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2  structures 219  species 0  interactions 220  sequences 5  architectures

Family: CpxA_peri (PF16527)

Summary: Two-component sensor protein CpxA, periplasmic domain

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This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Two-component sensor protein CpxA, periplasmic domain Provide feedback

CpxA_peri is the periplasmic domain-family of the Gram-negative Gammaproteobacteria two-component signalling system, Cpx. It represents the recognition-site for sensing specific envelope stress signals. The fold that the domain-core of CpxA_peri conforms to is a PAS fold. The domain senses the environmental change and triggers a signal transduction to the cytoplasmic domain. As well as the PAS-core, there is a C-terminal tail that is necessary for ligand-sensing and binding to CpxP, a CpxA-associated and a regulatory protein [1].

Literature references

  1. Kwon E, Kim DY, Ngo TD, Gross CA, Gross JD, Kim KK;, Protein Sci. 2012;21:1334-1343.: The crystal structure of the periplasmic domain of Vibrio parahaemolyticus CpxA. PUBMED:22760860 EPMC:22760860


This tab holds annotation information from the InterPro database.

InterPro entry IPR032404

This entry represents the periplasmic domain (also known as the VpCpxA-peri domain) of Vibrio parahaemolyticus CpxA. CpxA is a histidine kinase and a membrane-bound sensor acting in the Cpx two-component system of Gram-negative bacteria. The VpCpxA-peri domain possesses a PAS fold that may play a role in sensing envelope stress signals [PUBMED:22760860].

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 PAS_Fold (CL0183), which has the following description:

This clan contains PAS domains that are found in a wide variety of bacterial signaling proteins.

The clan contains the following 17 members:

AbfS_sensor CpxA_peri DUF5593 MEKHLA MLTR_LBD PAS PAS_10 PAS_11 PAS_12 PAS_2 PAS_3 PAS_4 PAS_5 PAS_6 PAS_7 PAS_8 PAS_9

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

View options

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
(10)
Full
(220)
Representative proteomes UniProt
(1231)
NCBI
(1753)
Meta
(1)
RP15
(14)
RP35
(77)
RP55
(213)
RP75
(496)
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HTML View  View               
PP/heatmap 1 View               

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(10)
Full
(220)
Representative proteomes UniProt
(1231)
NCBI
(1753)
Meta
(1)
RP15
(14)
RP35
(77)
RP55
(213)
RP75
(496)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(10)
Full
(220)
Representative proteomes UniProt
(1231)
NCBI
(1753)
Meta
(1)
RP15
(14)
RP35
(77)
RP55
(213)
RP75
(496)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: pdb_3v67
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Coggill P
Number in seed: 10
Number in full: 220
Average length of the domain: 117.90 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 26.30 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.5 23.5
Trusted cut-off 23.5 23.5
Noise cut-off 22.6 23.3
Model length: 134
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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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 CpxA_peri domain has been found. There are 2 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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