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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 (2,927) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 103,653 522,858 73
Proteins 98,911 507,396 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 stimulus0.000000018550Least InformativeDirect
Biological Process (BP)biological regulation0.00024220Least InformativeDirect
Biological Process (BP)single-organism cellular process0.22890.00000002226Least InformativeInherited
Biological Process (BP)signaling0.00000016660Moderately InformativeDirect
Biological Process (BP)cell communication0.00000058110Moderately InformativeDirect
Biological Process (BP)response to external stimulus0.00070160.9646Moderately InformativeInherited
Biological Process (BP)locomotion0.000000000000017080.0000006419InformativeDirect
Biological Process (BP)intracellular signal transduction0.0000000000018440InformativeDirect
Biological Process (BP)chemotaxis0.00000000000028040.00002497Highly InformativeDirect
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 0.00000002226 Least Informative Direct
Biological Process (BP) signaling 0 Moderately Informative Direct
Biological Process (BP) cell communication 0 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.000007166 Moderately Informative Direct
Biological Process (BP) regulation of nitrogen compound metabolic process 0.0008194 Moderately Informative Direct
Biological Process (BP) regulation of biosynthetic process 0.00004962 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) response to abiotic stimulus 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 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) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 1 Moderately Informative Inherited
Biological Process (BP) reproduction 1 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 1 Moderately Informative Inherited
Biological Process (BP) system development 1 Moderately Informative Inherited
Biological Process (BP) response to organic substance 1 Moderately Informative Inherited
Biological Process (BP) response to stress 1 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 1 Moderately Informative Inherited
Biological Process (BP) ion transport 0.5151 Moderately Informative Inherited
Biological Process (BP) organic substance transport 1 Moderately Informative Inherited
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 1 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.6101 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 0.9646 Moderately Informative Inherited
Biological Process (BP) locomotion 0.0000006419 Informative Direct
Biological Process (BP) intracellular signal transduction 0 Informative Direct
Biological Process (BP) regulation of transcription, DNA-templated 0.0000009402 Informative Direct
Biological Process (BP) cellular response to hormone stimulus 0.00000001123 Informative Direct
Biological Process (BP) regulation of growth 1 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.88 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.996 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 1 Informative Inherited
Biological Process (BP) reproductive system development 0.09796 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.7358 Informative Inherited
Biological Process (BP) growth 0.1884 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.1146 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 1 Informative Inherited
Biological Process (BP) organic acid transport 0.00617 Informative Inherited
Biological Process (BP) anion transport 0.05552 Informative Inherited
Biological Process (BP) response to radiation 1 Informative Inherited
Biological Process (BP) response to inorganic substance 0.2961 Informative Inherited
Biological Process (BP) response to acid chemical 0.6715 Informative Inherited
Biological Process (BP) chemotaxis 0.00002497 Highly Informative Direct
Biological Process (BP) hormone-mediated signaling pathway 0.00000000006325 Highly Informative Direct
Biological Process (BP) response to nutrient levels 0.00000008614 Highly Informative Direct
Biological Process (BP) pathogenesis 0.0000003176 Highly Informative Direct
Biological Process (BP) dicarboxylic acid transport 0.000001928 Highly Informative Direct
Biological Process (BP) response to red or far red light 0.000004443 Highly Informative Direct
Biological Process (BP) response to water deprivation 0.00002522 Highly Informative Direct
Biological Process (BP) circadian rhythm 0.00005061 Highly Informative Direct
Biological Process (BP) regulation of reproductive process 0.000142 Highly Informative Direct
Biological Process (BP) positive regulation of growth 0.2807 Highly Informative Inherited
Biological Process (BP) cellular response to abiotic stimulus 0.002424 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.1552 Highly Informative Inherited
Biological Process (BP) positive regulation of response to external stimulus 0.04007 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.2776 Highly Informative Inherited
Biological Process (BP) cellular response to external stimulus 0.002372 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.009792 Least Informative Inherited
Molecular Function (MF) binding 0.3985 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.00000000006824 Moderately Informative Direct
Molecular Function (MF) nucleic acid binding 0.01364 Moderately Informative Inherited
Molecular Function (MF) signal transducer activity 0 Informative Direct
Molecular Function (MF) transcription factor activity, sequence-specific DNA binding 0.0000000004373 Informative Direct
Molecular Function (MF) molecular transducer activity 0.000000001729 Informative Direct
Molecular Function (MF) DNA binding 0.000002582 Informative Direct
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.0007045 Informative Direct
Molecular Function (MF) kinase activity 0.001783 Informative Inherited
Molecular Function (MF) protein kinase activity 0.0000002382 Highly Informative Direct
Molecular Function (MF) transmembrane signaling receptor activity 1 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
Yeast Phenotype (YP)metabolism and growth0Least 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 tissue0.03852Least InformativeInherited
Plant ANatomical entity (PAN)cardinal part of multi-tissue plant structure0.06752Least InformativeInherited
Plant ANatomical entity (PAN)whole plant0.1157Least InformativeInherited
Plant ANatomical entity (PAN)leaf0.1915Least InformativeInherited
Plant ANatomical entity (PAN)shoot axis0.5691Least InformativeInherited
Plant ANatomical entity (PAN)root system0.5694Least InformativeInherited
Plant ANatomical entity (PAN)root tip0.000349InformativeDirect
Plant ANatomical entity (PAN)juvenile vascular leaf0.0000000000007768Highly InformativeDirect
Plant ANatomical entity (PAN)phyllome vascular system0.00000002078Highly InformativeDirect
Plant ANatomical entity (PAN)shoot apical meristem0.00001886Highly InformativeDirect
Plant ANatomical entity (PAN)root stele0.0003526Highly 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 phosphorus-containing groups0.0000000002253Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)Carboxylic ester hydrolases0InformativeDirect
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 processVirulence0Moderately InformativeDirect
Biological processChemotaxis0InformativeDirect
Biological processSporulation0InformativeDirect
Biological processBiological rhythms0.0000000000006631InformativeDirect
Biological processNitrogen fixation0.000000006997InformativeDirect
Biological processAntibiotic resistance0.00003161InformativeDirect
Biological processTwo-component regulatory system0Highly InformativeDirect
Biological processEthylene signaling pathway0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DiseaseCrown gall tumor0.000000009934InformativeDirect
Molecular functionDNA-binding0Least InformativeDirect
Molecular functionCopper0.000000000009998InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationKinase0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately 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 ]