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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 (2,926) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 103,622 522,858 73
Proteins 98,885 507,396 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 stimulus0.00000027510Least InformativeDirect
Biological Process (BP)regulation of cellular process0.00550.1259Least InformativeInherited
Biological Process (BP)single-organism cellular process0.59860.0000006664Least InformativeInherited
Biological Process (BP)response to endogenous stimulus0.3740.1817Moderately InformativeInherited
Biological Process (BP)response to organic substance11Moderately InformativeInherited
Biological Process (BP)signal transduction0.021280.000000000000003741Moderately InformativeInherited
Biological Process (BP)locomotion0.0000000000025990.0000783InformativeDirect
Biological Process (BP)response to hormone stimulus0.004060.0000000006185InformativeInherited
Biological Process (BP)response to cytokinin stimulus0.00000047650Highly InformativeDirect
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) response to stimulus 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0000006664 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 0.1259 Least Informative Inherited
Biological Process (BP) protein metabolic process 0.9056 Least Informative Inherited
Biological Process (BP) cellular macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) signal transduction 0.000000000000003741 Moderately Informative Direct
Biological Process (BP) regulation of cellular biosynthetic process 0.00005901 Moderately Informative Direct
Biological Process (BP) phosphate-containing compound metabolic process 0.00002329 Moderately Informative Direct
Biological Process (BP) regulation of gene expression 0.0001871 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 0.3633 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) multi-organism process 0.03999 Moderately Informative Inherited
Biological Process (BP) cellular response to stress 0.6779 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) response to endogenous stimulus 0.1817 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) response to abiotic stimulus 0.4239 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.04131 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 0.2731 Moderately Informative Inherited
Biological Process (BP) regulation of macromolecule biosynthetic process 0.01951 Moderately Informative Inherited
Biological Process (BP) positive regulation of response to stimulus 1 Moderately Informative Inherited
Biological Process (BP) locomotion 0.0000783 Informative Direct
Biological Process (BP) response to hormone stimulus 0.0000000006185 Informative Direct
Biological Process (BP) phosphorylation 0.0000000000003351 Informative Direct
Biological Process (BP) response to nutrient levels 0.0000217 Informative Direct
Biological Process (BP) response to oxidative stress 0.00006858 Informative Direct
Biological Process (BP) peptidyl-amino acid modification 0.0001233 Informative Direct
Biological Process (BP) reproductive system development 0.0006173 Informative Direct
Biological Process (BP) regulation of growth 1 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.189 Informative Inherited
Biological Process (BP) response to lipid 0.5843 Informative Inherited
Biological Process (BP) developmental process involved in reproduction 0.0409 Informative Inherited
Biological Process (BP) response to light stimulus 0.01924 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.7827 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.7905 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) growth 0.06125 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.237 Informative Inherited
Biological Process (BP) anatomical structure formation involved in morphogenesis 0.6081 Informative Inherited
Biological Process (BP) cellular response to endogenous stimulus 0.05003 Informative Inherited
Biological Process (BP) response to cytokinin stimulus 0 Highly Informative Direct
Biological Process (BP) circadian rhythm 0.00000000000006543 Highly Informative Direct
Biological Process (BP) hormone-mediated signaling pathway 0.00000002522 Highly Informative Direct
Biological Process (BP) pathogenesis 0.0000002248 Highly Informative Direct
Biological Process (BP) protein phosphorylation 0.00005815 Highly Informative Direct
Biological Process (BP) regulation of multi-organism process 0.000363 Highly Informative Direct
Biological Process (BP) positive regulation of growth 0.05614 Highly Informative Inherited
Biological Process (BP) response to alcohol 0.1437 Highly Informative Inherited
Biological Process (BP) multi-organism cellular process 0.01169 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 0.005809 Highly Informative Inherited
Biological Process (BP) regulation of developmental growth 0.1623 Highly Informative Inherited
Biological Process (BP) cellular response to radiation 0.2523 Highly Informative Inherited
Molecular Function (MF) transferase activity 0.0001703 Least Informative Direct
Molecular Function (MF) binding 0.2183 Least Informative Inherited
Molecular Function (MF) hydrolase activity 1 Least Informative Inherited
Molecular Function (MF) transferase activity, transferring phosphorus-containing groups 0.00000000009267 Moderately Informative Direct
Molecular Function (MF) hydrolase activity, acting on ester bonds 0.03759 Moderately Informative Inherited
Molecular Function (MF) nucleic acid binding 0.01853 Moderately Informative Inherited
Molecular Function (MF) molecular transducer activity 0 Informative Direct
Molecular Function (MF) nucleic acid binding transcription factor activity 0.000000002092 Informative Direct
Molecular Function (MF) receptor activity 0.00000001761 Informative Direct
Molecular Function (MF) DNA binding 0.00006188 Informative Direct
Molecular Function (MF) kinase activity 0.002467 Informative Inherited
Molecular Function (MF) phosphotransferase activity, alcohol group as acceptor 0.002693 Informative Inherited
Molecular Function (MF) phosphoric ester hydrolase activity 0.0171 Informative Inherited
Molecular Function (MF) sequence-specific DNA binding transcription factor activity 0.0000000001443 Highly Informative Direct
Molecular Function (MF) protein kinase activity 0.000009011 Highly Informative Direct
Molecular Function (MF) transcription regulatory region DNA binding 0.0004561 Highly Informative Direct
Molecular Function (MF) phosphoric diester hydrolase activity 0.005562 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 tissue0.03834Least 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 system0.00000000001574InformativeDirect
Plant ANatomical entity (PAN)root tip0.0003419InformativeDirect
Plant ANatomical entity (PAN)juvenile vascular leaf0.0000000000007755Highly InformativeDirect
Plant ANatomical entity (PAN)leaf vascular system0.00000001164Highly InformativeDirect
Plant ANatomical entity (PAN)shoot apical meristem0.00001882Highly 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 groups0.000001152Least InformativeDirect
Enzyme Commission (EC)Lyases1Least InformativeInherited
Enzyme Commission (EC)Carbon-carbon lyases1Moderately InformativeInherited
Enzyme Commission (EC)Carboxylic ester hydrolases0InformativeDirect
Enzyme Commission (EC)Carboxy-lyases0.9355InformativeInherited
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 processBiological rhythms2.37e-16InformativeDirect
Biological processNitrogen fixation0.000000003245InformativeDirect
Biological processAntibiotic resistance0.00001693InformativeDirect
Biological processTwo-component regulatory system0Highly InformativeDirect
Biological processEthylene signaling pathway0Highly InformativeDirect
Cellular componentCytoplasm0Least InformativeDirect
DiseaseCrown gall tumor0.000000005968InformativeDirect
Molecular functionDNA-binding0Moderately InformativeDirect
Molecular functionCopper0.00000002048InformativeDirect
Post-translational modificationHydrolase0Least InformativeDirect
Post-translational modificationTransferase1Least InformativeInherited
Post-translational modificationActivator0Moderately InformativeDirect
Post-translational modificationRepressor0Moderately InformativeDirect
Post-translational modificationKinase0.0000000000001665Moderately 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 ]