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18  structures 1  species 0  interactions 1  sequence 1  architecture

Family: Antig_Caf1 (PF09255)

Summary: Caf1 Capsule antigen

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Caf1 capsule antigen". More...

Caf1 capsule antigen Edit Wikipedia article

Antig_Caf1
PDB 1p5u EBI.jpg
x-ray structure of the ternary caf1m:caf1:caf1 chaperone:subunit:subunit complex
Identifiers
SymbolAntig_Caf1
PfamPF09255
InterProIPR015335
SCOP21p5v / SCOPe / SUPFAM

In molecular biology, Caf1 capsule antigen proteins are a family of the F1 capsule antigens Caf1 synthesised by Yersinia bacteria. They adopt a structure consisting of a seven strands arranged in two beta-sheets, in a Greek-key topology, and mediate targeting of the bacterium to sites of infection.[1]

References

  1. ^ Zavialov AV, Berglund J, Pudney AF, Fooks LJ, Ibrahim TM, MacIntyre S, Knight SD (2003). "Structure and biogenesis of the capsular F1 antigen from Yersinia pestis: preserved folding energy drives fiber formation". Cell. 113 (5): 587–96. PMID 12787500. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
This article incorporates text from the public domain Pfam and InterPro: IPR015335

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Caf1 Capsule antigen Provide feedback

Members of this family are predominantly found in the F1 capsule antigen Caf1 synthesised by Yersinia bacteria. They adopt a structure consisting of a seven strands arranged in two beta-sheets, in a Greek-key topology, and mediate targeting of the bacterium to sites of infection [1].

Literature references

  1. Zavialov AV, Berglund J, Pudney AF, Fooks LJ, Ibrahim TM, MacIntyre S, Knight SD; , Cell. 2003;113:587-596.: Structure and biogenesis of the capsular F1 antigen from Yersinia pestis: preserved folding energy drives fiber formation. PUBMED:12787500 EPMC:12787500


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR015335

Members of this family represent the F1 capsule antigen Caf1 synthesised by the Yersinia pestis bacteria. They adopt a structure consisting of a seven strands arranged in two beta-sheets, in a Greek-key topology, and mediate targeting of the bacterium to sites of infection [ PUBMED:12787500 ].

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_N2

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 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
(1)
Full
(1)
Representative proteomes UniProt
(27)
RP15
(0)
RP35
(1)
RP55
(1)
RP75
(2)
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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
(1)
Full
(1)
Representative proteomes UniProt
(27)
RP15
(0)
RP35
(1)
RP55
(1)
RP75
(2)
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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
(1)
Full
(1)
Representative proteomes UniProt
(27)
RP15
(0)
RP35
(1)
RP55
(1)
RP75
(2)
Raw Stockholm Download   Download     Download   Download   Download   Download  
Gzipped 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: pdb_1p5v
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Sammut SJ
Number in seed: 1
Number in full: 1
Average length of the domain: 136 aa
Average identity of full alignment: 100 %
Average coverage of the sequence by the domain: 80 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 37.6 307.3
Noise cut-off 23.6 21.9
Model length: 136
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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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 Antig_Caf1 domain has been found. There are 18 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
P26948 View 3D Structure Click here