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Ras GEF superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All alpha proteins [ 46456] (284)
Fold:   Ras GEF [ 48365]
Superfamily:   Ras GEF [ 48366]
Families:   Ras GEF [ 48367]


Superfamily statistics
Genomes (406) Uniprot 2017_06 genome PDB chains (SCOP 1.75)
Domains 5,688 13,926 6
Proteins 5,478 13,544 6


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)
Molecular Function (MF)molecular function regulator0.0000000031070Moderately InformativeDirect
Molecular Function (MF)guanyl-nucleotide exchange factor activity00Highly InformativeDirect

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) biological regulation 0 Least Informative Direct
Biological Process (BP) response to stimulus 0.0000000000007376 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.4448 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 0.4551 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 1 Least Informative Inherited
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) organonitrogen compound metabolic 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 signaling 0.000000000000007367 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 0.0000000000006912 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.0000000001228 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.000000004769 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.00000001113 Moderately Informative Direct
Biological Process (BP) regulation of localization 0.5824 Moderately Informative Inherited
Biological Process (BP) regulation of multicellular organismal process 0.6919 Moderately Informative Inherited
Biological Process (BP) regulation of nucleobase-containing compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.2739 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.4578 Moderately Informative Inherited
Biological Process (BP) response to organic substance 0.1942 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.01737 Moderately Informative Inherited
Biological Process (BP) positive regulation of cellular process 0.1808 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.1288 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 1 Moderately Informative Inherited
Biological Process (BP) regulation of cellular biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.4808 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 0.01448 Moderately Informative Inherited
Biological Process (BP) positive regulation of metabolic process 0.8662 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.1058 Moderately Informative Inherited
Biological Process (BP) system development 0.7843 Moderately Informative Inherited
Biological Process (BP) regulation of intracellular signal transduction 0.00000000000006092 Informative Direct
Biological Process (BP) regulation of protein modification process 0.0000000000002009 Informative Direct
Biological Process (BP) intracellular signal transduction 0.000000000001706 Informative Direct
Biological Process (BP) generation of neurons 0.000000152 Informative Direct
Biological Process (BP) positive regulation of catalytic activity 0.0000002926 Informative Direct
Biological Process (BP) locomotion 0.000003425 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0.00002384 Informative Direct
Biological Process (BP) regulation of hydrolase activity 0.00004147 Informative Direct
Biological Process (BP) response to organic cyclic compound 0.00005939 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.0006016 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.1928 Informative Inherited
Biological Process (BP) regulation of apoptotic process 0.005032 Informative Inherited
Biological Process (BP) positive regulation of phosphate metabolic process 0.224 Informative Inherited
Biological Process (BP) regulation of transferase activity 1 Informative Inherited
Biological Process (BP) regulation of cell proliferation 0.3933 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.6676 Informative Inherited
Biological Process (BP) positive regulation of cell death 0.1214 Informative Inherited
Biological Process (BP) positive regulation of developmental process 0.1856 Informative Inherited
Biological Process (BP) regulation of cellular component biogenesis 0.04162 Informative Inherited
Biological Process (BP) response to nitrogen compound 0.01194 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.7003 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.001134 Informative Inherited
Biological Process (BP) regulation of phosphorylation 0.202 Informative Inherited
Biological Process (BP) tissue development 0.5248 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 1 Informative Inherited
Biological Process (BP) negative regulation of cellular component organization 0.03891 Informative Inherited
Biological Process (BP) regulation of nervous system development 0.02959 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.3089 Informative Inherited
Biological Process (BP) post-embryonic development 0.8415 Informative Inherited
Biological Process (BP) animal organ morphogenesis 1 Informative Inherited
Biological Process (BP) negative regulation of cellular biosynthetic process 0.5476 Informative Inherited
Biological Process (BP) regulation of cellular component movement 0.1432 Informative Inherited
Biological Process (BP) regulation of locomotion 0.1555 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.8631 Informative Inherited
