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5  structures 478  species 0  interactions 807  sequences 2  architectures

Family: Autoind_synth (PF00765)

Summary: Autoinducer synthetase

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Autoinducer synthetase Provide feedback

No Pfam abstract.

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001690

Bacterial species have many methods of controlling gene expression and cell growth. Regulation of gene expression in response to changes in cell density is termed quorum sensing [PUBMED:10607620, PUBMED:9990077]. Quorum-sensing bacteria produce, release and respond to hormone-like molecules (autoinducers) that accumulate in the external environment as the cell population grows. Once a threshold of these molecules is reached, a signal transduction cascade is triggered that ultimately leads to behavioural changes in the bacterium [PUBMED:9990077]. Autoinducers are thus clearly important mediators of molecular communication.

Conjugal transfer of Agrobacterium octopine-type Ti plasmids is activated by octopine, a metabolite released from plant tumours [PUBMED:8188582]. Octopine causes conjugal donors to secrete a pheromone, Agrobacterium autoinducer (AAI), and exogenous AAI further stimulates conjugation. The putative AAI synthase and an AAI-responsive transcriptional regulator have been found to be encoded by the Ti plasmid traI and traR genes, respectively. TraR and TraI are similar to the LuxR and LuxI regulatory proteins of Vibrio fischeri, and AAI is similar in structure to the diffusable V. fischeri autoinducer, the inducing ligand of LuxR. TraR activates target genes in the presence of AAI and also activates traR and traI themselves, creating two positive-feedback loops. TraR-AAI-mediated activation in wild-type Agrobacterium strains is enhanced by culturing on solid media, suggesting a possible role in cell density sensing [PUBMED:8188582].

Production of light by the marine bacterium V. fischeri and by recombinant hosts containing cloned lux genes is controlled by the density of the culture [PUBMED:3697093]. Density-dependent regulation of lux gene expression has been shown to require a locus consisting of the luxR and luxI genes.

In these and other Gram-negative bacteria, N-(3-oxohexanoyl)-L-homoserine lactone (OHHL) acts as the autoinducer by binding to transcriptional regulatory proteins and activating them [PUBMED:7968529]. OHHL and related molecules, such as N-butanoyl- (BHL), N-hexanoyl- (HHL) and N-oxododecanoyl- (PAI) homoserine lactones, are produced by a family of proteins that share a high level of sequence similarity.

Proteins which currently members of this family include:

  • luxI from V. fischeri.
  • ahyI and asaI from Aeromonas species, which synthesize BHL and whose targets are ahyR and asaR respectively.
  • carI from Erwinia carotovora. The target of OHHL is carR which activates genes involved in the biosynthesis of carbapenem antibiotics.
  • eagI from Enterobacter agglomerans. The target of OHHL is not yet known.
  • esaI from Erwinia stewartii.
  • expI from Erwinia carotovora.
  • lasI from Pseudomonas aeruginosa, which synthesizes PAI and whose target is lasR which activates the transcription of the elastase gene.
  • rhlI (or vsmI) from P. aeruginosa, which synthesizes BHL and HHL and whose target is rhlR.
  • swrI from Serratia liquefaciens, which synthesizes BHL.
  • yenI from Yersinia enterocolitica.

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 Acetyltrans (CL0257), which has the following description:

This clan contains families related to N-acetyltransferases. N-acetyltransferases catalyse the transfer of acetyl groups from acetyl-CoA to arylamines.

The clan contains the following 31 members:

Acetyltransf_1 Acetyltransf_10 Acetyltransf_13 Acetyltransf_3 Acetyltransf_4 Acetyltransf_5 Acetyltransf_6 Acetyltransf_7 Acetyltransf_8 Acetyltransf_9 Acetyltransf_CG ATE_C ATE_N Autoind_synth DUF1248 DUF1999 DUF2156 DUF3749 DUF482 DUF619 FemAB FR47 Gly_acyl_tr_C GNAT_acetyltr_2 GNAT_acetyltran Leu_Phe_trans Mec-17 Mig-14 MOZ_SAS NMT NodA

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
(13)
Full
(807)
Representative proteomes NCBI
(757)
Meta
(67)
RP15
(22)
RP35
(84)
RP55
(121)
RP75
(184)
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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
(13)
Full
(807)
Representative proteomes NCBI
(757)
Meta
(67)
RP15
(22)
RP35
(84)
RP55
(121)
RP75
(184)
Alignment:
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Sequence:
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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
(13)
Full
(807)
Representative proteomes NCBI
(757)
Meta
(67)
RP15
(22)
RP35
(84)
RP55
(121)
RP75
(184)
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_881 (release 2.1)
Previous IDs: none
Type: Family
Author: Bateman A
Number in seed: 13
Number in full: 807
Average length of the domain: 174.20 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 85.33 %

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 20.1 20.1
Trusted cut-off 20.2 20.1
Noise cut-off 19.9 20.0
Model length: 182
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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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 Autoind_synth domain has been found. There are 5 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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