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0  structures 938  species 0  interactions 1282  sequences 83  architectures

Family: CZB (PF13682)

Summary: Chemoreceptor zinc-binding 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.

Chemoreceptor zinc-binding domain Provide feedback

The chemoreceptor zinc-binding domain (CZB) is found in bacterial signal transduction proteins - most frequently receptors involved in chemotaxis and motility, but also in c-di-GMP signalling and nitrate/nitrite-sensing. Originally discovered in the cytoplasmic chemoreceptor TlpD from Helicobacter pylori, it is often found C-terminal to the MCPsignal domain in cytoplasmic chemoreceptor proteins. The CZB domain contains a core sequence motif, Hxx[WFYL]x21-28Cx[LFMVI]Gx[WFLVI]x18-27HxxxH. The highly-conserved H-C-H-H residues of this motif are believed to coordinate zinc; mutating the latter two histidines of the motif to alanines abolishes Zn binding. This domain binds zinc with high affinity, with a Kd in the femtomolar range. Although the function of the CZB domain is not yet known, scientists have speculated that it may function as either an unknown signal input domain, based on its frequent association with signalling output domains, or as a domain that helps to stabilise protein tertiary or quaternary structure.

Literature references

  1. Draper J, Karplus K, Ottemann KM;, J Bacteriol. 2011;193:4338-4345.: Identification of a chemoreceptor zinc-binding domain common to cytoplasmic bacterial chemoreceptors. PUBMED:21725005 EPMC:21725005


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025991

This short domain contains four highly conserved histidines and one highly conserved cysteine. It is often found associated with an MCP-signal domain, and is sometimes found in association with a GGDEF domain.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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...

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
(345)
Full
(1282)
Representative proteomes NCBI
(896)
Meta
(70)
RP15
(135)
RP35
(281)
RP55
(309)
RP75
(334)
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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
(345)
Full
(1282)
Representative proteomes NCBI
(896)
Meta
(70)
RP15
(135)
RP35
(281)
RP55
(309)
RP75
(334)
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
(345)
Full
(1282)
Representative proteomes NCBI
(896)
Meta
(70)
RP15
(135)
RP35
(281)
RP55
(309)
RP75
(334)
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: Jackhmmer:Q47EQ8
Previous IDs: MCPsignal_assoc;
Type: Domain
Author: Coggill P
Number in seed: 345
Number in full: 1282
Average length of the domain: 71.70 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 17.09 %

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 20.0 20.0
Trusted cut-off 20.2 20.2
Noise cut-off 19.6 19.5
Model length: 70
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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