SUPERFAMILY 1.75 HMM library and genome assignments server


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 (2,895) Uniprot 2013_05 PDB chains (SCOP 1.75)
Domains 102,647 251,618 73
Proteins 98,006 242,431 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 stimulus4.755e-070Least InformativeDirect
Biological Process (BP)single-organism cellular process0.52171.338e-09Least InformativeInherited
Biological Process (BP)regulation of cellular process0.0031440.05564Least InformativeInherited
Biological Process (BP)response to endogenous stimulus0.32640.1873Moderately InformativeInherited
Biological Process (BP)response to organic substance11Moderately InformativeInherited
Biological Process (BP)signal transduction0.023090Moderately InformativeInherited
Biological Process (BP)locomotion1.052e-123.68e-05InformativeDirect
Biological Process (BP)response to hormone stimulus0.003115.317e-10InformativeInherited
Molecular Function (MF)molecular 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) single-organism cellular process 1.338e-09 Least Informative Direct
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) regulation of metabolic process 1 Least Informative Inherited
Biological Process (BP) developmental process 1 Least Informative Inherited
Biological Process (BP) multicellular organismal process 1 Least Informative Inherited
Biological Process (BP) regulation of cellular process 0.05564 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.8215 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) phosphate-containing compound metabolic process 4.59e-06 Moderately Informative Direct
Biological Process (BP) signal transduction 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0003417 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 6.004e-05 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) reproduction 0.5113 Moderately Informative Inherited
Biological Process (BP) regulation of signal transduction 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.8462 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1873 Moderately Informative Inherited
Biological Process (BP) single-organism developmental process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) cell differentiation 1 Moderately Informative Inherited
Biological Process (BP) organ development 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) tissue development 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.2239 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 0.7431 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.03071 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2888 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.04116 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to oxidative stress 1.013e-05 Informative Direct
Biological Process (BP) response to hormone stimulus 5.317e-10 Informative Direct
Biological Process (BP) phosphorylation 2.563e-13 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0001055 Informative Direct
Biological Process (BP) response to nutrient levels 3.668e-05 Informative Direct
Biological Process (BP) intracellular signal transduction 0 Informative Direct
Biological Process (BP) locomotion 3.68e-05 Informative Direct
Biological Process (BP) regulation of growth 0.9892 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.1917 Informative Inherited
Biological Process (BP) response to lipid 0.5875 Informative Inherited
Biological Process (BP) reproductive structure development 0.001096 Informative Inherited
Biological Process (BP) response to light stimulus 0.0379 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.7108 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.7023 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.9949 Informative Inherited
Biological Process (BP) growth 0.2194 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.1978 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.5428 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.06129 Informative Inherited
Biological Process (BP) regulation of response to biotic stimulus 0.0003905 Highly Informative Direct
Biological Process (BP) protein phosphorylation 0.0001149 Highly Informative Direct
Biological Process (BP) response to osmotic stress 8.959e-13 Highly Informative Direct
Biological Process (BP) pathogenesis 6.017e-07 Highly Informative Direct
Biological Process (BP) hormone-mediated signaling pathway 2.023e-07 Highly Informative Direct
Biological Process (BP) regulation of multi-organism process 0.0003745 Highly Informative Direct
Biological Process (BP) positive regulation of growth 0.05908 Highly Informative Inherited
Biological Process (BP) cellular response to alcohol 0.003346 Highly Informative Inherited
Biological Process (BP) regulation of response to nutrient levels 1 Highly Informative Inherited
Biological Process (BP) positive regulation of response to external stimulus 0.003766 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.1731 Highly Informative Inherited
Biological Process (BP) cellular response to radiation 0.1994 Highly Informative Inherited
Molecular Function (MF) binding 0.258 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 7.306e-11 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.01327 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.04482 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding transcription factor activity 5.977e-09 Informative Direct
Molecular Function (MF) DNA binding 0.0003 Informative Direct
Molecular Function (MF) receptor activity 8.125e-09 Informative Direct
Molecular Function (MF) molecular transducer activity 0 Informative Direct
Molecular Function (MF) kinase activity 0.002735 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.003145 Informative Inherited
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 4.875e-10 Highly Informative Direct
Molecular Function (MF) protein kinase activity 9.466e-06 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 4.683e-05 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 0.01172 Highly Informative Inherited

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

Yeast Phenotype (YP)

(show details)
YP termFDR (all)SDYP levelAnnotation (direct or inherited)
Yeast Phenotype (YP)resistance to chemicals0Least InformativeDirect

Document: YP annotation of SCOP domains

Arabidopsis Plant Ontology (AP)

(show details)
AP termFDR (all)SDAP levelAnnotation (direct or inherited)
Plant ANatomical entity (PAN)portion of meristem tissue0.03834Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.06717Least InformativeInherited
Plant ANatomical entity (PAN)whole plant0.1154Least InformativeInherited
Plant ANatomical entity (PAN)leaf0.1915Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.568Least InformativeInherited
Plant ANatomical entity (PAN)root system0.5687Least InformativeInherited
Plant ANatomical entity (PAN)vascular system1.574e-11InformativeDirect
Plant ANatomical entity (PAN)root tip0.0003419InformativeDirect
Plant ANatomical entity (PAN)juvenile vascular leaf7.755e-13Highly InformativeDirect
Plant ANatomical entity (PAN)leaf vascular system1.164e-08Highly InformativeDirect
Plant ANatomical entity (PAN)shoot apical meristem1.882e-05Highly InformativeDirect
Plant ANatomical entity (PAN)root stele0.0003347Highly InformativeDirect

Document: AP annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0Least InformativeDirect
Enzyme Commission (EC)Transferring phosphorous-containing groups4.692e-06Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)Carboxylic ester hydrolases0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.9241InformativeInherited
Enzyme Commission (EC)Protein-histidine kinases0Highly InformativeDirect

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 processChemotaxis0InformativeDirect
Biological processSporulation0InformativeDirect
Biological processVirulence0InformativeDirect
Biological processNitrogen fixation3.355e-09InformativeDirect
Biological processAntibiotic resistance1.594e-05InformativeDirect
Biological processBiological rhythms0Highly InformativeDirect
Biological processTwo-component regulatory system0Highly InformativeDirect
Biological processEthylene signaling pathway0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DiseaseCrown gall tumor5.742e-09InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionCopper2.043e-08InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationKinase9.666e-13Moderately InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect

Document: KW annotation of SCOP domains

UniProtKB UniPathway (UP)

(show details) Document: UP 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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) ]

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) · Yeast Phenotype (YP) · Arabidopsis Plant Ontology (AP) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · UniProtKB UniPathway (UP) · Internal database links ]