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0  structures 367  species 0  interactions 1162  sequences 3  architectures

Family: Bacteriocin_IIc (PF10439)

Summary: Bacteriocin class II with double-glycine leader peptide

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Bacteriocin class II with double-glycine leader peptide Provide feedback

This is a family of bacteriocidal bacteriocins secreted by Streptococcal species in order to kill off closely-related competitor Gram-positives. The sequence includes the peptide precursor, this being cleaved off proteolytically at the double-glycine. The family does not carry the YGNGVXC motif characteristic of pediocin-like Bacteriocins, Bacteriocin_II PF01721. The producer bacteria are protected from the effects of their own bacteriocins by production of a specific immunity protein which is co-transcribed with the genes encoding the bacteriocins, eg family EntA_Immun PF08951. The bacteriocins are structurally more specific than their immunity-protein counterparts. Typically, production of the bacteriocin gene is from within an operon carrying up to 6 genes including a typical two-component regulatory system (R and H), a small peptide pheromone (C), and a dedicated ABC transporter (A and -B) as well as an immunity protein [1]. The ABC transporter is thought to recognise the N termini of both the pheromone and the bacteriocins and to transport these peptides across the cytoplasmic membrane, concurrent with cleavage at the conserved double-glycine motif. Cleaved extracellular C can then bind to the sensor kinase, H, resulting in activation of R and up-regulation of the entire gene cluster via binding to consensus sequences within each promoter [2]. It seems likely that this whole regulon is carried on a transmissible plasmid which is passed between closely related Firmicute species since many clinical isolates from different Firmicutes can produce at least two bacteriocins. and the same bacteriocins can be produced by different species.

Literature references

  1. Dawid S, Roche AM, Weiser JN; , Infect Immun. 2007;75:443-451.: The blp bacteriocins of Streptococcus pneumoniae mediate intraspecies competition both in vitro and in vivo. PUBMED:17074857 EPMC:17074857

  2. Franz CM, van Belkum MJ, Holzapfel WH, Abriouel H, Galvez A; , FEMS Microbiol Rev. 2007;31:293-310.: Diversity of enterococcal bacteriocins and their grouping in a new classification scheme. PUBMED:17298586 EPMC:17298586


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR019493

Bacteriocins are proteinaceous toxins produced by bacteria to inhibit the growth of similar or closely related strains. The producer bacteria are protected from the effects of their own bacteriocins by production of a specific immunity protein which is co-transcribed with the genes encoding the bacteriocins, e.g. INTERPRO. The bacteriocins are structurally more specific than their immunity-protein counterparts. Typically, production of the bacteriocin gene is from within an operon carrying up to 6 genes including a typical two-component regulatory system (R and H), a small peptide pheromone (C), and a dedicated ABC transporter (A and -B) as well as an immunity protein [PUBMED:17074857]. The ABC transporter is thought to recognise the N termini of both the pheromone and the bacteriocins and to transport these peptides across the cytoplasmic membrane, concurrent with cleavage at the conserved double-glycine motif. Cleaved extracellular C can then bind to the sensor kinase, H, resulting in activation of R and up-regulation of the entire gene cluster via binding to consensus sequences within each promoter [PUBMED:17298586]. It seems likely that the whole regulon is carried on a transmissible plasmid which is passed between closely related Firmicute species since many clinical isolates from different Firmicutes can produce at least two bacteriocins, and the same bacteriocins can be produced by different species.

The proteins in this entry include amylovorin-L, lactacin-F and salivaricin CRL 1328, all of them class IIb two-peptide bacteriocins.

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 GG-leader (CL0400), which has the following description:

This is a collection of short bacterial families that carry a distinctive GG-cleavage motif. Conservation C-terminal to the GG-motif is not apparent. However, the families are all interconnected with critical virulence attributes of one kind or another.

The clan contains the following 5 members:

Antimicrobial17 Bacteriocin_IIc ComC L_biotic_typeA Lactococcin

Alignments

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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
(35)
Full
(1162)
Representative proteomes NCBI
(351)
Meta
(0)
RP15
(6)
RP35
(29)
RP55
(42)
RP75
(62)
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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
(35)
Full
(1162)
Representative proteomes NCBI
(351)
Meta
(0)
RP15
(6)
RP35
(29)
RP55
(42)
RP75
(62)
Alignment:
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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
(35)
Full
(1162)
Representative proteomes NCBI
(351)
Meta
(0)
RP15
(6)
RP35
(29)
RP55
(42)
RP75
(62)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
Gzipped 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: Manual
Previous IDs: none
Type: Family
Author: Coggill P
Number in seed: 35
Number in full: 1162
Average length of the domain: 66.30 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 90.98 %

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 27.0 27.0
Trusted cut-off 27.0 27.0
Noise cut-off 26.9 26.9
Model length: 65
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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