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0  structures 60  species 0  interactions 71  sequences 1  architecture

Family: Response_reg_2 (PF19192)

Summary: Response receiver 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.

Response receiver domain Provide feedback

This is a receiver domain (REC) commonly found in the same gene-neighbourhood of its cognate HK. Together they comprise a Two-Component System (TCS). There is a high degree of specificity among REC and DHp domains in a cognate pair. This domain is related to the Response_reg (PF00072) domain. We found that PF19191 and this domain show high degree of linkage in the same gene-neighbourhoods across several bacterial lineages. This implies that they comprise a TCS.

Literature references

  1. Gao R, Stock AM;, Annu Rev Microbiol. 2009;63:133-154.: Biological insights from structures of two-component proteins. PUBMED:19575571 EPMC:19575571

  2. Casino P, Rubio V, Marina A;, Curr Opin Struct Biol. 2010;20:763-771.: The mechanism of signal transduction by two-component systems. PUBMED:20951027 EPMC:20951027


This tab holds annotation information from the InterPro database.

InterPro entry IPR043834

Two-component systems (TCS) are widespread signal sensing and transduction machineries found mainly in bacteria and archaea, but can be also found in yeasts and plants. They comprise a homodimeric histidine kinase (HK) bound to the membrane that contains an extracellular sensor domain, and a response regulator (RR) that triggers the response modifying target genes expression. The signal transduction implies the ATP-dependent phosphorylation of a His residue present in the dimerisation and histidine phosphotransfer HK domain (DHp). The C-terminal catalytic domain (CA, also known as HATPase_c) binds ATP and phosphorylates the His residue. Then, the phosphoryl group in the His is transferred to an Asp present in a RR domain called the receiver domain (REC), which induces conformational changes of RR and modulates the affinity of an effector domain. In cases which lack an effector domain, the REC domain takes over that role [ PUBMED:20951027 , PUBMED:19575571 ].

This entry represents the receiver domain (REC) that, together with Histidine kinase (HK), constitutes the TCS system.

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 CheY (CL0304), which has the following description:

This clan includes the CheY-like response regulators from bacteria [1-2].

The clan contains the following 11 members:

cREC_REC FleQ NARF OKR_DC_1_N RcsC RcsD_ABL Response_reg Response_reg_2 TadZ_N UPF0004 VpsR

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
(42)
Full
(71)
Representative proteomes UniProt
(511)
RP15
(6)
RP35
(32)
RP55
(74)
RP75
(135)
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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
(42)
Full
(71)
Representative proteomes UniProt
(511)
RP15
(6)
RP35
(32)
RP55
(74)
RP75
(135)
Alignment:
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Sequence:
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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
(42)
Full
(71)
Representative proteomes UniProt
(511)
RP15
(6)
RP35
(32)
RP55
(74)
RP75
(135)
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: Daniel Bellieny-Rabelo
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Bellieny-Rabelo D
Number in seed: 42
Number in full: 71
Average length of the domain: 174.10 aa
Average identity of full alignment: 18 %
Average coverage of the sequence by the domain: 31.04 %

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 27.4 27.1
Noise cut-off 26.6 26.1
Model length: 181
Family (HMM) version: 3
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
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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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;