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0  structures 539  species 0  interactions 789  sequences 1  architecture

Family: AgrB (PF04647)

Summary: Accessory gene regulator B

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Accessory gene regulator B Provide feedback

The arg locus consists of two transcripts: RNAII and RNAIII. RNAII encodes four genes (agrA, B, C, and D) whose gene products assemble a quorum sensing system. AgrB and AgrD are essential for the production of the autoinducing peptide which functions as a signal for quorum sensing. AgrB is a transmembrane protein [1].

Literature references

  1. Saenz HL, Augsburger V, Vuong C, Jack RW, Gotz F, Otto M; , Arch Microbiol 2000;174:452-455.: Inducible expression and cellular location of AgrB, a protein involved in the maturation of the staphylococcal quorum-sensing pheromone. PUBMED:11195102 EPMC:11195102


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006741

The accessory gene regulator (agr) of Staphylococcus aureus is the central regulatory system that controls the gene expression for a large set of virulence factors. The arg locus consists of two transcripts: RNAII and RNAIII. RNAII encodes four genes (agrA, B, C, and D) whose gene products assemble a quorum sensing system. At low cell density, the agr genes are continuously expressed at basal levels. A signal molecule, autoinducing peptide (AIP), produced and secreted by the bacteria, accumulates outside of the cells. When the cell density increases and the AIP concentration reaches a threshold, it activates the agr response, i.e. activation of secreted protein gene expression and subsequent repression of cell wall-associated protein genes. AgrB and AgrD are essential for the production of the autoinducing peptide which functions as a signal for quorum sensing. AgrB is a transmembrane protein [PUBMED:11195102] involved in the proteolytic processing of AgrD, and may have both proteolytic and transporter activities, facilitating the export of the processed AgrD peptide [PUBMED:12122003].

Gene Ontology

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

Domain organisation

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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...

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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
(56)
Full
(789)
Representative proteomes NCBI
(491)
Meta
(7)
RP15
(69)
RP35
(107)
RP55
(116)
RP75
(119)
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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
(56)
Full
(789)
Representative proteomes NCBI
(491)
Meta
(7)
RP15
(69)
RP35
(107)
RP55
(116)
RP75
(119)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(56)
Full
(789)
Representative proteomes NCBI
(491)
Meta
(7)
RP15
(69)
RP35
(107)
RP55
(116)
RP75
(119)
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.

Pfam alignments:

HMM logo

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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_5200 (release 7.5)
Previous IDs: none
Type: Family
Author: Finn RD
Number in seed: 56
Number in full: 789
Average length of the domain: 179.40 aa
Average identity of full alignment: 24 %
Average coverage of the sequence by the domain: 93.29 %

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 23.0 23.0
Trusted cut-off 28.3 28.1
Noise cut-off 22.9 22.9
Model length: 185
Family (HMM) version: 10
Download: download the raw HMM for this family

Species distribution

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