Biological Process (BP) phosphorylation 0.001599 Informative Inherited
Biological Process (BP) central nervous system development 0.02951 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.01569 Informative Inherited
Biological Process (BP) G-protein coupled receptor signaling pathway 0.7723 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 1 Informative Inherited
Biological Process (BP) cell development 0.159 Informative Inherited
Biological Process (BP) circulatory system development 0.001908 Informative Inherited
Biological Process (BP) small GTPase mediated signal transduction 0 Highly Informative Direct
Biological Process (BP) regulation of GTPase activity 0 Highly Informative Direct
Biological Process (BP) transmembrane receptor protein tyrosine kinase signaling pathway 0 Highly Informative Direct
Biological Process (BP) response to organophosphorus 0.000000004559 Highly Informative Direct
Biological Process (BP) positive regulation of hydrolase activity 0.0000001249 Highly Informative Direct
Biological Process (BP) plasma membrane bounded cell projection organization 0.0000003281 Highly Informative Direct
Biological Process (BP) response to purine-containing compound 0.00000228 Highly Informative Direct
Biological Process (BP) cellular response to organonitrogen compound 0.000003458 Highly Informative Direct
Biological Process (BP) regulation of cyclic nucleotide metabolic process 0.00002837 Highly Informative Direct
Biological Process (BP) negative regulation of cell proliferation 0.00002973 Highly Informative Direct
Biological Process (BP) positive regulation of cell migration 0.0001197 Highly Informative Direct
Biological Process (BP) regulation of purine nucleotide metabolic process 0.0001593 Highly Informative Direct
Biological Process (BP) cellular response to growth factor stimulus 0.0002148 Highly Informative Direct
Biological Process (BP) positive regulation of nervous system development 0.05408 Highly Informative Inherited
Biological Process (BP) positive regulation of cell development 0.1157 Highly Informative Inherited
Biological Process (BP) positive regulation of protein serine/threonine kinase activity 0.002714 Highly Informative Inherited
Biological Process (BP) regulation of neuron projection development 0.3399 Highly Informative Inherited
Biological Process (BP) positive regulation of apoptotic process 0.003659 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.9855 Highly Informative Inherited
Biological Process (BP) negative regulation of nervous system development 0.09864 Highly Informative Inherited
Biological Process (BP) regulation of cell morphogenesis involved in differentiation 0.1305 Highly Informative Inherited
Biological Process (BP) epithelial cell differentiation 0.003718 Highly Informative Inherited
Biological Process (BP) appendage development 0.1322 Highly Informative Inherited
Biological Process (BP) regulation of binding 0.371 Highly Informative Inherited
Biological Process (BP) neuron development 0.2339 Highly Informative Inherited
Biological Process (BP) brain development 0.001422 Highly Informative Inherited
Biological Process (BP) negative regulation of cell development 0.1842 Highly Informative Inherited
Biological Process (BP) post-embryonic animal morphogenesis 0.002206 Highly Informative Inherited
Biological Process (BP) tube morphogenesis 0.5159 Highly Informative Inherited
Biological Process (BP) morphogenesis of an epithelium 1 Highly Informative Inherited
Biological Process (BP) biological adhesion 0.002199 Highly Informative Inherited
Molecular Function (MF) binding 0.01635 Least Informative Inherited
Molecular Function (MF) molecular function regulator 0 Moderately Informative Direct
Molecular Function (MF) carbohydrate derivative binding 0.0102 Moderately Informative Inherited
Molecular Function (MF) anion binding 0.007088 Moderately Informative Inherited
Molecular Function (MF) small molecule binding 0.05247 Moderately Informative Inherited
Molecular Function (MF) enzyme binding 0.00000008405 Informative Direct
Molecular Function (MF) purine nucleotide binding 0.00001002 Informative Direct
Molecular Function (MF) ribonucleotide binding 0.00001266 Informative Direct
Molecular Function (MF) receptor binding 0.2975 Informative Inherited
Molecular Function (MF) guanyl-nucleotide exchange factor activity 0 Highly Informative Direct
Molecular Function (MF) small GTPase binding 0 Highly Informative Direct
Molecular Function (MF) GTPase regulator activity 0.00000001937 Highly Informative Direct
Molecular Function (MF) G-protein coupled receptor binding 0.0004331 Highly Informative Direct
Molecular Function (MF) protein domain specific binding 0.003182 Highly Informative Inherited
Cellular Component (CC) membrane 0.00008552 Least Informative Direct
Cellular Component (CC) macromolecular complex 1 Least Informative Inherited
Cellular Component (CC) cytoplasmic part 0.04739 Least Informative Inherited
Cellular Component (CC) plasma membrane 0.0000000547 Moderately Informative Direct
Cellular Component (CC) vesicle 0.196 Moderately Informative Inherited
Cellular Component (CC) synapse 0.0006459 Informative Direct
Cellular Component (CC) plasma membrane region 0.03288 Informative Inherited
Cellular Component (CC) endosome 0.01673 Informative Inherited
Cellular Component (CC) perinuclear region of cytoplasm 0.000002802 Highly Informative Direct
Cellular Component (CC) neuronal cell body 0.00002158 Highly Informative Direct
Cellular Component (CC) late endosome 0.0006117 Highly Informative Direct

