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CheY-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   Alpha and beta proteins (a/b) [ 51349] (147)
Fold:   Flavodoxin-like [ 52171] (15)
Superfamily:   CheY-like [ 52172] (7)
Families:   CheY-related [ 52173] (25)
  Receiver domain of the ethylene receptor [ 52194]
  Positive regulator of the amidase operon AmiR [ 52197]
  Ornithine decarboxylase N-terminal "wing" domain [ 52252]
  N-terminal domain of the circadian clock protein KaiA [ 82344]
  RcsC linker domain-like [ 142037]
  AF1403 C-terminal domain-like [ 142040]


Superfamily statistics
Genomes (2,928) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 103,656 713,198 73
Proteins 98,914 682,819 71


Functional annotation
General category Regulation
Detailed category Signal transduction

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-quality)

(show details)
GO termFDR (singleton)FDR (all)SDFO levelAnnotation (direct or inherited)
Biological Process (BP)response to stimulus0.000000052940Least InformativeDirect
Biological Process (BP)biological regulation0.00029250Least InformativeDirect
Biological Process (BP)single organism signaling0.00000017660Moderately InformativeDirect
Biological Process (BP)cell communication0.00000068360Moderately InformativeDirect
Biological Process (BP)response to external stimulus0.00085891Moderately InformativeInherited
Biological Process (BP)locomotion0.00000000000019920.0000362InformativeDirect
Biological Process (BP)intracellular signal transduction0.0000000000020390InformativeDirect
Molecular Function (MF)signal transducer activity00InformativeDirect

Document: GO annotation of SCOP domains

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) biological regulation 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) single organism signaling 0 Moderately Informative Direct
Biological Process (BP) cell communication 0 Moderately Informative Direct
Biological Process (BP) regulation of macromolecule biosynthetic process 0.0000000801 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.00000007128 Moderately Informative Direct
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.00000004267 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.00000004679 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cell communication 1 Moderately Informative Inherited
Biological Process (BP) regulation of signaling 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.3651 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to biotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) ion transport 0.7703 Moderately Informative Inherited
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.006074 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 1 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) locomotion 0.0000362 Informative Direct
Biological Process (BP) intracellular signal transduction 0 Informative Direct
Biological Process (BP) cellular response to hormone stimulus 0.0000000005028 Informative Direct
Biological Process (BP) interspecies interaction between organisms 0.0001759 Informative Direct
Biological Process (BP) negative regulation of signaling 1 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) negative regulation of cell communication 1 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 1 Informative Inherited
Biological Process (BP) growth 0.2943 Informative Inherited
Biological Process (BP) response to extracellular stimulus 0.2669 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.4992 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) organic acid transport 0.0109 Informative Inherited
Biological Process (BP) regulation of growth 1 Informative Inherited
Biological Process (BP) response to radiation 1 Informative Inherited
Biological Process (BP) response to acid chemical 0.6794 Informative Inherited
Biological Process (BP) anion transport 0.1184 Informative Inherited
Biological Process (BP) hormone-mediated signaling pathway 0.000000000001326 Highly Informative Direct
Biological Process (BP) response to osmotic stress 0.000000002232 Highly Informative Direct
Biological Process (BP) dicarboxylic acid transport 0.00000422 Highly Informative Direct
Biological Process (BP) response to red or far red light 0.000009025 Highly Informative Direct
Biological Process (BP) response to water deprivation 0.00002586 Highly Informative Direct
Biological Process (BP) pathogenesis 0.00008889 Highly Informative Direct
Biological Process (BP) circadian rhythm 0.0001584 Highly Informative Direct
Biological Process (BP) positive regulation of growth 0.3887 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.2131 Highly Informative Inherited
Biological Process (BP) cellular response to extracellular stimulus 0.7125 Highly Informative Inherited
Biological Process (BP) multi-organism cellular process 0.04072 Highly Informative Inherited
Biological Process (BP) positive regulation of response to external stimulus 0.009922 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.3929 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.004403 Highly Informative Inherited
Biological Process (BP) response to nutrient levels 0.2684 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.03649 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) binding 0.001265 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.0000000004996 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.00000003251 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.3024 Moderately Informative Inherited
Molecular Function (MF) signal transducer activity 0 Informative Direct
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0 Informative Direct
Molecular Function (MF) DNA binding 0 Informative Direct
Molecular Function (MF) molecular transducer activity 0.0000001078 Informative Direct
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.0004168 Informative Direct
Molecular Function (MF) kinase activity 0.00122 Informative Inherited
Molecular Function (MF) carboxylic ester hydrolase activity 0.03661 Informative Inherited
Molecular Function (MF) transcription regulatory region DNA binding 0 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.000000112 Highly Informative Direct
Molecular Function (MF) double-stranded DNA binding 0.00004781 Highly Informative Direct
Molecular Function (MF) transmembrane signaling receptor activity 1 Highly Informative Inherited
Molecular Function (MF) sequence-specific DNA binding 0.01802 Highly Informative Inherited
Cellular Component (CC) protein-DNA complex 0 Informative Direct

