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6  structures 74  species 0  interactions 80  sequences 22  architectures

Family: LuxQ-periplasm (PF09308)

Summary: LuxQ, periplasmic

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LuxQ, periplasmic Provide feedback

Members of this family constitute the periplasmic sensor domain of the prokaryotic protein LuxQ, and assume a structure consisting of two tandem Per/ARNT/Simple-minded (PAS) folds [1].

Literature references

  1. Neiditch MB, Federle MJ, Miller ST, Bassler BL, Hughson FM; , Mol Cell. 2005;18:507-518.: Regulation of LuxPQ receptor activity by the quorum-sensing signal autoinducer-2. PUBMED:15916958 EPMC:15916958

This tab holds annotation information from the InterPro database.

InterPro entry IPR015387

This entry represents the periplasmic sensor domain of the prokaryotic protein LuxQ, that assumes a structure consisting of two tandem Per/ARNT/Simple-minded (PAS) folds [ PUBMED:15916958 ].

LuxQ is a sensor histidine kinase involved in quorum sensing in the marine bacterium Vibrio harveyi. Quorum sensing is a process of bacterial cell-cell communication driven by secreted signaling molecules called autoinducers such as AI-2. The receptor for this autoinducer is LuxPQ, formed as a result of the association between LuxQ and LuxP, a periplasmic binding protein, through the cited periplasmic domain of LuxQ [ PUBMED:16990134 ].

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 Cache (CL0165), which has the following description:

The Cache domain an extracellular domain that is thought to have a role in small-molecule recognition in a wide range of proteins, including the animal Ca(2+)-channel subunits and a class of prokaryotic chemotaxis receptors [1]. It is homologous to, but sufficiently different from the most common intracellular sensor module, the PAS domain. Furthermore, it is suggested that it might have originated from a simpler intracellular PAS/GAF ancestor as a benefit of extracellular sensing [2].

The clan contains the following 23 members:

2CSK_N ArlS_N Cache_3-Cache_2 CHASE CHASE4 CHASE7 CHASE8 dCache_1 dCache_2 dCache_3 Diacid_rec GAPES1 LuxQ-periplasm PhoQ_Sensor sCache_2 sCache_3_2 sCache_3_3 sCache_4 sCache_like SMP_2 Stimulus_sens_1 VGCC_alpha2 YkuI_C


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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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.

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Representative proteomes UniProt

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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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...


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.

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Curation and family details

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Curation View help on the curation process

Seed source: pdb_1zhh
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Mistry J , Sammut SJ
Number in seed: 6
Number in full: 80
Average length of the domain: 217.70 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 27.41 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.7 25.7
Trusted cut-off 26.5 26.1
Noise cut-off 25.3 25.6
Model length: 239
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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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 LuxQ-periplasm domain has been found. There are 6 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
Q7MD16 View 3D Structure Click here
Q87GU5 View 3D Structure Click here
Q9KLK7 View 3D Structure Click here