Document: GO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.03447Moderately InformativeInherited

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)cellular phenotype0.553Least InformativeInherited
Mammalian Phenotype (MP)abnormal cell adhesion0.0006307Highly InformativeDirect

Document: MP annotation of SCOP domains

Worm Phenotype (WP)

(show details) Document: WP 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

Zebrafish Anatomy (ZA)

(show details)
ZA termFDR (all)SDZA levelAnnotation (direct or inherited)
Zebrafish Anatomy (ZA)organism subdivision0Least InformativeDirect
Zebrafish Anatomy (ZA)multi-tissue structure0Least InformativeDirect
Zebrafish Anatomy (ZA)trunk0Moderately InformativeDirect

Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

Enzyme Commission (EC)

(show details)
EC termFDR (all)SDEC levelAnnotation (direct or inherited)
Enzyme Commission (EC)Hydrolases0.003285Least InformativeInherited
Enzyme Commission (EC)Phosphoric diester hydrolases0.00000000000561InformativeDirect
Enzyme Commission (EC)Phosphoinositide phospholipase C0Highly InformativeDirect

Document: EC annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processDifferentiation0.00000000000004324Moderately InformativeDirect
Biological processCell cycle0.000009966Moderately InformativeDirect
Biological processNeurogenesis0.00000002082InformativeDirect
Biological processMitosis0.0008751InformativeDirect
Cellular componentMembrane0.00000002099Least InformativeDirect
Cellular componentCell junction0.0000000003287Moderately InformativeDirect
Cellular componentEndosome0.0000000005172Moderately InformativeDirect
Cellular componentGolgi apparatus0.00001036Moderately InformativeDirect
Cellular componentEndoplasmic reticulum0.00005428Moderately InformativeDirect
Cellular componentCell projection0.0000828Moderately InformativeDirect
Cellular componentCell membrane0.0002803Moderately InformativeDirect
Cellular componentSynapse0.6392InformativeInherited
Cellular componentSynaptosome0.00000000001609Highly InformativeDirect
Coding sequence diversityAlternative splicing0.00008875Least InformativeDirect
DomainRepeat0.0001907Least InformativeDirect
DomainCoiled coil0.00000000356Moderately InformativeDirect
DomainZinc-finger0.0004069Moderately InformativeDirect
DomainSH2 domain0.00000000004581InformativeDirect
DomainSH3 domain0.00000003867InformativeDirect
Molecular functionNucleotide-binding1Least InformativeInherited
Molecular functionCalcium0Moderately InformativeDirect
Molecular functioncAMP-binding0.00000000004621Highly InformativeDirect
Molecular functioncAMP0.000000001911Highly InformativeDirect
Post-translational modificationGuanine-nucleotide releasing factor0InformativeDirect
Post-translational modificationGTPase activation0.000000000004051InformativeDirect
Post-translational modificationPhosphoprotein0Least InformativeDirect
Post-translational modificationUbl conjugation0.0001043Moderately InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008937 SSF48366 Protein matches
Abstract

Small GTPases of the Ras family alternate between 2 conformations induced by the binding of either GTP or GDP. Guanine nucleotide exchange factors (GEFs) induce the dissociation of GDP to allow association of the more abundant GTP. The Ras-like family of small GTPases includes, among others, Ras, Rap1, R-ras, and Ral. The family is characterised by similarities in the effector domain. The Ras GTPase Rap1 is activated rapidly in response to activation of a variety of receptors. Rap1 activation is mediated by several second messengers, including calcium, diacylglycerol, and cAMP. GEFs have been identified that mediate these effects. One such GEF is Epac, an exchange protein directly activated by cAMP, which represents a novel cAMP-induced, protein kinase A-independent pathway [PubMed10579920].


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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · 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 1 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 Ras GEF 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 1 hidden Markov models representing the Ras GEF 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) · Human Phenotype (HP) · Mouse Phenotype (MP) · Worm Phenotype (WP) · Yeast Phenotype (YP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · Enzyme Commission (EC) · UniProtKB KeyWords (KW) · Internal database links ]