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0  structures 0  species 7  interactions 0  sequences 0  architectures

Family: End_tail_spike (PF12219)

Summary: Catalytic domain of bacteriophage endosialidase

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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.

Catalytic domain of bacteriophage endosialidase Provide feedback

This domain family is found in bacteria and viruses, and is approximately 160 amino acids in length. There are two conserved sequence motifs: VSR and YGA. This domain is the C terminal domain of the bacteriophage protein endosialidase. The endosialidase protein forms homotrimeric molecules and this domain complexes into a tail-spike stalk. The stalk region folds in a triple beta-helix that is interrupted by a small triple beta-prism domain. The tail-spike is a multifunctional protein device used by the phage to fulfill the following functions: (i) to adsorb to the bacterial polySia capsule (ii) to de-polymerise the capsule to gain access to the outer bacterial membrane, and finally (iii) to mediate tight adhesion to the membrane, a prerequisite for the initiation of the infection cycle.

Literature references

  1. Stummeyer K, Dickmanns A, Muhlenhoff M, Gerardy-Schahn R, Ficner R;, Nat Struct Mol Biol. 2005;12:90-96.: Crystal structure of the polysialic acid-degrading endosialidase of bacteriophage K1F. PUBMED:15608653 EPMC:15608653


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024430

This entry represents the C-terminal domain of endosialidase, which is approximately 160 amino acids in length. There are two conserved sequence motifs: VSR and YGA. The endosialidase protein forms homotrimeric molecules and this domain complexes into a tail-spike stalk. The stalk region folds in a triple beta-helix that is interrupted by a small triple beta-prism domain. The tail-spike is a multifunctional protein device used by the phage to fulfil the following functions: (i) to adsorb to the bacterial polySia capsule (ii) to de-polymerise the capsule to gain access to the outer bacterial membrane, and finally (iii) to mediate tight adhesion to the membrane, a prerequisite for the initiation of the infection cycle [PUBMED:15608653].

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 Phage_fibre (CL0606), which has the following description:

According to SCOP this superfamily includes phage tail fibre proteins that form homotrimers with each chain donating 3 beta-strands per turn of the helix

The clan contains the following 4 members:

End_tail_spike gp12-short_mid Gp5_C Hyaluronidase_1

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
(5)
Full
(0)
Representative proteomes UniProt
(55)
NCBI
(161)
Meta
(2)
RP15
(0)
RP35
(0)
RP55
(1)
RP75
(6)
Jalview View        View  View  View  View  View 
HTML View                 
PP/heatmap 1                

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

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

Format an alignment

  Seed
(5)
Full
(0)
Representative proteomes UniProt
(55)
NCBI
(161)
Meta
(2)
RP15
(0)
RP35
(0)
RP55
(1)
RP75
(6)
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
(5)
Full
(0)
Representative proteomes UniProt
(55)
NCBI
(161)
Meta
(2)
RP15
(0)
RP35
(0)
RP55
(1)
RP75
(6)
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_1v0e
Previous IDs: none
Type: Domain
Author: Mistry J, Gavin OL
Number in seed: 5
Number in full: 0
Average length of the domain: 0.00 aa
Average identity of full alignment: 0 %
Average coverage of the sequence by the domain: 0.00 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 17690987 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.0 25.0
Trusted cut-off 25.3 29.5
Noise cut-off 24.9 24.8
Model length: 160
Family (HMM) version: 6
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 are 7 interactions for this family. More...

End_beta_barrel End_N_terminal End_beta_barrel End_beta_propel End_tail_spike End_N_terminal End_beta_propel