Document: GO annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEO levelAnnotation (direct or inherited)
Enzyme Commission (EC)Acting on ester bonds0Least InformativeDirect
Enzyme Commission (EC)Carboxylic ester hydrolases0Moderately InformativeDirect
Enzyme Commission (EC)Protein-histidine kinases0InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processTransport1Least InformativeInherited
Biological processTranscription regulation0Moderately InformativeDirect
Biological processVirulence0Moderately InformativeDirect
Biological processSporulation0InformativeDirect
Biological processChemotaxis0InformativeDirect
Biological processBiological rhythms0.0000000000007462InformativeDirect
Biological processNitrogen fixation0.00000000705InformativeDirect
Biological processAntibiotic resistance0.00003267InformativeDirect
Biological processEthylene signaling pathway0Highly InformativeDirect
Biological processTwo-component regulatory system0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DiseaseCrown gall tumor0.00000001022InformativeDirect
Molecular functionCopper0.000000000002964InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationDNA-binding0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR011006 SSF52172 Protein matches
Abstract

CheY is a member of the response regulator family in bacterial two-component signalling systems, where CheY receives the signal from the sensor partner, usually a histidine protein kinase. Signal transduction involves phosphotransfer, whereby the histidine kinase phosphorylates a conserved aspartate in the response regulator to activate responses to environmental signals [PubMed14636076]. CheY is a single domain protein that folds into a compact globular unit with a flavodoxin-like fold consisting of three-layer alpha/beta/alpha sandwich with 21345 beta topology, where the phosphorylation region lies in a cavity.

Other members of the response regulator family contain a CheY-like receiver domain, which is often found N-terminal to a DNA-binding effector domain. Examples include NarL (nitrate/nitrite response regulator), NtrC (nitrogen regulatory protein C), Spo0A and Spo0F (sporulation response) from Bacillus, PhoA and PhoB cyclin-dependent kinases from Aspergillus, among others.

AmiR, the positive regulator of the amidase operon in Psuedomonas, is an unusual member of the bacterial response regulator family; AmiR is able to bind RNA and uses ligand-regulated activation rather than phopho-activation. It has a CheY-like fold at its N-terminus, but contains two subdomains in a C-terminal extension, one forming a coiled-coil and the other a long alpha helix. As such AmiR may represent a new family of RNA-binding response regulators [PubMed10508151].

CheY-like domains can be found in other protein families as well. Examples include the receiver domain of the ethylene receptor (ETR1) from Arabidopsis, which is involved in ethylene detection and signal transduction [PubMed10647185]; the N-terminal wing' domain of ornithine decarboxylase from Lactobacilli, which catalyses the conversion of ornithine to putrescine at the beginning of the polyamine pathway [PubMed10666573]. The N-terminal domain of the circadian clock protein, KaiA, from cyanobacteria, acts as a psuedo-receiver domain, but lacks the conserved aspartyl residue required for phosphotransfer in response regulators [PubMed12438647].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) ]

Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 38 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a CheY-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 38 hidden Markov models representing the CheY-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-quality) · Gene Ontology (high-coverage) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]