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8  structures 167  species 0  interactions 258  sequences 25  architectures

Family: Pyocin_S (PF06958)

Summary: S-type Pyocin

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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.

S-type Pyocin Provide feedback

This family represents a conserved region approximately 180 residues long within bacterial S-type pyocins. Pyocins are polypeptide toxins produced by, and active against, bacteria. S-type pyocins cause cell death by DNA breakdown due to endonuclease activity [1].

Literature references

  1. Michel-Briand Y, Baysse C; , Biochimie 2002;84:499-510.: The pyocins of Pseudomonas aeruginosa. PUBMED:12423794 EPMC:12423794


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR016128

This entry represents a structural domain with a complex fold made of several coiled beta-sheets. This domain is found at the N-terminal of both colicin E3 and colicin B, and acts as a translocation domain. It also occurs in S-type pyocin. Both pyocin and cloacin are bacteriocins, protein antibiotics that kill bacteria closely related to the producing species. Colicins are a subgroup of bacteriocins that are produced by and target Escherichia coli. The lethal action of most colicins is exerted either by formation of a pore in the cytoplasmic membrane of the target cell, or by an enzymatic nuclease digestion mechanism [PUBMED:12409205].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 Bacteriocin_TLN (CL0446), which has the following description:

A number of different bacterial species produce bacteriocins to kill competitor species, and the colicin class is a group of complex three-domain structures. The receptor-binding domain recognises and binds to specific cell surface receptors on the target cells; the N-terminal translocation domain interacts with cell membrane proteins to gain access to the cell interior; the C-terminal domain specifies a killing activity, such as pore formation or nuclease activity. This superfamily is a collection of the translocating domains.

The clan contains the following 2 members:

Cloacin Pyocin_S

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
(39)
Full
(258)
Representative proteomes NCBI
(270)
Meta
(1)
RP15
(3)
RP35
(12)
RP55
(30)
RP75
(54)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(39)
Full
(258)
Representative proteomes NCBI
(270)
Meta
(1)
RP15
(3)
RP35
(12)
RP55
(30)
RP75
(54)
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
(39)
Full
(258)
Representative proteomes NCBI
(270)
Meta
(1)
RP15
(3)
RP35
(12)
RP55
(30)
RP75
(54)
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: Pfam-B_20020 (release 10.0)
Previous IDs: none
Type: Family
Author: Vella Briffa B
Number in seed: 39
Number in full: 258
Average length of the domain: 134.20 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 24.52 %

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 22.5 22.5
Trusted cut-off 23.0 22.5
Noise cut-off 21.7 21.7
Model length: 139
Family (HMM) version: 7
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 Pyocin_S 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 seqence.

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