Summary: S-type Pyocin
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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 .
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].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Biological process||pathogenesis (GO:0009405)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
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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
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
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Curation and family details
|Seed source:||Pfam-B_20020 (release 10.0)|
|Author:||Vella Briffa B|
|Number in seed:||39|
|Number in full:||1775|
|Average length of the domain:||137.20 aa|
|Average identity of full alignment:||33 %|
|Average coverage of the sequence by the domain:||25.30 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||8|
|Download:||download the raw HMM for this family|
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The tree shows the occurrence of this domain across different species. More...
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There are 4 interactions for this family. More...
We determine these interactions using iPfam, which considers the interactions between residues in three-dimensional protein structures and maps those interactions back to Pfam families. You can find more information about the iPfam algorithm in the journal article that accompanies the website.
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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