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0  structures 575  species 0  interactions 882  sequences 102  architectures

Family: CHASE8 (PF17152)

Summary: Periplasmic sensor domain

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Periplasmic sensor domain Provide feedback

CHASE8 is a conserved periplasmic sensor domain found in histidine kinases, diguanylate cyclases/phosphodiesterases and methyl-accepting chemotaxis proteins, including the diguanylate cyclase DgcN (YfiN) that regulates biofilm formation and motility in Escherichia coli [1, 2]. In Pseudomonas aeruginosa, CHASE8 is the sensor domain in the diguanylate cyclase TpbB that regulates biofilm formation [3] by controlling the levels of extracellular DNA [4].

Literature references

  1. Ueda A, Wood TK;, PLoS Pathog. 2009;5:e1000483.: Connecting quorum sensing, c-di-GMP, pel polysaccharide, and biofilm formation in Pseudomonas aeruginosa through tyrosine phosphatase TpbA (PA3885). PUBMED:19543378 EPMC:19543378

  2. Hengge R, Galperin MY, Ghigo JM, Gomelsky M, Green J, Hughes KT, Jenal U, Landini P;, J Bacteriol. 2015;198:7-11.: Systematic Nomenclature for GGDEF and EAL Domain-Containing Cyclic Di-GMP Turnover Proteins of Escherichia coli. PUBMED:26148715 EPMC:26148715

  3. Sanchez-Torres V, Hu H, Wood TK;, Appl Microbiol Biotechnol. 2011;90:651-658.: GGDEF proteins YeaI, YedQ, and YfiN reduce early biofilm formation and swimming motility in Escherichia coli. PUBMED:21181144 EPMC:21181144

  4. Ueda A, Wood TK;, Environ Microbiol. 2010;2:449-455.: Tyrosine Phosphatase TpbA of Pseudomonas aeruginosa Controls Extracellular DNA via Cyclic Diguanylic Acid Concentrations. PUBMED:21552365 EPMC:21552365


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR033417

CHASE8 is a conserved periplasmic sensor domain found in histidine kinases, diguanylate cyclases/phosphodiesterases and methyl-accepting chemotaxis proteins, including the diguanylate cyclase DgcN (YfiN) that regulates biofilm formation and motility in Escherichia coli [ PUBMED:21181144 , PUBMED:26148715 ]. In Pseudomonas aeruginosa, CHASE8 is the sensor domain in the diguanylate cyclase TpbB that regulates biofilm formation by controlling the levels of extracellular DNA [ PUBMED:19543378 , PUBMED:21552365 ].

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

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 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.

  Seed
(38)
Full
(882)
Representative proteomes UniProt
(6548)
RP15
(130)
RP35
(428)
RP55
(905)
RP75
(1746)
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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
(38)
Full
(882)
Representative proteomes UniProt
(6548)
RP15
(130)
RP35
(428)
RP55
(905)
RP75
(1746)
Alignment:
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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
(38)
Full
(882)
Representative proteomes UniProt
(6548)
RP15
(130)
RP35
(428)
RP55
(905)
RP75
(1746)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Phmmer:P46139
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Coggill P , El-Gebali S
Number in seed: 38
Number in full: 882
Average length of the domain: 105.80 aa
Average identity of full alignment: 20 %
Average coverage of the sequence by the domain: 16.09 %

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 27.0 27.0
Trusted cut-off 27.0 27.1
Noise cut-off 26.8 26.8
Model length: 102
Family (HMM) version: 7
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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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
P46139 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;