
(919)
NCBI
(8230)
Meta
(0)
RP15
(2)
RP35
(15)
RP55
(50)
RP75
(83)
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
(23)
Full
(48)
Representative proteomes UniProt
(919)
NCBI
(8230)
Meta
(0)
RP15
(2)
RP35
(15)
RP55
(50)
RP75
(83)
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.

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_2120 (release 7.5)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mifsud W , Bateman A
Number in seed: 23
Number in full: 48
Average length of the domain: 198.10 aa
Average identity of full alignment: 51 %
Average coverage of the sequence by the domain: 87.30 %

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 21.9 21.9
Trusted cut-off 23.0 38.3
Noise cut-off 21.3 18.1
Model length: 225
Family (HMM) version: 12
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...

DUF576

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 DUF576 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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