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13  structures 662  species 2  interactions 1993  sequences 14  architectures

Family: CheC (PF04509)

Summary: CheC-like family

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

CheC-like family Provide feedback

The restoration of pre-stimulus levels of the chemotactic response regulator, CheY-P, is important for allowing bacteria to respond to new environmental stimuli. The members of this family, CheC, CheX, CheA and FliY are CheY-P phosphatase [1,2]. CheC appears to be primarily involved in restoring normal CheY-P levels, whereas FliY seems to act on CheY-P constitutively. CheD enhances the activity of CheC 5-fold, which is normally relatively low [1,2]. In some cases, the region represented by this entry is present as multiple copies.

Literature references

  1. Szurmant H, Muff TJ, Ordal GW; , J Biol Chem 2004;279:21787-21792.: Bacillus subtilis CheC and FliY are members of a novel class of CheY-P-hydrolyzing proteins in the chemotactic signal transduction cascade. PUBMED:14749334 EPMC:14749334

  2. Szurmant H, Ordal GW; , Microbiol Mol Biol Rev 2004;68:301-319.: Diversity in chemotaxis mechanisms among the bacteria and archaea. PUBMED:15187186 EPMC:15187186


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR007597

The precise function of these proteins is unclear, but some of them are involved in flagella motor switch [PUBMED:11722727]. The region represented in this entry is found in the CheC, CheX, CheA and FliY proteins. In some cases, this region is repeated in multiple copies.

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 CheC-like (CL0355), which has the following description:

The chemotactic response regulator superfamily are CheY-P phosphatases. Their structure is two intertwined alpha-beta-(X)-beta(2) motifs. This superfamily comprises two classes of proteins each shown to interact with the chemotaxis response regulator CheY: the FliM switch proteins and the CheC-type phosphatases [1]. FliM is a component of the flagellar switch found across the bacteria and is responsible for binding CheY-P and changing the rotational direction of the flagella. The N-terminal domain is CheC-like and the C-terminal shares the SpoA domain with FliN and FliY. The CheC family is broadly broken down into three phosphatase subfamilies: CheC, CheX, and FliY. All three have an active site consensus sequence of D/S-X(3)-E-X(2)-N-X(22)-P.

The clan contains the following 4 members:

CheC CheX DUF3334 FliM

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...

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
(33)
Full
(1993)
Representative proteomes NCBI
(2015)
Meta
(46)
RP15
(261)
RP35
(447)
RP55
(522)
RP75
(597)
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PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

  Seed
(33)
Full
(1993)
Representative proteomes NCBI
(2015)
Meta
(46)
RP15
(261)
RP35
(447)
RP55
(522)
RP75
(597)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(33)
Full
(1993)
Representative proteomes NCBI
(2015)
Meta
(46)
RP15
(261)
RP35
(447)
RP55
(522)
RP75
(597)
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

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: COG1406
Previous IDs: none
Type: Domain
Author: Waterfield DI, Finn RD
Number in seed: 33
Number in full: 1993
Average length of the domain: 37.70 aa
Average identity of full alignment: 36 %
Average coverage of the sequence by the domain: 24.19 %

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 20.2 20.2
Trusted cut-off 20.2 20.2
Noise cut-off 20.0 20.1
Model length: 38
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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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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Interactions

There are 2 interactions for this family. More...

CheD CheC

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 CheC domain has been found. There are 13 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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